From 9802bcb9fea911fba27937decdb582fd733b9557 Mon Sep 17 00:00:00 2001 From: miconis Date: Wed, 1 Apr 2020 18:48:31 +0200 Subject: [PATCH 01/19] dedup testing --- dhp-workflows/dhp-dedup-openaire/pom.xml | 6 ++ .../dhp/oa/dedup/SparkCreateSimRels.java | 100 ++++++++++++----- .../oa/dedup/dedup/SparkCreateDedupTest.java | 77 ------------- .../dhp/oa/dedup/dedup/SparkDedupTest.java | 101 ++++++++++++++++++ 4 files changed, 179 insertions(+), 105 deletions(-) delete mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkCreateDedupTest.java create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkDedupTest.java diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index e7f2a926f4..6e3723ad8b 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -90,6 +90,12 @@ com.fasterxml.jackson.core jackson-core + + junit + junit + 4.12 + test + diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java index e1c1f581c3..6025a54c1b 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java @@ -5,7 +5,9 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.MapDocumentUtil; @@ -17,12 +19,18 @@ import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; +import org.dom4j.Document; import org.dom4j.DocumentException; +import org.dom4j.Element; +import org.dom4j.io.SAXReader; import scala.Tuple2; import java.io.Serializable; +import java.io.StringReader; +import java.util.ArrayList; import java.util.List; public class SparkCreateSimRels implements Serializable { @@ -51,35 +59,38 @@ public class SparkCreateSimRels implements Serializable { System.out.println(String.format("actionSetId: '%s'", actionSetId)); System.out.println(String.format("workingPath: '%s'", workingPath)); - try (SparkSession spark = getSparkSession(parser)) { - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + List configurations = getConfigurations(isLookUpUrl, actionSetId); + System.out.println("configurations = " + configurations.size()); - //for each dedup configuration - for (DedupConfig dedupConf: DedupUtility.getConfigurations(isLookUpUrl, actionSetId)) { - final String entity = dedupConf.getWf().getEntityType(); - final String subEntity = dedupConf.getWf().getSubEntityValue(); - - JavaPairRDD mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) - .mapToPair(s -> { - MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); - return new Tuple2<>(d.getIdentifier(), d); - }); - - //create blocks for deduplication - JavaPairRDD> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf); - - //create relations by comparing only elements in the same group - final JavaPairRDD dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf); - - JavaRDD relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity)); - - //save the simrel in the workingdir - spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class)) - .write() - .mode("overwrite") - .save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)); - } - } +// try (SparkSession spark = getSparkSession(parser)) { +// final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); +// +// //for each dedup configuration +// for (DedupConfig dedupConf: getConfigurations(isLookUpUrl, actionSetId)) { +// final String entity = dedupConf.getWf().getEntityType(); +// final String subEntity = dedupConf.getWf().getSubEntityValue(); +// +// JavaPairRDD mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) +// .mapToPair((PairFunction) s -> { +// MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); +// return new Tuple2(d.getIdentifier(), d); +// }); +// +// //create blocks for deduplication +// JavaPairRDD> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf); +// +// //create relations by comparing only elements in the same group +// final JavaPairRDD dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf); +// +// JavaRDD relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity)); +// +// //save the simrel in the workingdir +// spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class)) +// .write() +// .mode("overwrite") +// .save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)); +// } +// } } /** @@ -131,4 +142,37 @@ public class SparkCreateSimRels implements Serializable { .getOrCreate(); } + public List getConfigurations(String isLookUpUrl, String orchestrator) throws ISLookUpException, DocumentException { + final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookUpUrl); + + final String xquery = String.format("/RESOURCE_PROFILE[.//DEDUPLICATION/ACTION_SET/@id = '%s']", orchestrator); + + String orchestratorProfile = isLookUpService.getResourceProfileByQuery(xquery); + + final Document doc = new SAXReader().read(new StringReader(orchestratorProfile)); + + final String actionSetId = doc.valueOf("//DEDUPLICATION/ACTION_SET/@id"); + final List configurations = new ArrayList<>(); + + for (final Object o : doc.selectNodes("//SCAN_SEQUENCE/SCAN")) { + configurations.add(loadConfig(isLookUpService, actionSetId, o)); + } + + return configurations; + + } + + public DedupConfig loadConfig(final ISLookUpService isLookUpService, final String actionSetId, final Object o) + throws ISLookUpException { + final Element s = (Element) o; + final String configProfileId = s.attributeValue("id"); + final String conf = + isLookUpService.getResourceProfileByQuery(String.format( + "for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", + configProfileId)); + final DedupConfig dedupConfig = DedupConfig.load(conf); + dedupConfig.getWf().setConfigurationId(actionSetId); + return dedupConfig; + } + } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkCreateDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkCreateDedupTest.java deleted file mode 100644 index d7fc3f6949..0000000000 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkCreateDedupTest.java +++ /dev/null @@ -1,77 +0,0 @@ -package eu.dnetlib.dhp.oa.dedup.dedup; - -import com.google.common.hash.HashFunction; -import com.google.common.hash.Hashing; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.dedup.SparkCreateConnectedComponent; -import eu.dnetlib.dhp.oa.dedup.SparkCreateDedupRecord; -import eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Disabled; - -import java.io.IOException; - -public class SparkCreateDedupTest { - - String configuration; - String entity = "organization"; - - @BeforeEach - public void setUp() throws IOException { -// configuration = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dedup/conf/org.curr.conf.json")); - configuration = ""; - } - - @Disabled("must be parametrized to run locally") - public void createSimRelsTest() throws Exception { - SparkCreateSimRels.main(new String[]{ - "-mt", "local[*]", - "-i", "/Users/miconis/dumps", - "-o", "/tmp/dedup/rawset_test", - "-asi", "dedup-similarity-result-levenstein", - "-la", "lookupurl", - "-w", "workingPath" - }); - } - - @Disabled("must be parametrized to run locally") - public void createCCTest() throws Exception { - - SparkCreateConnectedComponent.main(new String[]{ - "-mt", "local[*]", - "-s", "/Users/miconis/dumps", - "-e", entity, - "-c", ArgumentApplicationParser.compressArgument(configuration), - "-t", "/tmp/dedup", - }); - } - - @Disabled("must be parametrized to run locally") - public void dedupRecordTest() throws Exception { - SparkCreateDedupRecord.main(new String[]{ - "-mt", "local[*]", - "-s", "/Users/miconis/dumps", - "-e", entity, - "-c", ArgumentApplicationParser.compressArgument(configuration), - "-d", "/tmp/dedup", - }); - } - - @Disabled("must be parametrized to run locally") - public void printConfiguration() throws Exception { - System.out.println(ArgumentApplicationParser.compressArgument(configuration)); - } - - @Disabled("must be parametrized to run locally") - public void testHashCode() { - final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f"; - final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46"; - - final HashFunction hashFunction = Hashing.murmur3_128(); - - System.out.println(s1.hashCode()); - System.out.println(hashFunction.hashString(s1).asLong()); - System.out.println(s2.hashCode()); - System.out.println(hashFunction.hashString(s2).asLong()); - } -} diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkDedupTest.java new file mode 100644 index 0000000000..c0ddaa8423 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkDedupTest.java @@ -0,0 +1,101 @@ +package eu.dnetlib.dhp.oa.dedup.dedup; + +import com.google.common.collect.Lists; +import com.google.common.hash.HashFunction; +import com.google.common.hash.Hashing; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.dedup.SparkCreateConnectedComponent; +import eu.dnetlib.dhp.oa.dedup.SparkCreateDedupRecord; +import eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.pace.config.DedupConfig; +import org.apache.commons.io.IOUtils; +import org.dom4j.DocumentException; +import org.junit.Before; +import org.junit.Test; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Disabled; +import org.mockito.Mock; +import org.mockito.junit.MockitoJUnitRunner; +import org.junit.runner.RunWith; + +import static org.junit.Assert.*; +import static org.mockito.ArgumentMatchers.anyString; +import static org.mockito.Mockito.when; + +import java.io.IOException; +import java.util.List; + +@RunWith(MockitoJUnitRunner.Silent.class) +public class SparkDedupTest { + + @Mock + SparkCreateSimRels sparkCreateSimRels; + + public List prepareConfigurations() throws IOException { + + return Lists.newArrayList( + DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))), + DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))) + ); + } + + @Before + public void setUp() throws IOException, ISLookUpException, DocumentException { + + when(sparkCreateSimRels.getConfigurations(anyString(), anyString())).thenReturn(prepareConfigurations()); + + } + + @Test + public void createSimRelsTest() throws Exception { + SparkCreateSimRels.main(new String[]{ + "-mt", "local[*]", + "-i", "/Users/miconis/dumps", + "-asi", "dedup-similarity-result-levenstein", + "-la", "lookupurl", + "-w", "workingPath" + }); + } + +// @Disabled("must be parametrized to run locally") +// public void createCCTest() throws Exception { +// +// SparkCreateConnectedComponent.main(new String[]{ +// "-mt", "local[*]", +// "-s", "/Users/miconis/dumps", +// "-e", entity, +// "-c", ArgumentApplicationParser.compressArgument(configuration), +// "-t", "/tmp/dedup", +// }); +// } +// +// @Disabled("must be parametrized to run locally") +// public void dedupRecordTest() throws Exception { +// SparkCreateDedupRecord.main(new String[]{ +// "-mt", "local[*]", +// "-s", "/Users/miconis/dumps", +// "-e", entity, +// "-c", ArgumentApplicationParser.compressArgument(configuration), +// "-d", "/tmp/dedup", +// }); +// } +// +// @Disabled("must be parametrized to run locally") +// public void printConfiguration() throws Exception { +// System.out.println(ArgumentApplicationParser.compressArgument(configuration)); +// } + + @Disabled("must be parametrized to run locally") + public void testHashCode() { + final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f"; + final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46"; + + final HashFunction hashFunction = Hashing.murmur3_128(); + + System.out.println(s1.hashCode()); + System.out.println(hashFunction.hashString(s1).asLong()); + System.out.println(s2.hashCode()); + System.out.println(hashFunction.hashString(s2).asLong()); + } +} From bfa5bc74dffada1b3e9963c5d72ce1f0eee6f8ff Mon Sep 17 00:00:00 2001 From: miconis Date: Wed, 1 Apr 2020 19:05:48 +0200 Subject: [PATCH 02/19] minor changes --- dhp-workflows/dhp-dedup-openaire/pom.xml | 6 ------ .../dhp/oa/dedup/dedup/SparkDedupTest.java | 21 +++++++------------ 2 files changed, 8 insertions(+), 19 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index 6e3723ad8b..e7f2a926f4 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -90,12 +90,6 @@ com.fasterxml.jackson.core jackson-core - - junit - junit - 4.12 - test - diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkDedupTest.java index c0ddaa8423..2b5efbf4fe 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkDedupTest.java @@ -3,30 +3,25 @@ package eu.dnetlib.dhp.oa.dedup.dedup; import com.google.common.collect.Lists; import com.google.common.hash.HashFunction; import com.google.common.hash.Hashing; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.dedup.SparkCreateConnectedComponent; -import eu.dnetlib.dhp.oa.dedup.SparkCreateDedupRecord; import eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.pace.config.DedupConfig; import org.apache.commons.io.IOUtils; import org.dom4j.DocumentException; -import org.junit.Before; -import org.junit.Test; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; -import org.mockito.junit.MockitoJUnitRunner; -import org.junit.runner.RunWith; - -import static org.junit.Assert.*; -import static org.mockito.ArgumentMatchers.anyString; -import static org.mockito.Mockito.when; +import org.mockito.junit.jupiter.MockitoExtension; import java.io.IOException; import java.util.List; -@RunWith(MockitoJUnitRunner.Silent.class) +import static org.mockito.ArgumentMatchers.anyString; +import static org.mockito.Mockito.when; + +@ExtendWith(MockitoExtension.class) public class SparkDedupTest { @Mock @@ -40,7 +35,7 @@ public class SparkDedupTest { ); } - @Before + @BeforeEach public void setUp() throws IOException, ISLookUpException, DocumentException { when(sparkCreateSimRels.getConfigurations(anyString(), anyString())).thenReturn(prepareConfigurations()); From a61763d149d33ebcb529f295755fccc3147d39ba Mon Sep 17 00:00:00 2001 From: miconis Date: Thu, 2 Apr 2020 18:37:53 +0200 Subject: [PATCH 03/19] structure for sparksimrel changed to be compliant with mockito testing --- .../dhp/oa/dedup/AbstractSparkAction.java | 83 ++++++++++++ .../dhp/oa/dedup/SparkCreateSimRels.java | 118 ++++++------------ .../oa/dedup/{dedup => }/MergeAuthorTest.java | 2 +- .../oa/dedup/{dedup => }/SparkDedupTest.java | 53 +++++--- .../dedup/{dedup => }/jpath/JsonPathTest.java | 2 +- .../dhp/dedup/profiles/mock_orchestrator.xml | 25 ++++ 6 files changed, 184 insertions(+), 99 deletions(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java rename dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/{dedup => }/MergeAuthorTest.java (97%) rename dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/{dedup => }/SparkDedupTest.java (66%) rename dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/{dedup => }/jpath/JsonPathTest.java (99%) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java new file mode 100644 index 0000000000..37ee1d8b3a --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java @@ -0,0 +1,83 @@ +package eu.dnetlib.dhp.oa.dedup; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import eu.dnetlib.pace.config.DedupConfig; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.SparkSession; +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.Element; +import org.dom4j.io.SAXReader; +import scala.xml.Elem; + +import java.io.IOException; +import java.io.Serializable; +import java.io.StringReader; +import java.util.ArrayList; +import java.util.List; + +abstract class AbstractSparkAction implements Serializable { + + public ArgumentApplicationParser parser; //parameters for the spark action + public ISLookUpService isLookUpService; //lookup service to take dedupconfig + + public AbstractSparkAction(ArgumentApplicationParser parser, ISLookUpService isLookUpService) throws Exception { + + this.parser = parser; + this.isLookUpService = isLookUpService; + } + + public List getConfigurations(String orchestrator) throws ISLookUpException, DocumentException, IOException { + + final String xquery = String.format("/RESOURCE_PROFILE[.//DEDUPLICATION/ACTION_SET/@id = '%s']", orchestrator); + + String orchestratorProfile = isLookUpService.getResourceProfileByQuery(xquery); + + final Document doc = new SAXReader().read(new StringReader(orchestratorProfile)); + + final String actionSetId = doc.valueOf("//DEDUPLICATION/ACTION_SET/@id"); + + final List configurations = new ArrayList<>(); + + for (final Object o : doc.selectNodes("//SCAN_SEQUENCE/SCAN")) { + configurations.add(loadConfig(isLookUpService, actionSetId, o)); + } + + return configurations; + } + + public DedupConfig loadConfig(final ISLookUpService isLookUpService, final String actionSetId, final Object o) + throws ISLookUpException, IOException { + final Element s = (Element) o; + final String configProfileId = s.attributeValue("id"); + final String conf = + isLookUpService.getResourceProfileByQuery(String.format( + "for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", + configProfileId)); + + DedupConfig dedupConfig = new ObjectMapper().readValue(conf, DedupConfig.class); + dedupConfig.getPace().initModel(); + dedupConfig.getPace().initTranslationMap(); + dedupConfig.getWf().setConfigurationId(actionSetId); + + return dedupConfig; + } + + abstract void run() throws DocumentException, IOException, ISLookUpException; + + protected SparkSession getSparkSession(ArgumentApplicationParser parser) { + SparkConf conf = new SparkConf(); + + return SparkSession + .builder() + .appName(SparkCreateSimRels.class.getSimpleName()) + .master(parser.get("master")) + .config(conf) + .getOrCreate(); + } +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java index 6025a54c1b..000a96a56c 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java @@ -28,25 +28,31 @@ import org.dom4j.Element; import org.dom4j.io.SAXReader; import scala.Tuple2; +import java.io.IOException; import java.io.Serializable; import java.io.StringReader; import java.util.ArrayList; import java.util.List; -public class SparkCreateSimRels implements Serializable { +public class SparkCreateSimRels extends AbstractSparkAction { private static final Log log = LogFactory.getLog(SparkCreateSimRels.class); + public SparkCreateSimRels(ArgumentApplicationParser parser, ISLookUpService isLookUpService) throws Exception { + super(parser, isLookUpService); + } + public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( + ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils.toString( SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); parser.parseArgument(args); - new SparkCreateSimRels().run(parser); + new SparkCreateSimRels(parser, ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))).run(); } - private void run(ArgumentApplicationParser parser) throws ISLookUpException, DocumentException { + @Override + public void run() throws DocumentException, IOException, ISLookUpException { //read oozie parameters final String graphBasePath = parser.get("graphBasePath"); @@ -59,38 +65,35 @@ public class SparkCreateSimRels implements Serializable { System.out.println(String.format("actionSetId: '%s'", actionSetId)); System.out.println(String.format("workingPath: '%s'", workingPath)); - List configurations = getConfigurations(isLookUpUrl, actionSetId); - System.out.println("configurations = " + configurations.size()); + try (SparkSession spark = getSparkSession(parser)) { + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); -// try (SparkSession spark = getSparkSession(parser)) { -// final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); -// -// //for each dedup configuration -// for (DedupConfig dedupConf: getConfigurations(isLookUpUrl, actionSetId)) { -// final String entity = dedupConf.getWf().getEntityType(); -// final String subEntity = dedupConf.getWf().getSubEntityValue(); -// -// JavaPairRDD mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) -// .mapToPair((PairFunction) s -> { -// MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); -// return new Tuple2(d.getIdentifier(), d); -// }); -// -// //create blocks for deduplication -// JavaPairRDD> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf); -// -// //create relations by comparing only elements in the same group -// final JavaPairRDD dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf); -// -// JavaRDD relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity)); -// -// //save the simrel in the workingdir -// spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class)) -// .write() -// .mode("overwrite") -// .save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)); -// } -// } + //for each dedup configuration + for (DedupConfig dedupConf: getConfigurations(actionSetId)) { + final String entity = dedupConf.getWf().getEntityType(); + final String subEntity = dedupConf.getWf().getSubEntityValue(); + + JavaPairRDD mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) + .mapToPair((PairFunction) s -> { + MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); + return new Tuple2(d.getIdentifier(), d); + }); + + //create blocks for deduplication + JavaPairRDD> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf); + + //create relations by comparing only elements in the same group + final JavaPairRDD dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf); + + JavaRDD relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity)); + + //save the simrel in the workingdir + spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class)) + .write() + .mode("overwrite") + .save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)); + } + } } /** @@ -130,49 +133,4 @@ public class SparkCreateSimRels implements Serializable { } return r; } - - private static SparkSession getSparkSession(ArgumentApplicationParser parser) { - SparkConf conf = new SparkConf(); - - return SparkSession - .builder() - .appName(SparkCreateSimRels.class.getSimpleName()) - .master(parser.get("master")) - .config(conf) - .getOrCreate(); - } - - public List getConfigurations(String isLookUpUrl, String orchestrator) throws ISLookUpException, DocumentException { - final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookUpUrl); - - final String xquery = String.format("/RESOURCE_PROFILE[.//DEDUPLICATION/ACTION_SET/@id = '%s']", orchestrator); - - String orchestratorProfile = isLookUpService.getResourceProfileByQuery(xquery); - - final Document doc = new SAXReader().read(new StringReader(orchestratorProfile)); - - final String actionSetId = doc.valueOf("//DEDUPLICATION/ACTION_SET/@id"); - final List configurations = new ArrayList<>(); - - for (final Object o : doc.selectNodes("//SCAN_SEQUENCE/SCAN")) { - configurations.add(loadConfig(isLookUpService, actionSetId, o)); - } - - return configurations; - - } - - public DedupConfig loadConfig(final ISLookUpService isLookUpService, final String actionSetId, final Object o) - throws ISLookUpException { - final Element s = (Element) o; - final String configProfileId = s.attributeValue("id"); - final String conf = - isLookUpService.getResourceProfileByQuery(String.format( - "for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", - configProfileId)); - final DedupConfig dedupConfig = DedupConfig.load(conf); - dedupConfig.getWf().setConfigurationId(actionSetId); - return dedupConfig; - } - } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/MergeAuthorTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java similarity index 97% rename from dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/MergeAuthorTest.java rename to dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java index a729eaa9d9..69edf63438 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/MergeAuthorTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.oa.dedup.dedup; +package eu.dnetlib.dhp.oa.dedup; import eu.dnetlib.dhp.oa.dedup.DedupUtility; import eu.dnetlib.dhp.schema.oaf.Publication; diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java similarity index 66% rename from dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkDedupTest.java rename to dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 2b5efbf4fe..421612265e 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -1,56 +1,67 @@ -package eu.dnetlib.dhp.oa.dedup.dedup; +package eu.dnetlib.dhp.oa.dedup; import com.google.common.collect.Lists; import com.google.common.hash.HashFunction; import com.google.common.hash.Hashing; -import eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; import org.apache.commons.io.IOUtils; import org.dom4j.DocumentException; +import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; +import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; import java.io.IOException; import java.util.List; import static org.mockito.ArgumentMatchers.anyString; +import static org.mockito.Mockito.mock; import static org.mockito.Mockito.when; +import static org.mockito.Mockito.withSettings; @ExtendWith(MockitoExtension.class) public class SparkDedupTest { - @Mock - SparkCreateSimRels sparkCreateSimRels; + ISLookUpService isLookUpService = mock(ISLookUpService.class, withSettings().serializable()); - public List prepareConfigurations() throws IOException { - - return Lists.newArrayList( - DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))), - DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))) - ); - } @BeforeEach public void setUp() throws IOException, ISLookUpException, DocumentException { - when(sparkCreateSimRels.getConfigurations(anyString(), anyString())).thenReturn(prepareConfigurations()); + withSettings().serializable(); + when(isLookUpService.getResourceProfileByQuery(Mockito.contains("test-orchestrator"))) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); + + when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); + + when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); } @Test public void createSimRelsTest() throws Exception { - SparkCreateSimRels.main(new String[]{ + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); + parser.parseArgument(new String[]{ "-mt", "local[*]", "-i", "/Users/miconis/dumps", - "-asi", "dedup-similarity-result-levenstein", + "-asi", "test-orchestrator", "-la", "lookupurl", - "-w", "workingPath" - }); + "-w", "workingPath"}); + + new SparkCreateSimRels(parser, isLookUpService).run(); + } // @Disabled("must be parametrized to run locally") @@ -93,4 +104,12 @@ public class SparkDedupTest { System.out.println(s2.hashCode()); System.out.println(hashFunction.hashString(s2).asLong()); } + + public List prepareConfigurations() throws IOException { + + return Lists.newArrayList( + DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))), + DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))) + ); + } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/jpath/JsonPathTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java similarity index 99% rename from dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/jpath/JsonPathTest.java rename to dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java index e1f92d867a..d72734ed5a 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/jpath/JsonPathTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.oa.dedup.dedup.jpath; +package eu.dnetlib.dhp.oa.dedup.jpath; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml new file mode 100644 index 0000000000..9a4871223c --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml @@ -0,0 +1,25 @@ + +
+ + + + + +
+ + + + + + + + + + + + + + + SECURITY_PARAMETERS + + \ No newline at end of file From 53fd624c347e1152491587546b13b0cb7f05ffcd Mon Sep 17 00:00:00 2001 From: miconis Date: Fri, 3 Apr 2020 18:32:25 +0200 Subject: [PATCH 04/19] implemented test for sparkcreatesimrels --- .../dhp/oa/dedup/AbstractSparkAction.java | 17 +- .../dhp/oa/dedup/SparkCreateSimRels.java | 50 ++-- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 102 ++++--- .../dnetlib/dhp/dedup/conf/org.curr.conf.json | 8 +- .../dnetlib/dhp/dedup/entities/organization | 257 ++++++++++++++++++ .../eu/dnetlib/dhp/dedup/entities/publication | 0 6 files changed, 355 insertions(+), 79 deletions(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/organization create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java index 37ee1d8b3a..8358939ff5 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java @@ -2,18 +2,15 @@ package eu.dnetlib.dhp.oa.dedup; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; -import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.sql.SparkSession; import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.Element; import org.dom4j.io.SAXReader; -import scala.xml.Elem; import java.io.IOException; import java.io.Serializable; @@ -24,15 +21,15 @@ import java.util.List; abstract class AbstractSparkAction implements Serializable { public ArgumentApplicationParser parser; //parameters for the spark action - public ISLookUpService isLookUpService; //lookup service to take dedupconfig + public SparkSession spark; //the spark session - public AbstractSparkAction(ArgumentApplicationParser parser, ISLookUpService isLookUpService) throws Exception { + public AbstractSparkAction(ArgumentApplicationParser parser, SparkSession spark) throws Exception { this.parser = parser; - this.isLookUpService = isLookUpService; + this.spark = spark; } - public List getConfigurations(String orchestrator) throws ISLookUpException, DocumentException, IOException { + public List getConfigurations(ISLookUpService isLookUpService, String orchestrator) throws ISLookUpException, DocumentException, IOException { final String xquery = String.format("/RESOURCE_PROFILE[.//DEDUPLICATION/ACTION_SET/@id = '%s']", orchestrator); @@ -51,7 +48,7 @@ abstract class AbstractSparkAction implements Serializable { return configurations; } - public DedupConfig loadConfig(final ISLookUpService isLookUpService, final String actionSetId, final Object o) + private DedupConfig loadConfig(final ISLookUpService isLookUpService, final String actionSetId, final Object o) throws ISLookUpException, IOException { final Element s = (Element) o; final String configProfileId = s.attributeValue("id"); @@ -68,9 +65,9 @@ abstract class AbstractSparkAction implements Serializable { return dedupConfig; } - abstract void run() throws DocumentException, IOException, ISLookUpException; + abstract void run(ISLookUpService isLookUpService) throws DocumentException, IOException, ISLookUpException; - protected SparkSession getSparkSession(ArgumentApplicationParser parser) { + protected static SparkSession getSparkSession(ArgumentApplicationParser parser) { SparkConf conf = new SparkConf(); return SparkSession diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java index 000a96a56c..a97e6d2ba6 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java @@ -38,8 +38,8 @@ public class SparkCreateSimRels extends AbstractSparkAction { private static final Log log = LogFactory.getLog(SparkCreateSimRels.class); - public SparkCreateSimRels(ArgumentApplicationParser parser, ISLookUpService isLookUpService) throws Exception { - super(parser, isLookUpService); + public SparkCreateSimRels(ArgumentApplicationParser parser, SparkSession spark) throws Exception { + super(parser, spark); } public static void main(String[] args) throws Exception { @@ -48,11 +48,11 @@ public class SparkCreateSimRels extends AbstractSparkAction { SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); parser.parseArgument(args); - new SparkCreateSimRels(parser, ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))).run(); + new SparkCreateSimRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } @Override - public void run() throws DocumentException, IOException, ISLookUpException { + public void run(ISLookUpService isLookUpService) throws DocumentException, IOException, ISLookUpException { //read oozie parameters final String graphBasePath = parser.get("graphBasePath"); @@ -65,34 +65,32 @@ public class SparkCreateSimRels extends AbstractSparkAction { System.out.println(String.format("actionSetId: '%s'", actionSetId)); System.out.println(String.format("workingPath: '%s'", workingPath)); - try (SparkSession spark = getSparkSession(parser)) { - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - //for each dedup configuration - for (DedupConfig dedupConf: getConfigurations(actionSetId)) { - final String entity = dedupConf.getWf().getEntityType(); - final String subEntity = dedupConf.getWf().getSubEntityValue(); + //for each dedup configuration + for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { + final String entity = dedupConf.getWf().getEntityType(); + final String subEntity = dedupConf.getWf().getSubEntityValue(); - JavaPairRDD mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) - .mapToPair((PairFunction) s -> { - MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); - return new Tuple2(d.getIdentifier(), d); - }); + JavaPairRDD mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) + .mapToPair((PairFunction) s -> { + MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); + return new Tuple2(d.getIdentifier(), d); + }); - //create blocks for deduplication - JavaPairRDD> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf); + //create blocks for deduplication + JavaPairRDD> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf); - //create relations by comparing only elements in the same group - final JavaPairRDD dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf); + //create relations by comparing only elements in the same group + final JavaPairRDD dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf); - JavaRDD relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity)); + JavaRDD relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity)); - //save the simrel in the workingdir - spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class)) - .write() - .mode("overwrite") - .save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)); - } + //save the simrel in the workingdir + spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class)) + .write() + .mode("overwrite") + .save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 421612265e..23685739b2 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -1,43 +1,54 @@ package eu.dnetlib.dhp.oa.dedup; -import com.google.common.collect.Lists; -import com.google.common.hash.HashFunction; -import com.google.common.hash.Hashing; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import eu.dnetlib.pace.config.DedupConfig; +import net.bytebuddy.utility.RandomString; +import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; +import org.junit.jupiter.api.*; import org.junit.jupiter.api.extension.ExtendWith; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Disabled; -import org.junit.jupiter.api.Test; import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; +import java.io.File; import java.io.IOException; -import java.util.List; +import java.net.URISyntaxException; +import java.nio.file.Paths; -import static org.mockito.ArgumentMatchers.anyString; -import static org.mockito.Mockito.mock; import static org.mockito.Mockito.when; -import static org.mockito.Mockito.withSettings; +import static org.junit.jupiter.api.Assertions.assertEquals; @ExtendWith(MockitoExtension.class) +@TestMethodOrder(MethodOrderer.OrderAnnotation.class) public class SparkDedupTest { - ISLookUpService isLookUpService = mock(ISLookUpService.class, withSettings().serializable()); + @Mock + ISLookUpService isLookUpService; + SparkSession spark; + + static String testGraphBasePath; + static String testOutputBasePath; + String testActionSetId = "test-orchestrator"; @BeforeEach - public void setUp() throws IOException, ISLookUpException, DocumentException { + public void setUp() throws IOException, ISLookUpException, DocumentException, URISyntaxException { - withSettings().serializable(); + testGraphBasePath = Paths.get(getClass().getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath(); + testOutputBasePath = "/tmp/" + RandomString.make(5).toLowerCase(); + spark = SparkSession + .builder() + .appName(SparkCreateSimRels.class.getSimpleName()) + .master("local[*]") + .config(new SparkConf()) + .getOrCreate(); - when(isLookUpService.getResourceProfileByQuery(Mockito.contains("test-orchestrator"))) + when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) .thenReturn(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) @@ -48,6 +59,7 @@ public class SparkDedupTest { } @Test + @Order(1) public void createSimRelsTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( @@ -55,12 +67,19 @@ public class SparkDedupTest { SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); parser.parseArgument(new String[]{ "-mt", "local[*]", - "-i", "/Users/miconis/dumps", - "-asi", "test-orchestrator", + "-i", testGraphBasePath, + "-asi", testActionSetId, "-la", "lookupurl", - "-w", "workingPath"}); + "-w", testOutputBasePath}); - new SparkCreateSimRels(parser, isLookUpService).run(); + new SparkCreateSimRels(parser, spark).run(isLookUpService); + + //test number of simrels + long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel").count(); + long pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count(); + + assertEquals(918, orgs_simrel); + assertEquals(0, pubs_simrel); } @@ -90,26 +109,31 @@ public class SparkDedupTest { // @Disabled("must be parametrized to run locally") // public void printConfiguration() throws Exception { // System.out.println(ArgumentApplicationParser.compressArgument(configuration)); +// } +// +// @Disabled("must be parametrized to run locally") +// public void testHashCode() { +// final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f"; +// final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46"; +// +// final HashFunction hashFunction = Hashing.murmur3_128(); +// +// System.out.println(s1.hashCode()); +// System.out.println(hashFunction.hashString(s1).asLong()); +// System.out.println(s2.hashCode()); +// System.out.println(hashFunction.hashString(s2).asLong()); +// } +// +// public List prepareConfigurations() throws IOException { +// +// return Lists.newArrayList( +// DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))), +// DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))) +// ); // } - @Disabled("must be parametrized to run locally") - public void testHashCode() { - final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f"; - final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46"; - - final HashFunction hashFunction = Hashing.murmur3_128(); - - System.out.println(s1.hashCode()); - System.out.println(hashFunction.hashString(s1).asLong()); - System.out.println(s2.hashCode()); - System.out.println(hashFunction.hashString(s2).asLong()); - } - - public List prepareConfigurations() throws IOException { - - return Lists.newArrayList( - DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))), - DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))) - ); + @AfterAll + public static void cleanUp() throws IOException { + FileUtils.deleteDirectory(new File(testOutputBasePath)); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json index 726f2b8997..1a4ec49e61 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json @@ -144,10 +144,10 @@ } }, "model" : [ - { "name" : "country", "type" : "String", "path" : "$.country.classid"}, - { "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"}, - { "name" : "legalname", "type" : "String", "path" : "$.legalname.value" }, - { "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" }, + { "name" : "country", "type" : "String", "path" : "$.organization.metadata.country.classid"}, + { "name" : "legalshortname", "type" : "String", "path" : "$.organization.metadata.legalshortname.value"}, + { "name" : "legalname", "type" : "String", "path" : "$.organization.metadata.legalname.value" }, + { "name" : "websiteurl", "type" : "URL", "path" : "$.organization.metadata.websiteurl.value" }, { "name" : "gridid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='grid')].value"}, { "name" : "originalId", "type" : "String", "path" : "$.id" } ], diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/organization b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/organization new file mode 100644 index 0000000000..f2adcf9bf1 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/organization @@ -0,0 +1,257 @@ 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a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication new file mode 100644 index 0000000000..e69de29bb2 From 56fbe689f06a955919dab6fd67e41e67e6ff472e Mon Sep 17 00:00:00 2001 From: miconis Date: Mon, 6 Apr 2020 16:30:31 +0200 Subject: [PATCH 05/19] implementation of the tests for each spark action --- .../dedup/SparkCreateConnectedComponent.java | 102 +- .../dhp/oa/dedup/SparkCreateDedupRecord.java | 68 +- .../dhp/oa/dedup/SparkPropagateRelation.java | 149 +- .../dhp/oa/dedup/SparkUpdateEntity.java | 72 +- .../dhp/oa/dedup/dedupRecord_parameters.json | 33 - .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 197 +- .../dnetlib/dhp/dedup/conf/org.curr.conf.json | 6 +- .../eu/dnetlib/dhp/dedup/entities/publication | 3793 +++++++++++++++++ 8 files changed, 4119 insertions(+), 301 deletions(-) delete mode 100644 dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/dedupRecord_parameters.json diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateConnectedComponent.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateConnectedComponent.java index 9d8d5944d7..b28d020b6f 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateConnectedComponent.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateConnectedComponent.java @@ -5,10 +5,14 @@ import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor; import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; @@ -23,79 +27,75 @@ import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; import scala.Tuple2; +import java.io.IOException; import java.util.ArrayList; import java.util.List; -public class SparkCreateConnectedComponent { +public class SparkCreateConnectedComponent extends AbstractSparkAction { - public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); - parser.parseArgument(args); + private static final Log log = LogFactory.getLog(SparkCreateConnectedComponent.class); - new SparkCreateConnectedComponent().run(parser); + public SparkCreateConnectedComponent(ArgumentApplicationParser parser, SparkSession spark) throws Exception { + super(parser, spark); } - private void run(ArgumentApplicationParser parser) throws ISLookUpException, DocumentException { + public static void main(String[] args) throws Exception { + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + parser.parseArgument(args); + + new SparkCreateSimRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); + } + + @Override + public void run(ISLookUpService isLookUpService) throws ISLookUpException, DocumentException, IOException { final String graphBasePath = parser.get("graphBasePath"); final String workingPath = parser.get("workingPath"); final String isLookUpUrl = parser.get("isLookUpUrl"); final String actionSetId = parser.get("actionSetId"); - try (SparkSession spark = getSparkSession(parser)) { + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { - for (DedupConfig dedupConf: DedupUtility.getConfigurations(isLookUpUrl, actionSetId)) { + final String entity = dedupConf.getWf().getEntityType(); + final String subEntity = dedupConf.getWf().getSubEntityValue(); - final String entity = dedupConf.getWf().getEntityType(); - final String subEntity = dedupConf.getWf().getSubEntityValue(); + final JavaPairRDD vertexes = sc.textFile(graphBasePath + "/" + subEntity) + .map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s)) + .mapToPair((PairFunction) + s -> new Tuple2(getHashcode(s), s) + ); - final JavaPairRDD vertexes = sc.textFile(graphBasePath + "/" + subEntity) - .map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s)) - .mapToPair((PairFunction) - s -> new Tuple2(getHashcode(s), s) - ); - - final Dataset similarityRelations = spark.read().load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)).as(Encoders.bean(Relation.class)); - final RDD> edgeRdd = similarityRelations.javaRDD().map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())).rdd(); - final JavaRDD cc = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations()).toJavaRDD(); - final Dataset mergeRelation = spark.createDataset(cc.filter(k -> k.getDocIds().size() > 1).flatMap((FlatMapFunction) c -> - c.getDocIds() - .stream() - .flatMap(id -> { - List tmp = new ArrayList<>(); - Relation r = new Relation(); - r.setSource(c.getCcId()); - r.setTarget(id); - r.setRelClass("merges"); - tmp.add(r); - r = new Relation(); - r.setTarget(c.getCcId()); - r.setSource(id); - r.setRelClass("isMergedIn"); - tmp.add(r); - return tmp.stream(); - }).iterator()).rdd(), Encoders.bean(Relation.class)); - mergeRelation.write().mode("overwrite").save(DedupUtility.createMergeRelPath(workingPath, actionSetId, entity)); - } + final Dataset similarityRelations = spark.read().load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)).as(Encoders.bean(Relation.class)); + final RDD> edgeRdd = similarityRelations.javaRDD().map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())).rdd(); + final JavaRDD cc = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations()).toJavaRDD(); + final Dataset mergeRelation = spark.createDataset(cc.filter(k -> k.getDocIds().size() > 1).flatMap((FlatMapFunction) c -> + c.getDocIds() + .stream() + .flatMap(id -> { + List tmp = new ArrayList<>(); + Relation r = new Relation(); + r.setSource(c.getCcId()); + r.setTarget(id); + r.setRelClass("merges"); + tmp.add(r); + r = new Relation(); + r.setTarget(c.getCcId()); + r.setSource(id); + r.setRelClass("isMergedIn"); + tmp.add(r); + return tmp.stream(); + }).iterator()).rdd(), Encoders.bean(Relation.class)); + mergeRelation.write().mode("overwrite").save(DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity)); } + } public static long getHashcode(final String id) { return Hashing.murmur3_128().hashString(id).asLong(); } - private static SparkSession getSparkSession(ArgumentApplicationParser parser) { - SparkConf conf = new SparkConf(); - - return SparkSession - .builder() - .appName(SparkCreateSimRels.class.getSimpleName()) - .master(parser.get("master")) - .config(conf) - .getOrCreate(); - } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java index 3271f2b4cc..099824051e 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java @@ -3,62 +3,62 @@ package eu.dnetlib.dhp.oa.dedup; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; -public class SparkCreateDedupRecord { +import java.io.IOException; - public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); - parser.parseArgument(args); +public class SparkCreateDedupRecord extends AbstractSparkAction { - new SparkCreateDedupRecord().run(parser); + private static final Log log = LogFactory.getLog(SparkCreateDedupRecord.class); + + public SparkCreateDedupRecord(ArgumentApplicationParser parser, SparkSession spark) throws Exception { + super(parser, spark); } - private void run(ArgumentApplicationParser parser) throws ISLookUpException, DocumentException { + public static void main(String[] args) throws Exception { + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); + parser.parseArgument(args); + + new SparkCreateSimRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); + } + + @Override + public void run(ISLookUpService isLookUpService) throws ISLookUpException, DocumentException, IOException { final String graphBasePath = parser.get("graphBasePath"); final String isLookUpUrl = parser.get("isLookUpUrl"); final String actionSetId = parser.get("actionSetId"); final String workingPath = parser.get("workingPath"); - try (SparkSession spark = getSparkSession(parser)) { - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - for (DedupConfig dedupConf: DedupUtility.getConfigurations(isLookUpUrl, actionSetId)) { - String subEntity = dedupConf.getWf().getSubEntityValue(); + for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { + String subEntity = dedupConf.getWf().getSubEntityValue(); - final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity); - final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity); - final OafEntityType entityType = OafEntityType.valueOf(subEntity); - final JavaRDD dedupRecord = - DedupRecordFactory.createDedupRecord(sc, spark, mergeRelPath, entityPath, entityType, dedupConf); - dedupRecord.map(r -> { - ObjectMapper mapper = new ObjectMapper(); - return mapper.writeValueAsString(r); - }).saveAsTextFile(DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity)); - } + final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity); + final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity); + final OafEntityType entityType = OafEntityType.valueOf(subEntity); + final JavaRDD dedupRecord = + DedupRecordFactory.createDedupRecord(sc, spark, mergeRelPath, entityPath, entityType, dedupConf); + dedupRecord.map(r -> { + ObjectMapper mapper = new ObjectMapper(); + return mapper.writeValueAsString(r); + }).saveAsTextFile(DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity)); } + } - private static SparkSession getSparkSession(ArgumentApplicationParser parser) { - SparkConf conf = new SparkConf(); - - return SparkSession - .builder() - .appName(SparkCreateDedupRecord.class.getSimpleName()) - .master(parser.get("master")) - .config(conf) - .enableHiveSupport() - .getOrCreate(); - } } - diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index 18fb199f62..f441851b45 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -6,8 +6,12 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; @@ -24,7 +28,7 @@ import scala.Tuple2; import java.io.IOException; -public class SparkPropagateRelation { +public class SparkPropagateRelation extends AbstractSparkAction { enum FieldType { SOURCE, @@ -34,83 +38,88 @@ public class SparkPropagateRelation { final static String SOURCEJSONPATH = "$.source"; final static String TARGETJSONPATH = "$.target"; - public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkPropagateRelation.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); - parser.parseArgument(args); + private static final Log log = LogFactory.getLog(SparkPropagateRelation.class); - new SparkPropagateRelation().run(parser); + public SparkPropagateRelation(ArgumentApplicationParser parser, SparkSession spark) throws Exception { + super(parser, spark); } - public void run(ArgumentApplicationParser parser) { + public static void main(String[] args) throws Exception { + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); + parser.parseArgument(args); + + new SparkPropagateRelation(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); + } + + @Override + public void run(ISLookUpService isLookUpService) { final String graphBasePath = parser.get("graphBasePath"); final String workingPath = parser.get("workingPath"); final String dedupGraphPath = parser.get("dedupGraphPath"); - try (SparkSession spark = getSparkSession(parser)) { - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - final Dataset mergeRels = spark.read().load(DedupUtility.createMergeRelPath(workingPath, "*", "*")).as(Encoders.bean(Relation.class)); + final Dataset mergeRels = spark.read().load(DedupUtility.createMergeRelPath(workingPath, "*", "*")).as(Encoders.bean(Relation.class)); - final JavaPairRDD mergedIds = mergeRels - .where("relClass == 'merges'") - .select(mergeRels.col("source"), mergeRels.col("target")) - .distinct() - .toJavaRDD() - .mapToPair((PairFunction) r -> new Tuple2<>(r.getString(1), r.getString(0))); + final JavaPairRDD mergedIds = mergeRels + .where("relClass == 'merges'") + .select(mergeRels.col("source"), mergeRels.col("target")) + .distinct() + .toJavaRDD() + .mapToPair((PairFunction) r -> new Tuple2(r.getString(1), r.getString(0))); - JavaRDD relations = sc.textFile(DedupUtility.createEntityPath(graphBasePath, "relation")); + JavaRDD relations = sc.textFile(DedupUtility.createEntityPath(graphBasePath, "relation")); - JavaRDD newRels = relations.mapToPair( - (PairFunction) s -> - new Tuple2<>(MapDocumentUtil.getJPathString(SOURCEJSONPATH, s), s)) - .leftOuterJoin(mergedIds) - .map((Function>>, String>) v1 -> { - if (v1._2()._2().isPresent()) { - return replaceField(v1._2()._1(), v1._2()._2().get(), FieldType.SOURCE); - } - return v1._2()._1(); - }) - .mapToPair( - (PairFunction) s -> - new Tuple2<>(MapDocumentUtil.getJPathString(TARGETJSONPATH, s), s)) - .leftOuterJoin(mergedIds) - .map((Function>>, String>) v1 -> { - if (v1._2()._2().isPresent()) { - return replaceField(v1._2()._1(), v1._2()._2().get(), FieldType.TARGET); - } - return v1._2()._1(); - }).filter(SparkPropagateRelation::containsDedup) - .repartition(500); + JavaRDD newRels = relations.mapToPair( + (PairFunction) s -> + new Tuple2(MapDocumentUtil.getJPathString(SOURCEJSONPATH, s), s)) + .leftOuterJoin(mergedIds) + .map((Function>>, String>) v1 -> { + if (v1._2()._2().isPresent()) { + return replaceField(v1._2()._1(), v1._2()._2().get(), FieldType.SOURCE); + } + return v1._2()._1(); + }) + .mapToPair( + (PairFunction) s -> + new Tuple2(MapDocumentUtil.getJPathString(TARGETJSONPATH, s), s)) + .leftOuterJoin(mergedIds) + .map((Function>>, String>) v1 -> { + if (v1._2()._2().isPresent()) { + return replaceField(v1._2()._1(), v1._2()._2().get(), FieldType.TARGET); + } + return v1._2()._1(); + }).filter(SparkPropagateRelation::containsDedup) + .repartition(500); - //update deleted by inference - relations = relations.mapToPair( - (PairFunction) s -> - new Tuple2<>(MapDocumentUtil.getJPathString(SOURCEJSONPATH, s), s)) - .leftOuterJoin(mergedIds) - .map((Function>>, String>) v1 -> { - if (v1._2()._2().isPresent()) { - return updateDeletedByInference(v1._2()._1(), Relation.class); - } - return v1._2()._1(); - }) - .mapToPair( - (PairFunction) s -> - new Tuple2<>(MapDocumentUtil.getJPathString(TARGETJSONPATH, s), s)) - .leftOuterJoin(mergedIds) - .map((Function>>, String>) v1 -> { - if (v1._2()._2().isPresent()) { - return updateDeletedByInference(v1._2()._1(), Relation.class); - } - return v1._2()._1(); - }) - .repartition(500); + //update deleted by inference + relations = relations.mapToPair( + (PairFunction) s -> + new Tuple2(MapDocumentUtil.getJPathString(SOURCEJSONPATH, s), s)) + .leftOuterJoin(mergedIds) + .map((Function>>, String>) v1 -> { + if (v1._2()._2().isPresent()) { + return updateDeletedByInference(v1._2()._1(), Relation.class); + } + return v1._2()._1(); + }) + .mapToPair( + (PairFunction) s -> + new Tuple2(MapDocumentUtil.getJPathString(TARGETJSONPATH, s), s)) + .leftOuterJoin(mergedIds) + .map((Function>>, String>) v1 -> { + if (v1._2()._2().isPresent()) { + return updateDeletedByInference(v1._2()._1(), Relation.class); + } + return v1._2()._1(); + }) + .repartition(500); - newRels.union(relations).repartition(1000) - .saveAsTextFile(DedupUtility.createEntityPath(dedupGraphPath, "relation"), GzipCodec.class); - } + newRels.union(relations).repartition(1000) + .saveAsTextFile(DedupUtility.createEntityPath(dedupGraphPath, "relation"), GzipCodec.class); } private static boolean containsDedup(final String json) { @@ -143,18 +152,6 @@ public class SparkPropagateRelation { } } - private static SparkSession getSparkSession(ArgumentApplicationParser parser) { - SparkConf conf = new SparkConf(); - - return SparkSession - .builder() - .appName(SparkPropagateRelation.class.getSimpleName()) - .master(parser.get("master")) - .config(conf) - .enableHiveSupport() - .getOrCreate(); - } - private static String updateDeletedByInference(final String json, final Class clazz) { final ObjectMapper mapper = new ObjectMapper(); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java index c490101f48..5c9d3c0e15 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java @@ -4,8 +4,12 @@ import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.*; import org.apache.hadoop.io.compress.GzipCodec; @@ -23,17 +27,23 @@ import scala.Tuple2; import java.io.IOException; import java.io.Serializable; -public class SparkUpdateEntity implements Serializable { +public class SparkUpdateEntity extends AbstractSparkAction { final String IDJSONPATH = "$.id"; + private static final Log log = LogFactory.getLog(SparkUpdateEntity.class); + + public SparkUpdateEntity(ArgumentApplicationParser parser, SparkSession spark) throws Exception { + super(parser, spark); + } + public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( + ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils.toString( SparkUpdateEntity.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); parser.parseArgument(args); - new SparkUpdateEntity().run(parser); + new SparkUpdateEntity(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } public boolean mergeRelExists(String basePath, String entity) throws IOException { @@ -53,45 +63,43 @@ public class SparkUpdateEntity implements Serializable { return result; } - public void run(ArgumentApplicationParser parser) throws IOException { + public void run(ISLookUpService isLookUpService) throws IOException { final String graphBasePath = parser.get("graphBasePath"); final String workingPath = parser.get("workingPath"); final String dedupGraphPath = parser.get("dedupGraphPath"); - try (SparkSession spark = getSparkSession(parser)) { + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + //for each entity + for (OafEntityType entity: OafEntityType.values()) { - //for each entity - for (OafEntityType entity: OafEntityType.values()) { + JavaRDD sourceEntity = sc.textFile(DedupUtility.createEntityPath(graphBasePath, entity.toString())); - JavaRDD sourceEntity = sc.textFile(DedupUtility.createEntityPath(graphBasePath, entity.toString())); + if (mergeRelExists(workingPath, entity.toString())) { - if (mergeRelExists(workingPath, entity.toString())) { + final Dataset rel = spark.read().load(DedupUtility.createMergeRelPath(workingPath, "*", entity.toString())).as(Encoders.bean(Relation.class)); - final Dataset rel = spark.read().load(DedupUtility.createMergeRelPath(workingPath, "*", entity.toString())).as(Encoders.bean(Relation.class)); + final JavaPairRDD mergedIds = rel + .where("relClass == 'merges'") + .select(rel.col("target")) + .distinct() + .toJavaRDD() + .mapToPair((PairFunction) r -> new Tuple2(r.getString(0), "d")); - final JavaPairRDD mergedIds = rel - .where("relClass == 'merges'") - .select(rel.col("target")) - .distinct() - .toJavaRDD() - .mapToPair((PairFunction) r -> new Tuple2<>(r.getString(0), "d")); + final JavaRDD dedupEntity = sc.textFile(DedupUtility.createDedupRecordPath(workingPath, "*", entity.toString())); - final JavaRDD dedupEntity = sc.textFile(DedupUtility.createDedupRecordPath(workingPath, "*", entity.toString())); + JavaPairRDD entitiesWithId = sourceEntity.mapToPair((PairFunction) s -> new Tuple2(MapDocumentUtil.getJPathString(IDJSONPATH, s), s)); - JavaPairRDD entitiesWithId = sourceEntity.mapToPair((PairFunction) s -> new Tuple2<>(MapDocumentUtil.getJPathString(IDJSONPATH, s), s)); - - JavaRDD map = entitiesWithId.leftOuterJoin(mergedIds).map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), getOafClass(entity)) : k._2()._1()); - sourceEntity = map.union(dedupEntity); - - } - - sourceEntity.saveAsTextFile(dedupGraphPath + "/" + entity, GzipCodec.class); + JavaRDD map = entitiesWithId.leftOuterJoin(mergedIds).map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), getOafClass(entity)) : k._2()._1()); + sourceEntity = map.union(dedupEntity); } + + sourceEntity.saveAsTextFile(dedupGraphPath + "/" + entity, GzipCodec.class); + } + } public Class getOafClass(OafEntityType className) { @@ -128,16 +136,4 @@ public class SparkUpdateEntity implements Serializable { throw new RuntimeException("Unable to convert json", e); } } - - private static SparkSession getSparkSession(ArgumentApplicationParser parser) { - SparkConf conf = new SparkConf(); - - return SparkSession - .builder() - .appName(SparkUpdateEntity.class.getSimpleName()) - .master(parser.get("master")) - .config(conf) - .enableHiveSupport() - .getOrCreate(); - } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/dedupRecord_parameters.json b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/dedupRecord_parameters.json deleted file mode 100644 index de744dfb63..0000000000 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/dedupRecord_parameters.json +++ /dev/null @@ -1,33 +0,0 @@ -[ - { - "paramName": "mt", - "paramLongName": "master", - "paramDescription": "should be local or yarn", - "paramRequired": true - }, - { - "paramName": "s", - "paramLongName": "sourcePath", - "paramDescription": "the path of the sequential file to read", - "paramRequired": true - }, - { - "paramName": "e", - "paramLongName": "entity", - "paramDescription": "the type of entity to be deduped", - "paramRequired": true - }, - { - "paramName": "c", - "paramLongName": "dedupConf", - "paramDescription": "dedup configuration to be used", - "compressed": true, - "paramRequired": true - }, - { - "paramName": "d", - "paramLongName": "dedupPath", - "paramDescription": "dedup path to load mergeRelation", - "paramRequired": true - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 23685739b2..8a7d77774c 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -1,14 +1,14 @@ package eu.dnetlib.dhp.oa.dedup; +import com.google.common.hash.HashFunction; +import com.google.common.hash.Hashing; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import net.bytebuddy.utility.RandomString; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.sql.SparkSession; -import org.dom4j.DocumentException; import org.junit.jupiter.api.*; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; @@ -30,17 +30,24 @@ public class SparkDedupTest { @Mock ISLookUpService isLookUpService; - SparkSession spark; + private SparkSession spark; - static String testGraphBasePath; - static String testOutputBasePath; - String testActionSetId = "test-orchestrator"; + private static String testGraphBasePath; + private final static String testOutputBasePath = "/tmp/test_dedup_workflow"; + private final static String testActionSetId = "test-orchestrator"; + private final static String testDedupGraphBasePath = "/tmp/test_dedup_workflow/dedup_graph"; + + @BeforeAll + private static void cleanUp() throws IOException, URISyntaxException { + + testGraphBasePath = Paths.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath(); + + FileUtils.deleteDirectory(new File(testOutputBasePath)); + } @BeforeEach - public void setUp() throws IOException, ISLookUpException, DocumentException, URISyntaxException { + private void setUp() throws IOException, ISLookUpException { - testGraphBasePath = Paths.get(getClass().getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath(); - testOutputBasePath = "/tmp/" + RandomString.make(5).toLowerCase(); spark = SparkSession .builder() .appName(SparkCreateSimRels.class.getSimpleName()) @@ -49,13 +56,14 @@ public class SparkDedupTest { .getOrCreate(); when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) - .thenReturn(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); + .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) - .thenReturn(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); + .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) - .thenReturn(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); + .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); + } @Test @@ -74,66 +82,123 @@ public class SparkDedupTest { new SparkCreateSimRels(parser, spark).run(isLookUpService); - //test number of simrels long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel").count(); long pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count(); - assertEquals(918, orgs_simrel); - assertEquals(0, pubs_simrel); + System.out.println("pubs_simrel = " + pubs_simrel); + System.out.println("orgs_simrel = " + orgs_simrel); +// assertEquals(918, orgs_simrel); +// assertEquals(0, pubs_simrel); } -// @Disabled("must be parametrized to run locally") -// public void createCCTest() throws Exception { -// -// SparkCreateConnectedComponent.main(new String[]{ -// "-mt", "local[*]", -// "-s", "/Users/miconis/dumps", -// "-e", entity, -// "-c", ArgumentApplicationParser.compressArgument(configuration), -// "-t", "/tmp/dedup", -// }); -// } -// -// @Disabled("must be parametrized to run locally") -// public void dedupRecordTest() throws Exception { -// SparkCreateDedupRecord.main(new String[]{ -// "-mt", "local[*]", -// "-s", "/Users/miconis/dumps", -// "-e", entity, -// "-c", ArgumentApplicationParser.compressArgument(configuration), -// "-d", "/tmp/dedup", -// }); -// } -// -// @Disabled("must be parametrized to run locally") -// public void printConfiguration() throws Exception { -// System.out.println(ArgumentApplicationParser.compressArgument(configuration)); -// } -// -// @Disabled("must be parametrized to run locally") -// public void testHashCode() { -// final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f"; -// final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46"; -// -// final HashFunction hashFunction = Hashing.murmur3_128(); -// -// System.out.println(s1.hashCode()); -// System.out.println(hashFunction.hashString(s1).asLong()); -// System.out.println(s2.hashCode()); -// System.out.println(hashFunction.hashString(s2).asLong()); -// } -// -// public List prepareConfigurations() throws IOException { -// -// return Lists.newArrayList( -// DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))), -// DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))) -// ); -// } + @Test + @Order(2) + public void createCCTest() throws Exception { - @AfterAll - public static void cleanUp() throws IOException { - FileUtils.deleteDirectory(new File(testOutputBasePath)); + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + parser.parseArgument(new String[]{ + "-mt", "local[*]", + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath}); + + new SparkCreateConnectedComponent(parser, spark).run(isLookUpService); + + long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count(); + long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count(); + + System.out.println("pubs_mergerel = " + pubs_mergerel); + System.out.println("orgs_mergerel = " + orgs_mergerel); +// assertEquals(458, orgs_mergerel); +// assertEquals(0, pubs_mergerel); + + } + + @Test + @Order(3) + public void dedupRecordTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); + parser.parseArgument(new String[]{ + "-mt", "local[*]", + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath}); + + new SparkCreateDedupRecord(parser, spark).run(isLookUpService); + + long orgs_deduprecord = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count(); + long pubs_deduprecord = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count(); + + System.out.println("pubs_deduprecord = " + pubs_deduprecord); + System.out.println("pubs_deduprecord = " + orgs_deduprecord); +// assertEquals(458, orgs_deduprecord); +// assertEquals(0, pubs_deduprecord); + } + + @Test + @Order(4) + public void updateEntityTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkUpdateEntity.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); + parser.parseArgument(new String[]{ + "-mt", "local[*]", + "-i", testGraphBasePath, + "-w", testOutputBasePath, + "-o", testDedupGraphBasePath + }); + + new SparkUpdateEntity(parser, spark).run(isLookUpService); + + long organizations = spark.read().load(testDedupGraphBasePath + "/organization").count(); + long publications = spark.read().load(testDedupGraphBasePath + "/publication").count(); + + System.out.println("publications = " + publications); + System.out.println("organizations = " + organizations); + + } + + @Test + @Order(5) + public void propagateRelationTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkPropagateRelation.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); + parser.parseArgument(new String[]{ + "-mt", "local[*]", + "-i", testGraphBasePath, + "-w", testOutputBasePath, + "-o", testDedupGraphBasePath + }); + + new SparkPropagateRelation(parser, spark).run(isLookUpService); + + long relations = spark.read().load(testDedupGraphBasePath + "/relation").count(); + + System.out.println("relations = " + relations); + + } + + @Disabled("must be parametrized to run locally") + public void testHashCode() { + final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f"; + final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46"; + + final HashFunction hashFunction = Hashing.murmur3_128(); + + System.out.println(s1.hashCode()); + System.out.println(hashFunction.hashString(s1).asLong()); + System.out.println(s2.hashCode()); + System.out.println(hashFunction.hashString(s2).asLong()); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json index 1a4ec49e61..2b02e99a32 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json @@ -145,9 +145,9 @@ }, "model" : [ { "name" : "country", "type" : "String", "path" : "$.organization.metadata.country.classid"}, - { "name" : "legalshortname", "type" : "String", "path" : "$.organization.metadata.legalshortname.value"}, - { "name" : "legalname", "type" : "String", "path" : "$.organization.metadata.legalname.value" }, - { "name" : "websiteurl", "type" : "URL", "path" : "$.organization.metadata.websiteurl.value" }, + { "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"}, + { "name" : "legalname", "type" : "String", "path" : "$.legalname.value" }, + { "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" }, { "name" : "gridid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='grid')].value"}, { "name" : "originalId", "type" : "String", "path" : "$.id" } ], diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication index e69de29bb2..62b997224c 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication @@ -0,0 +1,3793 @@ 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.../eu/dnetlib/dhp/dedup/entities/datasource | 0 .../dnetlib/dhp/dedup/entities/organization | 1010 +++- .../dhp/dedup/entities/otherresearchproduct | 0 .../eu/dnetlib/dhp/dedup/entities/project | 0 .../eu/dnetlib/dhp/dedup/entities/publication | 4624 +++-------------- .../eu/dnetlib/dhp/dedup/entities/relation | 500 ++ .../eu/dnetlib/dhp/dedup/entities/software | 0 11 files changed, 2144 insertions(+), 4098 deletions(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/dataset create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/otherresearchproduct create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/project create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/relation create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/software diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java index 69edf63438..970fc0ddbd 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java @@ -20,7 +20,6 @@ public class MergeAuthorTest { public void setUp() throws Exception { final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/json/authors_merge.json")); - publicationsToMerge = Arrays.asList(json.split("\n")).stream().map(s-> { try { return mapper.readValue(s, Publication.class); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 8a7d77774c..3d7f574608 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -1,13 +1,14 @@ package eu.dnetlib.dhp.oa.dedup; -import com.google.common.hash.HashFunction; -import com.google.common.hash.Hashing; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; import org.junit.jupiter.api.extension.ExtendWith; @@ -17,20 +18,22 @@ import org.mockito.junit.jupiter.MockitoExtension; import java.io.File; import java.io.IOException; +import java.io.Serializable; import java.net.URISyntaxException; import java.nio.file.Paths; -import static org.mockito.Mockito.when; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.mockito.Mockito.lenient; @ExtendWith(MockitoExtension.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class) -public class SparkDedupTest { +public class SparkDedupTest implements Serializable { - @Mock + @Mock(serializable = true) ISLookUpService isLookUpService; - private SparkSession spark; + private static SparkSession spark; + private static JavaSparkContext jsc; private static String testGraphBasePath; private final static String testOutputBasePath = "/tmp/test_dedup_workflow"; @@ -43,10 +46,6 @@ public class SparkDedupTest { testGraphBasePath = Paths.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath(); FileUtils.deleteDirectory(new File(testOutputBasePath)); - } - - @BeforeEach - private void setUp() throws IOException, ISLookUpException { spark = SparkSession .builder() @@ -55,13 +54,20 @@ public class SparkDedupTest { .config(new SparkConf()) .getOrCreate(); - when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) + jsc = new JavaSparkContext(spark.sparkContext()); + + } + + @BeforeEach + private void setUp() throws IOException, ISLookUpException { + + lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); - when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) + lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); - when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) + lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); } @@ -85,11 +91,8 @@ public class SparkDedupTest { long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel").count(); long pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count(); - System.out.println("pubs_simrel = " + pubs_simrel); - System.out.println("orgs_simrel = " + orgs_simrel); -// assertEquals(918, orgs_simrel); -// assertEquals(0, pubs_simrel); - + assertEquals(3288, orgs_simrel); + assertEquals(7260, pubs_simrel); } @Test @@ -111,16 +114,14 @@ public class SparkDedupTest { long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count(); long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count(); - System.out.println("pubs_mergerel = " + pubs_mergerel); - System.out.println("orgs_mergerel = " + orgs_mergerel); -// assertEquals(458, orgs_mergerel); -// assertEquals(0, pubs_mergerel); + assertEquals(1244, orgs_mergerel); + assertEquals(1460, pubs_mergerel); } @Test @Order(3) - public void dedupRecordTest() throws Exception { + public void createDedupRecordTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils.toString( @@ -134,13 +135,11 @@ public class SparkDedupTest { new SparkCreateDedupRecord(parser, spark).run(isLookUpService); - long orgs_deduprecord = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count(); - long pubs_deduprecord = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count(); + long orgs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count(); + long pubs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count(); - System.out.println("pubs_deduprecord = " + pubs_deduprecord); - System.out.println("pubs_deduprecord = " + orgs_deduprecord); -// assertEquals(458, orgs_deduprecord); -// assertEquals(0, pubs_deduprecord); + assertEquals(82, orgs_deduprecord); + assertEquals(66, pubs_deduprecord); } @Test @@ -159,12 +158,35 @@ public class SparkDedupTest { new SparkUpdateEntity(parser, spark).run(isLookUpService); - long organizations = spark.read().load(testDedupGraphBasePath + "/organization").count(); - long publications = spark.read().load(testDedupGraphBasePath + "/publication").count(); + long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count(); + long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count(); - System.out.println("publications = " + publications); - System.out.println("organizations = " + organizations); + long mergedOrgs = spark + .read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct().count(); + long mergedPubs = spark + .read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct().count(); + + assertEquals(897, publications); + assertEquals(835, organizations); + + long deletedOrgs = jsc.textFile(testDedupGraphBasePath + "/organization") + .filter(this::isDeletedByInference).count(); + long deletedPubs = jsc.textFile(testDedupGraphBasePath + "/publication") + .filter(this::isDeletedByInference).count(); + + assertEquals(mergedOrgs, deletedOrgs); + assertEquals(mergedPubs, deletedPubs); + + //TODO check the size of other entities not deduplicated } @Test @@ -183,22 +205,13 @@ public class SparkDedupTest { new SparkPropagateRelation(parser, spark).run(isLookUpService); - long relations = spark.read().load(testDedupGraphBasePath + "/relation").count(); + long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); - System.out.println("relations = " + relations); + assertEquals(826, relations); } - @Disabled("must be parametrized to run locally") - public void testHashCode() { - final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f"; - final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46"; - - final HashFunction hashFunction = Hashing.murmur3_128(); - - System.out.println(s1.hashCode()); - System.out.println(hashFunction.hashString(s1).asLong()); - System.out.println(s2.hashCode()); - System.out.println(hashFunction.hashString(s2).asLong()); + public boolean isDeletedByInference(String s) { + return s.contains("\"deletedbyinference\":true"); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json index 2b02e99a32..726f2b8997 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json @@ -144,7 +144,7 @@ } }, "model" : [ - { "name" : "country", "type" : "String", "path" : "$.organization.metadata.country.classid"}, + { "name" : "country", "type" : "String", "path" : "$.country.classid"}, { "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"}, { "name" : "legalname", "type" : "String", "path" : "$.legalname.value" }, { "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" }, diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/dataset b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/dataset new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/organization b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/organization index f2adcf9bf1..7e34ad1335 100644 --- 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We use data from direct numerical simulations up to R????280 following the evolution of about two million passive tracers advected by the flow over a time span of about three decades. We present data for both the separation distance and the relative velocity statistics. Statistics are measured along the particle pair trajectories both as a function of time and as a function of their separation, i.e., at fixed scales. We compare and contrast both sets of statistics in order to gain insight into the mechanisms governing the separation process. We find very high levels of intermittency in the early stages, that is, for travel times up to order ten Kolmogorov time scales. The fixed scale statistics allow us to quantify anomalous corrections to Richardson diffusion in the inertial range of scales for those pairs that separate rapidly. 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In this paper, the relations between the mobilisation and use of internal and external resources in innovation processes, and the innovative performance of firms, are explored empirically, using an adapted version of H\\xe5kansson's (1987) economic network model. The main research question was: to what extent do network variables contribute to the innovative performance of firms? To answer this question, we assessed the explanatory power of economic network theory within the empirical study of innovation. Firms were found to engage in various configurations of internal and external resource bases, enabling them to innovate with better results. The relations in the estimated models are strongly influenced by moderating variables such as sector, and type and level of innovations produced. 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The decays of entangled neutral B mesons into definite flavor states (B-0 or (B) over bar (0)), and J/psi K-L(0) or c (c) over barK(S)(0) final states (referred to as B+ or B-), allow comparisons between the probabilities of four pairs of T-conjugated transitions, for example, (B) over bar (0) -> B- and B- -> (B) over bar (0), as a function of the time difference between the two B decays. Using 468 X 10(6) B (B) over bar pairs produced in Y(4S) decays collected by the BABAR detector at SLAC, we measure T-violating parameters in the time evolution of neutral B mesons, yielding Delta S-T(+) = -137 +/- 0.14(stat) +/- 0.06(syst) and Delta S-T(-) = 1.17 +/- 0.18(stat) +/- 0.11(syst). 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Background: Use of whole-genome sequence data is expected to increase persistency of genomic prediction across generations and breeds but affects model performance and requires increased computing time. In this study, we investigated whether the split-and-merge Bayesian stochastic search variable selection (BSSVS) model could overcome these issues. BSSVS is performed first on subsets of sequence-based variants and then on a merged dataset containing variants selected in the first step. Results: We used a dataset that included 4,154,064 variants after editing and de-regressed proofs for 3415 reference and 2138 validation bulls for somatic cell score, protein yield and interval first to last insemination. In the first step, BSSVS was performed on 106 subsets each containing ~39,189 variants. In the second step, 1060 up to 472,492 variants, selected from the first step, were included to estimate the accuracy of genomic prediction. Accuracies were at best equal to those achieved with the commonly used Bovine 50k-SNP chip, although the number of variants within a few well-known quantitative trait loci regions was considerably enriched. When variant selection and the final genomic prediction were performed on the same data, predictions were biased. Predictions computed as the average of the predictions computed for each subset achieved the highest accuracies, i.e. 0.5 to 1.1 % higher than the accuracies obtained with the 50k-SNP chip, and yielded the least biased predictions. Finally, the accuracy of genomic predictions obtained when all sequence-based variants were included was similar or up to 1.4 % lower compared to that based on the average predictions across the subsets. By applying parallelization, the split-and-merge procedure was completed in 5 days, while the standard analysis including all sequence-based variants took more than three months. Conclusions: The split-and-merge approach splits one large computational task into many much smaller ones, which allows the use of parallel processing and thus efficient genomic prediction based on whole-genome sequence data. The split-and-merge approach did not improve prediction accuracy, probably because we used data on a single breed for which relationships between individuals were high. Nevertheless, the split-and-merge approach may have potential for applications on data from multiple breeds.

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The increase of private health care plans and the implementation of the \"Smiling Brazil\" Program, the largest public oral health care program in the world, could have influenced this increase in access. However, we do not yet know if inequalities in the use of dental health services persist after the improvement in access. The aims of this study are to analyze socioeconomic differences for dental health service use between 2003 and 2008 in S\\xe3o Paulo and to examine changes in these associations since the implementation of the Smiling Brazil program in 2003. \\n__Method:__ Data was obtained via two household health surveys (ISA-Capital 2003 and ISA-Capital 2008) which investigated living conditions, lifestyle, health status and use of health care services. Logistic regression was used to analyze associations between socioeconomic factors and dental services use. Additionally, trends from 2003 to 2008 regarding socioeconomic characteristics and dental health service use"}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-07"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "language": {"classid": "en", "classname": "en", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["https://www.narcis.nl/publication/RecordID/oai%3Arepub.eur.nl%3A94722", "urn:NBN:nl:ui:15-1765/94722", "10.1186/s12913-016-1928-y", "http://repub.eur.nl/pub/94722/REPUB_94722_OA.pdf", "1765/94722", "eur:oai:repub.eur.nl:94722"], "source": [], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Socioeconomic inequalities in dental health services in Sao Paulo, Brazil, 2003-2008"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:datasetarchive", "classname": "sysimport:crosswalk:datasetarchive", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:dataCite_resource", "schemename": "dnet:dataCite_resource"}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.1016/s0304-3975(97)00182-5"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "scp-number", "classname": "scp-number", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "0002794431"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "urn", "classname": "urn", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "urn:nbn:nl:ui:25-1aa61067-2f77-4f9b-a8ce-1e04c7c672a8"}], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "relevantdate": [], "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", "value": "DANS (Data Archiving and Networked Services)"}], "id": "50|DansKnawCris::6eec7225f3b545e6441dd8b7f39d25d2", "subject": [], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Aceto", "name": "L.", "pid": [], "rank": 1, "affiliation": [], "fullname": "Aceto, L."}, {"surname": "Groote", "name": "J. 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A large variety of studies suggest that biofilm formation by NTHi may be an important step in the pathogenesis of this bacterium. However, the underlying mechanisms involved in this process are poorly elucidated. In this study, we used a transposon mutant library to identify bacterial genes involved in biofilm formation. The growth and biofilm formation of 4,172 transposon mutants were determined, and the involvement of the identified genes in biofilm formation was validated in in vitro experiments. Here, we present experimental data showing that increased bacterial lysis, through interference with peptidoglycan synthesis, results in elevated levels of extracellular DNA, which increased biofilm formation. Interestingly, similar results were obtained with subinhibitory concentrations of beta-lactam antibiotics, known to interfere with peptidoglycan synthesis, but such an effect does not appear with other classes of antibiotics. These results indicate that treatment with beta-lactam antibiotics, especially for beta-lactam-resistant NTHi isolates, might increase resistance to antibiotics by increasing biofilm formation. IMPORTANCE Most, if not all, bacteria form a biofilm, a multicellular structure that protects them from antimicrobial actions of the host immune system and affords resistance to antibiotics. The latter is especially disturbing with the increase in multiresistant bacterial clones worldwide. Bacterial biofilm formation is a multistep process that starts with surface adhesion, after which attached bacteria divide and give rise to biomass. The actual steps required for Haemophilus influenzae biofilm formation are largely not known. We show that interference with peptidoglycan biosynthesis increases biofilm formation because of the release of bacterial genomic DNA. Subinhibitory concentrations of beta-lactam antibiotics, which are often prescribed to treat H. influenzae infections, increase biofilm formation through a similar mechanism. Therefore, when beta-lactam antibiotics do not reach their MIC in vivo, they might not only drive selection for beta-lactam-resistant clones but also increase biofilm formation and resistance to other antimicrobial compounds."}], "format": [], "journal": {"issnPrinted": "2379-5042", "conferencedate": "", "vol": "2", "conferenceplace": "", "name": "Msphere", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2017-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": 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"dnet:dataCite_title"}, "value": "Bacterial Lysis through Interference with Peptidoglycan Synthesis Increases Biofilm Formation by Nontypeable Haemophilus influenzae"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:datasetarchive", "classname": "sysimport:crosswalk:datasetarchive", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:dataCite_resource", "schemename": "dnet:dataCite_resource"}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "urn", "classname": "urn", "schemeid": "dnet:pid_types", "schemename": 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Warmer and relatively arid conditions prevailed during the Medieval Climate Anomaly (MCA, ca. 900-1300 AD), with a significant development of xerophytes and Mediterranean vegetation and limited deciduous tree formations (mesophytes). The Little Ice Age (LIA, 1300-1800 AD) was generally colder and moister, with an expansion of deciduous taxa and cold-adapted montane conifers. Two major phases occurred within this period: (i) a transition MCA-LIA, characterized by fluctuating, moist conditions and relatively cold temperatures (ca. 1300 and 1600 AD); and (ii) a second period, characterized by the coldest and most humid conditions, coinciding with maximum (recent) glacier advances (ca. 1600-1800 AD). Glaciers retreated after the LIA when warmer and more arid conditions dominated, interrupted by a short-living cooling episode during the late 19th to early 20th centuries. Some records suggest a response to solar activity with colder and slightly moister conditions during solar minima. Centennial-scale hydrological fluctuations are in phase with reconstructions of NAO variability, which appears to be one of the main climate mechanisms influencing rainfall variations in the region during the last millennium. \\xa9 2012 Author(s)."}], "format": [], "journal": {"issnPrinted": "1814-9324", "conferencedate": "", "vol": "8", "conferenceplace": "", "name": "Climate of the Past", "iss": "2 special issue", "sp": "683", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "700", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2012-03-30"}, "coverage": [], "publisher": 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String iteration is a variation on the original binary version of the Kleene star operation $p^* q$ obtained by restricting the first argument to be a non-empty sequence of atomic actions. We show that, for every positive integer $k$, bisimulation equivalence over the set of processes in this language with loops of length at most $k$ is finitely axiomatizable, provided that the set of actions is finite. We also offer an infinite equational theory that completely axiomatizes bisimulation equivalence over the whole language. 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In this study we not only aim to investigate if children's advertising exposure indeed affects their materialism, but also how it affects their materialism (i.e., by studying the mediating effects of advertised product desire and perceived reality of advertising). The study investigates 8- to 11-year-olds, because these children are in the midst of consumer development. Unlike previous studies, it focuses on the longitudinal rather than the cross-sectional relations. A sample of 466 children (ages 8-11 years; 55% girls) participated in a two-wave online survey with a one-year interval. We asked children questions about advertising and material possessions. We used structural equation modeling to study the relationship between these variables. Results indicated that children's advertising exposure increases materialism. 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In this study we not only aim to investigate if children's advertising exposure indeed affects their materialism, but also how it affects their materialism (i.e., by studying the mediating effects of advertised product desire and perceived reality of advertising). The study investigates 8- to 11-year-olds, because these children are in the midst of consumer development. Unlike previous studies, it focuses on the longitudinal rather than the cross-sectional relations. A sample of 466 children (ages 8-11 years; 55% girls) participated in a two-wave online survey with a one-year interval. We asked children questions about advertising and material possessions. We used structural equation modeling to study the relationship between these variables. Results indicated that children's advertising exposure increases materialism. The effect of children\\u2019s advertising exposure is mediated by advertised product desire: children's advertising exposure leads to an increase in advertised product desire that enhances materialism. The effect of children's advertising exposure is not mediated by perceived reality of advertising: children's advertising exposure does not lead to an increase perceived reality of advertising, yet, perceived reality of advertising does enhance materialism. 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"trust": ""}, "key": "10|opendoar____::269d837afada308dd4aeab28ca2d57e4", "value": "LSHTM Research Online"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["https://researchonline.lshtm.ac.uk/id/eprint/11161/1/Buprenorphine%20maintenance%20versus%20placebo%20or%20methadone%20maintenance%20for%20opioid%20dependence_GREEN%20VoR.pdf"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": 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{"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "https://researchonline.lshtm.ac.uk/id/eprint/11161/1/Buprenorphine%20maintenance%20versus%20placebo%20or%20methadone%20maintenance%20for%20opioid%20dependence_GREEN%20VoR.pdf"}], "dateoftransformation": "2020-03-05T20:28:44.964Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value":"BACKGROUND: Buprenorphine has recently been reported to be an alternative to methadone and LAAM for maintenance treatment of opioid dependent individuals, differing results are reported concerning its relative effectiveness indicating the need for an integrative review. OBJECTIVES: To evaluate the effects of buprenorphine maintenance against placebo and methadone maintenance in retaining patients in treatment and in suppressing illicit drug use. SEARCH STRATEGY: We searched the following databases up to 2001, inclusive: Cochrane Drugs and Alcohol Review Group Register, the Cochrane Controlled Trials Register, MEDLINE, EMBASE, Current Contents, Psychlit, CORK [www. state.vt.su/adap/cork], Alcohol and Drug Council of Australia (ADCA) [www.adca.org.au], Australian Drug Foundation (ADF -VIC) [www.adf.org.au], Centre for Education and Information on Drugs and Alcohol (CEIDA) [www.ceida.net.au], Australian Bibliographic Network (ABN), and Library of Congress databases, available NIDA monographs and the College on Problems of Drug Dependence Inc. proceedings, the reference lists of all identified studies and published reviews and authors of identified RCT's were asked about any other published or unpublished relevant RCT. SELECTION CRITERIA: Randomised clinical trials of buprenorphine maintenance compared with either placebo or methadone maintenance for opioid dependence. DATA COLLECTION AND ANALYSIS: Reviewers evaluated the papers separately and independently, rating methodological quality of concealment of allocation; data were extracted independently for meta-analysis and double-entered. MAIN RESULTS: Thirteen studies met the inclusion criteria, all were randomised clinical trials, all but one were double-blind. The method of concealment of allocation was not clearly described in 11 of the studies, otherwise methodological quality was good. Buprenorphine given in flexible doses appeared statistically significantly less effective than methadone in retaining patient in treatment (RR= 0.82; 95% CI: 0.69-0.96). Low dose buprenorphine is not superior to low dose methadone. High dose buprenorphine does not retain more patients than low dose methadone, but may suppress heroin use better. There was no advantage for high dose buprenorphine over high dose methadone in retention (RR=0.79; 95% CI:0.62-1.01), and high dose buprenorphine was inferior in suppression of heroin use. Buprenorphine was statistically significantly superior to placebo medication in retention of patients in treatment at low doses (RR=1.24; 95% CI: 1.06-1.45), high doses (RR=1.21; 95% CI: 1.02-1.44), and very high doses (RR=1.52; 95% CI: 1.23-1.88). However, only high and very high dose buprenorphine suppressed heroin use significantly above placebo. REVIEWERS' CONCLUSIONS: Buprenorphine is an effective intervention for use in the maintenance treatment of heroin dependence, but it is not more effective than methadone at adequate dosages."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "application/pdf"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, 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"value":"AbstractWe study equational axiomatizations of bisimulation equivalence for the language obtained by extending Milner's basic CCS with string iteration. String iteration is a variation on the original binary version of the Kleene star operation p\\u2217q obtained by restricting the first argument to be a non-empty sequence of atomic actions. We show that, for every positive integer k, bisimulation equivalence over the set of processes in this language with loops of length at most k is finitely axiomatizable, provided that the set of actions is finite. We also offer an infinite equational theory that completely axiomatizes bisimulation equivalence over the whole language. We prove that this result cannot be improved upon by showing that no finite equational axiomatization of bisimulation equivalence over basic CCS with string iteration can exist, unless the set of actions is empty."}], "format": [], "journal": {"issnPrinted": "03043975", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "Theoretical Computer Science", "iss": "1-2", "sp": "339", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "374", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", 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"dateofcollection": "2018-11-10T05:10:17.902Z", "fulltext": [], "dateoftransformation": "2020-02-27T19:29:46.391Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "SummarySIRT1 is a NAD+-dependent enzyme that affects metabolism by deacetylating key transcriptional regulators of energy expenditure. Here, we tested whether deletion of PARP-2, an alternative NAD+-consuming enzyme, impacts on NAD+ bioavailability and SIRT1 activity. Our results indicate that PARP-2 deficiency increases SIRT1 activity in cultured myotubes. However, this increase was not due to changes in NAD+ levels, but to an increase in SIRT1 expression, as PARP-2 acts as a direct negative regulator of the SIRT1 promoter. PARP-2 deletion in mice increases SIRT1 levels, promotes energy expenditure, and increases mitochondrial content. Furthermore, PARP-2\\u2212/\\u2212 mice were protected against diet-induced obesity. Despite being insulin sensitized, PARP-2\\u2212/\\u2212 mice were glucose intolerant due to a defective pancreatic function. 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Buprenorphine has recently been reported to be an alternative to methadone and LAAM for maintenance treatment of opioid dependent individuals, differing results are reported concerning its relative effectiveness indicating the need for an integrative review. OBJECTIVES: To evaluate the effects of buprenorphine maintenance against placebo and methadone maintenance in retaining patients in treatment and in suppressing illicit drug use. SEARCH STRATEGY: We searched the following databases up to 2001, inclusive: Cochrane Drugs and Alcohol Review Group Register, the Cochrane Controlled Trials Register, MEDLINE, EMBASE, Current Contents, Psychlit, CORK [www. state.vt.su/adap/cork], Alcohol and Drug Council of Australia (ADCA) [www.adca.org.au], Australian Drug Foundation (ADF -VIC) [www.adf.org.au], Centre for Education and Information on Drugs and Alcohol (CEIDA) [www.ceida.net.au], Australian Bibliographic Network (ABN), and Library of Congress databases, available NIDA monographs and the College on Problems of Drug Dependence Inc. proceedings, the reference lists of all identified studies and published reviews and authors of identified RCT's were asked about any other published or unpublished relevant RCT. SELECTION CRITERIA: Randomised clinical trials of buprenorphine maintenance compared with either placebo or methadone maintenance for opioid dependence. DATA COLLECTION AND ANALYSIS: Reviewers evaluated the papers separately and independently, rating methodological quality of concealment of allocation; data were extracted independently for meta-analysis and double-entered. MAIN RESULTS: Thirteen studies met the inclusion criteria, all were randomised clinical trials, all but one were double-blind. The method of concealment of allocation was not clearly described in 11 of the studies, otherwise methodological quality was good. Buprenorphine given in flexible doses appeared statistically significantly less effective than methadone in retaining patient in treatment (RR= 0.82; 95% CI: 0.69-0.96). Low dose buprenorphine is not superior to low dose methadone. High dose buprenorphine does not retain more patients than low dose methadone, but may suppress heroin use better. There was no advantage for high dose buprenorphine over high dose methadone in retention (RR=0.79; 95% CI:0.62-1.01), and high dose buprenorphine was inferior in suppression of heroin use. Buprenorphine was statistically significantly superior to placebo medication in retention of patients in treatment at low doses (RR=1.24; 95% CI: 1.06-1.45), high doses (RR=1.21; 95% CI: 1.02-1.44), and very high doses (RR=1.52; 95% CI: 1.23-1.88). However, only high and very high dose buprenorphine suppressed heroin use significantly above placebo. REVIEWER'S CONCLUSIONS: Buprenorphine is an effective intervention for use in the maintenance treatment of heroin dependence, but it is not more effective than methadone at adequate dosages."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "application/pdf"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, 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"dateofcollection": "2020-03-03T12:35:37.548Z", "fulltext": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "http://eprints.whiterose.ac.uk/98102/1/Angew.%20Chem.%202016%2C%20128%2C%204816-4820.pdf"}], "dateoftransformation": "2020-03-05T21:40:55.294Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "A highly efficient cap-exchange approach for preparing compact, dense polyvalent mannose-capped quantum dots (QDs) has been developed. The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC-SIGN and DC-SIGNR (collectively termed as DC-SIGN/R) using a sensitive, ratiometric F\\xf6rster resonance energy transfer (FRET) assay. The QD probes specifically bind DC-SIGN, but not its closely related receptor DC-SIGNR, which is further confirmed by its specific blocking of DC-SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC-SIGN binds more efficiently to densely packed mannosides. A FRET-based thermodynamic study reveals that the binding is enthalpy-driven. This work establishes QD FRET as a rapid, sensitive technique for probing structure and thermodynamics of multivalent protein\\u2013ligand interactions."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "application/pdf"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", 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"trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Anthelmintics"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Macrocyclic lactones"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": 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"pid": [], "rank": 4, "affiliation": [], "fullname": "Hashem, Shaima"}, {"surname": "Andre\\u0301", "name": "Franc\\u0327ois", "pid": [], "rank": 5, "affiliation": [], "fullname": "Andr\\xe9, Fran\\xe7ois"}, {"surname": "Lespine", "name": "Anne", "pid": [], "rank": 6, "affiliation": [], "fullname": "Lespine, Anne"}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::8f87e10869299a5fe80b315695296b88", "value": "Elsevier"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["http://dx.doi.org/10.1016/j.ijpddr.2016.09.001"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::437f4b072b1aa198adcbc35910ff3b98", "value": "CORE"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-11-09T09:48:56.28Z", "fulltext": [], "dateoftransformation": "2020-02-27T19:44:40.709Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "AbstractMacrocyclic lactones (ML) are important anthelmintics used in animals and humans against parasite nematodes, but their therapeutic success is compromised by the spread of ML resistance. Some ABC transporters, such as p-glycoproteins (Pgps), are selected and overexpressed in ML-resistant nematodes, supporting a role for some drug efflux proteins in ML resistance. However, the role of such proteins in ML transport remains to be clarified at the molecular level. Recently, Caenorhabditis elegans Pgp-1 (Cel-Pgp-1) has been crystallized, and its drug-modulated ATPase function characterized in\\xa0vitro revealed Cel-Pgp-1 as a multidrug transporter. Using this crystal structure, we have developed an in silico drug docking model in order to study the binding of ML and other anthelmintic drugs to Cel-Pgp-1. All tested ML bound with high affinity in a unique site, within the inner chamber of the protein, supporting that ML may be transported by Cel-Pgp-1. Interestingly, interacting residues delineate a ML specific fingerprint involving H-bonds, including T1028. In particular, benzofurane and spiroketal moieties bound to specific sub-sites. When compared with the aglycone ML, such as moxidectin and ivermectin aglycone, avermectin anthelmintics have significant higher affinity for Cel-Pgp-1, likely due to the sugar substituent(s) that bind to a specific area involving H-bonds at Y771. Triclabendazole, closantel and emodepside bound with good affinities to different sub-sites in the inner chamber, partially overlapping with the ML binding site, suggesting that they could compete for Cel-Pgp-1-mediated ML transport. In conclusion, this work provides novel information on the role of nematode Pgps in transporting anthelmintics, and a valuable tool to predict drug-drug interactions and to rationally design new competitive inhibitors of clinically-relevant nematode Pgps, to improve anthelmintic therapeutics."}], "format": [], "journal": {"issnPrinted": "22113207", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "International Journal for Parasitology: Drugs and Drug Resistance", "iss": "3", "sp": "299", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "313", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": 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"dateoftransformation": "2020-03-05T22:53:48.852Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value":"BACKGROUND: Buprenorphine has recently been reported to be an alternative to methadone and LAAM for maintenance treatment of opioid dependent individuals, differing results are reported concerning its relative effectiveness indicating the need for an integrative review. OBJECTIVES: To evaluate the effects of buprenorphine maintenance against placebo and methadone maintenance in retaining patients in treatment and in suppressing illicit drug use. SEARCH STRATEGY: We searched the following databases up to 2001, inclusive: Cochrane Drugs and Alcohol Review Group Register, the Cochrane Controlled Trials Register, MEDLINE, EMBASE, Current Contents, Psychlit, CORK [www. state.vt.su/adap/cork], Alcohol and Drug Council of Australia (ADCA) [www.adca.org.au], Australian Drug Foundation (ADF -VIC) [www.adf.org.au], Centre for Education and Information on Drugs and Alcohol (CEIDA) [www.ceida.net.au], Australian Bibliographic Network (ABN), and Library of Congress databases, available NIDA monographs and the College on Problems of Drug Dependence Inc. proceedings, the reference lists of all identified studies and published reviews and authors of identified RCT's were asked about any other published or unpublished relevant RCT. SELECTION CRITERIA: Randomised clinical trials of buprenorphine maintenance compared with either placebo or methadone maintenance for opioid dependence. DATA COLLECTION AND ANALYSIS: Reviewers evaluated the papers separately and independently, rating methodological quality of concealment of allocation; data were extracted independently for meta-analysis and double-entered. MAIN RESULTS: Thirteen studies met the inclusion criteria, all were randomised clinical trials, all but one were double-blind. The method of concealment of allocation was not clearly described in 11 of the studies, otherwise methodological quality was good. Buprenorphine given in flexible doses appeared statistically significantly less effective than methadone in retaining patient in treatment (RR= 0.82; 95% CI: 0.69-0.96). Low dose buprenorphine is not superior to low dose methadone. High dose buprenorphine does not retain more patients than low dose methadone, but may suppress heroin use better. There was no advantage for high dose buprenorphine over high dose methadone in retention (RR=0.79; 95% CI:0.62-1.01), and high dose buprenorphine was inferior in suppression of heroin use. Buprenorphine was statistically significantly superior to placebo medication in retention of patients in treatment at low doses (RR=1.24; 95% CI: 1.06-1.45), high doses (RR=1.21; 95% CI: 1.02-1.44), and very high doses (RR=1.52; 95% CI: 1.23-1.88). However, only high and very high dose buprenorphine suppressed heroin use significantly above placebo. REVIEWER'S CONCLUSIONS: Buprenorphine is an effective intervention for use in the maintenance treatment of heroin dependence, but it is not more effective than methadone at adequate dosages."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "application/pdf"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, 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They are usually maintained with 10% fetal bovine serum (FBS) in vitro. Modified platelet-rich plasma (mPRP) would be a safe alternative to 10% FBS during SHEDs culture. Therefore, our study aimed to compare the proliferation and differentiation of SHEDs cultured in mPRP and FBS medium to explore an optimal concentration of mPRP for SHEDs maintenance. Platelets were harvested by automatic blood cell analyzer and activated by repeated liquid nitrogen freezing and thawing. The platelet-related cytokines were examined and analyzed by ELISA. SHEDs were extracted and cultured with different concentrations of mPRP or 10% FBS medium. Alkaline phosphatase (ALP) activity was measured. Mineralization factors, RUNX2 and OCN, were measured by real-time PCR. SHEDs were characterized with mesenchymal stem cells (MSCs) markers including vimentin, CD44, and CD105. mPRP at different concentrations (2, 5, 10, and 20%) enhanced the growth of SHEDs. Moreover, mPRP significantly stimulated ALP activity and promoted expression of RUNX2 and OCN compared with 10% FBS. mPRP could efficiently facilitate proliferation and differentiation of SHEDs, and 2% mPRP would be an optimal substitute for 10% FBS during SHEDs expansion and differentiation in clinical scale manufacturing."}], "format": [], "journal": {"issnPrinted": "1414-431X", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "Brazilian Journal of Medical and Biological Research", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", 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The performance of both methods was analyzed based on two datasets: 1) a complete site x species matrix compiled from two studies in different land uses in the Amazon using direct analysis of field samples and trap cultures. 2) Total number of AMF morphotypes detected by both methods in published manuscripts across several ecosystems. From dataset 1, direct analysis of field samples revealed 57 morphotypes, whereas only 21 of these were detected by trap culture. Community variation (beta diversity) analysis revealed that field samples are far more sensitive in detecting shifts in AMF community composition among land uses than trap cultures in the Amazon region, with the combined results of both methods being not better than that obtained only by direct analysis of field samples. 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"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824", "value": "DOAJ-Articles"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2020-03-15T08:56:22.261Z", "fulltext": [], "dateoftransformation": "2020-03-15T12:41:38.508Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Abstract Objective This study analyzed the maintenance of lateral incisors in the dental rehabilitation of individuals with cleft lip and palate. Material and Methods The study was conducted on a tertiary craniofacial center and comprised retrospective analysis of panoramic and periapical radiographs of Caucasoid individuals with non-syndromic complete unilateral cleft lip and palate, analyzing all radiographs available on the records of each individual, from the first to the last up to 12 years of age. Overall, 2,826 records were reviewed to achieve a sample of 1,000 individuals. Among these, 487 individuals presented the permanent lateral incisors on both cleft and non-cleft sides, which were included in this study. Results The results were evaluated in percentages and by descriptive statistics. The association between maintenance of the lateral incisor and timing of alveolar bone graft were analyzed by the t test. Among the 487 individuals, 265 had not completed treatment, 62 presented insufficient information, and 44 concluded the treatment elsewhere. Among the remaining 116 individuals, the lateral incisor was extracted from 88 (75.86%) of them on the cleft side (CS) and from 23 (19.83%) people on the non-cleft side (NCS). The age at accomplishment of alveolar bone graft was significantly associated with maintenance of the lateral incisor on the cleft side (p<0.01). Most extractions were indicated because of the inadequate positioning on the CS and for midline correction on the NCS. Rehabilitation was primarily completed by orthodontic movement (53 individuals on the CS and 13 individuals on the NCS). Conclusion In conclusion, the lateral incisor on the cleft side was not maintained in most individuals. Positive relationship was observed between extraction of the lateral incisor and age at accomplishment of the alveolar bone graft, suggesting the need to anticipate the initial radiographic evaluation to enhance its maintenance and reduce the procedures required for rehabilitation."}], "format": [], "journal": {"issnPrinted": "1678-7765", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "Journal of Applied Oral Science", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-05-01"}, "coverage": 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"", "invisible": false, "trust": ""}, "value": "2012-08-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|driver______::bee53aa31dc2cbb538c10c2b65fa5824", "value": "DOAJ-Articles"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2020-03-15T10:45:17.338Z", "fulltext": [], "dateoftransformation": "2020-03-15T14:07:40.174Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", 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MATERIAL AND METHODS: Test groups consisted of aqueous and ethanolic Aroeira extracts and saline (control). For edema quantification, 18 rats received an intravenous injection of Evan's Blue. After 30 min, the extracts and saline were injected on the dorsum of the rats, which were then sacrificed after 3 and 6 h. Readings were performed in a spectrophotometer. For subcutaneous implantation, 30 rats received a polyethylene tube containing the extracts on their dorsum and then they were killed after 7 and 28 days. The samples were processed for histological analysis and evaluated with a light microscope. The inflammatory infiltrate was quantified. RESULTS: There were no statistically significant differences between aqueous extract and saline groups in relation to edema quantification in the different periods (p>0.05). Ethanolic solution resulted in more edema independently of the experimental period (p<0.05). Histological analysis showed similar results on the 7-day period for the 3 groups. There was a notable reduction on inflammatory cell number for saline and aqueous extract groups at 28 days. CONCLUSION: The aqueous extract showed biocompatible properties similar to those of saline."}], "format": [], "journal": {"issnPrinted": "1678-7757", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "Journal of Applied Oral Science", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1678-7765", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2012-08-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, 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"qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Evaluation of tissue reaction to Aroeira (Myracrodruon urundeuva) extracts: a histologic and edemogenic study"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", 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Some ABC transporters, such as p-glycoproteins (Pgps), are selected and overexpressed in ML-resistant nematodes, supporting a role for some drug efflux proteins in ML resistance. However, the role of such proteins in ML transport remains to be clarified at the molecular level. Recently, Caenorhabditis elegans Pgp-1 (Cel-Pgp-1) has been crystallized, and its drug-modulated ATPase function characterized in\\xa0vitro revealed Cel-Pgp-1 as a multidrug transporter. Using this crystal structure, we have developed an in silico drug docking model in order to study the binding of ML and other anthelmintic drugs to Cel-Pgp-1. All tested ML bound with high affinity in a unique site, within the inner chamber of the protein, supporting that ML may be transported by Cel-Pgp-1. Interestingly, interacting residues delineate a ML specific fingerprint involving H-bonds, including T1028. In particular, benzofurane and spiroketal moieties bound to specific sub-sites. When compared with the aglycone ML, such as moxidectin and ivermectin aglycone, avermectin anthelmintics have significant higher affinity for Cel-Pgp-1, likely due to the sugar substituent(s) that bind to a specific area involving H-bonds at Y771. Triclabendazole, closantel and emodepside bound with good affinities to different sub-sites in the inner chamber, partially overlapping with the ML binding site, suggesting that they could compete for Cel-Pgp-1-mediated ML transport. In conclusion, this work provides novel information on the role of nematode Pgps in transporting anthelmintics, and a valuable tool to predict drug-drug interactions and to rationally design new competitive inhibitors of clinically-relevant nematode Pgps, to improve anthelmintic therapeutics."}], "format": [], "journal": {"issnPrinted": "2211-3207", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "International Journal for Parasitology: Drugs and Drug Resistance", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, 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Abstract

Background

Mental health problems are a worldwide public health burden. The literature concerning the mental health benefits from physical activity among adults has grown. Adolescents are less studied, and especially longitudinal studies are lacking. This paper investigates the associations between weekly hours of physical activity at age 15\\u201316 and mental health three years later.

Methods

Longitudinal self-reported health survey. The baseline study consisted of participants from the youth section of the Oslo Health Study, carried out in schools in 2000\\u20132001 (n = 3811). The follow-up in 2003\\u20132004 was conducted partly at school and partly through mail. A total of 2489 (1112 boys and 1377 girls) participated in the follow-up. Mental health was measured by the Strengths and Difficulties Questionnaire with an impact supplement. Physical activity was measured by a question on weekly hours of physical activity outside of school, defined as exertion \"to an extent that made you sweat and/or out of breath\". Adjustments were made for well-documented confounders and mental health at baseline.

Results

In boys, the number of hours spent on physical activity per week at age 15\\u201316 was negatively associated with emotional symptoms [B (95%CI) = -0.09 (-0.15, -0.03)] and peer problems [B (95%CI) = -0.08 (-0.14, -0.03)] at age 18\\u201319 after adjustments. In girls, there were no significant differences in SDQ subscales at age 18\\u201319 according to weekly hours of physical activity at age 15\\u201316 after adjustments. Boys and girls with five to seven hours of physical activity per week at age 15\\u201316 had the lowest mean scores for total difficulties and the lowest percentage with high impact score at age 18\\u201319, but the differences were not statistically significant after adjustments.

Conclusion

Weekly hours of physical activity at age 15\\u201316 years was weakly associated with mental health at three-year follow-up in boys. Results encourage a search for further knowledge about physical activity as a possible protective factor in relation to mental health problems in adolescence.

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R.", "pid": [], "rank": 1, "affiliation": [], "fullname": "Nelson J.R. Fagundes"}, {"surname": "", "name": "", "pid": [], "rank": 2, "affiliation": [], "fullname": "Alice Tagliani-Ribeiro"}, {"surname": "", "name": "", "pid": [], "rank": 3, "affiliation": [], "fullname": "Rohina Rubicz"}, {"surname": "", "name": "", "pid": [], "rank": 4, "affiliation": [], "fullname": "Larissa Tarskaia"}, {"surname": "Crawford", "name": "Michael H.", "pid": [], "rank": 5, "affiliation": [], "fullname": "Michael H. Crawford"}, {"surname": "Salzano", "name": "Francisco M.", "pid": [], "rank": 6, "affiliation": [], "fullname": "Francisco M. Salzano"}, {"surname": "Bonatto", "name": "Sandro L.", "pid": [], "rank": 7, "affiliation": [], "fullname": "Sandro L. 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Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. Recognizing the size of the genetic bottleneck during the peopling of the Americas is important for determining the extent of genetic markers needed to characterize Native American populations in genome-wide studies and to evaluate the adaptive potential of genetic variants in this population."}], "format": [], "journal": {"issnPrinted": "1678-4685", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "Genetics and Molecular Biology", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Sociedade Brasileira de Gen\\xe9tica"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:doaj.org/article:890de7eabf9b4658b8ce208d6641178c"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Genetics and Molecular Biology, Vol 41, Iss 1 suppl 1, Pp 206-214"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.1590/S0100-204X2004000300001"}], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", 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"name": "", "pid": [], "rank": 3, "affiliation": [], "fullname": "Marise Ventura Coutinho"}, {"surname": "", "name": "", "pid": [], "rank": 4, "affiliation": [], "fullname": "Daniel John Rigden"}, {"surname": "", "name": "", "pid": [], "rank": 5, "affiliation": [], "fullname": "Goran Neshich"}, {"surname": "", "name": "", "pid": [], "rank": 6, "affiliation": [], "fullname": "Maarten John Chrispeels"}, {"surname": "", "name": "", "pid": [], "rank": 7, "affiliation": [], "fullname": "Maria F\\xe1tima Grossi-de-S\\xe1"}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|doajarticles::1c6d69b7645cde261d6e598085f9020d", "value": "Pesquisa Agropecu\\xe1ria Brasileira"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2004000300001", "https://doaj.org/toc/0100-204X", "https://doaj.org/toc/1678-3921"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": 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"description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Despite the presence of a family of defense proteins, Phaseolus vulgaris can be attacked by bruchid insects resulting in serious damage to stored grains. The two distinct active forms of a-amylase inhibitors, a-AI1 and a-AI2, in P. vulgaris show different specificity toward a-amylases. Zabrotes subfasciatus a-amylase is inhibited by a-AI2 but not by a-AI1. In contrast, porcine a-amylase is inhibited by a-AI1 but not by a-AI2. The objective of this work was to understand the molecular basis of the specificity of two inhibitors in P. vulgaris (a-AI1 and a-AI2) in relation to a-amylases. Mutants of a-AI2 were made and expressed in tobacco plants. The results showed that all the a-AI2 mutant inhibitors lost their activity against the insect a-amylases but none exhibited activity toward the mammalian a-amylase. The replacement of His33 of a-AI2 with the a-AI1-like sequence Ser-Tyr-Asn abolished inhibition of Z. subfasciatus a-amylase. From structural modeling, the conclusion is that the size and complexity of the amylase-inhibitor interface explain why mutation of the N-terminal loop and resultant abolition of Z. subfasciatus a-amylase inhibition are not accompanied by gain of inhibitory activity against porcine a-amylase.
Apesar de possuir uma fam\\xedlia de prote\\xednas de defesa, o feij\\xe3o-comum (Phaseolus vulgaris L.) pode ser atacado por insetos bruqu\\xeddeos causando s\\xe9rios danos aos gr\\xe3os armazenados. O P. vulgaris possui duas formas ativas de inibidores de a-amilases, denominadas a-AI1 e a-AI2, que apresentam diferentes especificidades em rela\\xe7\\xe3o \\xe0s a-amilases. A a-amilase de Zabrotes subfasciatus \\xe9 inibida por a-AI2 mas n\\xe3o por a-AI1. Em contraste, a a-amilase pancre\\xe1tica de porco \\xe9 inibida por a-AI1 mas n\\xe3o \\xe9 por a-AI2. O objetivo deste trabalho foi entender as bases moleculares da especificidade desses inibidores em rela\\xe7\\xe3o \\xe0s a-amilases. Para tanto, foram constru\\xeddos mutantes do a-AI2, os quais foram expressados em plantas de fumo. Todos os inibidores mutantes deixaram de inibir a a-amilase de inseto sem, contudo, passar a exibir atividade contra a a-amilase de mam\\xedfero. Os modelos estruturais explicam por que a substitui\\xe7\\xe3o de His33 do a-AI2 pela seq\\xfc\\xeancia correspondente do a-AI1 (Ser-Tyr-Asn) aboliu a inibi\\xe7\\xe3o da a-amilase de Z. subfasciatus. Dos estudos de modelagem molecular pode-se concluir que o tamanho e a complexidade da interface a-amilase-inibidor explicam por que a muta\\xe7\\xe3o da al\\xe7a N-terminal e a quebra da atividade inibit\\xf3ria para a-amilase de Z. subfasciatus n\\xe3o levam ao ganho de atividade inibit\\xf3ria do mutante em rela\\xe7\\xe3o \\xe0 a-amilase de porco."}], "format": [], "journal": {"issnPrinted": "0100-204X", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "Pesquisa Agropecu\\xe1ria Brasileira", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1678-3921", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, 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The high resolution allows an accurate representation of the submarine canyons that presides in the region. The model is one-way coupled to a large scale model of the Mediterranean Sea through open boundaries and uses the atmospheric forcing fields provided in terms of HIRLAM outputs by the Spanish National Institute of Meteorology. Results show that the model can successfully reproduce the complex general circulation characteristics of the area, including the modifications induced by canyons in their vicinity and other phenomena observed such as instabilities and coastal trapped waves. The sea surface temperature is similar to satellite observations except that simulated temperatures are slightly warmer near the coast than observations and colder near the open boundaries. An important topic of this work is the computation of the shelf-slope exchanges, which are able to renew shelf waters in a few months."}], "format": [], "journal": {"issnPrinted": "1812-0784", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "Ocean Science", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1812-0792", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2006-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, 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"dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-10-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|driver______::bee53aa31dc2cbb538c10c2b65fa5824", "value": "DOAJ-Articles"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2020-03-15T07:28:17.941Z", "fulltext": [], "dateoftransformation": "2020-03-15T22:18:49.506Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "BACKGROUND The first dengue cases in Brazil with laboratory confirmation occurred in the northern region of the country, with the isolation of two serotypes, dengue virus 1 (DENV-1) and DENV-4. In Cear\\xe1, the introduction of DENV-4 was reported during a DENV-1 epidemic in 2011, with only two isolations. OBJECTIVES The aim of this study was to characterise the first DENV-4 epidemic in the state of Cear\\xe1, Brazil. METHODS The study population was composed of patients with suspected dengue that were reported to health care units from January to December 2012. The laboratory confirmation of infection was made by viral isolation, reverse transcription polymerase chain reaction (RT-PCR), AgNS1, immunohistochemistry and IgM enzyme-linked immunosorbent assay (ELISA). MAIN CONCLUSIONS In the study year, 72,211 suspected dengue cases were reported and 51,865 of these cases (71.8%) were confirmed to be positive. Co-circulation of three serotypes, DENV-1, DENV-3 and DENV-4, was detected with a predominance of DENV-4 (95.3%). Most cases were not severe, but there were 44 fatal outcomes. 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"inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value": "Crossref"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2019-02-15", "fulltext": [], "dateoftransformation": "", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "<p><strong>Abstract.</strong> This paper reviews multi-proxy paleoclimatic reconstructions with robust age-control derived from lacustrine, dendrochronological and geomorphological records and characterizes the main environmental changes that occurred in the Southern Pyrenees during the last millennium. Warmer and relatively arid conditions prevailed during the Medieval Climate Anomaly (MCA, ca. 900\\u20131300 AD), with a significant development of xerophytes and Mediterranean vegetation and limited deciduous tree formations (mesophytes). The Little Ice Age (LIA, 1300\\u20131800 AD) was generally colder and moister, with an expansion of deciduous taxa and cold-adapted montane conifers. Two major phases occurred within this period: (i) a transition MCA\\u2013LIA, characterized by fluctuating, moist conditions and relatively cold temperatures (ca. 1300 and 1600 AD); and (ii) a second period, characterized by the coldest and most humid conditions, coinciding with maximum (recent) glacier advances (ca. 1600\\u20131800 AD). Glaciers retreated after the LIA when warmer and more arid conditions dominated, interrupted by a short-living cooling episode during the late 19th to early 20th centuries. Some records suggest a response to solar activity with colder and slightly moister conditions during solar minima. Centennial-scale hydrological fluctuations are in phase with reconstructions of NAO variability, which appears to be one of the main climate mechanisms influencing rainfall variations in the region during the last millennium.</p>"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "This paper reviews multi-proxy paleoclimatic reconstructions with robust age-control derived from lacustrine, dendrochronological and geomorphological records and characterizes the main environmental changes that occurred in the Southern Pyrenees during the last millennium. Warmer and relatively arid conditions prevailed during the Medieval Climate Anomaly (MCA, ca. 900\\u20131300 AD), with a significant development of xerophytes and Mediterranean vegetation and limited deciduous tree formations (mesophytes). The Little Ice Age (LIA, 1300\\u20131800 AD) was generally colder and moister, with an expansion of deciduous taxa and cold-adapted montane conifers. Two major phases occurred within this period: (i) a transition MCA\\u2013LIA, characterized by fluctuating, moist conditions and relatively cold temperatures (ca. 1300 and 1600 AD); and (ii) a second period, characterized by the coldest and most humid conditions, coinciding with maximum (recent) glacier advances (ca. 1600\\u20131800 AD). Glaciers retreated after the LIA when warmer and more arid conditions dominated, interrupted by a short-living cooling episode during the late 19th to early 20th centuries. Some records suggest a response to solar activity with colder and slightly moister conditions during solar minima. Centennial-scale hydrological fluctuations are in phase with reconstructions of NAO variability, which appears to be one of the main climate mechanisms influencing rainfall variations in the region during the last millennium."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "Copernicus GmbH", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1814-9332", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2012-3-30"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", 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String iteration is a variation on the original binary version of the Kleene star operation p*q obtained by restricting the first argument to be a non-empty sequence of atomic actions. We show that, for every positive integer k, bisimulation equivalence over the set of processes in this language with loops of length at most k is finitely axiomatizable. We also offer a countably infinite equational theory that completely axiomatizes bisimulation equivalence over the whole language. We prove that this result cannot be improved upon by showing that no finite equational axiomatization of bisimulation equivalence over basic CCS with string iteration can exist, unless the set of actions is empty."}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value":"We study equational axiomatizations of bisimulation equivalence for the language obtained by extending Milner's basic CCS with string iteration. String iteration is a variation on the original binary version of the Kleene star operation p*q obtained by restricting the first argument to be a non-empty sequence of atomic actions. We show that, for every positive integer k, bisimulation equivalence over the set of processes in this language with loops of length at most k is finitely axiomatizable. We also offer a countably infinite equational theory that completely axiomatizes bisimulation equivalence over the whole language. 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The increase of private health care plans and the implementation of the \\u201cSmiling Brazil\\u201d Program, the largest public oral health care program in the world, could have influenced this increase in access. However, we do not yet know if inequalities in the use of dental health services persist after the improvement in access. The aims of this study are to analyze socioeconomic differences for dental health service use between 2003 and 2008 in Sao Paulo and to examine changes in these associations since the implementation of the Smiling Brazil program in 2003. Data was obtained via two household health surveys (ISA-Capital 2003 and ISA-Capital 2008) which investigated living conditions, lifestyle, health status and use of health care services. Logistic regression was used to analyze associations between socioeconomic factors and dental services use. Additionally, trends from 2003 to 2008 regarding socioeconomic characteristics and dental health service use were explored. Overall, dental health service use increased between 2003 and 2008 and was at both time points more common among those who had higher income, better education, better housing conditions, private health care plans and were Caucasian. Inequalities in use of dental health care did not decrease over time. Among the reasons for not seeking dental care, not having teeth and financial difficulty were more common in lower socioeconomic groups, while thinking it was unnecessary was more common in higher socioeconomic groups. The Brazilian oral health policy is still in a period of expansion and seems to have contributed slightly to increased dental health service use, but has not influenced socioeconomic inequalities in the use of these services. Acquiring deeper knowledge about inequalities in dental health service use will contribute to better understanding of potential barriers to reducing them."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "Springer Nature", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1472-6963", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-1"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "language": {"classid": "und", "classname": "Undetermined", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["10.1186/s12913-016-1928-y"], "source": [], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Socioeconomic inequalities in dental health services in Sao Paulo, Brazil, 2003\\u20132008"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.1055/sos-sd-012-00797"}], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "relevantdate": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "published-online", "classname": "published-online", "schemeid": "dnet:dataCite_date", "schemename": "dnet:dataCite_date"}, "value": "2002-1-1"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "published-print", "classname": "published-print", "schemeid": "dnet:dataCite_date", "schemename": "dnet:dataCite_date"}, "value": "2002-1-1"}], "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value": "Crossref"}], "id": "50|doiboost____::0ec386b46d4571b066dd00d889c70bb4", "subject": [], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Hajos", "name": "G.", "pid": [], "rank": 1, "affiliation": [], "fullname": "G. 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Here, we tested whether deletion of PARP-2, an alternative NAD+-consuming enzyme, impacts on NAD+ bioavailability and SIRT1 activity. Our results indicate that PARP-2 deficiency increases SIRT1 activity in cultured myotubes. However, this increase was not due to changes in NAD+ levels, but to an increase in SIRT1 expression, as PARP-2 acts as a direct negative regulator of the SIRT1 promoter. PARP-2 deletion in mice increases SIRT1 levels, promotes energy expenditure, and increases mitochondrial content. Furthermore, PARP-2\\u2212/\\u2212 mice were protected against diet-induced obesity. Despite being insulin sensitized, PARP-2\\u2212/\\u2212 mice were glucose intolerant due to a defective pancreatic function. 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I would like to suggest three additional impeding factors. The first is that there are too many different kinds of providers' trying to address the same problem in sometimes incompatible ways. It is clearly essential to define health care in terms of what people actually need, but endeavors to do so have moved under a variety of banners\\u2014family medicine, holistic treatment, practices sponsored by hospitals and private corporations, and now community-oriented primary care. As a family physician, I see this as constantly reinventing the wheel, each time using new words that confuse people and creating new and overlapping constituencies. 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The MSV-MIDAS model is estimated via maximum likelihood (ML) methods. The estimation relies on a slightly modified version of Hamilton's recursive filter. We use Monte Carlo simulations to assess the robustness of the estimation procedure and related test statistics. The results show that ML provides accurate estimates, but they suggest some caution in interpreting the tests of the parameters involved in the transition probabilities. We apply this new model to the detection and forecasting of business cycle turning points in the United States. We properly detect recessions by exploiting the link between GDP growth and higher frequency variables from financial and energy markets. The spread term is a particularly useful indicator to predict recessions in the United States. 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The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC-SIGN and DC-SIGNR (collectively termed as DC-SIGN/R) using a sensitive, ratiometric Forster resonance energy transfer (FRET) assay. The QD probes specifically bind DC-SIGN, but not its closely related receptor DC-SIGNR, which is further confirmed by its specific blocking of DC-SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC-SIGN binds more efficiently to densely packed mannosides. A FRET-based thermodynamic study reveals that the binding is enthalpy-driven. 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"trust": ""}, "value": "Macrocyclic lactones (ML) are important anthelmintics used in animals and humans against parasite nematodes, but their therapeutic success is compromised by the spread of ML resistance. Some ABC transporters, such as p-glycoproteins (Pgps), are selected and overexpressed in ML-resistant nematodes, supporting a role for some drug efflux proteins in ML resistance. However, the role of such proteins in ML transport remains to be clarified at the molecular level. Recently, Caenorhabditis elegans Pgp-1 (Cel-Pgp-1) has been crystallized, and its drug-modulated ATPase function characterized in\\xa0vitro revealed Cel-Pgp-1 as a multidrug transporter. Using this crystal structure, we have developed an in silico drug docking model in order to study the binding of ML and other anthelmintic drugs to Cel-Pgp-1. All tested ML bound with high affinity in a unique site, within the inner chamber of the protein, supporting that ML may be transported by Cel-Pgp-1. Interestingly, interacting residues delineate a ML specific fingerprint involving H-bonds, including T1028. In particular, benzofurane and spiroketal moieties bound to specific sub-sites. When compared with the aglycone ML, such as moxidectin and ivermectin aglycone, avermectin anthelmintics have significant higher affinity for Cel-Pgp-1, likely due to the sugar substituent(s) that bind to a specific area involving H-bonds at Y771. Triclabendazole, closantel and emodepside bound with good affinities to different sub-sites in the inner chamber, partially overlapping with the ML binding site, suggesting that they could compete for Cel-Pgp-1-mediated ML transport. In conclusion, this work provides novel information on the role of nematode Pgps in transporting anthelmintics, and a valuable tool to predict drug-drug interactions and to rationally design new competitive inhibitors of clinically-relevant nematode Pgps, to improve anthelmintic therapeutics."}], "format": [], "journal": {"issnPrinted": "2211-3207", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "Elsevier BV", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-1"}, "coverage": [], 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Recently it has received a lot of attention as a substrate to grow and isolate graphene as well as for its intrinsic UV lasing response. Similar to carbon, one-dimensional boron nitride nanotubes (BNNTs) have been theoretically predicted and later synthesised. Here we use first principles simulations to unambiguously demonstrate that i) BN nanotubes inherit the highly efficient UV luminescence of hexagonal BN; ii) the application of an external perpendicular field closes the electronic gap keeping the UV lasing with lower yield; iii) defects in BNNTS are responsible for tunable light emission from the UV to the visible controlled by a transverse electric field (TEF). 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"inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "ABSTRACTThis paper introduces a Markov-switching model in which transition probabilities depend on higher frequency indicators and their lags through polynomial weighting schemes. The MSV-MIDAS model is estimated through maximum likelihood (ML) methods with a slightly modified version of Hamilton\\u2019s filter. Monte Carlo simulations show that ML provides accurate estimates, but they suggest some caution in interpreting the tests of the parameters in the transition probabilities. We apply this new model to forecast business cycle turning points in the United States. 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Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. 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The high resolution al- lows an accurate representation of the submarine canyons that presides in the region. The model is one-way coupled to a large scale model of the Mediterranean Sea through open boundaries and uses the atmospheric forcing fields provided in terms of HIRLAM outputs by the Spanish National Insti- tute of Meteorology. Results show that the model can suc- cessfully reproduce the complex general circulation charac- teristics of the area, including the modifications induced by canyons in their vicinity and other phenomena observed such as instabilities and coastal trapped waves. The sea surface temperature is similar to satellite observations except that simulated temperatures are slightly warmer near the coast than observations and colder near the open boundaries. 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Material and Methods The study was conducted on a tertiary craniofacial center and comprised retrospective analysis of panoramic and periapical radiographs of Caucasoid individuals with non-syndromic complete unilateral cleft lip and palate, analyzing all radiographs available on the records of each individual, from the first to the last up to 12 years of age. Overall, 2,826 records were reviewed to achieve a sample of 1,000 individuals. Among these, 487 individuals presented the permanent lateral incisors on both cleft and non-cleft sides, which were included in this study. Results The results were evaluated in percentages and by descriptive statistics. The association between maintenance of the lateral incisor and timing of alveolar bone graft were analyzed by the t test. Among the 487 individuals, 265 had not completed treatment, 62 presented insufficient information, and 44 concluded the treatment elsewhere. Among the remaining 116 individuals, the lateral incisor was extracted from 88 (75.86%) of them on the cleft side (CS) and from 23 (19.83%) people on the non-cleft side (NCS). The age at accomplishment of alveolar bone graft was significantly associated with maintenance of the lateral incisor on the cleft side (p<0.01). Most extractions were indicated because of the inadequate positioning on the CS and for midline correction on the NCS. Rehabilitation was primarily completed by orthodontic movement (53 individuals on the CS and 13 individuals on the NCS). Conclusion In conclusion, the lateral incisor on the cleft side was not maintained in most individuals. Positive relationship was observed between extraction of the lateral incisor and age at accomplishment of the alveolar bone graft, suggesting the need to anticipate the initial radiographic evaluation to enhance its maintenance and reduce the procedures required for rehabilitation."}], "format": [], "journal": {"issnPrinted": "1678-7757", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "FapUNIFESP (SciELO)", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1678-7765", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-5-7"}, "coverage": [], 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In Ceara, the introduction of DENV-4 was reported during a DENV-1 epidemic in 2011, with only two isolations. OBJECTIVES The aim of this study was to characterise the first DENV-4 epidemic in the state of Ceara, Brazil. METHODS The study population was composed of patients with suspected dengue that were reported to health care units from January to December 2012. The laboratory confirmation of infection was made by viral isolation, reverse transcription polymerase chain reaction (RT-PCR), AgNS1, immunohistochemistry and IgM enzyme-linked immunosorbent assay (ELISA). MAIN CONCLUSIONS In the study year, 72,211 suspected dengue cases were reported and 51,865 of these cases (71.8%) were confirmed to be positive. Co-circulation of three serotypes, DENV-1, DENV-3 and DENV-4, was detected with a predominance of DENV-4 (95.3%). Most cases were not severe, but there were 44 fatal outcomes. 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"dateofcollection": "2019-02-15", "fulltext": [], "dateoftransformation": "", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "ABSTRACT\\n \\n Nontypeable\\n Haemophilus influenzae\\n (NTHi) is an opportunistic pathogen that mainly causes otitis media in children and community-acquired pneumonia or exacerbations of chronic obstructive pulmonary disease in adults. A large variety of studies suggest that biofilm formation by NTHi may be an important step in the pathogenesis of this bacterium. However, the underlying mechanisms involved in this process are poorly elucidated. In this study, we used a transposon mutant library to identify bacterial genes involved in biofilm formation. The growth and biofilm formation of 4,172 transposon mutants were determined, and the involvement of the identified genes in biofilm formation was validated in\\n in vitro\\n experiments. Here, we present experimental data showing that increased bacterial lysis, through interference with peptidoglycan synthesis, results in elevated levels of extracellular DNA, which increased biofilm formation. Interestingly, similar results were obtained with subinhibitory concentrations of \\u03b2-lactam antibiotics, known to interfere with peptidoglycan synthesis, but such an effect does not appear with other classes of antibiotics. These results indicate that treatment with \\u03b2-lactam antibiotics, especially for \\u03b2-lactam-resistant NTHi isolates, might increase resistance to antibiotics by increasing biofilm formation.\\n \\n \\n IMPORTANCE\\n Most, if not all, bacteria form a biofilm, a multicellular structure that protects them from antimicrobial actions of the host immune system and affords resistance to antibiotics. The latter is especially disturbing with the increase in multiresistant bacterial clones worldwide. Bacterial biofilm formation is a multistep process that starts with surface adhesion, after which attached bacteria divide and give rise to biomass. The actual steps required for\\n Haemophilus influenzae\\n biofilm formation are largely not known. We show that interference with peptidoglycan biosynthesis increases biofilm formation because of the release of bacterial genomic DNA. Subinhibitory concentrations of \\u03b2-lactam antibiotics, which are often prescribed to treat\\n H.\\xa0influenzae\\n infections, increase biofilm formation through a similar mechanism. Therefore, when \\u03b2-lactam antibiotics do not reach their MIC\\n in vivo\\n , they might not only drive selection for \\u03b2-lactam-resistant clones but also increase biofilm formation and resistance to other antimicrobial compounds.\\n "}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "American Society for Microbiology", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "2379-5042", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2017-1-18"}, "coverage": [], "publisher": {"dataInfo": 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No thoughtful person can argue with the logic of this approach. How can one believe that improvements in health can occur without thorough epidemiologic knowledge of health problems that exist in a community or a society? How can preventive, rehabilitative, or curative services be fully effective if one knows little or nothing about the cultural, educational, economic, or psychological factors that can create barriers to care, isolate groups, and increase personal health risks for community inhabitants? No one in modern society can believe that a physician working in isolation, and simply treating those who come to him on a one-on-one basis, can produce a healthy society. 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Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. 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Material and methods: Test groups consisted of aqueous and ethanolic Aroeira extracts and saline (control). For groups consisted of aqueous and ethanolic Aroeira extracts and saline Blue. After 30 min, the extracts and saline were injected on the dorsum of the rats, which were then sacrificed after 3 and 6 h. Readings were performed in a spectrophotometer. For subcutaneous implantation, 30 rats received a polyethylene tube containing the extracts on their dorsum and then they were killed after 7 and 28 days. The samples were processed for histological analysis and evaluated with a light microscope. The inflammatory infiltrate was quantified. Results: There were no statistically significant differences between aqueous extract and saline groups in relation to edema quantification in the different periods (p > 0.05). Ethanolic solution resulted in more edema independently of the experimental period (p < 0.05). 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No. of bitstreams: 5\\nMutants of common bean alpha_amylase inhibitor_2.PDF: 128607 bytes, checksum: ea73a49dc66da14a08f402c9d8cfe551 (MD5)\\nlicense_url: 52 bytes, checksum: 2f32edb9c19a57e928372a33fd08dba5 (MD5)\\nlicense_text: 24372 bytes, checksum: 94b0a37ff5ec51de8c55507bff4a7ff9 (MD5)\\nlicense_rdf: 24623 bytes, checksum: 378d22d8fe50e084ee2f354be78cbe62 (MD5)\\nlicense.txt: 1887 bytes, checksum: 445d1980f282ec865917de35a4c622f6 (MD5)\\n Previous issue date: 2004-03\\nDespite the presence of a family of defense proteins, Phaseolus vulgaris can be attacked by bruchid\\ninsects resulting in serious damage to stored grains. The two distinct active forms of \\u03b1-amylase inhibitors, \\u03b1-AI1\\nand \\u03b1-AI2, in P. vulgaris show different specificity toward \\u03b1-amylases. Zabrotes subfasciatus \\u03b1-amylase is\\ninhibited by \\u03b1-AI2 but not by \\u03b1-AI1. In contrast, porcine \\u03b1-amylase is inhibited by \\u03b1-AI1 but not by \\u03b1-AI2. The\\nobjective of this work was to understand the molecular basis of the specificity of two inhibitors in P. vulgaris\\n(\\u03b1-AI1 and \\u03b1-AI2) in relation to \\u03b1-amylases. Mutants of \\u03b1-AI2 were made and expressed in tobacco plants. The\\nresults showed that all the \\u03b1-AI2 mutant inhibitors lost their activity against the insect \\u03b1-amylases but none\\nexhibited activity toward the mammalian \\u03b1-amylase. The replacement of His33 of \\u03b1-AI2 with the \\u03b1-AI1-like\\nsequence Ser-Tyr-Asn abolished inhibition of Z. subfasciatus \\u03b1-amylase. 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No. of bitstreams: 0\\n Previous issue date: 2012-07-01\\nMade available in DSpace on 2013-09-30T18:30:31Z (GMT). No. of bitstreams: 0\\n Previous issue date: 2012-07-01\\nSubmitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-20T13:44:11Z\\nNo. of bitstreams: 0\\nMade available in DSpace on 2014-05-20T13:44:11Z (GMT). No. of bitstreams: 0\\n Previous issue date: 2012-07-01\\nCoordena\\xe7\\xe3o de Aperfei\\xe7oamento de Pessoal de N\\xedvel Superior (CAPES)\\nObjectives: This study evaluated subcutaneous tissue response to Aroeira (Myracrodruon urundeuva) extract employing edemogenic and histological analyses. Material and methods: Test groups consisted of aqueous and ethanolic Aroeira extracts and saline (control). For groups consisted of aqueous and ethanolic Aroeira extracts and saline Blue. After 30 min, the extracts and saline were injected on the dorsum of the rats, which were then sacrificed after 3 and 6 h. Readings were performed in a spectrophotometer. For subcutaneous implantation, 30 rats received a polyethylene tube containing the extracts on their dorsum and then they were killed after 7 and 28 days. The samples were processed for histological analysis and evaluated with a light microscope. The inflammatory infiltrate was quantified. Results: There were no statistically significant differences between aqueous extract and saline groups in relation to edema quantification in the different periods (p > 0.05). Ethanolic solution resulted in more edema independently of the experimental period (p < 0.05). Histological analysis showed similar results on the 7-day period for the 3 groups. There was a notable reduction on inflammatory cell number for saline and aqueous extract groups at 28 days. 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The performance of both methods was analyzed based on two datasets: 1) a complete site x species matrix compiled from two studies in different land uses in the Amazon using direct analysis of field samples and trap cultures. 2) Total number of AMF morphotypes detected by both methods in published manuscripts across several ecosystems. From dataset 1, direct analysis of field samples revealed 57 morphotypes, whereas only 21 of these were detected by trap culture. Community variation (beta diversity) analysis revealed that field samples are far more sensitive in detecting shifts in AMF community composition among land uses than trap cultures in the Amazon region, with the combined results of both methods being not better than that obtained only by direct analysis of field samples. Analysis of dataset 2 showed that the relative performance of trap cultures, using direct analysis of field sample as reference, was inversely related to the total observed AMF species richness."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "text/html"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2017-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Academia Brasileira de Ci\\xeancias"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:scielo:S0001-37652017005017105"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Anais da Academia Brasileira de Ci\\xeancias n.ahead 2017"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "reponame:Anais da Academia Brasileira de Ci\\xeancias"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "instname:ABC"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "instacron:ABC"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Assessment of the occurrence and richness of arbuscular mycorrhizal fungal spores by direct analysis of field samples and trap culture - 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No. of bitstreams: 0\\n Previous issue date: 2009-12-01\\nMade available in DSpace on 2015-11-25T19:19:41Z (GMT). No. of bitstreams: 2\\nS1517-83822009000400019.pdf: 200940 bytes, checksum: 1777d3b67ffff6a12f7fd5e5d25fe530 (MD5)\\nS1517-83822009000400019.pdf.txt: 20125 bytes, checksum: 44e81b8448679e3abad7b2470dd24899 (MD5)\\n Previous issue date: 2009-12-01\\nThis study aimed at isolating and characterizing of microorganisms able to use linamarin as sole carbon source. Thirty one microbial strains were isolated from manipueira, a liquid effluent of cassava processing factories. 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{"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2020-03-06T22:08:30.467Z", "fulltext": [], "dateoftransformation": "2020-03-08T23:25:38.587Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "BACKGROUND The first dengue cases in Brazil with laboratory confirmation occurred in the northern region of the country, with the isolation of two serotypes, dengue virus 1 (DENV-1) and DENV-4. In Cear\\xe1, the introduction of DENV-4 was reported during a DENV-1 epidemic in 2011, with only two isolations. OBJECTIVES The aim of this study was to characterise the first DENV-4 epidemic in the state of Cear\\xe1, Brazil. METHODS The study population was composed of patients with suspected dengue that were reported to health care units from January to December 2012. The laboratory confirmation of infection was made by viral isolation, reverse transcription polymerase chain reaction (RT-PCR), AgNS1, immunohistochemistry and IgM enzyme-linked immunosorbent assay (ELISA). MAIN CONCLUSIONS In the study year, 72,211 suspected dengue cases were reported and 51,865 of these cases (71.8%) were confirmed to be positive. Co-circulation of three serotypes, DENV-1, DENV-3 and DENV-4, was detected with a predominance of DENV-4 (95.3%). Most cases were not severe, but there were 44 fatal outcomes. DENV-4 Genotype II was identified for the first time in Cear\\xe1."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "text/html"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-01-01"}, "coverage": [], "publisher": 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"Inequalities in health care services"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "Health surveys"}], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Monteiro", "name": "Camila Nascimento", "pid": [], "rank": 1, "affiliation": [], "fullname": "Monteiro, Camila Nascimento"}, {"surname": "Beenackers", "name": "Marie\\u0308lle A.", "pid": [], "rank": 2, "affiliation": [], "fullname": "Beenackers, Mari\\xeblle A."}, {"surname": "Goldbaum", "name": "Moises", "pid": [], "rank": 3, "affiliation": [], "fullname": "Goldbaum, Moises"}, {"surname": "Barros", "name": "Marilisa Berti Azevedo", "pid": [], "rank": 4, "affiliation": [], "fullname": "Barros, Marilisa Berti de Azevedo"}, {"surname": "Gianini", "name": "Reinaldo Jose\\u0301", "pid": [], "rank": 5, "affiliation": [], "fullname": "Gianini, Reinaldo Jos\\xe9"}, {"surname": "Cesar", "name": "Chester Luiz Galvao", "pid": [], "rank": 6, "affiliation": [], "fullname": "Cesar, Chester Luiz Galvao"}, {"surname": "Mackenbach", "name": "Johan P.", "pid": [], "rank": 7, "affiliation": [], "fullname": "Mackenbach, Johan P."}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::dc6e224a8d74ce03bf301152d6e33e97", "value": "LA Referencia"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["http://www.producao.usp.br/handle/BDPI/51184"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", 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"description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Abstract\\n \\n Background\\n Access to, and use of, dental health services in Brazil have improved since 2003. The increase of private health care plans and the implementation of the \\u201cSmiling Brazil\\u201d Program, the largest public oral health care program in the world, could have influenced this increase in access. However, we do not yet know if inequalities in the use of dental health services persist after the improvement in access. The aims of this study are to analyze socioeconomic differences for dental health service use between 2003 and 2008 in S\\xe3o Paulo and to examine changes in these associations since the implementation of the Smiling Brazil program in 2003.\\n \\n \\n Method\\n Data was obtained via two household health surveys (ISA-Capital 2003 and ISA-Capital 2008) which investigated living conditions, lifestyle, health status and use of health care services. Logistic regression was used to analyze associations between socioeconomic factors and dental services use. Additionally, trends from 2003 to 2008 regarding socioeconomic characteristics and dental health service use were explored.\\n \\n \\n Results\\n Overall, dental health service use increased between 2003 and 2008 and was at both time points more common among those who had higher income, better education, better housing conditions, private health care plans and were Caucasian. Inequalities in use of dental health care did not decrease over time. Among the reasons for not seeking dental care, not having teeth and financial difficulty were more common in lower socioeconomic groups, while thinking it was unnecessary was more common in higher socioeconomic groups.\\n \\n \\n Conclusions\\n The Brazilian oral health policy is still in a period of expansion and seems to have contributed slightly to increased dental health service use, but has not influenced socioeconomic inequalities in the use of these services. Acquiring deeper knowledge about inequalities in dental health service use will contribute to better understanding of potential barriers to reducing them."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, 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{"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "instname:USP"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Socioeconomic inequalities in dental health services in Sao Paulo, Brazil, 2003\\u20132008"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": 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C. M. Da", "pid": [], "rank": 1, "affiliation": [], "fullname": "SILVA, M.C.M. da"}, {"surname": "Mello", "name": "L. V.", "pid": [], "rank": 2, "affiliation": [], "fullname": "MELLO, L.V."}, {"surname": "Coutinho", "name": "M. V.", "pid": [], "rank": 3, "affiliation": [], "fullname": "COUTINHO, M.V."}, {"surname": "Rigden", "name": "D. J.", "pid": [], "rank": 4, "affiliation": [], "fullname": "RIGDEN, D.J."}, {"surname": "Neshich", "name": "G.", "pid": [], "rank": 5, "affiliation": [], "fullname": "NESHICH, G."}, {"surname": "Chrispeels", "name": "M. J.", "pid": [], "rank": 6, "affiliation": [], "fullname": "CHRISPEELS, M.J."}, {"surname": "Grossi-De-Sa\\u0301", "name": "M. F.", "pid": [], "rank": 7, "affiliation": [], "fullname": "GROSSI-DE-S\\xc1, M.F."}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::dc6e224a8d74ce03bf301152d6e33e97", "value": "LA Referencia"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["http://www.alice.cnptia.embrapa.br/handle/doc/110087", "http://ainfo.cnptia.embrapa.br/digital/bitstream/AI-SEDE/26490/1/v39n03a01.pdf"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2004-01-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::dc6e224a8d74ce03bf301152d6e33e97", "value": "LA Referencia"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2020-03-06T19:06:28.786Z", "fulltext": [], "dateoftransformation": "2020-03-09T11:05:49.071Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Despite the presence of a family of defense proteins, Phaseolus vulgaris can be attacked by bruchid insects resulting in serious damage to stored grains. The two distinct active forms of a-amylase inhibitors, a-AI1 and a-AI2, in P. vulgaris show different specificity toward a-amylases. Zabrotes subfasciatus a-amylase is inhibited by a-AI2 but not by a-AI1. In contrast, porcine a-amylase is inhibited by a-AI1 but not by a-AI2. The objective of this work was to understand the molecular basis of the specificity of two inhibitors in P. vulgaris (a-AI1 and a-AI2) in relation to a-amylases. Mutants of a-AI2 were made and expressed in tobacco plants. The results showed that all the a-AI2 mutant inhibitors lost their activity against the insect a-amylases but none exhibited activity toward the mammalian a-amylase. The replacement of His33 of a-AI2 with the a-AI1-like sequence Ser-Tyr-Asn abolished inhibition of Z. subfasciatus a-amylase. From structural modeling, the conclusion is that the size and complexity of the amylase-inhibitor interface explain why mutation of the N-terminal loop and resultant abolition of Z. subfasciatus a-amylase inhibition are not accompanied by gain of inhibitory activity against porcine a-amylase.\\nMade available in DSpace on 2011-04-09T12:30:48Z (GMT). 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Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. 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No. of bitstreams: 1\\nwos2012-2315_en.pdf: 1140692 bytes, checksum: 5d0dfabfd91477f637f156297db56f46 (MD5)\\n Previous issue date: 2012\\nCoordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)\\nCoordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)\\nObjectives: This study evaluated subcutaneous tissue response to Aroeira (Myracrodruon urundeuva) extract employing edemogenic and histological analyses. Material and methods: Test groups consisted of aqueous and ethanolic Aroeira extracts and saline (control). For groups consisted of aqueous and ethanolic Aroeira extracts and saline Blue. After 30 min, the extracts and saline were injected on the dorsum of the rats, which were then sacrificed after 3 and 6 h. Readings were performed in a spectrophotometer. For subcutaneous implantation, 30 rats received a polyethylene tube containing the extracts on their dorsum and then they were killed after 7 and 28 days. The samples were processed for histological analysis and evaluated with a light microscope. The inflammatory infiltrate was quantified. Results: There were no statistically significant differences between aqueous extract and saline groups in relation to edema quantification in the different periods (p > 0.05). Ethanolic solution resulted in more edema independently of the experimental period (p < 0.05). Histological analysis showed similar results on the 7-day period for the 3 groups. There was a notable reduction on inflammatory cell number for saline and aqueous extract groups at 28 days. 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No. of bitstreams: 0\\n Previous issue date: 1998\\nMade available in DSpace on 2015-11-26T15:21:42Z (GMT). No. of bitstreams: 0\\n Previous issue date: 1998\\nWe show that pulsar velocities may arise from anisotropic neutrino emission induced by resonant conversions of massless neutrinos in the presence of a strong magnetic field. The main ingredient is a small weak universality violation and neither neutrino masses nor magnetic moments are required.\\n81\\n12\\n2412\\n2415\\nLyne, A.G., Lorimer, D.R., (1994) Nature (London), 369, p. 127\\nChugai, N.N., (1984) Sov. Astron. Lett., 10, p. 87\\nVilenkin, A., (1995) Astrophys. J., 451, p. 700. , Dong Lai and Y.-Z. Qian, astro-ph/9712043\\nKusenko, A., Segre, G., (1996) Phys. Rev. Lett., 77, p. 4872\\nMikheyev, M., Smirnov, A., (1986) Sov. J. Nucl. Phys., 42, p. 913\\nWolfenstein, L., (1978) Phys. Rev. D, 17, p. 2369\\n(1979) Phys. Rev. D, 20, p. 2634\\nD'Olivo, J.C., Nieves, J.F., Pal, P.B., (1989) Phys. Rev. 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Phys., 26, p. 91\\nSchechter, J., Valle, J.W.F., (1980) Phys. Rev. D, 22, p. 2227\\nGronau, M., Leung, C.N., Rosner, J.L., (1984) Phys. Rev. D, 29, p. 2539\\nLangacker, P., London, D., (1988) Phys. Rev. D, 38, p. 886\\n(1988) Phys. Rev. D, 38, p. 907\\nIlakovac, A., Pilaftsis, A., (1995) Nucl. Phys., B437, p. 491\\nNardi, E., Roulet, E., Tommasini, D., (1995) Phys. Lett. B, 344, p. 225\\nSuzuki, H., (1994) Physics and Astrophysics of Neutrinos, p. 763. , edited by M. Fukugita and A. Suzuki Springer-Verlag, Tokyo\\nWilson, J.R., Mayle, R., (1989) Advanced Study Institute on the Nuclear Equation of State, 216 A, p. 731. , edited by Walter Greiner and Horst St\\xf6cker, NATO ASI, Ser. B, Plenum Press, New York, H.-Th. Janka and W. Keil, astro-ph/9709210\\nSusuki, H., private communicationNunokawa, H., Semikoz, V.B., Smirnov, A.Yu., Valle, J.W.F., (1997) Nucl. Phys., B501, p. 17\\nThompson, C., Duncan, R., (1993) Astrophys. 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Material and methods: Test groups consisted of aqueous and ethanolic Aroeira extracts and saline (control). For groups consisted of aqueous and ethanolic Aroeira extracts and saline Blue. After 30 min, the extracts and saline were injected on the dorsum of the rats, which were then sacrificed after 3 and 6 h. Readings were performed in a spectrophotometer. For subcutaneous implantation, 30 rats received a polyethylene tube containing the extracts on their dorsum and then they were killed after 7 and 28 days. The samples were processed for histological analysis and evaluated with a light microscope. The inflammatory infiltrate was quantified. Results: There were no statistically significant differences between aqueous extract and saline groups in relation to edema quantification in the different periods (p > 0.05). Ethanolic solution resulted in more edema independently of the experimental period (p < 0.05). 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No. of bitstreams: 1\\n12913_2016_Article_1928.pdf: 448641 bytes, checksum: 476068e13972398a4cf2ac850756e91e (MD5)\\n Previous issue date: 2016-12-07\\nS\\xe3o Paulo Research Foundation-FAPESP. Process 2012/214153-0 and\\n2013/26687-2.\\nNational Council for Scientific and Technological Development (CNPq).\\nThe surveys were financed by the Municipal Health Secretary of S\\xe3o Paulo.\\nResearchers from three universities in S\\xe3o Paulo state (University of Sao\\nPaulo, University of Campinas and University of the State of S\\xe3o Paulo)\\nparticipated in administering the surveys.\\nAbstract\\n \\n Background\\n Access to, and use of, dental health services in Brazil have improved since 2003. The increase of private health care plans and the implementation of the \\u201cSmiling Brazil\\u201d Program, the largest public oral health care program in the world, could have influenced this increase in access. However, we do not yet know if inequalities in the use of dental health services persist after the improvement in access. The aims of this study are to analyze socioeconomic differences for dental health service use between 2003 and 2008 in S\\xe3o Paulo and to examine changes in these associations since the implementation of the Smiling Brazil program in 2003.\\n \\n \\n Method\\n Data was obtained via two household health surveys (ISA-Capital 2003 and ISA-Capital 2008) which investigated living conditions, lifestyle, health status and use of health care services. Logistic regression was used to analyze associations between socioeconomic factors and dental services use. Additionally, trends from 2003 to 2008 regarding socioeconomic characteristics and dental health service use were explored.\\n \\n \\n Results\\n Overall, dental health service use increased between 2003 and 2008 and was at both time points more common among those who had higher income, better education, better housing conditions, private health care plans and were Caucasian. Inequalities in use of dental health care did not decrease over time. Among the reasons for not seeking dental care, not having teeth and financial difficulty were more common in lower socioeconomic groups, while thinking it was unnecessary was more common in higher socioeconomic groups.\\n \\n \\n Conclusions\\n The Brazilian oral health policy is still in a period of expansion and seems to have contributed slightly to increased dental health service use, but has not influenced socioeconomic inequalities in the use of these services. 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"instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2020-03-06T19:32:24.281Z", "fulltext": [], "dateoftransformation": "2020-03-10T13:01:30.394Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Sao Paulo Research Foundation-FAPESP [2012/214153-0, 2013/26687-2]\\nNational Council for Scientific and Technological Development (CNPq)\\nMade available in DSpace on 2017-11-13T13:21:11Z (GMT). No. of bitstreams: 1\\n000391882500001.pdf: 441415 bytes, checksum: f66ad4c53af317f4f6cec06ac56dfea6 (MD5)\\n Previous issue date: 2016\\nAccess to, and use of, dental health services in Brazil have improved since 2003. The increase of private health care plans and the implementation of the \"Smiling Brazil\" Program, the largest public oral health care program in the world, could have influenced this increase in access. However, we do not yet know if inequalities in the use of dental health services persist after the improvement in access. The aims of this study are to analyze socioeconomic differences for dental health service use between 2003 and 2008 in Sao Paulo and to examine changes in these associations since the implementation of the Smiling Brazil program in 2003. Method: Data was obtained via two household health surveys (ISA-Capital 2003 and ISA-Capital 2008) which investigated living conditions, lifestyle, health status and use of health care services. Logistic regression was used to analyze associations between socioeconomic factors and dental services use. Additionally, trends from 2003 to 2008 regarding socioeconomic characteristics and dental health service use were explored. Results: Overall, dental health service use increased between 2003 and 2008 and was at both time points more common among those who had higher income, better education, better housing conditions, private health care plans and were Caucasian. Inequalities in use of dental health care did not decrease over time. Among the reasons for not seeking dental care, not having teeth and financial difficulty were more common in lower socioeconomic groups, while thinking it was unnecessary was more common in higher socioeconomic groups. Conclusions: The Brazilian oral health policy is still in a period of expansion and seems to have contributed slightly to increased dental health service use, but has not influenced socioeconomic inequalities in the use of these services. 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The two distinct active forms of a-amylase inhibitors, a-AI1 and a-AI2, in P. vulgaris show different specificity toward a-amylases. Zabrotes subfasciatus a-amylase is inhibited by a-AI2 but not by a-AI1. In contrast, porcine a-amylase is inhibited by a-AI1 but not by a-AI2. The objective of this work was to understand the molecular basis of the specificity of two inhibitors in P. vulgaris (a-AI1 and a-AI2) in relation to a-amylases. Mutants of a-AI2 were made and expressed in tobacco plants. The results showed that all the a-AI2 mutant inhibitors lost their activity against the insect a-amylases but none exhibited activity toward the mammalian a-amylase. The replacement of His33 of a-AI2 with the a-AI1-like sequence Ser-Tyr-Asn abolished inhibition of Z. subfasciatus a-amylase. 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urundeuva) extract employing edemogenic and histological analyses. MATERIAL AND METHODS: Test groups consisted of aqueous and ethanolic Aroeira extracts and saline (control). For edema quantification, 18 rats received an intravenous injection of Evan's Blue. After 30 min, the extracts and saline were injected on the dorsum of the rats, which were then sacrificed after 3 and 6 h. Readings were performed in a spectrophotometer. For subcutaneous implantation, 30 rats received a polyethylene tube containing the extracts on their dorsum and then they were killed after 7 and 28 days. The samples were processed for histological analysis and evaluated with a light microscope. The inflammatory infiltrate was quantified. RESULTS: There were no statistically significant differences between aqueous extract and saline groups in relation to edema quantification in the different periods (p>0.05). Ethanolic solution resulted in more edema independently of the experimental period (p<0.05). 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They are usually maintained with 10% fetal bovine serum (FBS) in vitro. Modified platelet-rich plasma (mPRP) would be a safe alternative to 10% FBS during SHEDs culture. Therefore, our study aimed to compare the proliferation and differentiation of SHEDs cultured in mPRP and FBS medium to explore an optimal concentration of mPRP for SHEDs maintenance. Platelets were harvested by automatic blood cell analyzer and activated by repeated liquid nitrogen freezing and thawing. The platelet-related cytokines were examined and analyzed by ELISA. SHEDs were extracted and cultured with different concentrations of mPRP or 10% FBS medium. Alkaline phosphatase (ALP) activity was measured. Mineralization factors, RUNX2 and OCN, were measured by real-time PCR. SHEDs were characterized with mesenchymal stem cells (MSCs) markers including vimentin, CD44, and CD105. mPRP at different concentrations (2, 5, 10, and 20%) enhanced the growth of SHEDs. Moreover, mPRP significantly stimulated ALP activity and promoted expression of RUNX2 and OCN compared with 10% FBS. mPRP could efficiently facilitate proliferation and differentiation of SHEDs, and 2% mPRP would be an optimal substitute for 10% FBS during SHEDs expansion and differentiation in clinical scale manufacturing."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "text/html"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": 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[{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Investigation of modified platelet-rich plasma (mPRP) in promoting the proliferation and differentiation of dental pulp stem cells from deciduous teeth"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": 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"value": "Cleft palate"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "Oral rehabilitation"}], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Tereza", "name": "Guida Paola Genovez", "pid": [], "rank": 1, "affiliation": [], "fullname": "Tereza,Guida Paola Genovez"}, {"surname": "Santos", "name": "Marcos Anto\\u0302nio Corre\\u0302a Dos", "pid": [], "rank": 2, "affiliation": [], "fullname": "Santos,Marcos Ant\\xf4nio Corr\\xeaa dos"}, 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Referencia"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-77572018000100438"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-01-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::dc6e224a8d74ce03bf301152d6e33e97", "value": "LA Referencia"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2020-03-06T20:13:49.905Z", "fulltext": [], "dateoftransformation": "2020-03-10T21:25:42.582Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Abstract Objective This study analyzed the maintenance of lateral incisors in the dental rehabilitation of individuals with cleft lip and palate. Material and Methods The study was conducted on a tertiary craniofacial center and comprised retrospective analysis of panoramic and periapical radiographs of Caucasoid individuals with non-syndromic complete unilateral cleft lip and palate, analyzing all radiographs available on the records of each individual, from the first to the last up to 12 years of age. Overall, 2,826 records were reviewed to achieve a sample of 1,000 individuals. Among these, 487 individuals presented the permanent lateral incisors on both cleft and non-cleft sides, which were included in this study. Results The results were evaluated in percentages and by descriptive statistics. The association between maintenance of the lateral incisor and timing of alveolar bone graft were analyzed by the t test. Among the 487 individuals, 265 had not completed treatment, 62 presented insufficient information, and 44 concluded the treatment elsewhere. Among the remaining 116 individuals, the lateral incisor was extracted from 88 (75.86%) of them on the cleft side (CS) and from 23 (19.83%) people on the non-cleft side (NCS). The age at accomplishment of alveolar bone graft was significantly associated with maintenance of the lateral incisor on the cleft side (p<0.01). Most extractions were indicated because of the inadequate positioning on the CS and for midline correction on the NCS. Rehabilitation was primarily completed by orthodontic movement (53 individuals on the CS and 13 individuals on the NCS). Conclusion In conclusion, the lateral incisor on the cleft side was not maintained in most individuals. Positive relationship was observed between extraction of the lateral incisor and age at accomplishment of the alveolar bone graft, suggesting the need to anticipate the initial radiographic evaluation to enhance its maintenance and reduce the procedures required for rehabilitation."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "text/html"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", 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"inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Journal of Applied Oral Science v.26 2018"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "reponame:Journal of Applied Oral Science"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "instname:Universidade de S\\xe3o Paulo"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "instacron:USP"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", 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MATERIAL AND METHODS: Test groups consisted of aqueous and ethanolic Aroeira extracts and saline (control). For edema quantification, 18 rats received an intravenous injection of Evan's Blue. After 30 min, the extracts and saline were injected on the dorsum of the rats, which were then sacrificed after 3 and 6 h. Readings were performed in a spectrophotometer. For subcutaneous implantation, 30 rats received a polyethylene tube containing the extracts on their dorsum and then they were killed after 7 and 28 days. The samples were processed for histological analysis and evaluated with a light microscope. The inflammatory infiltrate was quantified. RESULTS: There were no statistically significant differences between aqueous extract and saline groups in relation to edema quantification in the different periods (p>0.05). Ethanolic solution resulted in more edema independently of the experimental period (p<0.05). 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The increase of private health care plans and the implementation of the \"Smiling Brazil\" Program, the largest public oral health care program in the world, could have influenced this increase in access. However, we do not yet know if inequalities in the use of dental health services persist after the improvement in access. The aims of this study are to analyze socioeconomic differences for dental health service use between 2003 and 2008 in S\\xe3o Paulo and to examine changes in these associations since the implementation of the Smiling Brazil program in 2003. __Method:__ Data was obtained via two household health surveys (ISA-Capital 2003 and ISA-Capital 2008) which investigated living conditions, lifestyle, health status and use of health care services. Logistic regression was used to analyze associations between socioeconomic factors and dental services use. 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The decays of entangled neutral B mesons into definite flavor states (B-0 or (B) over bar (0)), and J/psi K-L(0) or c (c) over barK(S)(0) final states (referred to as B+ or B-), allow comparisons between the probabilities of four pairs of T-conjugated transitions, for example, (B) over bar (0) -> B- and B- -> (B) over bar (0), as a function of the time difference between the two B decays. Using 468 X 10(6) B (B) over bar pairs produced in Y(4S) decays collected by the BABAR detector at SLAC, we measure T-violating parameters in the time evolution of neutral B mesons, yielding Delta S-T(+) = -137 +/- 0.14(stat) +/- 0.06(syst) and Delta S-T(-) = 1.17 +/- 0.18(stat) +/- 0.11(syst). 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A large variety of studies suggest that biofilm formation by NTHi may be an important step in the pathogenesis of this bacterium. However, the underlying mechanisms involved in this process are poorly elucidated. In this study, we used a transposon mutant library to identify bacterial genes involved in biofilm formation. The growth and biofilm formation of 4,172 transposon mutants were determined, and the involvement of the identified genes in biofilm formation was validated in in vitro experiments. Here, we present experimental data showing that increased bacterial lysis, through interference with peptidoglycan synthesis, results in elevated levels of extracellular DNA, which increased biofilm formation. Interestingly, similar results were obtained with subinhibitory concentrations of beta-lactam antibiotics, known to interfere with peptidoglycan synthesis, but such an effect does not appear with other classes of antibiotics. These results indicate that treatment with beta-lactam antibiotics, especially for beta-lactam-resistant NTHi isolates, might increase resistance to antibiotics by increasing biofilm formation. IMPORTANCE Most, if not all, bacteria form a biofilm, a multicellular structure that protects them from antimicrobial actions of the host immune system and affords resistance to antibiotics. The latter is especially disturbing with the increase in multiresistant bacterial clones worldwide. Bacterial biofilm formation is a multistep process that starts with surface adhesion, after which attached bacteria divide and give rise to biomass. The actual steps required for Haemophilus influenzae biofilm formation are largely not known. We show that interference with peptidoglycan biosynthesis increases biofilm formation because of the release of bacterial genomic DNA. Subinhibitory concentrations of beta-lactam antibiotics, which are often prescribed to treat H. influenzae infections, increase biofilm formation through a similar mechanism. 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Background: Use of whole-genome sequence data is expected to increase persistency of genomic prediction across generations and breeds but affects model performance and requires increased computing time. In this study, we investigated whether the split-and-merge Bayesian stochastic search variable selection (BSSVS) model could overcome these issues. BSSVS is performed first on subsets of sequence-based variants and then on a merged dataset containing variants selected in the first step. Results: We used a dataset that included 4,154,064 variants after editing and de-regressed proofs for 3415 reference and 2138 validation bulls for somatic cell score, protein yield and interval first to last insemination. In the first step, BSSVS was performed on 106 subsets each containing ~39,189 variants. In the second step, 1060 up to 472,492 variants, selected from the first step, were included to estimate the accuracy of genomic prediction. Accuracies were at best equal to those achieved with the commonly used Bovine 50k-SNP chip, although the number of variants within a few well-known quantitative trait loci regions was considerably enriched. When variant selection and the final genomic prediction were performed on the same data, predictions were biased. Predictions computed as the average of the predictions computed for each subset achieved the highest accuracies, i.e. 0.5 to 1.1 % higher than the accuracies obtained with the 50k-SNP chip, and yielded the least biased predictions. Finally, the accuracy of genomic predictions obtained when all sequence-based variants were included was similar or up to 1.4 % lower compared to that based on the average predictions across the subsets. By applying parallelization, the split-and-merge procedure was completed in 5 days, while the standard analysis including all sequence-based variants took more than three months. Conclusions: The split-and-merge approach splits one large computational task into many much smaller ones, which allows the use of parallel processing and thus efficient genomic prediction based on whole-genome sequence data. The split-and-merge approach did not improve prediction accuracy, probably because we used data on a single breed for which relationships between individuals were high. Nevertheless, the split-and-merge approach may have potential for applications on data from multiple breeds.

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Mental health problems are a worldwide public health burden. Among adults some evidence suggests that physical activity is a protective factor in relation to mental health problems. The same body of literature is not present among adolescents. With regard to prevention of mental health problems it is important to identify vulnerable groups that need special attention. If physical activity can be a preventive strategy,\\nknowledge of physical activity in subgroups of adolescents is important. With an increasing influx of immigrants to the Western parts of the world, cultural/ethnic background has become an important factor when studying health and health behaviour in a public health perspective. Inequality in health has also been a subject of increased attention during the last years, thus it is of great importance to study the significance of sociodemographic factors."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2010-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": 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The literature concerning the mental health benefits from physical activity among adults has grown. Adolescents are less studied, and especially longitudinal studies are lacking. This paper investigates the associations between weekly hours of physical activity at age 15\\u201316 and mental health three years later. \\n\\nMethods:\\n\\nLongitudinal self-reported health survey. The baseline study consisted of participants from the youth section of the Oslo Health Study, carried out in schools in 2000\\u20132001 (n = 3811). The follow-up in 2003\\u20132004 was conducted partly at school and partly through mail. A total of 2489 (1112 boys and 1377 girls) participated in the follow-up. Mental health was measured by the Strengths and Difficulties Questionnaire with an impact supplement. Physical activity was measured by a question on weekly hours of physical activity outside of school, defined as exertion \"to an extent that made you sweat and/or out of breath\". Adjustments were made for well-documented confounders and mental health at baseline. \\n\\nResults:\\n\\nIn boys, the number of hours spent on physical activity per week at age 15\\u201316 was negatively associated with emotional symptoms [B (95%CI) = -0.09 (-0.15, -0.03)] and peer problems [B (95%CI) = -0.08 (-0.14, -0.03)] at age 18\\u201319 after adjustments. In girls, there were no significant differences in SDQ subscales at age 18\\u201319 according to weekly hours of physical activity at age 15\\u201316 after adjustments. Boys and girls with five to seven hours of physical activity per week at age 15\\u201316 had the lowest mean scores for total difficulties and the lowest percentage with high impact score at age 18\\u201319, but the differences were not statistically significant after adjustments. \\n\\nConclusion:\\n\\nWeekly hours of physical activity at age 15\\u201316 years was weakly associated with mental health at three-year follow-up in boys. 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The literature concerning the mental health benefits from physical activity among adults has grown. Adolescents are less studied, and especially longitudinal studies are lacking. This paper investigates the associations between weekly hours of physical activity at age 15\\u201316 and mental health three years later. \\n\\nMethods:\\n\\nLongitudinal self-reported health survey. The baseline study consisted of participants from the youth section of the Oslo Health Study, carried out in schools in 2000\\u20132001 (n = 3811). The follow-up in 2003\\u20132004 was conducted partly at school and partly through mail. A total of 2489 (1112 boys and 1377 girls) participated in the follow-up. Mental health was measured by the Strengths and Difficulties Questionnaire with an impact supplement. Physical activity was measured by a question on weekly hours of physical activity outside of school, defined as exertion \"to an extent that made you sweat and/or out of breath\". 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Adjustments were made for well-documented confounders and mental health at baseline.\\n \\n \\n Results\\n In boys, the number of hours spent on physical activity per week at age 15\\u201316 was negatively associated with emotional symptoms [B (95%CI) = -0.09 (-0.15, -0.03)] and peer problems [B (95%CI) = -0.08 (-0.14, -0.03)] at age 18\\u201319 after adjustments. In girls, there were no significant differences in SDQ subscales at age 18\\u201319 according to weekly hours of physical activity at age 15\\u201316 after adjustments. Boys and girls with five to seven hours of physical activity per week at age 15\\u201316 had the lowest mean scores for total difficulties and the lowest percentage with high impact score at age 18\\u201319, but the differences were not statistically significant after adjustments.\\n \\n \\n Conclusion\\n Weekly hours of physical activity at age 15\\u201316 years was weakly associated with mental health at three-year follow-up in boys. 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The literature concerning the mental health benefits from physical activity among adults has grown. Adolescents are less studied, and especially longitudinal studies are lacking. This paper investigates the associations between weekly hours of physical activity at age 15\\u201316 and mental health three years later. \\n\\nMethods:\\n\\nLongitudinal self-reported health survey. The baseline study consisted of participants from the youth section of the Oslo Health Study, carried out in schools in 2000\\u20132001 (n = 3811). The follow-up in 2003\\u20132004 was conducted partly at school and partly through mail. A total of 2489 (1112 boys and 1377 girls) participated in the follow-up. Mental health was measured by the Strengths and Difficulties Questionnaire with an impact supplement. Physical activity was measured by a question on weekly hours of physical activity outside of school, defined as exertion \"to an extent that made you sweat and/or out of breath\". Adjustments were made for well-documented confounders and mental health at baseline. \\n\\nResults:\\n\\nIn boys, the number of hours spent on physical activity per week at age 15\\u201316 was negatively associated with emotional symptoms [B (95%CI) = -0.09 (-0.15, -0.03)] and peer problems [B (95%CI) = -0.08 (-0.14, -0.03)] at age 18\\u201319 after adjustments. In girls, there were no significant differences in SDQ subscales at age 18\\u201319 according to weekly hours of physical activity at age 15\\u201316 after adjustments. Boys and girls with five to seven hours of physical activity per week at age 15\\u201316 had the lowest mean scores for total difficulties and the lowest percentage with high impact score at age 18\\u201319, but the differences were not statistically significant after adjustments. \\n\\nConclusion:\\n\\nWeekly hours of physical activity at age 15\\u201316 years was weakly associated with mental health at three-year follow-up in boys. Results encourage a search for further knowledge about physical activity as a possible protective factor in relation to mental health problems in adolescence."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2007-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": 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"inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "In this paper, we present the results from a high horizontal resolution numerical simulation of the northwestern Mediterranean using a z-level, non-hydrostatic, primitive equation ocean model (DieCAST). The high resolution allows an accurate representation of the submarine canyons that presides in the region. The model is one-way coupled to a large scale model of the Mediterranean Sea through open boundaries and uses the atmospheric forcing fields provided in terms of HIRLAM outputs by the Spanish National Institute of Meteorology. Results show that the model can successfully reproduce the complex general circulation characteristics of the area, including the modifications induced by canyons in their vicinity and other phenomena observed such as instabilities and coastal trapped waves. The sea surface temperature is similar to satellite observations except that simulated temperatures are slightly warmer near the coast than observations and colder near the open boundaries. An important topic of this work is the computation of the shelf-slope exchanges, which are able to renew shelf waters in a few months."}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Peer Reviewed"}], "format": [], "journal": {"issnPrinted": "1812-0784", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "Ocean Science", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1812-0792", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, 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"schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "This work is licensed under a Creative Commons Attribution 3.0 Unported license."}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Boron nitride is a promising material for nanotechnology applications due to its two-dimensional graphene-like, insulating, and highly-resistant structure. Recently it has received a lot of attention as a substrate to grow and isolate graphene as well as for its intrinsic UV lasing response. Similar to carbon, one-dimensional boron nitride nanotubes (BNNTs) have been theoretically predicted and later synthesised. Here we use first principles simulations to unambiguously demonstrate that i) BN nanotubes inherit the highly efficient UV luminescence of hexagonal BN; ii) the application of an external perpendicular field closes the electronic gap keeping the UV lasing with lower yield; iii) defects in BNNTS are responsible for tunable light emission from the UV to the visible controlled by a transverse electric field (TEF). Our present findings pave the road towards optoelectronic applications of BN-nanotube-based devices that are simple to implement because they do not require any special doping or complex growth."}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "We acknowledge financial support also from the European Research Council Advanced Grant DYNamo (ERC-2010-AdG-267374), Spanish Grant (FIS2010-21282-C02-01), Grupos Consolidados UPV/EHU del Gobierno Vasco (IT578-13), Ikerbasque and the European Commission project CRONOS (Grant number 280879-2). Computational time was granted by i2basque and BSC Red Espanola de Supercomputacion and GENCI-IDRIS (Nos. 100063 and No. 091827). A. M. acknowledges funding by MIUR FIRB Grant No. RBFR12SW0J."}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Peer Reviewed"}], "format": [], "journal": {"issnPrinted": "2045-2322", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2013-01-01"}, "coverage": [], "publisher": 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We analyse two variants of such an extension and carry out a phenomenological study of regions of the parameter space satisfying current direct and indirect constraints, employing state-of-the-art two-loop RGE evolution and GMSB boundary conditions. We find that due to the appearance of non-decoupled D-terms it is possible to obtain a 125.5\\xa0GeV Higgs with stops below 2\\xa0TeV, while the uncoloured sparticles could still lie within reach of the LHC. We compare the contributions of the stop sector and the non-decoupled D-terms to the Higgs mass, and study their effect on the Higgs couplings. 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animals and humans against parasite nematodes, but their therapeutic success is compromised by the spread of ML resistance. Some ABC transporters, such as P-glycoproteins (Pgps), are selected and overexpressed in ML-resistant nematodes, supporting a role for some drug efflux proteins in ML resistance. However, the role of such proteins in ML transport remains to be clarified at the molecular level. Recently, Caenorhabditis elegans Pgp-1 (Cel-Pgp1) has been crystallized, and its drug-modulated ATPase function characterized in vitro revealed Cel-Pgp1 as a multidrug transporter. Using this crystal structure, we have developed an in silico drug docking model in order to study the binding of ML and other anthelmintic drugs to Cel-Pgp-1. All tested ML bound with high affinity in a unique site, within the inner chamber of the protein, supporting that ML may be transported by Cel-Pgp-1. Interestingly, interacting residues delineate a ML specific fingerprint involving H-bonds, including T1028. In particular, benzofurane and spiroketal moieties bound to specific sub-sites. When compared with the aglycone ML, such as moxidectin and ivermectin aglycone, avermectin anthelmintics have significant higher affinity for Cel-Pgp-1, likely due to the sugar substituent(s) that bind to a specific area involving H-bonds at Y771. Triclabendazole, closantel and emodepside bound with good affinities to different sub-sites in the inner chamber, partially overlapping with the ML binding site, suggesting that they could compete for Cel-Pgp-1-mediated ML transport. In conclusion, this work provides novel information on the role of nematode Pgps in transporting anthelmintics, and a valuable tool to predict drug-drug interactions and to rationally design new competitive inhibitors of clinically-relevant nematode Pgps, to improve anthelmintic therapeutics."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:prodinra.inra.fr:387545"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "International Journal for Parasitology: Drugs and Drug Resistance 3 (6), 299-313. 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Our present findings pave the road towards optoelectronic applications of BN-nanotube-based devices that are simple to implement because they do not require any special doping or complex growth\\nWe acknowledge financial support also from the European Research Council Advanced Grant DYNamo (ERC-2010-AdG-267374), Spanish Grant (FIS2010-21282-C02-01), Grupos Consolidados UPV/EHU del Gobierno Vasco (IT578-13), Ikerbasque and the European Commission project CRONOS (Grant number 280879-2). Computational time was granted by i2basque and BSC Red Espanola de Supercomputacion and GENCI-IDRIS (Nos. 100063 and No. 091827). A. 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"schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "International audience; The present paper describes the features and implementation of SmartVox an application designed to help vocal ensembles learn and perform polyphonic music.Technically, SmartVox is a distributed web application that delivers audiovisual scores through the performer\\u2019s mobile devices. From a singer\\u2019s point of view, this setup allows for the synergy between visual and acoustic stimuli, which facilitates the interpretive and performative processes, particularly in polyphonic passages. It also enables spatial separation of the performers (cori spezzati), and speeds up the learning process of unfamiliar musical materials (e.g. microtonal tuning, texts in a foreign language).The ubiquity of smartphones makes such a distributed system affordable and allows the use of SmartVox in multiple contexts, from professional ensembles to pedagogical and recreational practices."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2017-05-24"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "HAL CCSD"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:HAL:hal-01660184v1"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "TENOR 2017"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "https://hal.archives-ouvertes.fr/hal-01660184"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "TENOR 2017, May 2017, Coru\\xf1a, Spain. 2017"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "SMARTVOX - A Web-Based Distributed Media Player as Notation Tool For Choral Practices"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.1016/S0370-2693(01)00807-3"}], "contributor": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Institut de Physique Nucl\\xe9aire de Lyon\\n (\\nIPNL\\n)\\n\\n ; 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Recently it has received a lot of attention as a substrate to grow and isolate graphene as well as for its intrinsic UV lasing response. Similar to carbon, one-dimensional boron nitride nanotubes (BNNTs) have been theoretically predicted and later synthesised. Here we use first principles simulations to unambiguously demonstrate that i) BN nanotubes inherit the highly efficient UV luminescence of hexagonal BN; ii) the application of an external perpendicular field closes the electronic gap keeping the UV lasing with lower yield; iii) defects in BNNTS are responsible for tunable light emission from the UV to the visible controlled by a transverse electric field (TEF). 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\\nConsejo Superior de Investigaciones Cient\\xedficas [Spain]\\n (\\nCSIC\\n)\\n-Universidad de las Islas Baleares\\n (\\nUIB\\n)\\n"}], "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "relevantdate": [], "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::9766527f2b5d3e95d4a733fcfb77bd7e", "value": "INRIA a CCSD electronic archive server"}], "id": "50|od_______165::22ada9a6f80dad93f03b97f72543d8b4", "subject": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "[ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere"}], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Jordi", "name": "A.", "pid": [], "rank": 1, "affiliation": [], "fullname": "Jordi , A."}, {"surname": "Basterretxea", "name": "G.", "pid": [], "rank": 2, "affiliation": [], "fullname": "Basterretxea , G."}, {"surname": "Orfila", "name": "A.", "pid": [], "rank": 3, "affiliation": [], "fullname": "Orfila , A."}, {"surname": "Tintore\\u0301", "name": "J.", "pid": [], "rank": 4, "affiliation": [], "fullname": "Tintor\\xe9 , J."}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::9766527f2b5d3e95d4a733fcfb77bd7e", "value": "INRIA a CCSD electronic archive server"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["https://hal.archives-ouvertes.fr/hal-00298576", "https://hal.archives-ouvertes.fr/hal-00298576/document", "https://hal.archives-ouvertes.fr/hal-00298576/file/os-2-173-2006.pdf"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2006-10-17"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::9766527f2b5d3e95d4a733fcfb77bd7e", "value": "INRIA a CCSD electronic archive server"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-04-05T09:14:20.078Z", "fulltext": [], "dateoftransformation": "2020-03-05T18:16:37.315Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "\\nInternational audience\\n\\nIn this paper, we present the results from a high horizontal resolution numerical simulation of the northwestern Mediterranean using a z-level, non-hydrostatic, primitive equation ocean model (DieCAST). The high resolution allows an accurate representation of the submarine canyons that presides in the region. The model is one-way coupled to a large scale model of the Mediterranean Sea through open boundaries and uses the atmospheric forcing fields provided in terms of HIRLAM outputs by the Spanish National Institute of Meteorology. Results show that the model can successfully reproduce the complex general circulation characteristics of the area, including the modifications induced by canyons in their vicinity and other phenomena observed such as instabilities and coastal trapped waves. The sea surface temperature is similar to satellite observations except that simulated temperatures are slightly warmer near the coast than observations and colder near the open boundaries. An important topic of this work is the computation of the shelf-slope exchanges, which are able to renew shelf waters in a few months."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2006-10-17"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, 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"lastupdatetimestamp": 0, "author": [{"surname": "David", "name": "Marion A.", "pid": [], "rank": 1, "affiliation": [], "fullname": "David , Marion A."}, {"surname": "Orlowski", "name": "Ste\\u0301phane", "pid": [], "rank": 2, "affiliation": [], "fullname": "Orlowski , St\\xe9phane"}, {"surname": "Prichard", "name": "Roger K.", "pid": [], "rank": 3, "affiliation": [], "fullname": "Prichard , Roger K."}, {"surname": "Hashem", "name": "Shaima", "pid": [], "rank": 4, "affiliation": [], "fullname": "Hashem , Shaima"}, {"surname": "Andre\\u0301", "name": "Franc\\u0327ois", "pid": [], "rank": 5, "affiliation": [], "fullname": "Andr\\xe9 , Fran\\xe7ois"}, {"surname": "Lespine", "name": "Anne", "pid": [], "rank": 6, "affiliation": [], "fullname": "Lespine , Anne"}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": 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Some ABC transporters, such as p-glycoproteins (Pgps), are selected and overexpressed in ML-resistant nematodes, supporting a role for some drug efflux proteins in ML resistance. However, the role of such proteins in ML transport remains to be clarified at the molecular level. Recently, Caenorhabditis elegans Pgp-1 (Cel-Pgp-1) has been crystallized, and its drug-modulated ATPase function characterized in\\xa0vitro revealed Cel-Pgp-1 as a multidrug transporter. Using this crystal structure, we have developed an in silico drug docking model in order to study the binding of ML and other anthelmintic drugs to Cel-Pgp-1. All tested ML bound with high affinity in a unique site, within the inner chamber of the protein, supporting that ML may be transported by Cel-Pgp-1. Interestingly, interacting residues delineate a ML specific fingerprint involving H-bonds, including T1028. In particular, benzofurane and spiroketal moieties bound to specific sub-sites. When compared with the aglycone ML, such as moxidectin and ivermectin aglycone, avermectin anthelmintics have significant higher affinity for Cel-Pgp-1, likely due to the sugar substituent(s) that bind to a specific area involving H-bonds at Y771. Triclabendazole, closantel and emodepside bound with good affinities to different sub-sites in the inner chamber, partially overlapping with the ML binding site, suggesting that they could compete for Cel-Pgp-1-mediated ML transport. In conclusion, this work provides novel information on the role of nematode Pgps in transporting anthelmintics, and a valuable tool to predict drug-drug interactions and to rationally design new competitive inhibitors of clinically-relevant nematode Pgps, to improve anthelmintic therapeutics."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "HAL CCSD"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:HAL:hal-01451654v1"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "International journal for parasitology. 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From a singer\\u2019s point of view, this setup allows for the synergy between visual and acoustic stimuli, which facilitates the interpretive and performative processes, particularly in polyphonic passages. It also enables spatial separation of the performers (cori spezzati), and speeds up the learning process of unfamiliar musical materials (e.g. microtonal tuning, texts in a foreign language).The ubiquity of smartphones makes such a distributed system affordable and allows the use of SmartVox in multiple contexts, from professional ensembles to pedagogical and recreational practices."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2017-05-24"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "HAL CCSD"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:HAL:hal-01660184v1"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "TENOR"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "https://hal.archives-ouvertes.fr/hal-01660184"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "TENOR, May 2017, Coru\\xf1a, Spain"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "SMARTVOX - A Web-Based Distributed Media Player as Notation Tool For Choral Practices"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.1063/1.2130751"}], "contributor": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Dipartimento du Fisica ; 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We use data from direct numerical simulations up to Taylor\\\\'s Reynolds number 280 following the evolution of about two million passive tracers advected by the flow over a time span of about three decades. We present data for both the separation distance and the relative velocity statistics. Statistics are measured along the particle pair trajectories both as a function of time and as a function of their separation, i.e. at fixed scales. We compare and contrast both sets of statistics in order to gain an insight into the mechanisms governing the separation process. We find very high levels of intermittency in the early stages, that is, for travel times up to order ten Kolmogorov time scales. The fixed scale statistics allow us to quantify anomalous corrections to Richardson diffusion in the inertial range of scales for those pairs that separate rapidly. 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The MSV-MIDAS model is estimated via maximum likelihood methods.The estimation relies on a slightly modified version of Hamilton\\u2019s recursive filter.We use Monte Carlo simulations to assess the robustness of the estimation procedure and related test-statistics. The results show that ML provides accurateestimates, but they suggest some caution in the tests on the parameters involved inthe transition probabilities. We apply this new model to thedetection and forecastof business cycle turning points. We properly detect recessions in United States and United Kingdom by exploiting the link between GDP growth and higher frequency variables from financial and energy markets. Spread term is aparticularly usefulindicator to predict recessions in the United States, while stock returns have the strongest explanatory power around British turning points."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2015-06-22"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": 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"2018-04-04T15:41:58.595Z", "fulltext": [], "dateoftransformation": "2020-03-05T20:07:35.655Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value":"This paper introduces a Markov-switching model in which transition probabilities depend on higher frequency indicators and their lags through polynomial weight-ing schemes. The MSV-MIDAS model is estimated via maximum likelihood (ML) methods. The estimation relies on a slightly modified version of Hamilton's recursive filter. We use Monte Carlo simulations to assess the robustness of the estimation procedure and related test statistics. The results show that ML provides accurate estimates, but they suggest some caution in interpreting the tests of the parameters involved in the transition probabilities. We apply this new model to the detection and forecasting of business cycle turning points in the United States. We properly detect recessions by exploiting the link between GDP growth and higher frequency variables from financial and energy markets. The spread term is a particularly useful indicator to predict recessions in the United States. The empirical evidence also supports the use of functional polynomial weights in the MIDAS specification of the transition probabilities."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-09-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "HAL CCSD"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:HAL:hal-01358595v1"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "https://hal.archives-ouvertes.fr/hal-01358595"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Revisiting the transitional dynamics of business-cycle phases with mixed frequency data"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.1016/S0370-2693(01)00807-3"}], "contributor": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Institut de Physique Nucl\\xe9aire de Lyon\\n (\\nIPNL\\n)\\n\\n ; 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Submitted to Phys. Rev. Lett.\\nAlthough CP violation in the B meson system has been well established by the B factories, there has been no direct observation of time reversal violation. The decays of entangled neutral B mesons into definite flavor states ($B^0$ or $\\\\bar{B}^0$), and $J/\\\\psi K_S^0$ or $c\\\\bar{c} K_S^0$ final states (referred to as $B_+$ or $B_-$), allow comparisons between the probabilities of four pairs of T-conjugated transitions, for example, $\\\\bar{B}^0 \\\\rightarrow B_-$ and $B_- \\\\rightarrow \\\\bar{B}^0$, as a function of the time difference between the two B decays. Using 468 million $B\\\\bar{B}$ pairs produced in $\\\\Upsilon(4S)$ decays collected by the BABAR detector at SLAC, we measure T-violating parameters in the time evolution of neutral B mesons, yielding $\\\\Delta S_T^+ = -1.37 \\\\pm 0.14 (stat.) \\\\pm 0.06 (syst.)$ and $\\\\Delta S_T^- = 1.17 \\\\pm 0.18 (stat.) \\\\pm 0.11 (syst.)$. These nonzero results represent the first direct observation of T violation in the B meson system, through the exchange of initial and final states in transitions that can only be connected by a T-symmetry transformation."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2012-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", 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"dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "[ SDV ] Life Sciences [q-bio]"}], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Calus", "name": "Mario P. L.", "pid": [], "rank": 1, "affiliation": [], "fullname": "Calus , Mario P. L."}, {"surname": "Bouwman", "name": "Aniek C.", "pid": [], "rank": 2, "affiliation": [], "fullname": "Bouwman , Aniek C."}, {"surname": "Schrooten", "name": "Chris", "pid": [], "rank": 3, "affiliation": [], "fullname": "Schrooten , Chris"}, {"surname": "Veerkamp", "name": "Roel F.", "pid": [], "rank": 4, "affiliation": [], "fullname": "Veerkamp , Roel F."}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::9766527f2b5d3e95d4a733fcfb77bd7e", "value": "INRIA a CCSD electronic archive server"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["https://hal.archives-ouvertes.fr/hal-01341383", "https://hal.archives-ouvertes.fr/hal-01341383/document", "https://hal.archives-ouvertes.fr/hal-01341383/file/12711_2016_Article_225.pdf"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::9766527f2b5d3e95d4a733fcfb77bd7e", "value": "INRIA a CCSD electronic archive server"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-04-04T15:53:20.027Z", "fulltext": [], "dateoftransformation": "2020-03-05T23:23:59.768Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "\\nInternational audience\\n\\nBackgroundUse of whole-genome sequence data is expected to increase persistency of genomic prediction across generations and breeds but affects model performance and requires increased computing time. In this study, we investigated whether the split-and-merge Bayesian stochastic search variable selection (BSSVS) model could overcome these issues. BSSVS is performed first on subsets of sequence-based variants and then on a merged dataset containing variants selected in the first step.ResultsWe used a dataset that included 4,154,064 variants after editing and de-regressed proofs for 3415 reference and 2138 validation bulls for somatic cell score, protein yield and interval first to last insemination. In the first step, BSSVS was performed on 106 subsets each containing ~39,189 variants. In the second step, 1060 up to 472,492 variants, selected from the first step, were included to estimate the accuracy of genomic prediction. Accuracies were at best equal to those achieved with the commonly used Bovine 50k-SNP chip, although the number of variants within a few well-known quantitative trait loci regions was considerably enriched. When variant selection and the final genomic prediction were performed on the same data, predictions were biased. Predictions computed as the average of the predictions computed for each subset achieved the highest accuracies, i.e. 0.5\\xa0to\\xa01.1\\xa0% higher than the accuracies obtained with the 50k-SNP chip, and yielded the least biased predictions. Finally, the accuracy of genomic predictions obtained when all sequence-based variants were included was similar or up to 1.4\\xa0% lower compared to that based on the average predictions across the subsets. By applying parallelization, the split-and-merge procedure was completed in 5\\xa0days, while the standard analysis including all sequence-based variants took more than three\\xa0months.ConclusionsThe split-and-merge approach splits one large computational task into many much smaller ones, which allows the use of parallel processing and thus efficient genomic prediction based on whole-genome sequence data. The split-and-merge approach did not improve prediction accuracy, probably because we used data on a single breed for which relationships between individuals were high. Nevertheless, the split-and-merge approach may have potential for applications on data from multiple breeds."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "HAL CCSD"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:HAL:hal-01341383v1"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "EISSN: 1297-9686"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Genetics Selection Evolution"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, 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Recently it has received a lot of attention as a substrate to grow and isolate graphene as well as for its intrinsic UV lasing response. Similar to carbon, one-dimensional boron nitride nanotubes (BNNTs) have been theoretically predicted and later synthesised. Here we use first principles simulations to unambiguously demonstrate that i) BN nanotubes inherit the highly efficient UV luminescence of hexagonal BN; ii) the application of an external perpendicular field closes the electronic gap keeping the UV lasing with lower yield; iii) defects in BNNTS are responsible for tunable light emission from the UV to the visible controlled by a transverse electric field (TEF). 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The high resolution allows an accurate representation of the submarine canyons that presides in the region. The model is one-way coupled to a large scale model of the Mediterranean Sea through open boundaries and uses the atmospheric forcing fields provided in terms of HIRLAM outputs by the Spanish National Institute of Meteorology. Results show that the model can successfully reproduce the complex general circulation characteristics of the area, including the modifications induced by canyons in their vicinity and other phenomena observed such as instabilities and coastal trapped waves. The sea surface temperature is similar to satellite observations except that simulated temperatures are slightly warmer near the coast than observations and colder near the open boundaries. An important topic of this work is the computation of the shelf-slope exchanges, which are able to renew shelf waters in a few months."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2006-10-17"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, 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"value": "International audience; Macrocyclic lactones (ML) are important anthelmintics used in animals and humans against parasite nematodes, but their therapeutic success is compromised by the spread of ML resistance. Some ABC transporters, such as p-glycoproteins (Pgps), are selected and overexpressed in ML-resistant nematodes, supporting a role for some drug efflux proteins in ML resistance. However, the role of such proteins in ML transport remains to be clarified at the molecular level. Recently, Caenorhabditis elegans Pgp-1 (Cel-Pgp-1) has been crystallized, and its drug-modulated ATPase function characterized in\\xa0vitro revealed Cel-Pgp-1 as a multidrug transporter. Using this crystal structure, we have developed an in silico drug docking model in order to study the binding of ML and other anthelmintic drugs to Cel-Pgp-1. All tested ML bound with high affinity in a unique site, within the inner chamber of the protein, supporting that ML may be transported by Cel-Pgp-1. Interestingly, interacting residues delineate a ML specific fingerprint involving H-bonds, including T1028. In particular, benzofurane and spiroketal moieties bound to specific sub-sites. When compared with the aglycone ML, such as moxidectin and ivermectin aglycone, avermectin anthelmintics have significant higher affinity for Cel-Pgp-1, likely due to the sugar substituent(s) that bind to a specific area involving H-bonds at Y771. Triclabendazole, closantel and emodepside bound with good affinities to different sub-sites in the inner chamber, partially overlapping with the ML binding site, suggesting that they could compete for Cel-Pgp-1-mediated ML transport. In conclusion, this work provides novel information on the role of nematode Pgps in transporting anthelmintics, and a valuable tool to predict drug-drug interactions and to rationally design new competitive inhibitors of clinically-relevant nematode Pgps, to improve anthelmintic therapeutics."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Elsevier"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:HAL:hal-01451654v1"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "ISSN: 2211-3207"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "International journal for parasitology. 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The discovery of a 125.5 GeV Higgs with standard model-like couplings andnaturalness considerations motivate gauge extensions of the MSSM. We analysetwo variants of such an extension and carry out a phenomenological study ofregions of the parameter space satisfying current direct and indirectconstraints, employing state-of-the art two-loop RGE evolution and GMSBboundary conditions. We find that due to the appearance of non-decoupledD-terms it is possible to obtain a 125.5 GeV Higgs with stops below 2 TeV,while the uncolored sparticles could still lie within reach of the LHC. Wecompare the contributions of the stop sector and the non-decoupled D-terms tothe Higgs mass, and study their effect on the Higgs couplings. 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Submitted to Phys. Rev. Lett.; Although CP violation in the B meson system has been well established by the B factories, there has been no direct observation of time reversal violation. The decays of entangled neutral B mesons into definite flavor states ($B^0$ or $\\\\bar{B}^0$), and $J/\\\\psi K_S^0$ or $c\\\\bar{c} K_S^0$ final states (referred to as $B_+$ or $B_-$), allow comparisons between the probabilities of four pairs of T-conjugated transitions, for example, $\\\\bar{B}^0 \\\\rightarrow B_-$ and $B_- \\\\rightarrow \\\\bar{B}^0$, as a function of the time difference between the two B decays. Using 468 million $B\\\\bar{B}$ pairs produced in $\\\\Upsilon(4S)$ decays collected by the BABAR detector at SLAC, we measure T-violating parameters in the time evolution of neutral B mesons, yielding $\\\\Delta S_T^+ = -1.37 \\\\pm 0.14 (stat.) \\\\pm 0.06 (syst.)$ and $\\\\Delta S_T^- = 1.17 \\\\pm 0.18 (stat.) \\\\pm 0.11 (syst.)$. These nonzero results represent the first direct observation of T violation in the B meson system, through the exchange of initial and final states in transitions that can only be connected by a T-symmetry transformation."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2012-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", 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L.", "pid": [], "rank": 1, "affiliation": [], "fullname": "Calus, Mario P. L."}, {"surname": "Bouwman", "name": "Aniek C.", "pid": [], "rank": 2, "affiliation": [], "fullname": "Bouwman, Aniek C."}, {"surname": "Schrooten", "name": "Chris", "pid": [], "rank": 3, "affiliation": [], "fullname": "Schrooten, Chris"}, {"surname": "Veerkamp", "name": "Roel F.", "pid": [], "rank": 4, "affiliation": [], "fullname": "Veerkamp, Roel F."}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a", "value": "Hyper Article en Ligne"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["https://hal.archives-ouvertes.fr/hal-01341383", "https://hal.archives-ouvertes.fr/hal-01341383/document", "https://hal.archives-ouvertes.fr/hal-01341383/file/12711_2016_Article_225.pdf"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a", "value": "Hyper Article en Ligne"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2019-07-27T14:15:08.792Z", "fulltext": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "https://hal.archives-ouvertes.fr/hal-01341383/document"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "https://hal.archives-ouvertes.fr/hal-01341383/file/12711_2016_Article_225.pdf"}], "dateoftransformation": "2019-07-30T10:15:45.374Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "International audience; BackgroundUse of whole-genome sequence data is expected to increase persistency of genomic prediction across generations and breeds but affects model performance and requires increased computing time. In this study, we investigated whether the split-and-merge Bayesian stochastic search variable selection (BSSVS) model could overcome these issues. BSSVS is performed first on subsets of sequence-based variants and then on a merged dataset containing variants selected in the first step.ResultsWe used a dataset that included 4,154,064 variants after editing and de-regressed proofs for 3415 reference and 2138 validation bulls for somatic cell score, protein yield and interval first to last insemination. In the first step, BSSVS was performed on 106 subsets each containing ~39,189 variants. In the second step, 1060 up to 472,492 variants, selected from the first step, were included to estimate the accuracy of genomic prediction. Accuracies were at best equal to those achieved with the commonly used Bovine 50k-SNP chip, although the number of variants within a few well-known quantitative trait loci regions was considerably enriched. When variant selection and the final genomic prediction were performed on the same data, predictions were biased. Predictions computed as the average of the predictions computed for each subset achieved the highest accuracies, i.e. 0.5\\xa0to\\xa01.1\\xa0% higher than the accuracies obtained with the 50k-SNP chip, and yielded the least biased predictions. Finally, the accuracy of genomic predictions obtained when all sequence-based variants were included was similar or up to 1.4\\xa0% lower compared to that based on the average predictions across the subsets. By applying parallelization, the split-and-merge procedure was completed in 5\\xa0days, while the standard analysis including all sequence-based variants took more than three\\xa0months.ConclusionsThe split-and-merge approach splits one large computational task into many much smaller ones, which allows the use of parallel processing and thus efficient genomic prediction based on whole-genome sequence data. The split-and-merge approach did not improve prediction accuracy, probably because we used data on a single breed for which relationships between individuals were high. Nevertheless, the split-and-merge approach may have potential for applications on data from multiple breeds."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, 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"instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-06-11T08:32:15.261Z", "fulltext": [], "dateoftransformation": "2018-08-29T16:51:34.05Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value":"Objectives This study evaluated subcutaneous tissue response to Aroeira (Myracrodruon urundeuva) extract employing edemogenic and histological analyses. Material and methods Test groups consisted of aqueous and ethanolic Aroeira extracts and saline (control). For edema quantification, 18 rats received an intravenous injection of Evan's Blue. After 30 min, the extracts and saline were injected on the dorsum of the rats, which were then sacrificed after 3 and 6 h. Readings were performed in a spectrophotometer. For subcutaneous implantation, 30 rats received a polyethylene tube containing the extracts on their dorsum and then they were killed after 7 and 28 days. The samples were processed for histological analysis and evaluated with a light microscope. The inflammatory infiltrate was quantified. Results There were no statistically significant differences between aqueous extract and saline groups in relation to edema quantification in the different periods (p>0.05). Ethanolic solution resulted in more edema independently of the experimental period (p<0.05). Histological analysis showed similar results on the 7-day period for the 3 groups. There was a notable reduction on inflammatory cell number for saline and aqueous extract groups at 28 days. 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L."}, {"surname": "Bouwman", "name": "Aniek C.", "pid": [], "rank": 2, "affiliation": [], "fullname": "Bouwman, Aniek C."}, {"surname": "Schrooten", "name": "Chris", "pid": [], "rank": 3, "affiliation": [], "fullname": "Schrooten, Chris"}, {"surname": "Veerkamp", "name": "Roel F.", "pid": [], "rank": 4, "affiliation": [], "fullname": "Veerkamp, Roel F."}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c", "value": "Europe PubMed Central"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["http://europepmc.org/articles/PMC4926307"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-06-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357", "value": "PubMed Central"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-06-13T04:51:09.291Z", "fulltext": [], "dateoftransformation": "2018-08-29T18:39:14.858Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Background Use of whole-genome sequence data is expected to increase persistency of genomic prediction across generations and breeds but affects model performance and requires increased computing time. In this study, we investigated whether the split-and-merge Bayesian stochastic search variable selection (BSSVS) model could overcome these issues. BSSVS is performed first on subsets of sequence-based variants and then on a merged dataset containing variants selected in the first step. Results We used a dataset that included 4,154,064 variants after editing and de-regressed proofs for 3415 reference and 2138 validation bulls for somatic cell score, protein yield and interval first to last insemination. In the first step, BSSVS was performed on 106 subsets each containing ~39,189 variants. In the second step, 1060 up to 472,492 variants, selected from the first step, were included to estimate the accuracy of genomic prediction. Accuracies were at best equal to those achieved with the commonly used Bovine 50k-SNP chip, although the number of variants within a few well-known quantitative trait loci regions was considerably enriched. When variant selection and the final genomic prediction were performed on the same data, predictions were biased. Predictions computed as the average of the predictions computed for each subset achieved the highest accuracies, i.e. 0.5\\xa0to\\xa01.1\\xa0% higher than the accuracies obtained with the 50k-SNP chip, and yielded the least biased predictions. Finally, the accuracy of genomic predictions obtained when all sequence-based variants were included was similar or up to 1.4\\xa0% lower compared to that based on the average predictions across the subsets. By applying parallelization, the split-and-merge procedure was completed in 5\\xa0days, while the standard analysis including all sequence-based variants took more than three\\xa0months. Conclusions The split-and-merge approach splits one large computational task into many much smaller ones, which allows the use of parallel processing and thus efficient genomic prediction based on whole-genome sequence data. The split-and-merge approach did not improve prediction accuracy, probably because we used data on a single breed for which relationships between individuals were high. Nevertheless, the split-and-merge approach may have potential for applications on data from multiple breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0225-x) contains supplementary material, which is available to authorized users."}], "format": [], "journal": {"issnPrinted": "0999-193X", "conferencedate": "", "vol": "48", "conferenceplace": "", "name": "Genetics, Selection, Evolution : GSE", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1297-9686", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-06-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", 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false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Efficient genomic prediction based on whole-genome sequence data using split-and-merge Bayesian variable selection"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "doi", "classname": "doi", 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"Zhang", "name": "Ming", "pid": [], "rank": 3, "affiliation": [], "fullname": "Zhang, Ming"}, {"surname": "Neres", "name": "Joa\\u0303o", "pid": [], "rank": 4, "affiliation": [], "fullname": "Neres, Jo\\xe3o"}, {"surname": "Sar", "name": "Astrid M.", "pid": [], "rank": 5, "affiliation": [], "fullname": "Sar, Astrid M"}, {"surname": "Raadsen", "name": "Susanne A.", "pid": [], "rank": 6, "affiliation": [], "fullname": "Raadsen, Susanne A"}, {"surname": "Hartkoorn", "name": "Ruben C.", "pid": [], "rank": 7, "affiliation": [], "fullname": "Hartkoorn, Ruben C"}, {"surname": "Ryabova", "name": "Olga B.", "pid": [], "rank": 8, "affiliation": [], "fullname": "Ryabova, Olga B"}, {"surname": "Vocat", "name": "Anthony", "pid": [], "rank": 9, "affiliation": [], "fullname": "Vocat, Anthony"}, {"surname": "Decosterd", "name": "Laurent A.", "pid": [], "rank": 10, "affiliation": [], "fullname": "Decosterd, Laurent A"}, {"surname": "Widmer", "name": "Nicolas", "pid": [], "rank": 11, "affiliation": [], "fullname": "Widmer, Nicolas"}, {"surname": "Buclin", "name": "Thierry", "pid": [], "rank": 12, "affiliation": [], "fullname": "Buclin, Thierry"}, {"surname": "Bitter", "name": "Wilbert", "pid": [], "rank": 13, "affiliation": [], "fullname": "Bitter, Wilbert"}, {"surname": "Andries", "name": "Koen", "pid": [], "rank": 14, "affiliation": [], "fullname": "Andries, Koen"}, {"surname": "Pojer", "name": "Florence", "pid": [], "rank": 15, "affiliation": [], "fullname": "Pojer, Florence"}, {"surname": "Dyson", "name": "Paul J.", "pid": [], "rank": 16, "affiliation": [], "fullname": "Dyson, Paul J"}, {"surname": "Cole", "name": "Stewart T.", "pid": [], "rank": 17, "affiliation": [], "fullname": "Cole, Stewart T"}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c", "value": "Europe PubMed Central"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["http://europepmc.org/articles/PMC3958311"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2014-02-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357", "value": "PubMed Central"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-06-11T11:32:00.492Z", "fulltext": [], "dateoftransformation": "2018-08-29T19:41:29.552Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "The benzothiazinone lead compound, BTZ043, kills Mycobacterium tuberculosis by inhibiting the essential flavo-enzyme DprE1, decaprenylphosphoryl-beta-D-ribose 2-epimerase. Here, we synthesized a new series of piperazine-containing benzothiazinones (PBTZ) and show that, like BTZ043, the preclinical candidate PBTZ169 binds covalently to DprE1. The crystal structure of the DprE1-PBTZ169 complex reveals formation of a semimercaptal adduct with Cys387 in the active site and explains the irreversible inactivation of the enzyme. Compared to BTZ043, PBTZ169 has improved potency, safety and efficacy in zebrafish and mouse models of tuberculosis (TB). When combined with other TB drugs, PBTZ169 showed additive activity against M.\\xa0tuberculosis in vitro except with bedaquiline (BDQ) where synergy was observed. A new regimen comprising PBTZ169, BDQ and pyrazinamide was found to be more efficacious than the standard three drug treatment in a murine model of chronic disease. PBTZ169 is thus an attractive drug candidate to treat TB in humans. Subject Categories Microbiology, Virology & Host Pathogen Interaction; Pharmacology & Drug Discovery"}], "format": [], "journal": {"issnPrinted": "1757-4676", "conferencedate": "", "vol": "6", "conferenceplace": "", "name": "EMBO Molecular Medicine", "iss": "3", "sp": "372", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1757-4684", "ep": "383", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2014-02-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, 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"schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Towards a new combination therapy for tuberculosis with next generation benzothiazinones"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "pmid", "classname": "pmid", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "26990806"}, {"dataInfo": 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The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC\\u2010SIGN and DC\\u2010SIGNR (collectively termed as DC\\u2010SIGN/R) using a sensitive, ratiometric F\\xf6rster resonance energy transfer (FRET) assay. The QD probes specifically bind DC\\u2010SIGN, but not its closely related receptor DC\\u2010SIGNR, which is further confirmed by its specific blocking of DC\\u2010SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC\\u2010SIGN binds more efficiently to densely packed mannosides. A FRET\\u2010based thermodynamic study reveals that the binding is enthalpy\\u2010driven. This work establishes QD FRET as a rapid, sensitive technique for probing structure and thermodynamics of multivalent protein\\u2013ligand interactions."}], "format": [], "journal": {"issnPrinted": "1433-7851", "conferencedate": "", "vol": "55", "conferenceplace": "", "name": "Angewandte Chemie (International Ed. in English)", "iss": "15", "sp": "4738", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1521-3773", "ep": "4742", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-03-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", 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"dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2007-07-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357", "value": "PubMed Central"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-06-09T13:09:56.823Z", "fulltext": [], "dateoftransformation": "2018-08-30T01:37:41.001Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value":"Background Mental health problems are a worldwide public health burden. The literature concerning the mental health benefits from physical activity among adults has grown. Adolescents are less studied, and especially longitudinal studies are lacking. This paper investigates the associations between weekly hours of physical activity at age 15\\u201316 and mental health three years later. Methods Longitudinal self-reported health survey. The baseline study consisted of participants from the youth section of the Oslo Health Study, carried out in schools in 2000\\u20132001 (n = 3811). The follow-up in 2003\\u20132004 was conducted partly at school and partly through mail. A total of 2489 (1112 boys and 1377 girls) participated in the follow-up. Mental health was measured by the Strengths and Difficulties Questionnaire with an impact supplement. Physical activity was measured by a question on weekly hours of physical activity outside of school, defined as exertion \"to an extent that made you sweat and/or out of breath\". Adjustments were made for well-documented confounders and mental health at baseline. Results In boys, the number of hours spent on physical activity per week at age 15\\u201316 was negatively associated with emotional symptoms [B (95%CI) = -0.09 (-0.15, -0.03)] and peer problems [B (95%CI) = -0.08 (-0.14, -0.03)] at age 18\\u201319 after adjustments. In girls, there were no significant differences in SDQ subscales at age 18\\u201319 according to weekly hours of physical activity at age 15\\u201316 after adjustments. Boys and girls with five to seven hours of physical activity per week at age 15\\u201316 had the lowest mean scores for total difficulties and the lowest percentage with high impact score at age 18\\u201319, but the differences were not statistically significant after adjustments. Conclusion Weekly hours of physical activity at age 15\\u201316 years was weakly associated with mental health at three-year follow-up in boys. Results encourage a search for further knowledge about physical activity as a possible protective factor in relation to mental health problems in adolescence."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "7", "conferenceplace": "", "name": "BMC Public Health", "iss": "", "sp": "155", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1471-2458", "ep": "155", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2007-07-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "BioMed Central"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:pubmedcentral.nih.gov:1955440"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "BMC Public Health"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "The association between weekly hours of physical activity and mental health: A three-year follow-up study of 15\\u201316-year-old students in the city of Oslo, Norway"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "pmid", "classname": "pmid", 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"deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-04-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357", "value": "PubMed Central"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-06-15T02:59:16.126Z", "fulltext": [], "dateoftransformation": "2018-08-30T02:39:11.807Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Abstract Objective This study analyzed the maintenance of lateral incisors in the dental rehabilitation of individuals with cleft lip and palate. Material and Methods The study was conducted on a tertiary craniofacial center and comprised retrospective analysis of panoramic and periapical radiographs of Caucasoid individuals with non-syndromic complete unilateral cleft lip and palate, analyzing all radiographs available on the records of each individual, from the first to the last up to 12 years of age. Overall, 2,826 records were reviewed to achieve a sample of 1,000 individuals. Among these, 487 individuals presented the permanent lateral incisors on both cleft and non-cleft sides, which were included in this study. Results The results were evaluated in percentages and by descriptive statistics. The association between maintenance of the lateral incisor and timing of alveolar bone graft were analyzed by the t test. Among the 487 individuals, 265 had not completed treatment, 62 presented insufficient information, and 44 concluded the treatment elsewhere. Among the remaining 116 individuals, the lateral incisor was extracted from 88 (75.86%) of them on the cleft side (CS) and from 23 (19.83%) people on the non-cleft side (NCS). The age at accomplishment of alveolar bone graft was significantly associated with maintenance of the lateral incisor on the cleft side (p<0.01). Most extractions were indicated because of the inadequate positioning on the CS and for midline correction on the NCS. Rehabilitation was primarily completed by orthodontic movement (53 individuals on the CS and 13 individuals on the NCS). Conclusion In conclusion, the lateral incisor on the cleft side was not maintained in most individuals. Positive relationship was observed between extraction of the lateral incisor and age at accomplishment of the alveolar bone graft, suggesting the need to anticipate the initial radiographic evaluation to enhance its maintenance and reduce the procedures required for rehabilitation."}], "format": [], "journal": {"issnPrinted": "1678-7757", "conferencedate": "", "vol": "26", "conferenceplace": "", "name": "Journal of Applied Oral Science", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1678-7765", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-04-01"}, 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"dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Dental health services"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Dental care"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Inequalities in health care services"}, {"dataInfo": 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"Moise\\u0301s", "pid": [], "rank": 3, "affiliation": [], "fullname": "Goldbaum, Mois\\xe9s"}, {"surname": "Azevedo Barros", "name": "Marilisa Berti", "pid": [], "rank": 4, "affiliation": [], "fullname": "de Azevedo Barros, Marilisa Berti"}, {"surname": "Gianini", "name": "Reinaldo Jose\\u0301", "pid": [], "rank": 5, "affiliation": [], "fullname": "Gianini, Reinaldo Jos\\xe9"}, {"surname": "Cesar", "name": "Chester Luiz Galva\\u0303o", "pid": [], "rank": 6, "affiliation": [], "fullname": "Cesar, Chester Luiz Galv\\xe3o"}, {"surname": "Mackenbach", "name": "Johan P.", "pid": [], "rank": 7, "affiliation": [], "fullname": "Mackenbach, Johan P."}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", 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"classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357", "value": "PubMed Central"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-06-13T14:33:43.886Z", "fulltext": [], "dateoftransformation": "2018-08-30T03:52:36.376Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Background Access to, and use of, dental health services in Brazil have improved since 2003. The increase of private health care plans and the implementation of the \\u201cSmiling Brazil\\u201d Program, the largest public oral health care program in the world, could have influenced this increase in access. However, we do not yet know if inequalities in the use of dental health services persist after the improvement in access. The aims of this study are to analyze socioeconomic differences for dental health service use between 2003 and 2008 in S\\xe3o Paulo and to examine changes in these associations since the implementation of the Smiling Brazil program in 2003. Method Data was obtained via two household health surveys (ISA-Capital 2003 and ISA-Capital 2008) which investigated living conditions, lifestyle, health status and use of health care services. Logistic regression was used to analyze associations between socioeconomic factors and dental services use. Additionally, trends from 2003 to 2008 regarding socioeconomic characteristics and dental health service use were explored. Results Overall, dental health service use increased between 2003 and 2008 and was at both time points more common among those who had higher income, better education, better housing conditions, private health care plans and were Caucasian. Inequalities in use of dental health care did not decrease over time. Among the reasons for not seeking dental care, not having teeth and financial difficulty were more common in lower socioeconomic groups, while thinking it was unnecessary was more common in higher socioeconomic groups. Conclusions The Brazilian oral health policy is still in a period of expansion and seems to have contributed slightly to increased dental health service use, but has not influenced socioeconomic inequalities in the use of these services. Acquiring deeper knowledge about inequalities in dental health service use will contribute to better understanding of potential barriers to reducing them. Electronic supplementary material The online version of this article (doi:10.1186/s12913-016-1928-y) contains supplementary material, which is available to authorized users."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "16", "conferenceplace": "", "name": "BMC Health Services Research", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1472-6963", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", 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"Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-06-13T18:26:05.733Z", "fulltext": [], "dateoftransformation": "2018-08-30T05:30:36.107Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Most, if not all, bacteria form a biofilm, a multicellular structure that protects them from antimicrobial actions of the host immune system and affords resistance to antibiotics. The latter is especially disturbing with the increase in multiresistant bacterial clones worldwide. Bacterial biofilm formation is a multistep process that starts with surface adhesion, after which attached bacteria divide and give rise to biomass. The actual steps required for Haemophilus influenzae biofilm formation are largely not known. We show that interference with peptidoglycan biosynthesis increases biofilm formation because of the release of bacterial genomic DNA. Subinhibitory concentrations of \\u03b2-lactam antibiotics, which are often prescribed to treat H.\\xa0influenzae infections, increase biofilm formation through a similar mechanism. Therefore, when \\u03b2-lactam antibiotics do not reach their MIC in vivo, they might not only drive selection for \\u03b2-lactam-resistant clones but also increase biofilm formation and resistance to other antimicrobial compounds."}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "ABSTRACT Nontypeable Haemophilus influenzae (NTHi) is an opportunistic pathogen that mainly causes otitis media in children and community-acquired pneumonia or exacerbations of chronic obstructive pulmonary disease in adults. A large variety of studies suggest that biofilm formation by NTHi may be an important step in the pathogenesis of this bacterium. However, the underlying mechanisms involved in this process are poorly elucidated. In this study, we used a transposon mutant library to identify bacterial genes involved in biofilm formation. The growth and biofilm formation of 4,172 transposon mutants were determined, and the involvement of the identified genes in biofilm formation was validated in in vitro experiments. Here, we present experimental data showing that increased bacterial lysis, through interference with peptidoglycan synthesis, results in elevated levels of extracellular DNA, which increased biofilm formation. Interestingly, similar results were obtained with subinhibitory concentrations of \\u03b2-lactam antibiotics, known to interfere with peptidoglycan synthesis, but such an effect does not appear with other classes of antibiotics. These results indicate that treatment with \\u03b2-lactam antibiotics, especially for \\u03b2-lactam-resistant NTHi isolates, might increase resistance to antibiotics by increasing biofilm formation. IMPORTANCE Most, if not all, bacteria form a biofilm, a multicellular structure that protects them from antimicrobial actions of the host immune system and affords resistance to antibiotics. The latter is especially disturbing with the increase in multiresistant bacterial clones worldwide. Bacterial biofilm formation is a multistep process that starts with surface adhesion, after which attached bacteria divide and give rise to biomass. The actual steps required for Haemophilus influenzae biofilm formation are largely not known. We show that interference with peptidoglycan biosynthesis increases biofilm formation because of the release of bacterial genomic DNA. Subinhibitory concentrations of \\u03b2-lactam antibiotics, which are often prescribed to treat H.\\xa0influenzae infections, increase biofilm formation through a similar mechanism. Therefore, when \\u03b2-lactam antibiotics do not reach their MIC in vivo, they might not only drive selection for \\u03b2-lactam-resistant clones but also increase biofilm formation and resistance to other antimicrobial compounds."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "2", "conferenceplace": "", "name": "mSphere", "iss": "1", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "2379-5042", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2017-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", 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"deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357", "value": "PubMed Central"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-06-13T16:32:55.324Z", "fulltext": [], "dateoftransformation": "2018-08-30T08:27:50.134Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Macrocyclic lactones (ML) are important anthelmintics used in animals and humans against parasite nematodes, but their therapeutic success is compromised by the spread of ML resistance. Some ABC transporters, such as p-glycoproteins (Pgps), are selected and overexpressed in ML-resistant nematodes, supporting a role for some drug efflux proteins in ML resistance. However, the role of such proteins in ML transport remains to be clarified at the molecular level. Recently, Caenorhabditis elegans Pgp-1 (Cel-Pgp-1) has been crystallized, and its drug-modulated ATPase function characterized in\\xa0vitro revealed Cel-Pgp-1 as a multidrug transporter. Using this crystal structure, we have developed an in silico drug docking model in order to study the binding of ML and other anthelmintic drugs to Cel-Pgp-1. All tested ML bound with high affinity in a unique site, within the inner chamber of the protein, supporting that ML may be transported by Cel-Pgp-1. Interestingly, interacting residues delineate a ML specific fingerprint involving H-bonds, including T1028. In particular, benzofurane and spiroketal moieties bound to specific sub-sites. When compared with the aglycone ML, such as moxidectin and ivermectin aglycone, avermectin anthelmintics have significant higher affinity for Cel-Pgp-1, likely due to the sugar substituent(s) that bind to a specific area involving H-bonds at Y771. Triclabendazole, closantel and emodepside bound with good affinities to different sub-sites in the inner chamber, partially overlapping with the ML binding site, suggesting that they could compete for Cel-Pgp-1-mediated ML transport. In conclusion, this work provides novel information on the role of nematode Pgps in transporting anthelmintics, and a valuable tool to predict drug-drug interactions and to rationally design new competitive inhibitors of clinically-relevant nematode Pgps, to improve anthelmintic therapeutics."}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Graphical abstract Ivermectin (red spheres) binding to Cel-Pgp-1 (blue ribbon: N-term, yellow ribbon: C-term).Image 1"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Highlights \\u2022 Cel-Pgp-1 cristal provides a valuable tool to study anthelmintic interactions. \\u2022 Cel-Pgp-1 recognizes a broad panel of anthelmintics, including macrocyclic lactones. \\u2022 Cel-Pgp-1 is predicted to transport MLs and contribute to anthelmintic resistance. \\u2022 Sugars in avermectins increase the affinity to Cel-Pgp-1 compared with moxidectin. \\u2022 These data provide a basis for modelling ABC homologs in parasitic nematodes."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "6", "conferenceplace": "", "name": "International Journal for Parasitology: Drugs and Drug Resistance", "iss": "3", "sp": "299", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "2211-3207", "ep": "313", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, 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Recently it has received a lot of attention as a substrate to grow and isolate graphene as well as for its intrinsic UV lasing response. Similar to carbon, one-dimensional boron nitride nanotubes (BNNTs) have been theoretically predicted and later synthesised. Here we use first principles simulations to unambiguously demonstrate that i) BN nanotubes inherit the highly efficient UV luminescence of hexagonal BN; ii) the application of an external perpendicular field closes the electronic gap keeping the UV lasing with lower yield; iii) defects in BNNTS are responsible for tunable light emission from the UV to the visible controlled by a transverse electric field (TEF). 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Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. 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They are usually maintained with 10% fetal bovine serum (FBS) in vitro. Modified platelet-rich plasma (mPRP) would be a safe alternative to 10% FBS during SHEDs culture. Therefore, our study aimed to compare the proliferation and differentiation of SHEDs cultured in mPRP and FBS medium to explore an optimal concentration of mPRP for SHEDs maintenance. Platelets were harvested by automatic blood cell analyzer and activated by repeated liquid nitrogen freezing and thawing. The platelet-related cytokines were examined and analyzed by ELISA. SHEDs were extracted and cultured with different concentrations of mPRP or 10% FBS medium. Alkaline phosphatase (ALP) activity was measured. Mineralization factors, RUNX2 and OCN, were measured by real-time PCR. SHEDs were characterized with mesenchymal stem cells (MSCs) markers including vimentin, CD44, and CD105. mPRP at different concentrations (2, 5, 10, and 20%) enhanced the growth of SHEDs. 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A large variety of studies suggest that biofilm formation by NTHi may be an important step in the pathogenesis of this bacterium. However, the underlying mechanisms involved in this process are poorly elucidated. In this study, we used a transposon mutant library to identify bacterial genes involved in biofilm formation. The growth and biofilm formation of 4,172 transposon mutants were determined, and the involvement of the identified genes in biofilm formation was validated in in vitro experiments. Here, we present experimental data showing that increased bacterial lysis, through interference with peptidoglycan synthesis, results in elevated levels of extracellular DNA, which increased biofilm formation. Interestingly, similar results were obtained with subinhibitory concentrations of \\u03b2-lactam antibiotics, known to interfere with peptidoglycan synthesis, but such an effect does not appear with other classes of antibiotics. These results indicate that treatment with \\u03b2-lactam antibiotics, especially for \\u03b2-lactam-resistant NTHi isolates, might increase resistance to antibiotics by increasing biofilm formation. IMPORTANCE Most, if not all, bacteria form a biofilm, a multicellular structure that protects them from antimicrobial actions of the host immune system and affords resistance to antibiotics. The latter is especially disturbing with the increase in multiresistant bacterial clones worldwide. Bacterial biofilm formation is a multistep process that starts with surface adhesion, after which attached bacteria divide and give rise to biomass. The actual steps required for Haemophilus influenzae biofilm formation are largely not known. We show that interference with peptidoglycan biosynthesis increases biofilm formation because of the release of bacterial genomic DNA. Subinhibitory concentrations of \\u03b2-lactam antibiotics, which are often prescribed to treat H. influenzae infections, increase biofilm formation through a similar mechanism. Therefore, when \\u03b2-lactam antibiotics do not reach their MIC in vivo, they might not only drive selection for \\u03b2-lactam-resistant clones but also increase biofilm formation and resistance to other antimicrobial compounds."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", 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These results indicate that treatment with \\u03b2-lactam antibiotics, especially for \\u03b2-lactam-resistant NTHi isolates, might increase resistance to antibiotics by increasing biofilm formation. IMPORTANCE Most, if not all, bacteria form a biofilm, a multicellular structure that protects them from antimicrobial actions of the host immune system and affords resistance to antibiotics. The latter is especially disturbing with the increase in multiresistant bacterial clones worldwide. Bacterial biofilm formation is a multistep process that starts with surface adhesion, after which attached bacteria divide and give rise to biomass. The actual steps required for Haemophilus influenzae biofilm formation are largely not known. We show that interference with peptidoglycan biosynthesis increases biofilm formation because of the release of bacterial genomic DNA. Subinhibitory concentrations of \\u03b2-lactam antibiotics, which are often prescribed to treat H. influenzae infections, increase biofilm formation through a similar mechanism. 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Using 468 X 10(6) B (B) over bar pairs produced in Y(4S) decays collected by the BABAR detector at SLAC, we measure T-violating parameters in the time evolution of neutral B mesons, yielding Delta S-T(+) = -137 +/- 0.14(stat) +/- 0.06(syst) and Delta S-T(-) = 1.17 +/- 0.18(stat) +/- 0.11(syst). 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Background: Use of whole-genome sequence data is expected to increase persistency of genomic prediction across generations and breeds but affects model performance and requires increased computing time. In this study, we investigated whether the split-and-merge Bayesian stochastic search variable selection (BSSVS) model could overcome these issues. BSSVS is performed first on subsets of sequence-based variants and then on a merged dataset containing variants selected in the first step. Results: We used a dataset that included 4,154,064 variants after editing and de-regressed proofs for 3415 reference and 2138 validation bulls for somatic cell score, protein yield and interval first to last insemination. In the first step, BSSVS was performed on 106 subsets each containing ~39,189 variants. In the second step, 1060 up to 472,492 variants, selected from the first step, were included to estimate the accuracy of genomic prediction. Accuracies were at best equal to those achieved with the commonly used Bovine 50k-SNP chip, although the number of variants within a few well-known quantitative trait loci regions was considerably enriched. When variant selection and the final genomic prediction were performed on the same data, predictions were biased. Predictions computed as the average of the predictions computed for each subset achieved the highest accuracies, i.e. 0.5 to 1.1 % higher than the accuracies obtained with the 50k-SNP chip, and yielded the least biased predictions. Finally, the accuracy of genomic predictions obtained when all sequence-based variants were included was similar or up to 1.4 % lower compared to that based on the average predictions across the subsets. By applying parallelization, the split-and-merge procedure was completed in 5 days, while the standard analysis including all sequence-based variants took more than three months. Conclusions: The split-and-merge approach splits one large computational task into many much smaller ones, which allows the use of parallel processing and thus efficient genomic prediction based on whole-genome sequence data. The split-and-merge approach did not improve prediction accuracy, probably because we used data on a single breed for which relationships between individuals were high. Nevertheless, the split-and-merge approach may have potential for applications on data from multiple breeds.

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Carvalho", "pid": [], "rank": 2, "affiliation": [], "fullname": "Ara\\xfajo, Fernanda Montenegro de Carvalho"}, {"surname": "Cavalcanti", "name": "Luciano Pamplona Go\\u0301es", "pid": [], "rank": 3, "affiliation": [], "fullname": "Cavalcanti, Luciano Pamplona de G\\xf3es"}, {"surname": "Braga", "name": "Deborah Nunes Melo", "pid": [], "rank": 4, "affiliation": [], "fullname": "Braga, Deborah Nunes Melo"}, {"surname": "Perdiga\\u0303o", "name": "Anne Carolinne Bezerra", "pid": [], "rank": 5, "affiliation": [], "fullname": "Perdig\\xe3o, Anne Carolinne Bezerra"}, {"surname": "Santos", "name": "Flavia Barreto Dos", "pid": [], "rank": 6, "affiliation": [], "fullname": "Santos, Flavia Barreto dos"}, {"surname": "Nogueira", "name": "Fernanda Bruycker", "pid": [], "rank": 7, "affiliation": [], "fullname": "Nogueira, Fernanda de Bruycker"}, {"surname": "Esco\\u0301ssia", "name": "Kiliana Nogueira Farias Da", "pid": [], "rank": 8, "affiliation": [], "fullname": "Esc\\xf3ssia, Kiliana Nogueira Farias da"}, {"surname": "Guedes", "name": "Maria Izabel Florindo", "pid": [], "rank": 9, "affiliation": [], "fullname": "Guedes, Maria Izabel Florindo"}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - Brazil"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "http://creativecommons.org/licenses/by/4.0/"}, "url": ["http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762018001100300&lng=en&tlng=en"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-10-18"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - Brazil"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-10-17T15:29:29.5Z", "fulltext": [], "dateoftransformation": "2020-03-05T17:09:49.618Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "BACKGROUND The first dengue cases in Brazil with laboratory confirmation occurred in the northern region of the country, with the isolation of two serotypes, dengue virus 1 (DENV-1) and DENV-4. In Cear\\xe1, the introduction of DENV-4 was reported during a DENV-1 epidemic in 2011, with only two isolations. OBJECTIVES The aim of this study was to characterise the first DENV-4 epidemic in the state of Cear\\xe1, Brazil. METHODS The study population was composed of patients with suspected dengue that were reported to health care units from January to December 2012. The laboratory confirmation of infection was made by viral isolation, reverse transcription polymerase chain reaction (RT-PCR), AgNS1, immunohistochemistry and IgM enzyme-linked immunosorbent assay (ELISA). MAIN CONCLUSIONS In the study year, 72,211 suspected dengue cases were reported and 51,865 of these cases (71.8%) were confirmed to be positive. Co-circulation of three serotypes, DENV-1, DENV-3 and DENV-4, was detected with a predominance of DENV-4 (95.3%). Most cases were not severe, but there were 44 fatal outcomes. DENV-4 Genotype II was identified for the first time in Cear\\xe1."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "text/html"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-10-18"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Instituto Oswaldo Cruz, Minist\\xe9rio da Sa\\xfade"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:scielo:S0074-02762018001100300"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Mem\\xf3rias do Instituto Oswaldo Cruz, Volume: 113, Issue: 11, Article number: e180320, Published: 18 OCT 2018"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Dengue 4 in Cear\\xe1, Brazil: characterisation of epidemiological and laboratorial aspects and causes of death during the first epidemic in the state"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "relevantdate": [], "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - Brazil"}], "id": "50|od_______608::a09f60767c9565c03a40c6991f3d7c39", "subject": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "Isolation with Migration model"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "coalescent analysis"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "native Siberians"}], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Fagundes", "name": "Nelson J. R.", "pid": [], "rank": 1, "affiliation": [], "fullname": "Fagundes, Nelson J.R."}, {"surname": "Tagliani-Ribeiro", "name": "Alice", "pid": [], "rank": 2, "affiliation": [], "fullname": "Tagliani-Ribeiro, Alice"}, {"surname": "Rubicz", "name": "Rohina", "pid": [], "rank": 3, "affiliation": [], "fullname": "Rubicz, Rohina"}, {"surname": "Tarskaia", "name": "Larissa", "pid": [], "rank": 4, "affiliation": [], "fullname": "Tarskaia, Larissa"}, {"surname": "Crawford", "name": "Michael H.", "pid": [], "rank": 5, "affiliation": [], "fullname": "Crawford, Michael H."}, {"surname": "Salzano", "name": "Francisco M.", "pid": [], "rank": 6, "affiliation": [], "fullname": "Salzano, Francisco M."}, {"surname": "Bonatto", "name": "Sandro L.", "pid": [], "rank": 7, "affiliation": [], "fullname": "Bonatto, Sandro L."}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - Brazil"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "http://creativecommons.org/licenses/by/4.0/"}, "url": ["http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000200206&lng=en&tlng=en"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-01-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - Brazil"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-04-22T15:08:13.708Z", "fulltext": [], "dateoftransformation": "2020-03-05T17:56:15.371Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Abstract In spite of many genetic studies that contributed for a deep knowledge about the peopling of the Americas, no consensus has emerged about important parameters such as the effective size of the Native Americans founder population. Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. Recognizing the size of the genetic bottleneck during the peopling of the Americas is important for determining the extent of genetic markers needed to characterize Native American populations in genome-wide studies and to evaluate the adaptive potential of genetic variants in this population."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "text/html"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Sociedade Brasileira de Gen\\xe9tica"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:scielo:S1415-47572018000200206"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Genetics and Molecular Biology, Volume: 41, Issue: 1 Supplement 1, Pages: 206-214, Published: 2018"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "relevantdate": [], "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - Brazil"}], "id": "50|od_______608::c18e77bcf6417b170f22ed36a62ef13d", "subject": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "Bacillus"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "degradation"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "manipueira"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "fertirrigation"}], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Vasconcellos", "name": "S. 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Thirty one microbial strains were isolated from manipueira, a liquid effluent of cassava processing factories. Among these strains, Bacillus licheniformis (isolate 2_2) and Rhodotorulla glutinis (isolate L1) were able to degrade 71% and 95% of added linamarin, respectively, within 7 days, showing high biodegradation activity and great potential for detoxification of cassava processing wastewaters."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "text/html"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2009-12-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Sociedade Brasileira de Microbiologia"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:scielo:S1517-83822009000400019"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Brazilian Journal of Microbiology, Volume: 40, Issue: 4, Pages: 879-883, Published: DEC 2009"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "In vitro degradation of linamarin by microorganisms isolated from cassava wastewater treatment lagoons"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "relevantdate": [], "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - 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The performance of both methods was analyzed based on two datasets: 1) a complete site x species matrix compiled from two studies in different land uses in the Amazon using direct analysis of field samples and trap cultures. 2) Total number of AMF morphotypes detected by both methods in published manuscripts across several ecosystems. From dataset 1, direct analysis of field samples revealed 57 morphotypes, whereas only 21 of these were detected by trap culture. Community variation (beta diversity) analysis revealed that field samples are far more sensitive in detecting shifts in AMF community composition among land uses than trap cultures in the Amazon region, with the combined results of both methods being not better than that obtained only by direct analysis of field samples. 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a comparative study"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "relevantdate": [], "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - Brazil"}], "id": "50|od_______608::de715689eb8cf69f5c93275d325a152b", "subject": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "Inflammation"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "Edema"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "Medicinal plants"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "Anacardiaceae"}], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Machado", "name": "Alessandra Cury", "pid": [], "rank": 1, "affiliation": [], "fullname": "Machado, Alessandra Cury"}, {"surname": "Dezan Junior", "name": "Eloi", "pid": [], "rank": 2, "affiliation": [], "fullname": "Dezan Junior, Eloi"}, {"surname": "Gomes-Filho", "name": "Joa\\u0303o Eduardo", "pid": [], "rank": 3, "affiliation": [], "fullname": "Gomes-Filho, Jo\\xe3o Eduardo"}, {"surname": "Cintra", "name": "Luciano Tavares Angelo", "pid": [], "rank": 4, "affiliation": [], "fullname": "Cintra, Luciano Tavares Angelo"}, {"surname": "Ruvie\\u0301re", "name": "Denise Belucio", "pid": [], "rank": 5, "affiliation": [], "fullname": "Ruvi\\xe9re, Denise Belucio"}, {"surname": "Zoccal", "name": "Renata", "pid": [], "rank": 6, "affiliation": [], "fullname": "Zoccal, Renata"}, {"surname": "Damante", "name": "Carla Andreotti", "pid": [], "rank": 7, "affiliation": [], "fullname": "Damante, Carla Andreotti"}, {"surname": "Jardim Junior", "name": "Elerson Gaetti", "pid": [], "rank": 8, "affiliation": [], "fullname": "Jardim Junior, Elerson Gaetti"}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - 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MATERIAL AND METHODS: Test groups consisted of aqueous and ethanolic Aroeira extracts and saline (control). For edema quantification, 18 rats received an intravenous injection of Evan's Blue. After 30 min, the extracts and saline were injected on the dorsum of the rats, which were then sacrificed after 3 and 6 h. Readings were performed in a spectrophotometer. For subcutaneous implantation, 30 rats received a polyethylene tube containing the extracts on their dorsum and then they were killed after 7 and 28 days. The samples were processed for histological analysis and evaluated with a light microscope. The inflammatory infiltrate was quantified. RESULTS: There were no statistically significant differences between aqueous extract and saline groups in relation to edema quantification in the different periods (p>0.05). Ethanolic solution resulted in more edema independently of the experimental period (p<0.05). Histological analysis showed similar results on the 7-day period for the 3 groups. There was a notable reduction on inflammatory cell number for saline and aqueous extract groups at 28 days. CONCLUSION: The aqueous extract showed biocompatible properties similar to those of saline."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "text/html"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2012-08-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Faculdade De Odontologia De Bauru - 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T.", "pid": [], "rank": 2, "affiliation": [], "fullname": "Li, H.T."}, {"surname": "Li", "name": "S. H.", "pid": [], "rank": 3, "affiliation": [], "fullname": "Li, S.H."}, {"surname": "Li", "name": "X.", "pid": [], "rank": 4, "affiliation": [], "fullname": "Li, X."}, {"surname": "Duan", "name": "J. M.", "pid": [], "rank": 5, "affiliation": [], "fullname": "Duan, J.M."}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - Brazil"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "http://creativecommons.org/licenses/by/4.0/"}, "url": ["http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2016001000604&lng=en&tlng=en"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-09-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - Brazil"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2017-11-22T20:05:23.65Z", "fulltext": [], "dateoftransformation": "2020-03-05T18:32:46.905Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Stem cells from human exfoliated deciduous teeth (SHEDs) have great potential to treat various dental-related diseases in regenerative medicine. They are usually maintained with 10% fetal bovine serum (FBS) in vitro. Modified platelet-rich plasma (mPRP) would be a safe alternative to 10% FBS during SHEDs culture. Therefore, our study aimed to compare the proliferation and differentiation of SHEDs cultured in mPRP and FBS medium to explore an optimal concentration of mPRP for SHEDs maintenance. Platelets were harvested by automatic blood cell analyzer and activated by repeated liquid nitrogen freezing and thawing. The platelet-related cytokines were examined and analyzed by ELISA. SHEDs were extracted and cultured with different concentrations of mPRP or 10% FBS medium. Alkaline phosphatase (ALP) activity was measured. Mineralization factors, RUNX2 and OCN, were measured by real-time PCR. SHEDs were characterized with mesenchymal stem cells (MSCs) markers including vimentin, CD44, and CD105. mPRP at different concentrations (2, 5, 10, and 20%) enhanced the growth of SHEDs. Moreover, mPRP significantly stimulated ALP activity and promoted expression of RUNX2 and OCN compared with 10% FBS. mPRP could efficiently facilitate proliferation and differentiation of SHEDs, and 2% mPRP would be an optimal substitute for 10% FBS during SHEDs expansion and differentiation in clinical scale manufacturing."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "text/html"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-09-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Associa\\xe7\\xe3o Brasileira de Divulga\\xe7\\xe3o Cient\\xedfica"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:scielo:S0100-879X2016001000604"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Brazilian Journal of Medical and Biological Research, Volume: 49, Issue: 10, Article number: e5373, Published: 01 SEP 2016"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Investigation of modified platelet-rich plasma (mPRP) in promoting the proliferation and differentiation of dental pulp stem cells from deciduous teeth"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "relevantdate": [], "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - Brazil"}], "id": "50|od_______608::ecbd7f91aa73268b8d3dfb4493862b0c", "subject": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "Incisor"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "Cleft lip"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "Cleft palate"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:result_subject", "schemename": "dnet:result_subject"}, "value": "Oral rehabilitation"}], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Tereza", "name": "Guida Paola Genovez", "pid": [], "rank": 1, "affiliation": [], "fullname": "Tereza, Guida Paola Genovez"}, {"surname": "Santos", "name": "Marcos Anto\\u0302nio Corre\\u0302a Dos", "pid": [], "rank": 2, "affiliation": [], "fullname": "Santos, Marcos Ant\\xf4nio Corr\\xeaa dos"}, {"surname": "Winckler", "name": "Vivian Patricia Saldias Vargas", "pid": [], "rank": 3, "affiliation": [], "fullname": "Winckler, Vivian Patricia Saldias Vargas"}, {"surname": "Almeida", "name": "Ana Lu\\u0301cia Pompeia Fraga", "pid": [], "rank": 4, "affiliation": [], "fullname": "Almeida, Ana L\\xfacia Pompeia Fraga de"}, {"surname": "Dalben", "name": "Gisele Da Silva", "pid": [], "rank": 5, "affiliation": [], "fullname": "Dalben, Gisele da Silva"}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - Brazil"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "http://creativecommons.org/licenses/by/4.0/"}, "url": ["http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-77572018000100438&lng=en&tlng=en"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-05-07"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::996a7fa078cc36c46d02f9af3bef918b", "value": "Scientific Electronic Library Online - Brazil"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2018-07-07T15:09:37.426Z", "fulltext": [], "dateoftransformation": "2020-03-05T18:38:07.379Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Abstract Objective This study analyzed the maintenance of lateral incisors in the dental rehabilitation of individuals with cleft lip and palate. Material and Methods The study was conducted on a tertiary craniofacial center and comprised retrospective analysis of panoramic and periapical radiographs of Caucasoid individuals with non-syndromic complete unilateral cleft lip and palate, analyzing all radiographs available on the records of each individual, from the first to the last up to 12 years of age. Overall, 2,826 records were reviewed to achieve a sample of 1,000 individuals. Among these, 487 individuals presented the permanent lateral incisors on both cleft and non-cleft sides, which were included in this study. Results The results were evaluated in percentages and by descriptive statistics. The association between maintenance of the lateral incisor and timing of alveolar bone graft were analyzed by the t test. Among the 487 individuals, 265 had not completed treatment, 62 presented insufficient information, and 44 concluded the treatment elsewhere. Among the remaining 116 individuals, the lateral incisor was extracted from 88 (75.86%) of them on the cleft side (CS) and from 23 (19.83%) people on the non-cleft side (NCS). The age at accomplishment of alveolar bone graft was significantly associated with maintenance of the lateral incisor on the cleft side (p<0.01). Most extractions were indicated because of the inadequate positioning on the CS and for midline correction on the NCS. Rehabilitation was primarily completed by orthodontic movement (53 individuals on the CS and 13 individuals on the NCS). Conclusion In conclusion, the lateral incisor on the cleft side was not maintained in most individuals. 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"dnet:publication_resource"}}], "dateofcollection": "2017-09-25T14:02:01.908Z", "fulltext": [], "dateoftransformation": "2019-07-02T09:47:50.826Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value":"Background Mental health problems are a worldwide public health burden. The literature concerning the mental health benefits from physical activity among adults has grown. Adolescents are less studied, and especially longitudinal studies are lacking. This paper investigates the associations between weekly hours of physical activity at age 15?16 and mental health three years later. Methods Longitudinal self-reported health survey. The baseline study consisted of participants from the youth section of the Oslo Health Study, carried out in schools in 2000?2001 (n = 3811). The follow-up in 2003?2004 was conducted partly at school and partly through mail. A total of 2489 (1112 boys and 1377 girls) participated in the follow-up. Mental health was measured by the Strengths and Difficulties Questionnaire with an impact supplement. Physical activity was measured by a question on weekly hours of physical activity outside of school, defined as exertion \"to an extent that made you sweat and/or out of breath\". Adjustments were made for well-documented confounders and mental health at baseline. Results In boys, the number of hours spent on physical activity per week at age 15?16 was negatively associated with emotional symptoms [B (95%CI) = -0.09 (-0.15, -0.03)] and peer problems [B (95%CI) = -0.08 (-0.14, -0.03)] at age 18?19 after adjustments. In girls, there were no significant differences in SDQ subscales at age 18?19 according to weekly hours of physical activity at age 15?16 after adjustments. Boys and girls with five to seven hours of physical activity per week at age 15?16 had the lowest mean scores for total difficulties and the lowest percentage with high impact score at age 18?19, but the differences were not statistically significant after adjustments. Conclusion Weekly hours of physical activity at age 15?16 years was weakly associated with mental health at three-year follow-up in boys. Results encourage a search for further knowledge about physical activity as a possible protective factor in relation to mental health problems in adolescence."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "7", "conferenceplace": "", "name": "BMC Public Health", "iss": "", "sp": "155", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1471-2458", "ep": "155", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2007-07-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, 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Here, we synthesized a new series of piperazine-containing benzothiazinones (PBTZ) and show that, like BTZ043, the preclinical candidate PBTZ169 binds covalently to DprE1. The crystal structure of the DprE1-PBTZ169 complex reveals formation of a semimercaptal adduct with Cys387 in the active site and explains the irreversible inactivation of the enzyme. Compared to BTZ043, PBTZ169 has improved potency, safety and efficacy in zebrafish and mouse models of tuberculosis (TB). When combined with other TB drugs, PBTZ169 showed additive activity against M.\\xa0tuberculosis in vitro except with bedaquiline (BDQ) where synergy was observed. A new regimen comprising PBTZ169, BDQ and pyrazinamide was found to be more efficacious than the standard three drug treatment in a murine model of chronic disease. PBTZ169 is thus an attractive drug candidate to treat TB in humans. 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Material and methods Test groups consisted of aqueous and ethanolic Aroeira extracts and saline (control). For edema quantification, 18 rats received an intravenous injection of Evan's Blue. After 30 min, the extracts and saline were injected on the dorsum of the rats, which were then sacrificed after 3 and 6 h. Readings were performed in a spectrophotometer. For subcutaneous implantation, 30 rats received a polyethylene tube containing the extracts on their dorsum and then they were killed after 7 and 28 days. The samples were processed for histological analysis and evaluated with a light microscope. The inflammatory infiltrate was quantified. Results There were no statistically significant differences between aqueous extract and saline groups in relation to edema quantification in the different periods (p>0.05). Ethanolic solution resulted in more edema independently of the experimental period (p<0.05). Histological analysis showed similar results on the 7-day period for the 3 groups. There was a notable reduction on inflammatory cell number for saline and aqueous extract groups at 28 days. Conclusion The aqueous extract showed biocompatible properties similar to those of saline."}], "format": [], "journal": {"issnPrinted": "1678-7757", "conferencedate": "", "vol": "20", "conferenceplace": "", "name": "Journal of Applied Oral Science", "iss": "4", "sp": "414", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1678-7765", "ep": "418", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2012-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, 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"main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Evaluation of tissue reaction to Aroeira (Myracrodruon urundeuva) extracts: a histologic and edemogenic study"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "pmc", "classname": "pmc", "schemeid": "dnet:pid_types", "schemename": 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"value": "Most, if not all, bacteria form a biofilm, a multicellular structure that protects them from antimicrobial actions of the host immune system and affords resistance to antibiotics. The latter is especially disturbing with the increase in multiresistant bacterial clones worldwide. Bacterial biofilm formation is a multistep process that starts with surface adhesion, after which attached bacteria divide and give rise to biomass. The actual steps required for Haemophilus influenzae biofilm formation are largely not known. We show that interference with peptidoglycan biosynthesis increases biofilm formation because of the release of bacterial genomic DNA. Subinhibitory concentrations of ?-lactam antibiotics, which are often prescribed to treat H.?influenzae infections, increase biofilm formation through a similar mechanism. Therefore, when ?-lactam antibiotics do not reach their MIC in vivo, they might not only drive selection for ?-lactam-resistant clones but also increase biofilm formation and resistance to other antimicrobial compounds."}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "ABSTRACT Nontypeable Haemophilus influenzae (NTHi) is an opportunistic pathogen that mainly causes otitis media in children and community-acquired pneumonia or exacerbations of chronic obstructive pulmonary disease in adults. A large variety of studies suggest that biofilm formation by NTHi may be an important step in the pathogenesis of this bacterium. However, the underlying mechanisms involved in this process are poorly elucidated. In this study, we used a transposon mutant library to identify bacterial genes involved in biofilm formation. The growth and biofilm formation of 4,172 transposon mutants were determined, and the involvement of the identified genes in biofilm formation was validated in in vitro experiments. Here, we present experimental data showing that increased bacterial lysis, through interference with peptidoglycan synthesis, results in elevated levels of extracellular DNA, which increased biofilm formation. Interestingly, similar results were obtained with subinhibitory concentrations of ?-lactam antibiotics, known to interfere with peptidoglycan synthesis, but such an effect does not appear with other classes of antibiotics. These results indicate that treatment with ?-lactam antibiotics, especially for ?-lactam-resistant NTHi isolates, might increase resistance to antibiotics by increasing biofilm formation. IMPORTANCE Most, if not all, bacteria form a biofilm, a multicellular structure that protects them from antimicrobial actions of the host immune system and affords resistance to antibiotics. The latter is especially disturbing with the increase in multiresistant bacterial clones worldwide. Bacterial biofilm formation is a multistep process that starts with surface adhesion, after which attached bacteria divide and give rise to biomass. The actual steps required for Haemophilus influenzae biofilm formation are largely not known. We show that interference with peptidoglycan biosynthesis increases biofilm formation because of the release of bacterial genomic DNA. Subinhibitory concentrations of ?-lactam antibiotics, which are often prescribed to treat H.?influenzae infections, increase biofilm formation through a similar mechanism. Therefore, when ?-lactam antibiotics do not reach their MIC in vivo, they might not only drive selection for ?-lactam-resistant clones but also increase biofilm formation and resistance to other antimicrobial compounds."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "2", "conferenceplace": "", "name": "mSphere", "iss": "1", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "2379-5042", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2017-01-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", 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"rank": 1, "affiliation": [], "fullname": "David, Marion A."}, {"surname": "Orlowski", "name": "St Phane", "pid": [], "rank": 2, "affiliation": [], "fullname": "Orlowski, St?phane"}, {"surname": "Prichard", "name": "Roger K.", "pid": [], "rank": 3, "affiliation": [], "fullname": "Prichard, Roger K."}, {"surname": "Hashem", "name": "Shaima", "pid": [], "rank": 4, "affiliation": [], "fullname": "Hashem, Shaima"}, {"surname": "Andr", "name": "Fran Ois", "pid": [], "rank": 5, "affiliation": [], "fullname": "Andr?, Fran?ois"}, {"surname": "Lespine", "name": "Anne", "pid": [], "rank": 6, "affiliation": [], "fullname": "Lespine, Anne"}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": 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"2019-07-02T18:03:05.132Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Macrocyclic lactones (ML) are important anthelmintics used in animals and humans against parasite nematodes, but their therapeutic success is compromised by the spread of ML resistance. Some ABC transporters, such as p-glycoproteins (Pgps), are selected and overexpressed in ML-resistant nematodes, supporting a role for some drug efflux proteins in ML resistance. However, the role of such proteins in ML transport remains to be clarified at the molecular level. Recently, Caenorhabditis elegans Pgp-1 (Cel-Pgp-1) has been crystallized, and its drug-modulated ATPase function characterized in?vitro revealed Cel-Pgp-1 as a multidrug transporter. Using this crystal structure, we have developed an in silico drug docking model in order to study the binding of ML and other anthelmintic drugs to Cel-Pgp-1. All tested ML bound with high affinity in a unique site, within the inner chamber of the protein, supporting that ML may be transported by Cel-Pgp-1. Interestingly, interacting residues delineate a ML specific fingerprint involving H-bonds, including T1028. In particular, benzofurane and spiroketal moieties bound to specific sub-sites. When compared with the aglycone ML, such as moxidectin and ivermectin aglycone, avermectin anthelmintics have significant higher affinity for Cel-Pgp-1, likely due to the sugar substituent(s) that bind to a specific area involving H-bonds at Y771. Triclabendazole, closantel and emodepside bound with good affinities to different sub-sites in the inner chamber, partially overlapping with the ML binding site, suggesting that they could compete for Cel-Pgp-1-mediated ML transport. In conclusion, this work provides novel information on the role of nematode Pgps in transporting anthelmintics, and a valuable tool to predict drug-drug interactions and to rationally design new competitive inhibitors of clinically-relevant nematode Pgps, to improve anthelmintic therapeutics."}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Graphical abstract Ivermectin (red spheres) binding to Cel-Pgp-1 (blue ribbon: N-term, yellow ribbon: C-term). Image 1"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Highlights ? Cel-Pgp-1 cristal provides a valuable tool to study anthelmintic interactions. ? Cel-Pgp-1 recognizes a broad panel of anthelmintics, including macrocyclic lactones. ? Cel-Pgp-1 is predicted to transport MLs and contribute to anthelmintic resistance. ? Sugars in avermectins increase the affinity to Cel-Pgp-1 compared with moxidectin. ? 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They are usually maintained with 10% fetal bovine serum (FBS) in vitro. Modified platelet-rich plasma (mPRP) would be a safe alternative to 10% FBS during SHEDs culture. Therefore, our study aimed to compare the proliferation and differentiation of SHEDs cultured in mPRP and FBS medium to explore an optimal concentration of mPRP for SHEDs maintenance. Platelets were harvested by automatic blood cell analyzer and activated by repeated liquid nitrogen freezing and thawing. The platelet-related cytokines were examined and analyzed by ELISA. SHEDs were extracted and cultured with different concentrations of mPRP or 10% FBS medium. Alkaline phosphatase (ALP) activity was measured. Mineralization factors, RUNX2 and OCN, were measured by real-time PCR. SHEDs were characterized with mesenchymal stem cells (MSCs) markers including vimentin, CD44, and CD105. mPRP at different concentrations (2, 5, 10, and 20%) enhanced the growth of SHEDs. 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Bruce"}, {"surname": "Zho", "name": "Dejian", "pid": [{"qualifier": {"classid": "ORCID", "classname": "ORCID"}, "value": "0000-0003-3314-9242"}], "rank": 9, "affiliation": [], "fullname": "Zhou, Dejian"}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c", "value": "Europe PubMed Central"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["http://europepmc.org/articles/PMC4979658"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-03-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c", "value": "Europe PubMed Central"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2017-09-25T16:15:20.935Z", "fulltext": [], "dateoftransformation": "2019-07-02T21:52:19.156Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Abstract A highly efficient cap?exchange approach for preparing compact, dense polyvalent mannose?capped quantum dots (QDs) has been developed. The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC?SIGN and DC?SIGNR (collectively termed as DC?SIGN/R) using a sensitive, ratiometric F?rster resonance energy transfer (FRET) assay. The QD probes specifically bind DC?SIGN, but not its closely related receptor DC?SIGNR, which is further confirmed by its specific blocking of DC?SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC?SIGN binds more efficiently to densely packed mannosides. A FRET?based thermodynamic study reveals that the binding is enthalpy?driven. This work establishes QD FRET as a rapid, sensitive technique for probing structure and thermodynamics of multivalent protein?ligand interactions."}], "format": [], "journal": {"issnPrinted": "1433-7851", "conferencedate": "", "vol": "55", "conferenceplace": "", "name": "Angewandte Chemie (International Ed. in English)", "iss": "15", "sp": "4738", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1521-3773", "ep": "4742", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-03-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "John Wiley and Sons Inc."}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:europepmc.org:3953534"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Angewandte Chemie (International Ed. in English)"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Compact, Polyvalent Mannose Quantum Dots as Sensitive, Ratiometric FRET Probes for Multivalent Protein?Ligand Interactions"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "pmc", "classname": 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false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Dental health services"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Dental care"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Inequalities in health care services"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Health surveys"}], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Monteiro", "name": "Camila Nascimento", "pid": [], "rank": 1, "affiliation": [], "fullname": "Monteiro, Camila Nascimento"}, {"surname": "Beenackers", "name": "Mari Lle A.", "pid": [], "rank": 2, "affiliation": [], "fullname": "Beenackers, Mari?lle A."}, {"surname": "Goldbaum", "name": "Mois S.", "pid": [], "rank": 3, "affiliation": [], "fullname": "Goldbaum, Mois?s"}, {"surname": "Azevedo Barros", "name": "Marilisa Berti", "pid": [], "rank": 4, "affiliation": [], "fullname": "de Azevedo Barros, Marilisa Berti"}, {"surname": "Gianini", "name": "Reinaldo Jos", "pid": [], "rank": 5, "affiliation": [], "fullname": "Gianini, Reinaldo Jos?"}, {"surname": "Cesar", "name": "Chester Luiz Galv O.", "pid": [], "rank": 6, "affiliation": [], "fullname": "Cesar, Chester Luiz Galv?o"}, {"surname": "Mackenbach", "name": "Johan P.", "pid": [], "rank": 7, "affiliation": [], "fullname": "Mackenbach, Johan P."}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c", "value": "Europe PubMed Central"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["http://europepmc.org/articles/PMC5142432"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c", "value": "Europe PubMed Central"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2017-09-25T16:02:23.936Z", "fulltext": [], "dateoftransformation": "2019-07-02T22:26:52.735Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Background Access to, and use of, dental health services in Brazil have improved since 2003. The increase of private health care plans and the implementation of the ?Smiling Brazil? Program, the largest public oral health care program in the world, could have influenced this increase in access. However, we do not yet know if inequalities in the use of dental health services persist after the improvement in access. The aims of this study are to analyze socioeconomic differences for dental health service use between 2003 and 2008 in S?o Paulo and to examine changes in these associations since the implementation of the Smiling Brazil program in 2003. Method Data was obtained via two household health surveys (ISA-Capital 2003 and ISA-Capital 2008) which investigated living conditions, lifestyle, health status and use of health care services. Logistic regression was used to analyze associations between socioeconomic factors and dental services use. Additionally, trends from 2003 to 2008 regarding socioeconomic characteristics and dental health service use were explored. Results Overall, dental health service use increased between 2003 and 2008 and was at both time points more common among those who had higher income, better education, better housing conditions, private health care plans and were Caucasian. Inequalities in use of dental health care did not decrease over time. Among the reasons for not seeking dental care, not having teeth and financial difficulty were more common in lower socioeconomic groups, while thinking it was unnecessary was more common in higher socioeconomic groups. Conclusions The Brazilian oral health policy is still in a period of expansion and seems to have contributed slightly to increased dental health service use, but has not influenced socioeconomic inequalities in the use of these services. Acquiring deeper knowledge about inequalities in dental health service use will contribute to better understanding of potential barriers to reducing them. Electronic supplementary material The online version of this article (doi:10.1186/s12913-016-1928-y) contains supplementary material, which is available to authorized users."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "16", "conferenceplace": "", "name": "BMC Health Services Research", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1472-6963", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-12-01"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "BioMed Central"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:europepmc.org:4095602"], "source": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "BMC Health Services Research"}], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Socioeconomic inequalities in dental health services in Sao Paulo, Brazil, 2003?2008"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "pmc", "classname": "pmc", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "PMC4926307"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.1186/s12711-016-0225-x"}], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "relevantdate": [], "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c", "value": "Europe PubMed Central"}], "id": "50|od_______908::b331440083ff90d987942554a6ef0e60", "subject": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Research Article"}], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Calus", "name": "Mario P. L.", "pid": [{"qualifier": {"classid": "ORCID", "classname": "ORCID"}, "value": "0000-0002-3213-704X"}], "rank": 1, "affiliation": [], "fullname": "Calus, Mario P. L."}, {"surname": "Bouwman", "name": "Aniek C.", "pid": [], "rank": 2, "affiliation": [], "fullname": "Bouwman, Aniek C."}, {"surname": "Schrooten", "name": "Chris", "pid": [], "rank": 3, "affiliation": [], "fullname": "Schrooten, Chris"}, {"surname": "Veerkamp", "name": "Roel F.", "pid": [], "rank": 4, "affiliation": [], "fullname": "Veerkamp, Roel F."}], "instance": [{"refereed": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c", "value": "Europe PubMed Central"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "license": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": ["http://europepmc.org/articles/PMC4926307"], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-06-01"}, "collectedfrom": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c", "value": "Europe PubMed Central"}, "processingchargeamount": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2017-09-25T16:18:06.421Z", "fulltext": [], "dateoftransformation": "2019-07-02T22:46:54.79Z", "description": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Background Use of whole-genome sequence data is expected to increase persistency of genomic prediction across generations and breeds but affects model performance and requires increased computing time. In this study, we investigated whether the split-and-merge Bayesian stochastic search variable selection (BSSVS) model could overcome these issues. BSSVS is performed first on subsets of sequence-based variants and then on a merged dataset containing variants selected in the first step. Results We used a dataset that included 4,154,064 variants after editing and de-regressed proofs for 3415 reference and 2138 validation bulls for somatic cell score, protein yield and interval first to last insemination. In the first step, BSSVS was performed on 106 subsets each containing ~39,189 variants. In the second step, 1060 up to 472,492 variants, selected from the first step, were included to estimate the accuracy of genomic prediction. Accuracies were at best equal to those achieved with the commonly used Bovine 50k-SNP chip, although the number of variants within a few well-known quantitative trait loci regions was considerably enriched. When variant selection and the final genomic prediction were performed on the same data, predictions were biased. Predictions computed as the average of the predictions computed for each subset achieved the highest accuracies, i.e. 0.5?to?1.1?% higher than the accuracies obtained with the 50k-SNP chip, and yielded the least biased predictions. Finally, the accuracy of genomic predictions obtained when all sequence-based variants were included was similar or up to 1.4?% lower compared to that based on the average predictions across the subsets. By applying parallelization, the split-and-merge procedure was completed in 5?days, while the standard analysis including all sequence-based variants took more than three?months. Conclusions The split-and-merge approach splits one large computational task into many much smaller ones, which allows the use of parallel processing and thus efficient genomic prediction based on whole-genome sequence data. The split-and-merge approach did not improve prediction accuracy, probably because we used data on a single breed for which relationships between individuals were high. Nevertheless, the split-and-merge approach may have potential for applications on data from multiple breeds. 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Enucleation is frequently the only management option for this condition, resulting in blindness and psychosocial distress. Even when the cornea remains grossly intact, visual function could also be impaired by a high degree of myopia and keratoconus. Deafness is another common feature and results in combined sensory deprivation. Using autozygosity mapping, we identified mutations in PRDM5 in families with BCS. We demonstrate that regulation of expression of extracellular matrix components, particularly fibrillar collagens, by PRDM5 is a key molecular mechanism that underlies corneal fragility in BCS and controls normal corneal development and maintenance. ZNF469, encoding a zinc finger protein of hitherto undefined function, has been identified as a quantitative trait locus for central corneal thickness, and mutations in this gene have been demonstrated in Tunisian Jewish and Palestinian kindreds with BCS. 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The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC?SIGN and DC?SIGNR (collectively termed as DC?SIGN/R) using a sensitive, ratiometric F?rster resonance energy transfer (FRET) assay. The QD probes specifically bind DC?SIGN, but not its closely related receptor DC?SIGNR, which is further confirmed by its specific blocking of DC?SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC?SIGN binds more efficiently to densely packed mannosides. A FRET?based thermodynamic study reveals that the binding is enthalpy?driven. 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observation of time-reversal violation. The decays of entangled neutral B mesons into definite flavor states ( B 0 or \\xaf\\xaf\\xaf B 0 ), and J / \\u03c8 K 0 L or c \\xaf c K 0 S final states (referred to as B + or B \\u2212 ), allow comparisons between the probabilities of four pairs of T -conjugated transitions, for example, \\xaf\\xaf\\xaf B 0 \\u2192 B \\u2212 and B \\u2212 \\u2192 \\xaf\\xaf\\xaf B 0 , as a function of the time difference between the two B decays. Using 468 \\xd7 10 6 B \\xaf\\xaf\\xaf B pairs produced in \\u03a5 ( 4 S ) decays collected by the BABAR detector at SLAC, we measure T -violating parameters in the time evolution of neutral B mesons, yielding \\u0394 S + T = \\u2212 1.37 \\xb1 0.14 ( stat ) \\xb1 0.06 ( syst ) and \\u0394 S \\u2212 T = 1.17 \\xb1 0.18 ( stat ) \\xb1 0.11 ( syst ) . These nonzero results represent the first direct observation of T violation through the exchange of initial and final states in transitions that can only be connected by a T -symmetry transformation."}], "format": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "8 p."}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "application/pdf"}], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2012-11-19"}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "American Physical Society"}, "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["oai:diposit.ub.edu:2445/133262"], "source": [], "context": [], "title": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Observation of Time-Reversal Violation in the B0 Meson System"}]} +{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "pid": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.1103/PhysRevLett.109.211801"}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "pmid", "classname": "pmid", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "23215586"}], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "relevantdate": [], "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42", "value": "Archivio Istituzionale"}], "id": "50|od_______970::4a33e89a1336f15c6c259086b34890ad", "subject": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Physics and Astronomy (all)"}], "embargoenddate": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Lees", "name": "J. 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The decays of entangled neutral B mesons into definite flavor states ($B^0$ or $\\\\bar{B}^0$), and $J/\\\\psi K_S^0$ or $c\\\\bar{c} K_S^0$ final states (referred to as $B_+$ or $B_-$), allow comparisons between the probabilities of four pairs of T-conjugated transitions, for example, $\\\\bar{B}^0 \\\\rightarrow B_-$ and $B_- \\\\rightarrow \\\\bar{B}^0$, as a function of the time difference between the two B decays. Using 468 million $B\\\\bar{B}$ pairs produced in $\\\\Upsilon(4S)$ decays collected by the BABAR detector at SLAC, we measure T-violating parameters in the time evolution of neutral B mesons, yielding $\\\\Delta S_T^+ = -1.37 \\\\pm 0.14 (stat.) \\\\pm 0.06 (syst.)$ and $\\\\Delta S_T^- = 1.17 \\\\pm 0.18 (stat.) \\\\pm 0.11 (syst.)$. These nonzero results represent the first direct observation of T violation through the exchange of initial and final states in transitions that can only be connected by a T-symmetry transformation."}, {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Comment: 7 pages, 3 postscript figures, 1 table, appendix with 4 pages containing supplementary material. Accepted by Phys. Rev. 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We use data from direct numerical simulations up to Taylor's Reynolds number 280 following the evolution of about two million passive tracers advected by the flow over a time span of about three decades. We present data for both the separation distance and the relative velocity statistics. Statistics are measured along the particle pair trajectories both as a function of time and as a function of their separation, i.e. at fixed scales. We compare and contrast both sets of statistics in order to gain an insight into the mechanisms governing the separation process. We find very high levels of intermittency in the early stages, that is, for travel times up to order ten Kolmogorov time scales. The fixed scale statistics allow us to quantify anomalous corrections to Richardson diffusion in the inertial range of scales for those pairs that separate rapidly. 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In Cear\\xe1, the introduction of DENV-4 was reported during a DENV-1 epidemic in 2011, with only two isolations. OBJECTIVES The aim of this study was to characterise the first DENV-4 epidemic in the state of Cear\\xe1, Brazil. METHODS The study population was composed of patients with suspected dengue that were reported to health care units from January to December 2012. The laboratory confirmation of infection was made by viral isolation, reverse transcription polymerase chain reaction (RT-PCR), AgNS1, immunohistochemistry and IgM enzyme-linked immunosorbent assay (ELISA). MAIN CONCLUSIONS In the study year, 72,211 suspected dengue cases were reported and 51,865 of these cases (71.8%) were confirmed to be positive. Co-circulation of three serotypes, DENV-1, DENV-3 and DENV-4, was detected with a predominance of DENV-4 (95.3%). Most cases were not severe, but there were 44 fatal outcomes. 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The decays of entangled neutral B mesons into definite flavor states (B(0) or B(0)), and J/\\u03c8K(L)(0) or ccK(S)(0) final states (referred to as B(+) or B(-)), allow comparisons between the probabilities of four pairs of T-conjugated transitions, for example, B(0) \\u2192 B(-) and B(-) \\u2192 B(0), as a function of the time difference between the two B decays. Using 468 \\xd7 10(6) BB pairs produced in \\u03a5(4S) decays collected by the BABAR detector at SLAC, we measure T-violating parameters in the time evolution of neutral B mesons, yielding \\u0394S(T)(+) = -1.37 \\xb1 0.14(stat) \\xb1 0.06(syst) and \\u0394S(T)(-) = 1.17 \\xb1 0.18(stat) \\xb1 0.11(syst). These nonzero results represent the first direct observation of T violation through the exchange of initial and final states in transitions that can only be connected by a T-symmetry transformation."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, 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Here, we tested whether deletion of PARP-2, an alternative NAD(+)-consuming enzyme, impacts on NAD(+) bioavailability and SIRT1 activity. Our results indicate that PARP-2 deficiency increases SIRT1 activity in cultured myotubes. However, this increase was not due to changes in NAD(+) levels, but to an increase in SIRT1 expression, as PARP-2 acts as a direct negative regulator of the SIRT1 promoter. PARP-2 deletion in mice increases SIRT1 levels, promotes energy expenditure, and increases mitochondrial content. Furthermore, PARP-2(-/-) mice were protected against diet-induced obesity. Despite being insulin sensitized, PARP-2(-/-) mice were glucose intolerant due to a defective pancreatic function. Hence, while inhibition of PARP activity promotes oxidative metabolism through SIRT1 activation, the use of PARP inhibitors for metabolic purposes will require further understanding of the specific functions of different PARP family members."}], "format": [], "journal": {"issnPrinted": "", "conferencedate": "", "vol": "", "conferenceplace": "", "name": "", "iss": "", "sp": "", "edition": "", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "coverage": [], "publisher": {"dataInfo": {"provenanceaction": {"classid": "", "classname": "", 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The increase of private health care plans and the implementation of the \\u201cSmiling Brazil\\u201d Program, the largest public oral health care program in the world, could have influenced this increase in access. However, we do not yet know if inequalities in the use of dental health services persist after the improvement in access. The aims of this study are to analyze socioeconomic differences for dental health service use between 2003 and 2008 in Sao Paulo and to examine changes in these associations since the implementation of the Smiling Brazil program in 2003. Data was obtained via two household health surveys (ISA-Capital 2003 and ISA-Capital 2008) which investigated living conditions, lifestyle, health status and use of health care services. Logistic regression was used to analyze associations between socioeconomic factors and dental services use. Additionally, trends from 2003 to 2008 regarding socioeconomic characteristics and dental health service use were explored. Overall, dental health service use increased between 2003 and 2008 and was at both time points more common among those who had higher income, better education, better housing conditions, private health care plans and were Caucasian. Inequalities in use of dental health care did not decrease over time. Among the reasons for not seeking dental care, not having teeth and financial difficulty were more common in lower socioeconomic groups, while thinking it was unnecessary was more common in higher socioeconomic groups. The Brazilian oral health policy is still in a period of expansion and seems to have contributed slightly to increased dental health service use, but has not influenced socioeconomic inequalities in the use of these services. 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Technically, SmartVox is a distributed web application that delivers audiovisual scores through the performer's mobile devices. From a singer's point of view, this setup allows for the synergy between visual and acoustic stimuli, which facilitates the interpretive and performative processes, particularly in polyphonic passages. It also enables spatial separation of the performers (cori spezzati ), and speeds up the learning process of unfamiliar musical materials (e.g. microtonal tuning, texts in a foreign language). 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"50|datacite____::4d444c00a5a83437106f588506c29871"} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/software b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/software new file mode 100644 index 0000000000..e69de29bb2 From 5689d49689b50373aaeec95859a9288fa9b75307 Mon Sep 17 00:00:00 2001 From: miconis Date: Wed, 15 Apr 2020 16:34:06 +0200 Subject: [PATCH 07/19] minor changes --- .../dedup/SparkCreateConnectedComponent.java | 55 +++++++++++-------- .../dhp/oa/dedup/SparkCreateDedupRecord.java | 8 ++- .../dhp/oa/dedup/SparkCreateSimRels.java | 8 ++- .../dhp/oa/dedup/SparkPropagateRelation.java | 4 ++ .../dhp/oa/dedup/SparkUpdateEntity.java | 4 ++ 5 files changed, 53 insertions(+), 26 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateConnectedComponent.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateConnectedComponent.java index b28d020b6f..d0ef580342 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateConnectedComponent.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateConnectedComponent.java @@ -13,7 +13,6 @@ import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -29,6 +28,7 @@ import scala.Tuple2; import java.io.IOException; import java.util.ArrayList; +import java.util.Iterator; import java.util.List; public class SparkCreateConnectedComponent extends AbstractSparkAction { @@ -45,7 +45,7 @@ public class SparkCreateConnectedComponent extends AbstractSparkAction { SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); parser.parseArgument(args); - new SparkCreateSimRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); + new SparkCreateConnectedComponent(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } @Override @@ -56,12 +56,16 @@ public class SparkCreateConnectedComponent extends AbstractSparkAction { final String isLookUpUrl = parser.get("isLookUpUrl"); final String actionSetId = parser.get("actionSetId"); + System.out.println(String.format("graphBasePath: '%s'", graphBasePath)); + System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl)); + System.out.println(String.format("actionSetId: '%s'", actionSetId)); + System.out.println(String.format("workingPath: '%s'", workingPath)); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { - - final String entity = dedupConf.getWf().getEntityType(); final String subEntity = dedupConf.getWf().getSubEntityValue(); + System.out.println(String.format("Creating mergerels for: '%s'", subEntity)); final JavaPairRDD vertexes = sc.textFile(graphBasePath + "/" + subEntity) .map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s)) @@ -72,28 +76,35 @@ public class SparkCreateConnectedComponent extends AbstractSparkAction { final Dataset similarityRelations = spark.read().load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)).as(Encoders.bean(Relation.class)); final RDD> edgeRdd = similarityRelations.javaRDD().map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())).rdd(); final JavaRDD cc = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations()).toJavaRDD(); - final Dataset mergeRelation = spark.createDataset(cc.filter(k -> k.getDocIds().size() > 1).flatMap((FlatMapFunction) c -> - c.getDocIds() - .stream() - .flatMap(id -> { - List tmp = new ArrayList<>(); - Relation r = new Relation(); - r.setSource(c.getCcId()); - r.setTarget(id); - r.setRelClass("merges"); - tmp.add(r); - r = new Relation(); - r.setTarget(c.getCcId()); - r.setSource(id); - r.setRelClass("isMergedIn"); - tmp.add(r); - return tmp.stream(); - }).iterator()).rdd(), Encoders.bean(Relation.class)); - mergeRelation.write().mode("overwrite").save(DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity)); + final Dataset mergeRelation = spark.createDataset(cc.filter(k -> k.getDocIds().size() > 1) + .flatMap(this::ccToMergeRel).rdd(), Encoders.bean(Relation.class)); + + mergeRelation + .write().mode("overwrite") + .save(DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity)); } } + public Iterator ccToMergeRel(ConnectedComponent cc){ + return cc.getDocIds() + .stream() + .flatMap(id -> { + List tmp = new ArrayList<>(); + Relation r = new Relation(); + r.setSource(cc.getCcId()); + r.setTarget(id); + r.setRelClass("merges"); + tmp.add(r); + r = new Relation(); + r.setTarget(cc.getCcId()); + r.setSource(id); + r.setRelClass("isMergedIn"); + tmp.add(r); + return tmp.stream(); + }).iterator(); + } + public static long getHashcode(final String id) { return Hashing.murmur3_128().hashString(id).asLong(); } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java index 099824051e..2c065253a6 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java @@ -32,7 +32,7 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); parser.parseArgument(args); - new SparkCreateSimRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); + new SparkCreateDedupRecord(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } @Override @@ -43,10 +43,16 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { final String actionSetId = parser.get("actionSetId"); final String workingPath = parser.get("workingPath"); + System.out.println(String.format("graphBasePath: '%s'", graphBasePath)); + System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl)); + System.out.println(String.format("actionSetId: '%s'", actionSetId)); + System.out.println(String.format("workingPath: '%s'", workingPath)); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { String subEntity = dedupConf.getWf().getSubEntityValue(); + System.out.println(String.format("Creating deduprecords for: '%s'", subEntity)); final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity); final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java index a97e6d2ba6..0d07d1fe18 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java @@ -61,16 +61,18 @@ public class SparkCreateSimRels extends AbstractSparkAction { final String workingPath = parser.get("workingPath"); System.out.println(String.format("graphBasePath: '%s'", graphBasePath)); - System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl)); - System.out.println(String.format("actionSetId: '%s'", actionSetId)); - System.out.println(String.format("workingPath: '%s'", workingPath)); + System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl)); + System.out.println(String.format("actionSetId: '%s'", actionSetId)); + System.out.println(String.format("workingPath: '%s'", workingPath)); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); //for each dedup configuration for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { + final String entity = dedupConf.getWf().getEntityType(); final String subEntity = dedupConf.getWf().getSubEntityValue(); + System.out.println(String.format("Creating simrels for: '%s'", subEntity)); JavaPairRDD mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) .mapToPair((PairFunction) s -> { diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index f441851b45..e00c8767e6 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -60,6 +60,10 @@ public class SparkPropagateRelation extends AbstractSparkAction { final String workingPath = parser.get("workingPath"); final String dedupGraphPath = parser.get("dedupGraphPath"); + System.out.println(String.format("graphBasePath: '%s'", graphBasePath)); + System.out.println(String.format("workingPath: '%s'", workingPath)); + System.out.println(String.format("dedupGraphPath:'%s'", dedupGraphPath)); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final Dataset mergeRels = spark.read().load(DedupUtility.createMergeRelPath(workingPath, "*", "*")).as(Encoders.bean(Relation.class)); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java index 5c9d3c0e15..f92fcf3ce9 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java @@ -69,6 +69,10 @@ public class SparkUpdateEntity extends AbstractSparkAction { final String workingPath = parser.get("workingPath"); final String dedupGraphPath = parser.get("dedupGraphPath"); + System.out.println(String.format("graphBasePath: '%s'", graphBasePath)); + System.out.println(String.format("workingPath: '%s'", workingPath)); + System.out.println(String.format("dedupGraphPath: '%s'", dedupGraphPath)); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); //for each entity From 8eedfefc98ce53bd08ea35e2d814bddc9d3c8f86 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 15 Apr 2020 18:35:35 +0200 Subject: [PATCH 08/19] try to introduce intermediate serialization on hdfs to avoid OOM --- .../dhp/oa/dedup/SparkPropagateRelation.java | 20 +++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index e00c8767e6..47a2acf373 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -77,7 +77,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { JavaRDD relations = sc.textFile(DedupUtility.createEntityPath(graphBasePath, "relation")); - JavaRDD newRels = relations.mapToPair( + relations.mapToPair( (PairFunction) s -> new Tuple2(MapDocumentUtil.getJPathString(SOURCEJSONPATH, s), s)) .leftOuterJoin(mergedIds) @@ -97,10 +97,11 @@ public class SparkPropagateRelation extends AbstractSparkAction { } return v1._2()._1(); }).filter(SparkPropagateRelation::containsDedup) - .repartition(500); + .repartition(500) + .saveAsTextFile(DedupUtility.createEntityPath(workingPath, "newRels"), GzipCodec.class); //update deleted by inference - relations = relations.mapToPair( + relations.mapToPair( (PairFunction) s -> new Tuple2(MapDocumentUtil.getJPathString(SOURCEJSONPATH, s), s)) .leftOuterJoin(mergedIds) @@ -120,9 +121,16 @@ public class SparkPropagateRelation extends AbstractSparkAction { } return v1._2()._1(); }) - .repartition(500); + .repartition(500) + .saveAsTextFile(DedupUtility.createEntityPath(workingPath, "updated"), GzipCodec.class); - newRels.union(relations).repartition(1000) + JavaRDD newRels = sc + .textFile(DedupUtility.createEntityPath(workingPath, "newRels")); + + sc + .textFile(DedupUtility.createEntityPath(workingPath, "updated")) + .union(newRels) + .repartition(1000) .saveAsTextFile(DedupUtility.createEntityPath(dedupGraphPath, "relation"), GzipCodec.class); } @@ -169,4 +177,4 @@ public class SparkPropagateRelation extends AbstractSparkAction { throw new RuntimeException("Unable to convert json", e); } } -} +} \ No newline at end of file From 069ef5eaedee294be727924f31bf602188f9d50f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 15 Apr 2020 21:23:21 +0200 Subject: [PATCH 09/19] trying to avoid OOM in SparkPropagateRelation --- .../dhp/oa/dedup/SparkPropagateRelation.java | 81 ++++++++++++++----- .../dedup/consistency/oozie_app/workflow.xml | 57 ++++++++++--- 2 files changed, 104 insertions(+), 34 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index 47a2acf373..02db60f440 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -12,6 +12,9 @@ import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.fs.FileStatus; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; @@ -30,6 +33,11 @@ import java.io.IOException; public class SparkPropagateRelation extends AbstractSparkAction { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);; + + public static final int NUM_PARTITIONS = 3000; + enum FieldType { SOURCE, TARGET @@ -64,8 +72,18 @@ public class SparkPropagateRelation extends AbstractSparkAction { System.out.println(String.format("workingPath: '%s'", workingPath)); System.out.println(String.format("dedupGraphPath:'%s'", dedupGraphPath)); + final String relationsPath = DedupUtility.createEntityPath(dedupGraphPath, "relation"); + final String newRelsPath = DedupUtility.createEntityPath(workingPath, "newRels"); + final String fixedSourceId = DedupUtility.createEntityPath(workingPath, "fixedSourceId"); + final String deletedSourceId = DedupUtility.createEntityPath(workingPath, "deletedSourceId"); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + deletePath(relationsPath); + deletePath(newRelsPath); + deletePath(fixedSourceId); + deletePath(deletedSourceId); + final Dataset mergeRels = spark.read().load(DedupUtility.createMergeRelPath(workingPath, "*", "*")).as(Encoders.bean(Relation.class)); final JavaPairRDD mergedIds = mergeRels @@ -75,9 +93,9 @@ public class SparkPropagateRelation extends AbstractSparkAction { .toJavaRDD() .mapToPair((PairFunction) r -> new Tuple2(r.getString(1), r.getString(0))); - JavaRDD relations = sc.textFile(DedupUtility.createEntityPath(graphBasePath, "relation")); - - relations.mapToPair( + sc.textFile(DedupUtility.createEntityPath(graphBasePath, "relation")) + .repartition(NUM_PARTITIONS) + .mapToPair( (PairFunction) s -> new Tuple2(MapDocumentUtil.getJPathString(SOURCEJSONPATH, s), s)) .leftOuterJoin(mergedIds) @@ -87,6 +105,9 @@ public class SparkPropagateRelation extends AbstractSparkAction { } return v1._2()._1(); }) + .saveAsTextFile(fixedSourceId, GzipCodec.class); + + sc.textFile(fixedSourceId) .mapToPair( (PairFunction) s -> new Tuple2(MapDocumentUtil.getJPathString(TARGETJSONPATH, s), s)) @@ -97,12 +118,13 @@ public class SparkPropagateRelation extends AbstractSparkAction { } return v1._2()._1(); }).filter(SparkPropagateRelation::containsDedup) - .repartition(500) - .saveAsTextFile(DedupUtility.createEntityPath(workingPath, "newRels"), GzipCodec.class); + .repartition(NUM_PARTITIONS) + .saveAsTextFile(newRelsPath, GzipCodec.class); //update deleted by inference - relations.mapToPair( - (PairFunction) s -> + sc.textFile(DedupUtility.createEntityPath(graphBasePath, "relation")) + .repartition(NUM_PARTITIONS) + .mapToPair((PairFunction) s -> new Tuple2(MapDocumentUtil.getJPathString(SOURCEJSONPATH, s), s)) .leftOuterJoin(mergedIds) .map((Function>>, String>) v1 -> { @@ -111,6 +133,10 @@ public class SparkPropagateRelation extends AbstractSparkAction { } return v1._2()._1(); }) + .saveAsTextFile(deletedSourceId, GzipCodec.class); + + sc.textFile(deletedSourceId) + .repartition(NUM_PARTITIONS) .mapToPair( (PairFunction) s -> new Tuple2(MapDocumentUtil.getJPathString(TARGETJSONPATH, s), s)) @@ -121,17 +147,30 @@ public class SparkPropagateRelation extends AbstractSparkAction { } return v1._2()._1(); }) - .repartition(500) + .repartition(NUM_PARTITIONS) .saveAsTextFile(DedupUtility.createEntityPath(workingPath, "updated"), GzipCodec.class); JavaRDD newRels = sc - .textFile(DedupUtility.createEntityPath(workingPath, "newRels")); + .textFile(newRelsPath); sc .textFile(DedupUtility.createEntityPath(workingPath, "updated")) .union(newRels) - .repartition(1000) - .saveAsTextFile(DedupUtility.createEntityPath(dedupGraphPath, "relation"), GzipCodec.class); + .repartition(NUM_PARTITIONS) + .saveAsTextFile(relationsPath, GzipCodec.class); + } + + private void deletePath(String path) { + try { + Path p = new Path(path); + FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration()); + + if (fs.exists(p)) { + fs.delete(p, true); + } + } catch (IOException e) { + throw new RuntimeException(e); + } } private static boolean containsDedup(final String json) { @@ -142,20 +181,19 @@ public class SparkPropagateRelation extends AbstractSparkAction { } private static String replaceField(final String json, final String id, final FieldType type) { - ObjectMapper mapper = new ObjectMapper(); - mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); try { - Relation relation = mapper.readValue(json, Relation.class); - if (relation.getDataInfo() == null) + Relation relation = OBJECT_MAPPER.readValue(json, Relation.class); + if (relation.getDataInfo() == null) { relation.setDataInfo(new DataInfo()); + } relation.getDataInfo().setDeletedbyinference(false); switch (type) { case SOURCE: relation.setSource(id); - return mapper.writeValueAsString(relation); + return OBJECT_MAPPER.writeValueAsString(relation); case TARGET: relation.setTarget(id); - return mapper.writeValueAsString(relation); + return OBJECT_MAPPER.writeValueAsString(relation); default: throw new IllegalArgumentException(""); } @@ -165,14 +203,13 @@ public class SparkPropagateRelation extends AbstractSparkAction { } private static String updateDeletedByInference(final String json, final Class clazz) { - final ObjectMapper mapper = new ObjectMapper(); - mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); try { - Oaf entity = mapper.readValue(json, clazz); - if (entity.getDataInfo()== null) + Oaf entity = OBJECT_MAPPER.readValue(json, clazz); + if (entity.getDataInfo() == null) { entity.setDataInfo(new DataInfo()); + } entity.getDataInfo().setDeletedbyinference(true); - return mapper.writeValueAsString(entity); + return OBJECT_MAPPER.writeValueAsString(entity); } catch (IOException e) { throw new RuntimeException("Unable to convert json", e); } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml index 32f4e7db01..66dbdea733 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml @@ -24,6 +24,29 @@ sparkExecutorCores number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + @@ -38,6 +61,10 @@ oozie.launcher.mapred.job.queue.name ${oozieLauncherQueueName} + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + @@ -50,7 +77,7 @@ - + yarn cluster @@ -58,12 +85,14 @@ eu.dnetlib.dhp.oa.dedup.SparkUpdateEntity dhp-dedup-openaire-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} - --executor-cores ${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" - --conf spark.sql.warehouse.dir="/user/hive/warehouse" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 -mtyarn --i${graphBasePath} @@ -77,7 +106,9 @@ - + + + yarn cluster @@ -85,12 +116,14 @@ eu.dnetlib.dhp.oa.dedup.SparkPropagateRelation dhp-dedup-openaire-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} - --executor-cores ${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" - --conf spark.sql.warehouse.dir="/user/hive/warehouse" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 -mtyarn --i${graphBasePath} From 011b342bc9256f6d216227a2f051fb7998b28d31 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 16 Apr 2020 11:13:51 +0200 Subject: [PATCH 10/19] trying to avoid OOM in SparkPropagateRelation --- .../dhp/oa/dedup/AbstractSparkAction.java | 31 +++ .../dhp/oa/dedup/SparkPropagateRelation.java | 259 ++++++++---------- .../dedup/consistency/oozie_app/workflow.xml | 5 - 3 files changed, 149 insertions(+), 146 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java index 8358939ff5..58875eec07 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.oa.dedup; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; @@ -70,6 +71,36 @@ abstract class AbstractSparkAction implements Serializable { protected static SparkSession getSparkSession(ArgumentApplicationParser parser) { SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(new Class[] { + Author.class, + Context.class, + Country.class, + DataInfo.class, + Dataset.class, + Datasource.class, + ExternalReference.class, + ExtraInfo.class, + Field.class, + GeoLocation.class, + Instance.class, + Journal.class, + KeyValue.class, + Oaf.class, + OafEntity.class, + OAIProvenance.class, + Organization.class, + OriginDescription.class, + OtherResearchProduct.class, + Project.class, + Publication.class, + Qualifier.class, + Relation.class, + Result.class, + Software.class, + StructuredProperty.class + }); + return SparkSession .builder() .appName(SparkCreateSimRels.class.getSimpleName()) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index 02db60f440..4e012293b9 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -4,61 +4,50 @@ import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.hadoop.fs.FileStatus; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; -import org.apache.hadoop.io.compress.GzipCodec; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaPairRDD; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.Optional; -import org.apache.spark.api.java.function.Function; -import org.apache.spark.api.java.function.PairFunction; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import scala.Tuple2; import java.io.IOException; +import static org.apache.spark.sql.functions.col; + public class SparkPropagateRelation extends AbstractSparkAction { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() - .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);; + private static final Logger log = LoggerFactory.getLogger(SparkPropagateRelation.class); - public static final int NUM_PARTITIONS = 3000; + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); enum FieldType { SOURCE, TARGET } - final static String SOURCEJSONPATH = "$.source"; - final static String TARGETJSONPATH = "$.target"; - - private static final Log log = LogFactory.getLog(SparkPropagateRelation.class); - public SparkPropagateRelation(ArgumentApplicationParser parser, SparkSession spark) throws Exception { super(parser, spark); } public static void main(String[] args) throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); + IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); + parser.parseArgument(args); - new SparkPropagateRelation(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); + new SparkPropagateRelation(parser, getSparkSession(parser)) + .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } @Override @@ -68,96 +57,114 @@ public class SparkPropagateRelation extends AbstractSparkAction { final String workingPath = parser.get("workingPath"); final String dedupGraphPath = parser.get("dedupGraphPath"); - System.out.println(String.format("graphBasePath: '%s'", graphBasePath)); - System.out.println(String.format("workingPath: '%s'", workingPath)); - System.out.println(String.format("dedupGraphPath:'%s'", dedupGraphPath)); + log.info("graphBasePath: '{}'", graphBasePath); + log.info("workingPath: '{}'", workingPath); + log.info("dedupGraphPath: '{}'", dedupGraphPath); - final String relationsPath = DedupUtility.createEntityPath(dedupGraphPath, "relation"); - final String newRelsPath = DedupUtility.createEntityPath(workingPath, "newRels"); - final String fixedSourceId = DedupUtility.createEntityPath(workingPath, "fixedSourceId"); - final String deletedSourceId = DedupUtility.createEntityPath(workingPath, "deletedSourceId"); + final String outputRelationPath = DedupUtility.createEntityPath(dedupGraphPath, "relation"); + deletePath(outputRelationPath); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + Dataset mergeRels = spark.read() + .load(DedupUtility.createMergeRelPath(workingPath, "*", "*")) + .as(Encoders.bean(Relation.class)); - deletePath(relationsPath); - deletePath(newRelsPath); - deletePath(fixedSourceId); - deletePath(deletedSourceId); - - final Dataset mergeRels = spark.read().load(DedupUtility.createMergeRelPath(workingPath, "*", "*")).as(Encoders.bean(Relation.class)); - - final JavaPairRDD mergedIds = mergeRels - .where("relClass == 'merges'") - .select(mergeRels.col("source"), mergeRels.col("target")) + Dataset> mergedIds = mergeRels + .where(col("relClass").equalTo("merges")) + .select(col("source"), col("target")) .distinct() - .toJavaRDD() - .mapToPair((PairFunction) r -> new Tuple2(r.getString(1), r.getString(0))); + .map((MapFunction>) + r -> new Tuple2<>(r.getString(1), r.getString(0)), + Encoders.tuple(Encoders.STRING(), Encoders.STRING())) + .cache(); - sc.textFile(DedupUtility.createEntityPath(graphBasePath, "relation")) - .repartition(NUM_PARTITIONS) - .mapToPair( - (PairFunction) s -> - new Tuple2(MapDocumentUtil.getJPathString(SOURCEJSONPATH, s), s)) - .leftOuterJoin(mergedIds) - .map((Function>>, String>) v1 -> { - if (v1._2()._2().isPresent()) { - return replaceField(v1._2()._1(), v1._2()._2().get(), FieldType.SOURCE); - } - return v1._2()._1(); - }) - .saveAsTextFile(fixedSourceId, GzipCodec.class); + final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation"); - sc.textFile(fixedSourceId) - .mapToPair( - (PairFunction) s -> - new Tuple2(MapDocumentUtil.getJPathString(TARGETJSONPATH, s), s)) - .leftOuterJoin(mergedIds) - .map((Function>>, String>) v1 -> { - if (v1._2()._2().isPresent()) { - return replaceField(v1._2()._1(), v1._2()._2().get(), FieldType.TARGET); - } - return v1._2()._1(); - }).filter(SparkPropagateRelation::containsDedup) - .repartition(NUM_PARTITIONS) - .saveAsTextFile(newRelsPath, GzipCodec.class); + Dataset rels = spark.read() + .textFile(relationPath) + .map(patchRelFn(), Encoders.bean(Relation.class)); - //update deleted by inference - sc.textFile(DedupUtility.createEntityPath(graphBasePath, "relation")) - .repartition(NUM_PARTITIONS) - .mapToPair((PairFunction) s -> - new Tuple2(MapDocumentUtil.getJPathString(SOURCEJSONPATH, s), s)) - .leftOuterJoin(mergedIds) - .map((Function>>, String>) v1 -> { - if (v1._2()._2().isPresent()) { - return updateDeletedByInference(v1._2()._1(), Relation.class); - } - return v1._2()._1(); - }) - .saveAsTextFile(deletedSourceId, GzipCodec.class); + Dataset newRels = + processDataset( + processDataset(rels, mergedIds, FieldType.SOURCE, getFixRelFn(FieldType.SOURCE)), + mergedIds, FieldType.TARGET, getFixRelFn(FieldType.TARGET)) + .filter(SparkPropagateRelation::containsDedup); - sc.textFile(deletedSourceId) - .repartition(NUM_PARTITIONS) - .mapToPair( - (PairFunction) s -> - new Tuple2(MapDocumentUtil.getJPathString(TARGETJSONPATH, s), s)) - .leftOuterJoin(mergedIds) - .map((Function>>, String>) v1 -> { - if (v1._2()._2().isPresent()) { - return updateDeletedByInference(v1._2()._1(), Relation.class); - } - return v1._2()._1(); - }) - .repartition(NUM_PARTITIONS) - .saveAsTextFile(DedupUtility.createEntityPath(workingPath, "updated"), GzipCodec.class); + Dataset updated = processDataset( + processDataset(rels, mergedIds, FieldType.SOURCE, getDeletedFn()), + mergedIds, FieldType.TARGET, getDeletedFn()); - JavaRDD newRels = sc - .textFile(newRelsPath); + save(newRels.union(updated), outputRelationPath); - sc - .textFile(DedupUtility.createEntityPath(workingPath, "updated")) - .union(newRels) - .repartition(NUM_PARTITIONS) - .saveAsTextFile(relationsPath, GzipCodec.class); + } + + private static Dataset processDataset(Dataset rels, Dataset> mergedIds, FieldType type, + MapFunction, Tuple2>, Relation> mapFn) { + final Dataset> mapped = rels + .map((MapFunction>) + r -> new Tuple2<>(getId(r, type), r), + Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class))); + return mapped + .joinWith(mergedIds, mapped.col("_1").equalTo(mergedIds.col("_1")), "left_outer") + .map(mapFn, Encoders.bean(Relation.class)); + } + + private static MapFunction patchRelFn() { + return value -> { + final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class); + if (rel.getDataInfo() == null) { + rel.setDataInfo(new DataInfo()); + } + return rel; + }; + } + + private static String getId(Relation r, FieldType type) { + switch (type) { + case SOURCE: + return r.getSource(); + case TARGET: + return r.getTarget(); + default: + throw new IllegalArgumentException(""); + } + } + + private static MapFunction, Tuple2>, Relation> getFixRelFn(FieldType type) { + return value -> { + if (value._2() != null) { + Relation r = value._1()._2(); + String id = value._2()._2(); + if (r.getDataInfo() == null) { + r.setDataInfo(new DataInfo()); + } + r.getDataInfo().setDeletedbyinference(false); + switch (type) { + case SOURCE: + r.setSource(id); + return r; + case TARGET: + r.setTarget(id); + return r; + default: + throw new IllegalArgumentException(""); + } + } + return value._1()._2(); + }; + } + + private static MapFunction, Tuple2>, Relation> getDeletedFn() { + return value -> { + if (value._2() != null) { + Relation r = value._1()._2(); + if (r.getDataInfo() == null) { + r.setDataInfo(new DataInfo()); + } + r.getDataInfo().setDeletedbyinference(true); + return r; + } + return value._1()._2(); + }; } private void deletePath(String path) { @@ -173,45 +180,15 @@ public class SparkPropagateRelation extends AbstractSparkAction { } } - private static boolean containsDedup(final String json) { - final String source = MapDocumentUtil.getJPathString(SOURCEJSONPATH, json); - final String target = MapDocumentUtil.getJPathString(TARGETJSONPATH, json); - - return source.toLowerCase().contains("dedup") || target.toLowerCase().contains("dedup"); + private static void save(Dataset dataset, String outPath) { + dataset + .write() + .option("compression", "gzip") + .json(outPath); } - private static String replaceField(final String json, final String id, final FieldType type) { - try { - Relation relation = OBJECT_MAPPER.readValue(json, Relation.class); - if (relation.getDataInfo() == null) { - relation.setDataInfo(new DataInfo()); - } - relation.getDataInfo().setDeletedbyinference(false); - switch (type) { - case SOURCE: - relation.setSource(id); - return OBJECT_MAPPER.writeValueAsString(relation); - case TARGET: - relation.setTarget(id); - return OBJECT_MAPPER.writeValueAsString(relation); - default: - throw new IllegalArgumentException(""); - } - } catch (IOException e) { - throw new RuntimeException("unable to deserialize json relation: " + json, e); - } + private static boolean containsDedup(final Relation r) { + return r.getSource().toLowerCase().contains("dedup") || r.getTarget().toLowerCase().contains("dedup"); } - private static String updateDeletedByInference(final String json, final Class clazz) { - try { - Oaf entity = OBJECT_MAPPER.readValue(json, clazz); - if (entity.getDataInfo() == null) { - entity.setDataInfo(new DataInfo()); - } - entity.getDataInfo().setDeletedbyinference(true); - return OBJECT_MAPPER.writeValueAsString(entity); - } catch (IOException e) { - throw new RuntimeException("Unable to convert json", e); - } - } } \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml index 66dbdea733..b34466d8e7 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml @@ -105,11 +105,6 @@ - - - - - yarn cluster Update Relations From b39ff36c1641c647368006a35e4bfb278c75ab26 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 16 Apr 2020 12:11:37 +0200 Subject: [PATCH 11/19] improving the wf definitions --- .../dhp/oa/dedup/scan/oozie_app/workflow.xml | 67 ++++++++++++------- 1 file changed, 44 insertions(+), 23 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml index 25596bc2ff..b50241b8f8 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml @@ -28,6 +28,28 @@ sparkExecutorCores number of cores used by single executor + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + @@ -42,6 +64,10 @@ oozie.launcher.mapred.job.queue.name ${oozieLauncherQueueName} + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + @@ -53,20 +79,19 @@ - - - yarn cluster Create Similarity Relations eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels dhp-dedup-openaire-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} - --executor-cores ${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} -mtyarn --i${graphBasePath} @@ -80,21 +105,19 @@ - - - yarn cluster Create Merge Relations eu.dnetlib.dhp.oa.dedup.SparkCreateConnectedComponent dhp-dedup-openaire-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} - --executor-cores ${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" - --conf spark.sql.warehouse.dir="/user/hive/warehouse" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} -mtyarn --i${graphBasePath} @@ -108,21 +131,19 @@ - - - yarn cluster Create Dedup Record eu.dnetlib.dhp.oa.dedup.SparkCreateDedupRecord dhp-dedup-openaire-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} - --executor-cores ${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" - --conf spark.sql.warehouse.dir="/user/hive/warehouse" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} -mtyarn --i${graphBasePath} From cd4d9a148f84cebbfd0b2af446735acba3da3c5a Mon Sep 17 00:00:00 2001 From: miconis Date: Thu, 16 Apr 2020 12:13:26 +0200 Subject: [PATCH 12/19] creating temporary directories in dedup test --- .../dhp/oa/dedup/AbstractSparkAction.java | 2 +- ...mponent.java => SparkCreateMergeRels.java} | 9 +++---- .../dhp/oa/dedup/scan/oozie_app/workflow.xml | 2 +- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 26 ++++++++++++------- 4 files changed, 23 insertions(+), 16 deletions(-) rename dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/{SparkCreateConnectedComponent.java => SparkCreateMergeRels.java} (91%) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java index 58875eec07..8549839fca 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java @@ -24,7 +24,7 @@ abstract class AbstractSparkAction implements Serializable { public ArgumentApplicationParser parser; //parameters for the spark action public SparkSession spark; //the spark session - public AbstractSparkAction(ArgumentApplicationParser parser, SparkSession spark) throws Exception { + public AbstractSparkAction(ArgumentApplicationParser parser, SparkSession spark) { this.parser = parser; this.spark = spark; diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateConnectedComponent.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java similarity index 91% rename from dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateConnectedComponent.java rename to dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java index d0ef580342..1425422f80 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateConnectedComponent.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java @@ -16,7 +16,6 @@ import org.apache.commons.logging.LogFactory; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.graphx.Edge; import org.apache.spark.rdd.RDD; @@ -31,11 +30,11 @@ import java.util.ArrayList; import java.util.Iterator; import java.util.List; -public class SparkCreateConnectedComponent extends AbstractSparkAction { +public class SparkCreateMergeRels extends AbstractSparkAction { - private static final Log log = LogFactory.getLog(SparkCreateConnectedComponent.class); + private static final Log log = LogFactory.getLog(SparkCreateMergeRels.class); - public SparkCreateConnectedComponent(ArgumentApplicationParser parser, SparkSession spark) throws Exception { + public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) throws Exception { super(parser, spark); } @@ -45,7 +44,7 @@ public class SparkCreateConnectedComponent extends AbstractSparkAction { SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); parser.parseArgument(args); - new SparkCreateConnectedComponent(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); + new SparkCreateMergeRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } @Override diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml index 25596bc2ff..3c73fefb6a 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml @@ -86,7 +86,7 @@ yarn cluster Create Merge Relations - eu.dnetlib.dhp.oa.dedup.SparkCreateConnectedComponent + eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels dhp-dedup-openaire-${projectVersion}.jar --executor-memory ${sparkExecutorMemory} diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 3d7f574608..0a43003968 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -22,6 +22,7 @@ import java.io.Serializable; import java.net.URISyntaxException; import java.nio.file.Paths; +import static java.nio.file.Files.createTempDirectory; import static org.junit.jupiter.api.Assertions.assertEquals; import static org.mockito.Mockito.lenient; @@ -36,16 +37,20 @@ public class SparkDedupTest implements Serializable { private static JavaSparkContext jsc; private static String testGraphBasePath; - private final static String testOutputBasePath = "/tmp/test_dedup_workflow"; + private static String testOutputBasePath = "/tmp/test_dedup_workflow"; private final static String testActionSetId = "test-orchestrator"; - private final static String testDedupGraphBasePath = "/tmp/test_dedup_workflow/dedup_graph"; + private static String testDedupGraphBasePath = "/tmp/test_dedup_workflow/dedup_graph"; @BeforeAll private static void cleanUp() throws IOException, URISyntaxException { testGraphBasePath = Paths.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath(); + testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString(); + testDedupGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString(); + FileUtils.deleteDirectory(new File(testOutputBasePath)); + FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); spark = SparkSession .builder() @@ -54,7 +59,7 @@ public class SparkDedupTest implements Serializable { .config(new SparkConf()) .getOrCreate(); - jsc = new JavaSparkContext(spark.sparkContext()); + jsc = JavaSparkContext.fromSparkContext(spark.sparkContext()); } @@ -69,7 +74,6 @@ public class SparkDedupTest implements Serializable { lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); - } @Test @@ -97,11 +101,11 @@ public class SparkDedupTest implements Serializable { @Test @Order(2) - public void createCCTest() throws Exception { + public void createMergeRelsTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils.toString( - SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + SparkCreateMergeRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); parser.parseArgument(new String[]{ "-mt", "local[*]", "-i", testGraphBasePath, @@ -109,7 +113,7 @@ public class SparkDedupTest implements Serializable { "-la", "lookupurl", "-w", testOutputBasePath}); - new SparkCreateConnectedComponent(parser, spark).run(isLookUpService); + new SparkCreateMergeRels(parser, spark).run(isLookUpService); long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count(); long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count(); @@ -185,8 +189,6 @@ public class SparkDedupTest implements Serializable { assertEquals(mergedOrgs, deletedOrgs); assertEquals(mergedPubs, deletedPubs); - - //TODO check the size of other entities not deduplicated } @Test @@ -211,6 +213,12 @@ public class SparkDedupTest implements Serializable { } + @AfterAll + public static void finalCleanUp() throws IOException { + FileUtils.deleteDirectory(new File(testOutputBasePath)); + FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); + } + public boolean isDeletedByInference(String s) { return s.contains("\"deletedbyinference\":true"); } From 376efd67debef33b61d88dd900a062973b6b7dea Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 16 Apr 2020 12:14:16 +0200 Subject: [PATCH 13/19] removed prepare statement in spark action --- .../eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml | 3 --- 1 file changed, 3 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml index b34466d8e7..69411701b8 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml @@ -76,9 +76,6 @@ - - - yarn cluster Update Entity From 6a089ec2870a5e14f0faabec7543b6e505cce965 Mon Sep 17 00:00:00 2001 From: miconis Date: Thu, 16 Apr 2020 12:15:38 +0200 Subject: [PATCH 14/19] minor changes --- .../src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 0a43003968..880e917ce7 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -37,9 +37,9 @@ public class SparkDedupTest implements Serializable { private static JavaSparkContext jsc; private static String testGraphBasePath; - private static String testOutputBasePath = "/tmp/test_dedup_workflow"; + private static String testOutputBasePath; + private static String testDedupGraphBasePath; private final static String testActionSetId = "test-orchestrator"; - private static String testDedupGraphBasePath = "/tmp/test_dedup_workflow/dedup_graph"; @BeforeAll private static void cleanUp() throws IOException, URISyntaxException { From 0eccbc318b0e039538a0971b4828305562a2ecb6 Mon Sep 17 00:00:00 2001 From: miconis Date: Thu, 16 Apr 2020 12:36:37 +0200 Subject: [PATCH 15/19] Deduper class (utilities for dedup) cleaned. Useless methods removed --- .../java/eu/dnetlib/dhp/oa/dedup/Deduper.java | 121 +++--------------- .../dhp/oa/dedup/SparkCreateDedupRecord.java | 9 +- .../dhp/oa/dedup/SparkCreateMergeRels.java | 8 +- .../dhp/oa/dedup/SparkCreateSimRels.java | 19 +-- .../dhp/oa/dedup/SparkUpdateEntity.java | 8 +- 5 files changed, 36 insertions(+), 129 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java index d8de489469..1f9f84c552 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java @@ -4,8 +4,6 @@ import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.BlockProcessor; import eu.dnetlib.pace.util.MapDocumentUtil; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -13,59 +11,32 @@ import org.apache.spark.api.java.function.Function2; import org.apache.spark.api.java.function.PairFlatMapFunction; import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.util.LongAccumulator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import scala.Serializable; import scala.Tuple2; -import java.util.*; +import java.util.ArrayList; +import java.util.Comparator; +import java.util.List; +import java.util.Map; import java.util.stream.Collectors; public class Deduper implements Serializable { - private static final Log log = LogFactory.getLog(Deduper.class); - - /** - * @return the list of relations generated by the deduplication - * @param: the spark context - * @param: list of JSON entities to be deduped - * @param: the dedup configuration - */ - public static JavaPairRDD dedup(JavaSparkContext context, JavaRDD entities, DedupConfig config) { + private static final Logger log = LoggerFactory.getLogger(Deduper.class); + public static JavaPairRDD computeRelations(JavaSparkContext context, JavaPairRDD> blocks, DedupConfig config) { Map accumulators = DedupUtility.constructAccumulator(config, context.sc()); - //create vertexes of the graph: - JavaPairRDD mapDocs = mapToVertexes(context, entities, config); - - - //create blocks for deduplication - JavaPairRDD> blocks = createBlocks(context, mapDocs, config); - - //create relations by comparing only elements in the same group - return computeRelations(context, blocks, config); - -// final RDD> edgeRdd = relationRDD.map(it -> new Edge<>(it._1().hashCode(), it._2().hashCode(), "equalTo")).rdd(); -// -// RDD> vertexes = mapDocs.mapToPair((PairFunction, Object, MapDocument>) t -> new Tuple2((long) t._1().hashCode(), t._2())).rdd(); -// accumulators.forEach((name, acc) -> log.info(name + " -> " + acc.value())); -// -// return GraphProcessor.findCCs(vertexes, edgeRdd, 20).toJavaRDD(); - } - - /** - * @return the list of relations generated by the deduplication - * @param: the spark context - * @param: list of blocks - * @param: the dedup configuration - */ - public static JavaPairRDD computeRelations(JavaSparkContext context, JavaPairRDD> blocks, DedupConfig config) { - - Map accumulators = DedupUtility.constructAccumulator(config, context.sc()); - - return blocks.flatMapToPair((PairFlatMapFunction>, String, String>) it -> { - final SparkReporter reporter = new SparkReporter(accumulators); - new BlockProcessor(config).process(it._1(), it._2(), reporter); - return reporter.getRelations().iterator(); - + return blocks.flatMapToPair((PairFlatMapFunction>, String, String>) it -> { + try { + final SparkReporter reporter = new SparkReporter(accumulators); + new BlockProcessor(config).processSortedBlock(it._1(), it._2(), reporter); + return reporter.getRelations().iterator(); + } catch (Exception e) { + throw new RuntimeException(it._2().get(0).getIdentifier(), e); + } }).mapToPair( (PairFunction, String, Tuple2>) item -> new Tuple2>(item._1() + item._2(), item)) @@ -73,30 +44,7 @@ public class Deduper implements Serializable { .mapToPair((PairFunction>, String, String>) Tuple2::_2); } - - /** - * @return the list of blocks based on clustering of dedup configuration - * @param: the spark context - * @param: list of entities: - * @param: the dedup configuration - */ - public static JavaPairRDD> createBlocks(JavaSparkContext context, JavaPairRDD mapDocs, DedupConfig config) { - return mapDocs - //the reduce is just to be sure that we haven't document with same id - .reduceByKey((a, b) -> a) - .map(Tuple2::_2) - //Clustering: from to List - .flatMapToPair((PairFlatMapFunction) a -> - DedupUtility.getGroupingKeys(config, a) - .stream() - .map(it -> new Tuple2<>(it, a)) - .collect(Collectors.toList()) - .iterator()) - .groupByKey(); - } - - - public static JavaPairRDD> createsortedBlocks(JavaSparkContext context, JavaPairRDD mapDocs, DedupConfig config) { + public static JavaPairRDD> createSortedBlocks(JavaSparkContext context, JavaPairRDD mapDocs, DedupConfig config) { final String of = config.getWf().getOrderField(); final int maxQueueSize = config.getWf().getGroupMaxSize(); return mapDocs @@ -123,39 +71,4 @@ public class Deduper implements Serializable { return v1; }); } - - /** - * @return the list of vertexes: - * @param: the spark context - * @param: list of JSON entities - * @param: the dedup configuration - */ - public static JavaPairRDD mapToVertexes(JavaSparkContext context, JavaRDD entities, DedupConfig config) { - - return entities.mapToPair((PairFunction) s -> { - - MapDocument mapDocument = MapDocumentUtil.asMapDocumentWithJPath(config, s); - return new Tuple2(mapDocument.getIdentifier(), mapDocument); - - - }); - } - - public static JavaPairRDD computeRelations2(JavaSparkContext context, JavaPairRDD> blocks, DedupConfig config) { - Map accumulators = DedupUtility.constructAccumulator(config, context.sc()); - - return blocks.flatMapToPair((PairFlatMapFunction>, String, String>) it -> { - try { - final SparkReporter reporter = new SparkReporter(accumulators); - new BlockProcessor(config).processSortedBlock(it._1(), it._2(), reporter); - return reporter.getRelations().iterator(); - } catch (Exception e) { - throw new RuntimeException(it._2().get(0).getIdentifier(), e); - } - }).mapToPair( - (PairFunction, String, Tuple2>) item -> - new Tuple2>(item._1() + item._2(), item)) - .reduceByKey((a, b) -> a) - .mapToPair((PairFunction>, String, String>) Tuple2::_2); - } } \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java index 2c065253a6..22e6f145ef 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java @@ -8,21 +8,20 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import java.io.IOException; public class SparkCreateDedupRecord extends AbstractSparkAction { - private static final Log log = LogFactory.getLog(SparkCreateDedupRecord.class); + private static final Logger log = LoggerFactory.getLogger(SparkCreateDedupRecord.class); - public SparkCreateDedupRecord(ArgumentApplicationParser parser, SparkSession spark) throws Exception { + public SparkCreateDedupRecord(ArgumentApplicationParser parser, SparkSession spark) { super(parser, spark); } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java index 1425422f80..fb607a87ef 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java @@ -11,8 +11,6 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -24,6 +22,8 @@ import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; import scala.Tuple2; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import java.io.IOException; import java.util.ArrayList; @@ -32,9 +32,9 @@ import java.util.List; public class SparkCreateMergeRels extends AbstractSparkAction { - private static final Log log = LogFactory.getLog(SparkCreateMergeRels.class); + private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class); - public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) throws Exception { + public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) { super(parser, spark); } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java index 0d07d1fe18..a2b7e7b5d7 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java @@ -12,33 +12,26 @@ import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.hadoop.io.Text; -import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; -import org.dom4j.Document; import org.dom4j.DocumentException; -import org.dom4j.Element; -import org.dom4j.io.SAXReader; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import scala.Tuple2; import java.io.IOException; -import java.io.Serializable; -import java.io.StringReader; -import java.util.ArrayList; import java.util.List; public class SparkCreateSimRels extends AbstractSparkAction { - private static final Log log = LogFactory.getLog(SparkCreateSimRels.class); + private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class); - public SparkCreateSimRels(ArgumentApplicationParser parser, SparkSession spark) throws Exception { + public SparkCreateSimRels(ArgumentApplicationParser parser, SparkSession spark) { super(parser, spark); } @@ -81,10 +74,10 @@ public class SparkCreateSimRels extends AbstractSparkAction { }); //create blocks for deduplication - JavaPairRDD> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf); + JavaPairRDD> blocks = Deduper.createSortedBlocks(sc, mapDocument, dedupConf); //create relations by comparing only elements in the same group - final JavaPairRDD dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf); + final JavaPairRDD dedupRels = Deduper.computeRelations(sc, blocks, dedupConf); JavaRDD relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity)); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java index f92fcf3ce9..c2e1df78ca 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java @@ -22,6 +22,8 @@ import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import scala.Tuple2; import java.io.IOException; @@ -29,11 +31,11 @@ import java.io.Serializable; public class SparkUpdateEntity extends AbstractSparkAction { + private static final Logger log = LoggerFactory.getLogger(SparkUpdateEntity.class); + final String IDJSONPATH = "$.id"; - private static final Log log = LogFactory.getLog(SparkUpdateEntity.class); - - public SparkUpdateEntity(ArgumentApplicationParser parser, SparkSession spark) throws Exception { + public SparkUpdateEntity(ArgumentApplicationParser parser, SparkSession spark) { super(parser, spark); } From ec5dfc068db477fbbb8e335b52a6a06f8517d125 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 16 Apr 2020 14:41:28 +0200 Subject: [PATCH 16/19] added spark.sql.shuffle.partitions=3840 to dedup scan wf --- .../eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml index 250f7398fe..6c74a204dc 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml @@ -92,6 +92,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 -mtyarn --i${graphBasePath} @@ -118,6 +119,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 -mtyarn --i${graphBasePath} From 038ac7afd71a01efd02dca666c27dca8044d09e0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 17 Apr 2020 13:12:44 +0200 Subject: [PATCH 17/19] relation consistency workflow separated from dedup scan and creation of CCs --- .../eu/dnetlib/dhp/common/HdfsSupport.java | 15 ++ .../PartitionActionSetsByPayloadTypeJob.java | 2 + .../dhp/oa/dedup/AbstractSparkAction.java | 9 ++ .../dhp/oa/dedup/SparkCreateDedupRecord.java | 20 +-- .../dhp/oa/dedup/SparkCreateMergeRels.java | 100 +++++++++---- .../dhp/oa/dedup/SparkCreateSimRels.java | 55 +++----- .../dhp/oa/dedup/SparkPropagateRelation.java | 5 +- .../dhp/oa/dedup/SparkUpdateEntity.java | 110 +++++++-------- .../dedup/consistency/oozie_app/workflow.xml | 133 ++++++++++++++---- .../dhp/oa/dedup/scan/oozie_app/workflow.xml | 44 ++++++ 10 files changed, 330 insertions(+), 163 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java index 05beaa51e1..f6b94c9211 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java @@ -22,6 +22,21 @@ public class HdfsSupport { private HdfsSupport() { } + /** + * Checks a path (file or dir) exists on HDFS. + * + * @param path Path to be checked + * @param configuration Configuration of hadoop env + */ + public static boolean exists(String path, Configuration configuration) { + logger.info("Removing path: {}", path); + return rethrowAsRuntimeException(() -> { + Path f = new Path(path); + FileSystem fileSystem = FileSystem.get(configuration); + return fileSystem.exists(f); + }); + } + /** * Removes a path (file or dir) from HDFS. * diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java index 31a4da1902..7c4d0616cb 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java @@ -99,6 +99,8 @@ public class PartitionActionSetsByPayloadTypeJob { List inputActionSetPaths, String outputPath) { inputActionSetPaths + .stream() + .filter(path -> HdfsSupport.exists(path, spark.sparkContext().hadoopConfiguration())) .forEach(inputActionSetPath -> { Dataset actionDS = readActionSetFromPath(spark, inputActionSetPath); saveActions(actionDS, outputPath); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java index 8549839fca..6213f342a9 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java @@ -1,7 +1,9 @@ package eu.dnetlib.dhp.oa.dedup; +import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -21,6 +23,9 @@ import java.util.List; abstract class AbstractSparkAction implements Serializable { + protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + public ArgumentApplicationParser parser; //parameters for the spark action public SparkSession spark; //the spark session @@ -108,4 +113,8 @@ abstract class AbstractSparkAction implements Serializable { .config(conf) .getOrCreate(); } + + protected static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java index 22e6f145ef..02cf6587a1 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java @@ -1,6 +1,5 @@ package eu.dnetlib.dhp.oa.dedup; -import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.utils.ISLookupClientFactory; @@ -42,26 +41,27 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { final String actionSetId = parser.get("actionSetId"); final String workingPath = parser.get("workingPath"); - System.out.println(String.format("graphBasePath: '%s'", graphBasePath)); - System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl)); - System.out.println(String.format("actionSetId: '%s'", actionSetId)); - System.out.println(String.format("workingPath: '%s'", workingPath)); + log.info("graphBasePath: '{}'", graphBasePath); + log.info("isLookUpUrl: '{}'", isLookUpUrl); + log.info("actionSetId: '{}'", actionSetId); + log.info("workingPath: '{}'", workingPath); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { String subEntity = dedupConf.getWf().getSubEntityValue(); - System.out.println(String.format("Creating deduprecords for: '%s'", subEntity)); + log.info("Creating deduprecords for: '{}'", subEntity); + + final String outputPath = DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity); + removeOutputDir(spark, outputPath); final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity); final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity); final OafEntityType entityType = OafEntityType.valueOf(subEntity); final JavaRDD dedupRecord = DedupRecordFactory.createDedupRecord(sc, spark, mergeRelPath, entityPath, entityType, dedupConf); - dedupRecord.map(r -> { - ObjectMapper mapper = new ObjectMapper(); - return mapper.writeValueAsString(r); - }).saveAsTextFile(DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity)); + + dedupRecord.map(r -> OBJECT_MAPPER.writeValueAsString(r)).saveAsTextFile(outputPath); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java index fb607a87ef..ef82b4eaf6 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java @@ -4,6 +4,8 @@ import com.google.common.hash.Hashing; import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; @@ -19,6 +21,7 @@ import org.apache.spark.graphx.Edge; import org.apache.spark.rdd.RDD; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; import scala.Tuple2; @@ -32,7 +35,9 @@ import java.util.List; public class SparkCreateMergeRels extends AbstractSparkAction { + public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup"; private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class); + public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions"; public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) { super(parser, spark); @@ -44,7 +49,10 @@ public class SparkCreateMergeRels extends AbstractSparkAction { SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); parser.parseArgument(args); - new SparkCreateMergeRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); + final String isLookUpUrl = parser.get("isLookUpUrl"); + log.info("isLookupUrl {}", isLookUpUrl); + + new SparkCreateMergeRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(isLookUpUrl)); } @Override @@ -55,55 +63,91 @@ public class SparkCreateMergeRels extends AbstractSparkAction { final String isLookUpUrl = parser.get("isLookUpUrl"); final String actionSetId = parser.get("actionSetId"); - System.out.println(String.format("graphBasePath: '%s'", graphBasePath)); - System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl)); - System.out.println(String.format("actionSetId: '%s'", actionSetId)); - System.out.println(String.format("workingPath: '%s'", workingPath)); + log.info("graphBasePath: '{}'", graphBasePath); + log.info("isLookUpUrl: '{}'", isLookUpUrl); + log.info("actionSetId: '{}'", actionSetId); + log.info("workingPath: '{}'", workingPath); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { final String subEntity = dedupConf.getWf().getSubEntityValue(); - System.out.println(String.format("Creating mergerels for: '%s'", subEntity)); + log.info("Creating mergerels for: '{}'", subEntity); + + final int maxIterations = dedupConf.getWf().getMaxIterations(); + log.info("Max iterations {}", maxIterations); + + final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity); final JavaPairRDD vertexes = sc.textFile(graphBasePath + "/" + subEntity) .map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s)) .mapToPair((PairFunction) - s -> new Tuple2(getHashcode(s), s) - ); + s -> new Tuple2<>(getHashcode(s), s)); - final Dataset similarityRelations = spark.read().load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)).as(Encoders.bean(Relation.class)); - final RDD> edgeRdd = similarityRelations.javaRDD().map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())).rdd(); - final JavaRDD cc = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations()).toJavaRDD(); - final Dataset mergeRelation = spark.createDataset(cc.filter(k -> k.getDocIds().size() > 1) - .flatMap(this::ccToMergeRel).rdd(), Encoders.bean(Relation.class)); + final Dataset similarityRelations = spark + .read() + .load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)) + .as(Encoders.bean(Relation.class)); - mergeRelation - .write().mode("overwrite") - .save(DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity)); + final RDD> edgeRdd = similarityRelations + .javaRDD() + .map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())) + .rdd(); + + final RDD connectedComponents = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, maxIterations) + .toJavaRDD() + .filter(k -> k.getDocIds().size() > 1) + .flatMap(cc -> ccToMergeRel(cc, dedupConf)) + .rdd(); + + spark + .createDataset(connectedComponents, Encoders.bean(Relation.class)) + .write() + .mode(SaveMode.Append) + .save(mergeRelPath); } } - public Iterator ccToMergeRel(ConnectedComponent cc){ + public Iterator ccToMergeRel(ConnectedComponent cc, DedupConfig dedupConf){ return cc.getDocIds() .stream() .flatMap(id -> { List tmp = new ArrayList<>(); - Relation r = new Relation(); - r.setSource(cc.getCcId()); - r.setTarget(id); - r.setRelClass("merges"); - tmp.add(r); - r = new Relation(); - r.setTarget(cc.getCcId()); - r.setSource(id); - r.setRelClass("isMergedIn"); - tmp.add(r); + + tmp.add(rel(cc.getCcId(), id, "merges", dedupConf)); + tmp.add(rel(id, cc.getCcId(), "isMergedIn", dedupConf)); + return tmp.stream(); }).iterator(); } + private Relation rel(String source, String target, String relClass, DedupConfig dedupConf) { + Relation r = new Relation(); + r.setSource(source); + r.setTarget(target); + r.setRelClass(relClass); + r.setSubRelType("dedup"); + + DataInfo info = new DataInfo(); + info.setDeletedbyinference(false); + info.setInferred(true); + info.setInvisible(false); + info.setInferenceprovenance(dedupConf.getWf().getConfigurationId()); + Qualifier provenanceAction = new Qualifier(); + provenanceAction.setClassid(PROVENANCE_ACTION_CLASS); + provenanceAction.setClassname(PROVENANCE_ACTION_CLASS); + provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS); + provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS); + info.setProvenanceaction(provenanceAction); + + //TODO calculate the trust value based on the similarity score of the elements in the CC + //info.setTrust(); + + r.setDataInfo(info); + return r; + } + public static long getHashcode(final String id) { return Hashing.murmur3_128().hashString(id).asLong(); } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java index a2b7e7b5d7..de842d822b 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java @@ -4,6 +4,7 @@ import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; @@ -18,6 +19,7 @@ import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; import org.slf4j.Logger; @@ -53,24 +55,27 @@ public class SparkCreateSimRels extends AbstractSparkAction { final String actionSetId = parser.get("actionSetId"); final String workingPath = parser.get("workingPath"); - System.out.println(String.format("graphBasePath: '%s'", graphBasePath)); - System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl)); - System.out.println(String.format("actionSetId: '%s'", actionSetId)); - System.out.println(String.format("workingPath: '%s'", workingPath)); + log.info("graphBasePath: '{}'", graphBasePath); + log.info("isLookUpUrl: '{}'", isLookUpUrl); + log.info("actionSetId: '{}'", actionSetId); + log.info("workingPath: '{}'", workingPath); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); //for each dedup configuration for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { final String entity = dedupConf.getWf().getEntityType(); final String subEntity = dedupConf.getWf().getSubEntityValue(); - System.out.println(String.format("Creating simrels for: '%s'", subEntity)); + log.info("Creating simrels for: '{}'", subEntity); + + final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity); + removeOutputDir(spark, outputPath); JavaPairRDD mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) .mapToPair((PairFunction) s -> { MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); - return new Tuple2(d.getIdentifier(), d); + return new Tuple2<>(d.getIdentifier(), d); }); //create blocks for deduplication @@ -84,46 +89,30 @@ public class SparkCreateSimRels extends AbstractSparkAction { //save the simrel in the workingdir spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class)) .write() - .mode("overwrite") - .save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)); + .mode(SaveMode.Append) + .save(outputPath); } } - /** - * Utility method used to create an atomic action from a Relation object - * @param relation input relation - * @return A tuple2 with [id, json serialization of the atomic action] - * @throws JsonProcessingException - */ - public Tuple2 createSequenceFileRow(Relation relation) throws JsonProcessingException { - - ObjectMapper mapper = new ObjectMapper(); - - String id = relation.getSource() + "@" + relation.getRelClass() + "@" + relation.getTarget(); - AtomicAction aa = new AtomicAction<>(Relation.class, relation); - - return new Tuple2<>( - new Text(id), - new Text(mapper.writeValueAsString(aa)) - ); - } - - public Relation createSimRel(String source, String target, String entity){ + public Relation createSimRel(String source, String target, String entity) { final Relation r = new Relation(); r.setSource(source); r.setTarget(target); + r.setSubRelType("dedupSimilarity"); + r.setRelClass("isSimilarTo"); + r.setDataInfo(new DataInfo()); switch(entity){ case "result": - r.setRelClass("resultResult_dedupSimilarity_isSimilarTo"); + r.setRelType("resultResult"); break; case "organization": - r.setRelClass("organizationOrganization_dedupSimilarity_isSimilarTo"); + r.setRelType("organizationOrganization"); break; default: - r.setRelClass("isSimilarTo"); - break; + throw new IllegalArgumentException("unmanaged entity type: " + entity); } return r; } + } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index 4e012293b9..371d70ba2d 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -27,9 +27,6 @@ public class SparkPropagateRelation extends AbstractSparkAction { private static final Logger log = LoggerFactory.getLogger(SparkPropagateRelation.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() - .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - enum FieldType { SOURCE, TARGET @@ -62,7 +59,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { log.info("dedupGraphPath: '{}'", dedupGraphPath); final String outputRelationPath = DedupUtility.createEntityPath(dedupGraphPath, "relation"); - deletePath(outputRelationPath); + removeOutputDir(spark, outputRelationPath); Dataset mergeRels = spark.read() .load(DedupUtility.createMergeRelPath(workingPath, "*", "*")) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java index c2e1df78ca..5347489e70 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java @@ -3,17 +3,18 @@ package eu.dnetlib.dhp.oa.dedup; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.*; +import org.apache.hadoop.fs.FileStatus; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.compress.GzipCodec; -import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -27,7 +28,7 @@ import org.slf4j.LoggerFactory; import scala.Tuple2; import java.io.IOException; -import java.io.Serializable; +import java.util.Map; public class SparkUpdateEntity extends AbstractSparkAction { @@ -48,98 +49,87 @@ public class SparkUpdateEntity extends AbstractSparkAction { new SparkUpdateEntity(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } - public boolean mergeRelExists(String basePath, String entity) throws IOException { - - boolean result = false; - - FileSystem fileSystem = FileSystem.get(new Configuration()); - - FileStatus[] fileStatuses = fileSystem.listStatus(new Path(basePath)); - - for (FileStatus fs : fileStatuses) { - if (fs.isDirectory()) - if (fileSystem.exists(new Path(DedupUtility.createMergeRelPath(basePath, fs.getPath().getName(), entity)))) - result = true; - } - - return result; - } - public void run(ISLookUpService isLookUpService) throws IOException { final String graphBasePath = parser.get("graphBasePath"); final String workingPath = parser.get("workingPath"); final String dedupGraphPath = parser.get("dedupGraphPath"); - System.out.println(String.format("graphBasePath: '%s'", graphBasePath)); - System.out.println(String.format("workingPath: '%s'", workingPath)); - System.out.println(String.format("dedupGraphPath: '%s'", dedupGraphPath)); + log.info("graphBasePath: '{}'", graphBasePath); + log.info("workingPath: '{}'", workingPath); + log.info("dedupGraphPath: '{}'", dedupGraphPath); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); //for each entity - for (OafEntityType entity: OafEntityType.values()) { + ModelSupport.entityTypes.forEach((entity, clazz) -> { + final String outputPath = dedupGraphPath + "/" + entity; + removeOutputDir(spark, outputPath); JavaRDD sourceEntity = sc.textFile(DedupUtility.createEntityPath(graphBasePath, entity.toString())); if (mergeRelExists(workingPath, entity.toString())) { - final Dataset rel = spark.read().load(DedupUtility.createMergeRelPath(workingPath, "*", entity.toString())).as(Encoders.bean(Relation.class)); + final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, "*", entity.toString()); + final String dedupRecordPath = DedupUtility.createDedupRecordPath(workingPath, "*", entity.toString()); + + final Dataset rel = spark.read() + .load(mergeRelPath) + .as(Encoders.bean(Relation.class)); final JavaPairRDD mergedIds = rel .where("relClass == 'merges'") .select(rel.col("target")) .distinct() .toJavaRDD() - .mapToPair((PairFunction) r -> new Tuple2(r.getString(0), "d")); + .mapToPair((PairFunction) r -> new Tuple2<>(r.getString(0), "d")); - final JavaRDD dedupEntity = sc.textFile(DedupUtility.createDedupRecordPath(workingPath, "*", entity.toString())); + JavaPairRDD entitiesWithId = sourceEntity + .mapToPair((PairFunction) s -> new Tuple2<>(MapDocumentUtil.getJPathString(IDJSONPATH, s), s)); - JavaPairRDD entitiesWithId = sourceEntity.mapToPair((PairFunction) s -> new Tuple2(MapDocumentUtil.getJPathString(IDJSONPATH, s), s)); - - JavaRDD map = entitiesWithId.leftOuterJoin(mergedIds).map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), getOafClass(entity)) : k._2()._1()); - sourceEntity = map.union(dedupEntity); + JavaRDD map = entitiesWithId + .leftOuterJoin(mergedIds) + .map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), clazz) : k._2()._1()); + sourceEntity = map.union(sc.textFile(dedupRecordPath)); } - sourceEntity.saveAsTextFile(dedupGraphPath + "/" + entity, GzipCodec.class); + sourceEntity.saveAsTextFile(outputPath, GzipCodec.class); - } + }); } - public Class getOafClass(OafEntityType className) { - switch (className.toString()) { - case "publication": - return Publication.class; - case "dataset": - return eu.dnetlib.dhp.schema.oaf.Dataset.class; - case "datasource": - return Datasource.class; - case "software": - return Software.class; - case "organization": - return Organization.class; - case "otherresearchproduct": - return OtherResearchProduct.class; - case "project": - return Project.class; - default: - throw new IllegalArgumentException("Illegal type " + className); - } - } + public boolean mergeRelExists(String basePath, String entity) { - private static String updateDeletedByInference(final String json, final Class clazz) { - final ObjectMapper mapper = new ObjectMapper(); - mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + boolean result = false; try { - Oaf entity = mapper.readValue(json, clazz); + FileSystem fileSystem = FileSystem.get(new Configuration()); + + FileStatus[] fileStatuses = fileSystem.listStatus(new Path(basePath)); + + for (FileStatus fs : fileStatuses) { + if (fs.isDirectory()) + if (fileSystem.exists(new Path(DedupUtility.createMergeRelPath(basePath, fs.getPath().getName(), entity)))) + result = true; + } + + return result; + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + private static String updateDeletedByInference(final String json, final Class clazz) { + try { + Oaf entity = OBJECT_MAPPER.readValue(json, clazz); if (entity.getDataInfo()== null) entity.setDataInfo(new DataInfo()); entity.getDataInfo().setDeletedbyinference(true); - return mapper.writeValueAsString(entity); + return OBJECT_MAPPER.writeValueAsString(entity); } catch (IOException e) { throw new RuntimeException("Unable to convert json", e); } } + } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml index 69411701b8..df6877dfac 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml @@ -68,38 +68,12 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - yarn - cluster - Update Entity - eu.dnetlib.dhp.oa.dedup.SparkUpdateEntity - dhp-dedup-openaire-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=3840 - - -mtyarn - --i${graphBasePath} - --w${workingPath} - --o${dedupGraphPath} - - - - - yarn @@ -122,9 +96,112 @@ --o${dedupGraphPath} --w${workingPath} - + + + + + + + + + + + + + + + + + -pb + ${graphBasePath}/datasource + ${dedupGraphPath}/datasource + + + + + + + + + + + -pb + ${graphBasePath}/project + ${dedupGraphPath}/project + + + + + + + + + + + -pb + ${graphBasePath}/organization + ${dedupGraphPath}/organization + + + + + + + + + + + -pb + ${graphBasePath}/publication + ${dedupGraphPath}/publication + + + + + + + + + + + -pb + ${graphBasePath}/dataset + ${dedupGraphPath}/dataset + + + + + + + + + + + -pb + ${graphBasePath}/software + ${dedupGraphPath}/software + + + + + + + + + + + -pb + ${graphBasePath}/otherresearchproduct + ${dedupGraphPath}/otherresearchproduct + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml index 6c74a204dc..6790dde32a 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml @@ -16,6 +16,10 @@ workingPath path for the working directory + + dedupGraphPath + path for the output graph + sparkDriverMemory memory for driver process @@ -146,6 +150,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 -mtyarn --i${graphBasePath} @@ -153,6 +158,45 @@ --la${isLookUpUrl} --asi${actionSetId} + + + + + + + yarn + cluster + Update Entity + eu.dnetlib.dhp.oa.dedup.SparkUpdateEntity + dhp-dedup-openaire-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + -mtyarn + --i${graphBasePath} + --w${workingPath} + --o${dedupGraphPath} + + + + + + + + + + + -pb + ${graphBasePath}/relation + ${dedupGraphPath}/relation + From 71813795f61a1ce23944d107145c4a994a7f9425 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Sat, 18 Apr 2020 12:06:23 +0200 Subject: [PATCH 18/19] various refactorings on the dnet-dedup-openaire workflow --- .../dhp/oa/dedup/AbstractSparkAction.java | 47 +-- .../dhp/oa/dedup/DedupRecordFactory.java | 303 ++++-------------- .../java/eu/dnetlib/dhp/oa/dedup/Deduper.java | 58 +--- .../dnetlib/dhp/oa/dedup/OafEntityType.java | 15 - .../dhp/oa/dedup/SparkCreateDedupRecord.java | 27 +- .../dhp/oa/dedup/SparkCreateMergeRels.java | 33 +- .../dhp/oa/dedup/SparkCreateSimRels.java | 45 ++- .../dhp/oa/dedup/SparkPropagateRelation.java | 35 +- .../dnetlib/dhp/oa/dedup/SparkReporter.java | 6 +- .../dhp/oa/dedup/SparkUpdateEntity.java | 24 +- .../eu/dnetlib/dhp/oa/dedup/model/Block.java | 76 +++++ .../dedup/consistency/oozie_app/workflow.xml | 1 - .../dhp/oa/dedup/createCC_parameters.json | 6 - .../dedup/createDedupRecord_parameters.json | 6 - .../oa/dedup/createSimRels_parameters.json | 6 - .../dedup/propagateRelation_parameters.json | 6 - .../dhp/oa/dedup/scan/oozie_app/workflow.xml | 4 - .../dhp/oa/dedup/updateEntity_parameters.json | 6 - 18 files changed, 262 insertions(+), 442 deletions(-) delete mode 100644 dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/OafEntityType.java create mode 100644 dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Block.java diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java index 6213f342a9..f52e4bb39a 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java @@ -4,11 +4,14 @@ import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.Document; import org.dom4j.DocumentException; @@ -73,47 +76,21 @@ abstract class AbstractSparkAction implements Serializable { abstract void run(ISLookUpService isLookUpService) throws DocumentException, IOException, ISLookUpException; - protected static SparkSession getSparkSession(ArgumentApplicationParser parser) { - SparkConf conf = new SparkConf(); - - conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - conf.registerKryoClasses(new Class[] { - Author.class, - Context.class, - Country.class, - DataInfo.class, - Dataset.class, - Datasource.class, - ExternalReference.class, - ExtraInfo.class, - Field.class, - GeoLocation.class, - Instance.class, - Journal.class, - KeyValue.class, - Oaf.class, - OafEntity.class, - OAIProvenance.class, - Organization.class, - OriginDescription.class, - OtherResearchProduct.class, - Project.class, - Publication.class, - Qualifier.class, - Relation.class, - Result.class, - Software.class, - StructuredProperty.class - }); - + protected static SparkSession getSparkSession(SparkConf conf) { return SparkSession .builder() - .appName(SparkCreateSimRels.class.getSimpleName()) - .master(parser.get("master")) .config(conf) .getOrCreate(); } + protected static void save(Dataset dataset, String outPath, SaveMode mode) { + dataset + .write() + .option("compression", "gzip") + .mode(mode) + .json(outPath); + } + protected static void removeOutputDir(SparkSession spark, String path) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index df64d1011f..da16e6dffe 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -1,274 +1,95 @@ package eu.dnetlib.dhp.oa.dedup; +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.pace.config.DedupConfig; -import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.spark.api.java.JavaPairRDD; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.api.java.function.PairFunction; +import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; -import org.codehaus.jackson.map.ObjectMapper; + import scala.Tuple2; import java.util.Collection; +import java.util.Iterator; public class DedupRecordFactory { - public static JavaRDD createDedupRecord(final JavaSparkContext sc, final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, final OafEntityType entityType, final DedupConfig dedupConf) { + protected static final ObjectMapper OBJECT_MAPPER = new com.fasterxml.jackson.databind.ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + public static Dataset createDedupRecord( + final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, final Class clazz, final DedupConfig dedupConf) { + long ts = System.currentTimeMillis(); + // - final JavaPairRDD inputJsonEntities = sc.textFile(entitiesInputPath) - .mapToPair((PairFunction) it -> - new Tuple2(MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), it), it) - ); + Dataset> entities = spark.read() + .textFile(entitiesInputPath) + .map((MapFunction>) it -> { + T entity = OBJECT_MAPPER.readValue(it, clazz); + return new Tuple2<>(entity.getId(), entity); + }, Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); + //: source is the dedup_id, target is the id of the mergedIn - JavaPairRDD mergeRels = spark - .read().load(mergeRelsInputPath).as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .mapToPair( - (PairFunction) r -> - new Tuple2(r.getTarget(), r.getSource()) - ); + Dataset> mergeRels = spark + .read() + .load(mergeRelsInputPath) + .as(Encoders.bean(Relation.class)) + .where("relClass == 'merges'") + .map((MapFunction>) + r -> new Tuple2<>(r.getSource(), r.getTarget()), Encoders.tuple(Encoders.STRING(), Encoders.STRING())); // - final JavaPairRDD joinResult = mergeRels.join(inputJsonEntities).mapToPair((PairFunction>, String, String>) Tuple2::_2); - - JavaPairRDD> sortedJoinResult = joinResult.groupByKey(); - - switch (entityType) { - case publication: - return sortedJoinResult.map(p -> DedupRecordFactory.publicationMerger(p, ts)); - case dataset: - return sortedJoinResult.map(d -> DedupRecordFactory.datasetMerger(d, ts)); - case project: - return sortedJoinResult.map(p -> DedupRecordFactory.projectMerger(p, ts)); - case software: - return sortedJoinResult.map(s -> DedupRecordFactory.softwareMerger(s, ts)); - case datasource: - return sortedJoinResult.map(d -> DedupRecordFactory.datasourceMerger(d, ts)); - case organization: - return sortedJoinResult.map(o -> DedupRecordFactory.organizationMerger(o, ts)); - case otherresearchproduct: - return sortedJoinResult.map(o -> DedupRecordFactory.otherresearchproductMerger(o, ts)); - default: - return null; - } - + return mergeRels.joinWith(entities, mergeRels.col("_1").equalTo(entities.col("_1")), "left_outer") + .filter((FilterFunction, Tuple2>>) value -> value._2() != null) + .map((MapFunction, Tuple2>, T>) + value -> value._2()._2(), Encoders.kryo(clazz)) + .groupByKey((MapFunction) value -> value.getId(), Encoders.STRING()) + .mapGroups((MapGroupsFunction) + (key, values) -> entityMerger(key, values, ts, clazz), Encoders.bean(clazz)); } - private static Publication publicationMerger(Tuple2> e, final long ts) { + private static T entityMerger(String id, Iterator entities, final long ts, Class clazz) { + try { + T entity = clazz.newInstance(); + entity.setId(id); + if (entity.getDataInfo() == null) { + entity.setDataInfo(new DataInfo()); + } + entity.getDataInfo().setTrust("0.9"); + entity.setLastupdatetimestamp(ts); - Publication p = new Publication(); //the result of the merge, to be returned at the end + final Collection dates = Lists.newArrayList(); + entities.forEachRemaining(e -> { + entity.mergeFrom(e); + if (ModelSupport.isSubClass(e, Result.class)) { + Result r1 = (Result) e; + Result er = (Result) entity; + er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor())); - p.setId(e._1()); - - final ObjectMapper mapper = new ObjectMapper(); - - final Collection dateofacceptance = Lists.newArrayList(); - - if (e._2() != null) - e._2().forEach(pub -> { - try { - Publication publication = mapper.readValue(pub, Publication.class); - - p.mergeFrom(publication); - p.setAuthor(DedupUtility.mergeAuthor(p.getAuthor(), publication.getAuthor())); - //add to the list if they are not null - if (publication.getDateofacceptance() != null) - dateofacceptance.add(publication.getDateofacceptance().getValue()); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); - p.setDateofacceptance(DatePicker.pick(dateofacceptance)); - if (p.getDataInfo() == null) - p.setDataInfo(new DataInfo()); - p.getDataInfo().setTrust("0.9"); - p.setLastupdatetimestamp(ts); - return p; - } - - private static Dataset datasetMerger(Tuple2> e, final long ts) { - - Dataset d = new Dataset(); //the result of the merge, to be returned at the end - - d.setId(e._1()); - - final ObjectMapper mapper = new ObjectMapper(); - - final Collection dateofacceptance = Lists.newArrayList(); - - if (e._2() != null) - e._2().forEach(dat -> { - try { - Dataset dataset = mapper.readValue(dat, Dataset.class); - - d.mergeFrom(dataset); - d.setAuthor(DedupUtility.mergeAuthor(d.getAuthor(), dataset.getAuthor())); - //add to the list if they are not null - if (dataset.getDateofacceptance() != null) - dateofacceptance.add(dataset.getDateofacceptance().getValue()); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); - d.setDateofacceptance(DatePicker.pick(dateofacceptance)); - if (d.getDataInfo() == null) - d.setDataInfo(new DataInfo()); - d.getDataInfo().setTrust("0.9"); - d.setLastupdatetimestamp(ts); - return d; - } - - private static Project projectMerger(Tuple2> e, final long ts) { - - Project p = new Project(); //the result of the merge, to be returned at the end - - p.setId(e._1()); - - final ObjectMapper mapper = new ObjectMapper(); - if (e._2() != null) - e._2().forEach(proj -> { - try { - Project project = mapper.readValue(proj, Project.class); - - p.mergeFrom(project); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); - if (p.getDataInfo() == null) - p.setDataInfo(new DataInfo()); - p.getDataInfo().setTrust("0.9"); - p.setLastupdatetimestamp(ts); - return p; - } - - private static Software softwareMerger(Tuple2> e, final long ts) { - - Software s = new Software(); //the result of the merge, to be returned at the end - - s.setId(e._1()); - final ObjectMapper mapper = new ObjectMapper(); - final Collection dateofacceptance = Lists.newArrayList(); - if (e._2() != null) - e._2().forEach(soft -> { - try { - Software software = mapper.readValue(soft, Software.class); - - s.mergeFrom(software); - s.setAuthor(DedupUtility.mergeAuthor(s.getAuthor(), software.getAuthor())); - //add to the list if they are not null - if (software.getDateofacceptance() != null) - dateofacceptance.add(software.getDateofacceptance().getValue()); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); - s.setDateofacceptance(DatePicker.pick(dateofacceptance)); - if (s.getDataInfo() == null) - s.setDataInfo(new DataInfo()); - s.getDataInfo().setTrust("0.9"); - s.setLastupdatetimestamp(ts); - return s; - } - - private static Datasource datasourceMerger(Tuple2> e, final long ts) { - Datasource d = new Datasource(); //the result of the merge, to be returned at the end - d.setId(e._1()); - final ObjectMapper mapper = new ObjectMapper(); - if (e._2() != null) - e._2().forEach(dat -> { - try { - Datasource datasource = mapper.readValue(dat, Datasource.class); - - d.mergeFrom(datasource); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); - if (d.getDataInfo() == null) - d.setDataInfo(new DataInfo()); - d.getDataInfo().setTrust("0.9"); - d.setLastupdatetimestamp(ts); - return d; - } - - private static Organization organizationMerger(Tuple2> e, final long ts) { - - Organization o = new Organization(); //the result of the merge, to be returned at the end - - o.setId(e._1()); - - final ObjectMapper mapper = new ObjectMapper(); - - - StringBuilder trust = new StringBuilder("0.0"); - - if (e._2() != null) - e._2().forEach(pub -> { - try { - Organization organization = mapper.readValue(pub, Organization.class); - - final String currentTrust = organization.getDataInfo().getTrust(); - if (!"1.0".equals(currentTrust)) { - trust.setLength(0); - trust.append(currentTrust); + if (er.getDateofacceptance() != null) { + dates.add(r1.getDateofacceptance().getValue()); } - o.mergeFrom(organization); - - } catch (Exception exc) { - throw new RuntimeException(exc); } }); - if (o.getDataInfo() == null) - { - o.setDataInfo(new DataInfo()); + if (ModelSupport.isSubClass(entity, Result.class)) { + ((Result) entity).setDateofacceptance(DatePicker.pick(dates)); + } + return entity; + } catch (IllegalAccessException | InstantiationException e) { + throw new RuntimeException(e); } - if (o.getDataInfo() == null) - o.setDataInfo(new DataInfo()); - o.getDataInfo().setTrust("0.9"); - o.setLastupdatetimestamp(ts); - - return o; - } - - private static OtherResearchProduct otherresearchproductMerger(Tuple2> e, final long ts) { - - OtherResearchProduct o = new OtherResearchProduct(); //the result of the merge, to be returned at the end - - o.setId(e._1()); - - final ObjectMapper mapper = new ObjectMapper(); - - final Collection dateofacceptance = Lists.newArrayList(); - - if (e._2() != null) - e._2().forEach(orp -> { - try { - OtherResearchProduct otherResearchProduct = mapper.readValue(orp, OtherResearchProduct.class); - - o.mergeFrom(otherResearchProduct); - o.setAuthor(DedupUtility.mergeAuthor(o.getAuthor(), otherResearchProduct.getAuthor())); - //add to the list if they are not null - if (otherResearchProduct.getDateofacceptance() != null) - dateofacceptance.add(otherResearchProduct.getDateofacceptance().getValue()); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); - if (o.getDataInfo() == null) - o.setDataInfo(new DataInfo()); - o.setDateofacceptance(DatePicker.pick(dateofacceptance)); - o.getDataInfo().setTrust("0.9"); - o.setLastupdatetimestamp(ts); - return o; } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java index 1f9f84c552..28b85853f8 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java @@ -1,74 +1,50 @@ package eu.dnetlib.dhp.oa.dedup; +import eu.dnetlib.dhp.oa.dedup.model.Block; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.BlockProcessor; -import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.spark.api.java.JavaPairRDD; -import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.Function2; -import org.apache.spark.api.java.function.PairFlatMapFunction; -import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.util.LongAccumulator; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; import scala.Serializable; import scala.Tuple2; -import java.util.ArrayList; -import java.util.Comparator; -import java.util.List; import java.util.Map; import java.util.stream.Collectors; public class Deduper implements Serializable { - private static final Logger log = LoggerFactory.getLogger(Deduper.class); - - public static JavaPairRDD computeRelations(JavaSparkContext context, JavaPairRDD> blocks, DedupConfig config) { + public static JavaPairRDD computeRelations(JavaSparkContext context, JavaPairRDD blocks, DedupConfig config) { Map accumulators = DedupUtility.constructAccumulator(config, context.sc()); - return blocks.flatMapToPair((PairFlatMapFunction>, String, String>) it -> { - try { - final SparkReporter reporter = new SparkReporter(accumulators); - new BlockProcessor(config).processSortedBlock(it._1(), it._2(), reporter); - return reporter.getRelations().iterator(); - } catch (Exception e) { - throw new RuntimeException(it._2().get(0).getIdentifier(), e); - } - }).mapToPair( - (PairFunction, String, Tuple2>) item -> - new Tuple2>(item._1() + item._2(), item)) + return blocks + .flatMapToPair(it -> { + final SparkReporter reporter = new SparkReporter(accumulators); + new BlockProcessor(config).processSortedBlock(it._1(), it._2().getDocuments(), reporter); + return reporter.getRelations().iterator(); + }) + .mapToPair(it -> new Tuple2<>(it._1() + it._2(), it)) .reduceByKey((a, b) -> a) - .mapToPair((PairFunction>, String, String>) Tuple2::_2); + .mapToPair(Tuple2::_2); } - public static JavaPairRDD> createSortedBlocks(JavaSparkContext context, JavaPairRDD mapDocs, DedupConfig config) { + public static JavaPairRDD createSortedBlocks(JavaPairRDD mapDocs, DedupConfig config) { final String of = config.getWf().getOrderField(); final int maxQueueSize = config.getWf().getGroupMaxSize(); + return mapDocs //the reduce is just to be sure that we haven't document with same id .reduceByKey((a, b) -> a) .map(Tuple2::_2) //Clustering: from to List - .flatMapToPair((PairFlatMapFunction>) a -> - DedupUtility.getGroupingKeys(config, a) + .flatMap(a -> DedupUtility.getGroupingKeys(config, a) .stream() - .map(it -> { - List tmp = new ArrayList<>(); - tmp.add(a); - return new Tuple2<>(it, tmp); - } - ) + .map(it -> Block.from(it, a)) .collect(Collectors.toList()) .iterator()) - .reduceByKey((Function2, List, List>) (v1, v2) -> { - v1.addAll(v2); - v1.sort(Comparator.comparing(a -> a.getFieldMap().get(of).stringValue())); - if (v1.size() > maxQueueSize) - return new ArrayList<>(v1.subList(0, maxQueueSize)); - return v1; - }); + .mapToPair(block -> new Tuple2<>(block.getKey(), block)) + .reduceByKey((b1, b2) -> Block.from(b1, b2, of, maxQueueSize)); } + } \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/OafEntityType.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/OafEntityType.java deleted file mode 100644 index da2bc3a370..0000000000 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/OafEntityType.java +++ /dev/null @@ -1,15 +0,0 @@ -package eu.dnetlib.dhp.oa.dedup; - -public enum OafEntityType { - - datasource, - organization, - project, - dataset, - otherresearchproduct, - software, - publication - - - -} diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java index 02cf6587a1..c2b1fc9c24 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java @@ -1,14 +1,21 @@ package eu.dnetlib.dhp.oa.dedup; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; import org.slf4j.Logger; @@ -30,7 +37,12 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); parser.parseArgument(args); - new SparkCreateDedupRecord(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + + new SparkCreateDedupRecord(parser, getSparkSession(conf)) + .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } @Override @@ -46,8 +58,6 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { log.info("actionSetId: '{}'", actionSetId); log.info("workingPath: '{}'", workingPath); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { String subEntity = dedupConf.getWf().getSubEntityValue(); log.info("Creating deduprecords for: '{}'", subEntity); @@ -57,11 +67,14 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity); final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity); - final OafEntityType entityType = OafEntityType.valueOf(subEntity); - final JavaRDD dedupRecord = - DedupRecordFactory.createDedupRecord(sc, spark, mergeRelPath, entityPath, entityType, dedupConf); - dedupRecord.map(r -> OBJECT_MAPPER.writeValueAsString(r)).saveAsTextFile(outputPath); + Class clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); + + DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz, dedupConf) + .map((MapFunction) value -> OBJECT_MAPPER.writeValueAsString(value), Encoders.STRING()) + .write() + .mode(SaveMode.Overwrite) + .json(outputPath); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java index ef82b4eaf6..9c46404b7b 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java @@ -4,6 +4,7 @@ import com.google.common.hash.Hashing; import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -13,8 +14,8 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; -import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.graphx.Edge; @@ -52,7 +53,11 @@ public class SparkCreateMergeRels extends AbstractSparkAction { final String isLookUpUrl = parser.get("isLookUpUrl"); log.info("isLookupUrl {}", isLookUpUrl); - new SparkCreateMergeRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(isLookUpUrl)); + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + + new SparkCreateMergeRels(parser, getSparkSession(conf)).run(ISLookupClientFactory.getLookUpService(isLookUpUrl)); } @Override @@ -79,32 +84,30 @@ public class SparkCreateMergeRels extends AbstractSparkAction { log.info("Max iterations {}", maxIterations); final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity); + final JavaPairRDD vertexes = sc.textFile(graphBasePath + "/" + subEntity) .map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s)) - .mapToPair((PairFunction) - s -> new Tuple2<>(getHashcode(s), s)); + .mapToPair((PairFunction) s -> new Tuple2<>(hash(s), s)); - final Dataset similarityRelations = spark + final RDD> edgeRdd = spark .read() .load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)) - .as(Encoders.bean(Relation.class)); - - final RDD> edgeRdd = similarityRelations + .as(Encoders.bean(Relation.class)) .javaRDD() - .map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())) + .map(it -> new Edge<>(hash(it.getSource()), hash(it.getTarget()), it.getRelClass())) .rdd(); - final RDD connectedComponents = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, maxIterations) + final Dataset mergeRels = spark + .createDataset(GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, maxIterations) .toJavaRDD() .filter(k -> k.getDocIds().size() > 1) .flatMap(cc -> ccToMergeRel(cc, dedupConf)) - .rdd(); + .rdd(), Encoders.bean(Relation.class)); - spark - .createDataset(connectedComponents, Encoders.bean(Relation.class)) + mergeRels .write() .mode(SaveMode.Append) - .save(mergeRelPath); + .parquet(mergeRelPath); } } @@ -148,7 +151,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction { return r; } - public static long getHashcode(final String id) { + public static long hash(final String id) { return Hashing.murmur3_128().hashString(id).asLong(); } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java index de842d822b..d02aef64cb 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java @@ -1,23 +1,26 @@ package eu.dnetlib.dhp.oa.dedup; -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.oa.dedup.model.Block; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; +import eu.dnetlib.pace.model.FieldListImpl; +import eu.dnetlib.pace.model.FieldValueImpl; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; -import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.PairFunction; +import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; @@ -27,7 +30,6 @@ import org.slf4j.LoggerFactory; import scala.Tuple2; import java.io.IOException; -import java.util.List; public class SparkCreateSimRels extends AbstractSparkAction { @@ -43,7 +45,17 @@ public class SparkCreateSimRels extends AbstractSparkAction { SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); parser.parseArgument(args); - new SparkCreateSimRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(new Class[] { + MapDocument.class, + FieldListImpl.class, + FieldValueImpl.class, + Block.class + }); + + new SparkCreateSimRels(parser, getSparkSession(conf)) + .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } @Override @@ -60,8 +72,6 @@ public class SparkCreateSimRels extends AbstractSparkAction { log.info("actionSetId: '{}'", actionSetId); log.info("workingPath: '{}'", workingPath); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - //for each dedup configuration for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { @@ -72,29 +82,30 @@ public class SparkCreateSimRels extends AbstractSparkAction { final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity); removeOutputDir(spark, outputPath); - JavaPairRDD mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) - .mapToPair((PairFunction) s -> { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaPairRDD mapDocuments = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) + .mapToPair((PairFunction) s -> { MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); return new Tuple2<>(d.getIdentifier(), d); }); //create blocks for deduplication - JavaPairRDD> blocks = Deduper.createSortedBlocks(sc, mapDocument, dedupConf); + JavaPairRDD blocks = Deduper.createSortedBlocks(mapDocuments, dedupConf); //create relations by comparing only elements in the same group - final JavaPairRDD dedupRels = Deduper.computeRelations(sc, blocks, dedupConf); - - JavaRDD relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity)); + JavaRDD relations = Deduper.computeRelations(sc, blocks, dedupConf) + .map(t -> createSimRel(t._1(), t._2(), entity)); //save the simrel in the workingdir - spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class)) + spark.createDataset(relations.rdd(), Encoders.bean(Relation.class)) .write() .mode(SaveMode.Append) .save(outputPath); } } - public Relation createSimRel(String source, String target, String entity) { + private Relation createSimRel(String source, String target, String entity) { final Relation r = new Relation(); r.setSource(source); r.setTarget(target); @@ -102,7 +113,7 @@ public class SparkCreateSimRels extends AbstractSparkAction { r.setRelClass("isSimilarTo"); r.setDataInfo(new DataInfo()); - switch(entity){ + switch(entity) { case "result": r.setRelType("resultResult"); break; diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index 371d70ba2d..86d19d96d4 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.dedup; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; @@ -10,11 +11,9 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.IOUtils; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; +import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import scala.Tuple2; @@ -43,7 +42,11 @@ public class SparkPropagateRelation extends AbstractSparkAction { parser.parseArgument(args); - new SparkPropagateRelation(parser, getSparkSession(parser)) + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + + new SparkPropagateRelation(parser, getSparkSession(conf)) .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } @@ -90,7 +93,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { processDataset(rels, mergedIds, FieldType.SOURCE, getDeletedFn()), mergedIds, FieldType.TARGET, getDeletedFn()); - save(newRels.union(updated), outputRelationPath); + save(newRels.union(updated), outputRelationPath, SaveMode.Overwrite); } @@ -164,26 +167,6 @@ public class SparkPropagateRelation extends AbstractSparkAction { }; } - private void deletePath(String path) { - try { - Path p = new Path(path); - FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration()); - - if (fs.exists(p)) { - fs.delete(p, true); - } - } catch (IOException e) { - throw new RuntimeException(e); - } - } - - private static void save(Dataset dataset, String outPath) { - dataset - .write() - .option("compression", "gzip") - .json(outPath); - } - private static boolean containsDedup(final Relation r) { return r.getSource().toLowerCase().contains("dedup") || r.getTarget().toLowerCase().contains("dedup"); } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkReporter.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkReporter.java index cc03db3856..98ee37e14f 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkReporter.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkReporter.java @@ -13,9 +13,9 @@ import java.util.Map; public class SparkReporter implements Serializable, Reporter { - final List> relations = new ArrayList<>(); - private static final Log log = LogFactory.getLog(SparkReporter.class); - Map accumulators; + private final List> relations = new ArrayList<>(); + + private Map accumulators; public SparkReporter(Map accumulators){ this.accumulators = accumulators; diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java index 5347489e70..ea0a06bbe9 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java @@ -1,13 +1,17 @@ package eu.dnetlib.dhp.oa.dedup; -import com.fasterxml.jackson.databind.DeserializationFeature; -import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.oa.dedup.model.Block; import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import eu.dnetlib.pace.model.FieldListImpl; +import eu.dnetlib.pace.model.FieldValueImpl; +import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; @@ -15,6 +19,7 @@ import org.apache.hadoop.fs.FileStatus; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.compress.GzipCodec; +import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -28,7 +33,6 @@ import org.slf4j.LoggerFactory; import scala.Tuple2; import java.io.IOException; -import java.util.Map; public class SparkUpdateEntity extends AbstractSparkAction { @@ -43,10 +47,16 @@ public class SparkUpdateEntity extends AbstractSparkAction { public static void main(String[] args) throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils.toString( - SparkUpdateEntity.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); + SparkUpdateEntity.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); parser.parseArgument(args); - new SparkUpdateEntity(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + + new SparkUpdateEntity(parser, getSparkSession(conf)) + .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } public void run(ISLookUpService isLookUpService) throws IOException { diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Block.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Block.java new file mode 100644 index 0000000000..e1ccf143c9 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Block.java @@ -0,0 +1,76 @@ +package eu.dnetlib.dhp.oa.dedup.model; + +import com.google.common.collect.Lists; +import eu.dnetlib.pace.model.MapDocument; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.Comparator; +import java.util.Iterator; +import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.Stream; +import java.util.stream.StreamSupport; + +public class Block implements Serializable { + + private String key; + + private List documents; + + public Block() { + super(); + } + + public static Block from(String key, MapDocument doc) { + Block block = new Block(); + block.setKey(key); + block.setDocuments(Lists.newArrayList(doc)); + return block; + } + + public static Block from(String key, Iterator blocks, String orderField, int maxSize) { + Block block = new Block(); + block.setKey(key); + + Iterable it = () -> blocks; + + block.setDocuments( + StreamSupport.stream(it.spliterator(), false) + .flatMap(b -> b.getDocuments().stream()) + .sorted(Comparator.comparing(a -> a.getFieldMap().get(orderField).stringValue())) + .limit(maxSize) + .collect(Collectors.toCollection(ArrayList::new))); + return block; + } + + public static Block from(Block b1, Block b2, String orderField, int maxSize) { + Block block = new Block(); + block.setKey(b1.getKey()); + block.setDocuments( + Stream.concat( + b1.getDocuments().stream(), + b2.getDocuments().stream()) + .sorted(Comparator.comparing(a -> a.getFieldMap().get(orderField).stringValue())) + .limit(maxSize) + .collect(Collectors.toCollection(ArrayList::new))); + + return block; + } + + public String getKey() { + return key; + } + + public void setKey(String key) { + this.key = key; + } + + public List getDocuments() { + return documents; + } + + public void setDocuments(List documents) { + this.documents = documents; + } +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml index df6877dfac..9262870324 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml @@ -91,7 +91,6 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=7680 - -mtyarn --i${graphBasePath} --o${dedupGraphPath} --w${workingPath} diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json index 42ef2b78e3..6eedd54321 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json @@ -1,10 +1,4 @@ [ - { - "paramName": "mt", - "paramLongName": "master", - "paramDescription": "should be local or yarn", - "paramRequired": true - }, { "paramName": "asi", "paramLongName": "actionSetId", diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json index f7bf5e518a..3d48cb2d8d 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json @@ -1,10 +1,4 @@ [ - { - "paramName": "mt", - "paramLongName": "master", - "paramDescription": "should be local or yarn", - "paramRequired": true - }, { "paramName": "i", "paramLongName": "graphBasePath", diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json index 8cffa86dc8..ce38dc6f00 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json @@ -1,10 +1,4 @@ [ - { - "paramName": "mt", - "paramLongName": "master", - "paramDescription": "should be local or yarn", - "paramRequired": true - }, { "paramName": "la", "paramLongName": "isLookUpUrl", diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json index 721a783e12..6a2a48746b 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json @@ -1,10 +1,4 @@ [ - { - "paramName": "mt", - "paramLongName": "master", - "paramDescription": "should be local or yarn", - "paramRequired": true - }, { "paramName": "i", "paramLongName": "graphBasePath", diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml index 6790dde32a..2451947a18 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml @@ -98,7 +98,6 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - -mtyarn --i${graphBasePath} --la${isLookUpUrl} --asi${actionSetId} @@ -125,7 +124,6 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - -mtyarn --i${graphBasePath} --w${workingPath} --la${isLookUpUrl} @@ -152,7 +150,6 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - -mtyarn --i${graphBasePath} --w${workingPath} --la${isLookUpUrl} @@ -179,7 +176,6 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - -mtyarn --i${graphBasePath} --w${workingPath} --o${dedupGraphPath} diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json index 06b67f7322..c91f3c04bc 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json @@ -1,10 +1,4 @@ [ -{ - "paramName": "mt", - "paramLongName": "master", - "paramDescription": "should be local or yarn", - "paramRequired": true -}, { "paramName": "i", "paramLongName": "graphBasePath", From ad7a131b182e47936a6cf8432b7576a4774cbef5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Sat, 18 Apr 2020 12:42:58 +0200 Subject: [PATCH 19/19] introduced common project code formatting plugin, works on the commit hook, based on https://github.com/Cosium/git-code-format-maven-plugin, applied to each java class in the project --- .../GenerateOoziePropertiesMojo.java | 86 +- .../WritePredefinedProjectProperties.java | 198 ++-- .../GenerateOoziePropertiesMojoTest.java | 48 +- .../WritePredefinedProjectPropertiesTest.java | 165 +-- .../collector/worker/model/ApiDescriptor.java | 58 +- .../mdstore/manager/common/model/MDStore.java | 162 ++- .../common/model/MDStoreCurrentVersion.java | 59 +- .../manager/common/model/MDStoreVersion.java | 128 +- .../manager/common/model/MDStoreWithInfo.java | 188 ++- .../ArgumentApplicationParser.java | 51 +- .../dhp/application/OptionsParameter.java | 4 +- .../common/FunctionalInterfaceSupport.java | 17 +- .../eu/dnetlib/dhp/common/HdfsSupport.java | 61 +- .../dhp/common/SparkSessionSupport.java | 88 +- .../dnetlib/dhp/common/ThrowingSupport.java | 24 +- .../dhp/model/mdstore/MetadataRecord.java | 49 +- .../dnetlib/dhp/model/mdstore/Provenance.java | 13 +- .../dhp/parser/utility/VtdException.java | 2 +- .../dhp/parser/utility/VtdUtilityParser.java | 47 +- .../java/eu/dnetlib/dhp/utils/DHPUtils.java | 30 +- .../saxon/AbstractExtensionFunction.java | 10 +- .../dnetlib/dhp/utils/saxon/ExtractYear.java | 16 +- .../dhp/utils/saxon/NormalizeDate.java | 17 +- .../eu/dnetlib/dhp/utils/saxon/PickFirst.java | 6 +- .../utils/saxon/SaxonTransformerFactory.java | 9 +- .../main/java/eu/dnetlib/message/Message.java | 11 +- .../eu/dnetlib/message/MessageConsumer.java | 13 +- .../eu/dnetlib/message/MessageManager.java | 69 +- .../java/eu/dnetlib/message/MessageType.java | 2 - .../scholexplorer/relation/RelInfo.java | 2 +- .../relation/RelationMapper.java | 9 +- .../ArgumentApplicationParserTest.java | 54 +- .../dnetlib/dhp/common/HdfsSupportTest.java | 27 +- .../dhp/common/SparkSessionSupportTest.java | 15 +- .../dhp/model/mdstore/MetadataRecordTest.java | 6 +- .../java/eu/dnetlib/message/MessageTest.java | 25 +- .../relation/RelationMapperTest.java | 4 +- .../dhp/schema/action/AtomicAction.java | 4 +- .../action/AtomicActionDeserializer.java | 4 +- .../dnetlib/dhp/schema/common/EntityType.java | 15 +- .../dhp/schema/common/MainEntityType.java | 12 +- .../dhp/schema/common/ModelSupport.java | 120 +- .../eu/dnetlib/dhp/schema/oaf/Author.java | 12 +- .../eu/dnetlib/dhp/schema/oaf/Context.java | 11 +- .../eu/dnetlib/dhp/schema/oaf/DataInfo.java | 22 +- .../eu/dnetlib/dhp/schema/oaf/Dataset.java | 49 +- .../eu/dnetlib/dhp/schema/oaf/Datasource.java | 259 ++-- .../dhp/schema/oaf/ExternalReference.java | 19 +- .../eu/dnetlib/dhp/schema/oaf/ExtraInfo.java | 10 +- .../java/eu/dnetlib/dhp/schema/oaf/Field.java | 9 +- .../dnetlib/dhp/schema/oaf/GeoLocation.java | 27 +- .../eu/dnetlib/dhp/schema/oaf/Instance.java | 41 +- .../eu/dnetlib/dhp/schema/oaf/Journal.java | 38 +- .../eu/dnetlib/dhp/schema/oaf/KeyValue.java | 19 +- .../dnetlib/dhp/schema/oaf/OAIProvenance.java | 2 +- .../java/eu/dnetlib/dhp/schema/oaf/Oaf.java | 18 +- .../eu/dnetlib/dhp/schema/oaf/OafEntity.java | 38 +- .../dnetlib/dhp/schema/oaf/Organization.java | 128 +- .../dhp/schema/oaf/OriginDescription.java | 15 +- .../dhp/schema/oaf/OtherResearchProduct.java | 10 +- .../eu/dnetlib/dhp/schema/oaf/Project.java | 188 ++- .../dnetlib/dhp/schema/oaf/Publication.java | 5 +- .../eu/dnetlib/dhp/schema/oaf/Qualifier.java | 37 +- .../eu/dnetlib/dhp/schema/oaf/Relation.java | 150 +-- .../eu/dnetlib/dhp/schema/oaf/Result.java | 98 +- .../eu/dnetlib/dhp/schema/oaf/Software.java | 27 +- .../dhp/schema/oaf/StructuredProperty.java | 18 +- .../dhp/schema/scholexplorer/DLIDataset.java | 53 +- .../schema/scholexplorer/DLIPublication.java | 52 +- .../dhp/schema/scholexplorer/DLIUnknown.java | 55 +- .../schema/scholexplorer/ProvenaceInfo.java | 2 +- .../dhp/schema/action/AtomicActionTest.java | 20 +- .../dhp/schema/common/ModelSupportTest.java | 8 +- .../eu/dnetlib/dhp/schema/oaf/MergeTest.java | 11 +- .../dhp/schema/scholexplorer/DLItest.java | 39 +- .../dnetlib/dhp/actionmanager/ISClient.java | 189 +-- .../PartitionActionSetsByPayloadTypeJob.java | 116 +- .../actionmanager/promote/MergeAndGet.java | 56 +- .../PromoteActionPayloadForGraphTableJob.java | 225 ++-- .../PromoteActionPayloadFunctions.java | 166 +-- ...rtitionActionSetsByPayloadTypeJobTest.java | 204 ++-- .../promote/MergeAndGetTest.java | 102 +- ...moteActionPayloadForGraphTableJobTest.java | 276 +++-- .../PromoteActionPayloadFunctionsTest.java | 325 ++--- .../GenerateNativeStoreSparkJob.java | 124 +- .../collection/plugin/CollectorPlugin.java | 3 +- .../plugin/oai/OaiCollectorPlugin.java | 104 +- .../collection/plugin/oai/OaiIterator.java | 268 +++-- .../plugin/oai/OaiIteratorFactory.java | 28 +- .../worker/DnetCollectorException.java | 41 +- .../worker/DnetCollectorWorker.java | 115 +- .../DnetCollectorWorkerApplication.java | 37 +- .../utils/CollectorPluginErrorLogList.java | 21 +- .../worker/utils/CollectorPluginFactory.java | 13 +- .../worker/utils/HttpConnector.java | 385 +++--- .../collection/worker/utils/XmlCleaner.java | 606 ++++++---- .../migration/actions/LicenseComparator.java | 2 - .../migration/actions/MigrateActionSet.java | 115 +- .../dhp/migration/actions/ProtoConverter.java | 316 ++--- .../migration/actions/TransformActions.java | 85 +- .../dhp/transformation/TransformFunction.java | 44 +- .../transformation/TransformSparkJobNode.java | 89 +- .../dhp/transformation/functions/Cleaner.java | 29 +- .../dhp/transformation/vocabulary/Term.java | 1 - .../transformation/vocabulary/Vocabulary.java | 4 - .../vocabulary/VocabularyHelper.java | 10 +- .../dhp/collection/CollectionJobTest.java | 163 +-- .../DnetCollectorWorkerApplicationTests.java | 43 +- .../transformation/TransformationJobTest.java | 102 +- .../vocabulary/VocabularyTest.java | 10 +- .../dhp/oa/dedup/AbstractSparkAction.java | 51 +- .../eu/dnetlib/dhp/oa/dedup/DatePicker.java | 84 +- .../dhp/oa/dedup/DedupRecordFactory.java | 105 +- .../eu/dnetlib/dhp/oa/dedup/DedupUtility.java | 150 ++- .../java/eu/dnetlib/dhp/oa/dedup/Deduper.java | 45 +- .../dhp/oa/dedup/SparkCreateDedupRecord.java | 38 +- .../dhp/oa/dedup/SparkCreateMergeRels.java | 109 +- .../dhp/oa/dedup/SparkCreateSimRels.java | 65 +- .../dhp/oa/dedup/SparkPropagateRelation.java | 103 +- .../dnetlib/dhp/oa/dedup/SparkReporter.java | 20 +- .../dhp/oa/dedup/SparkUpdateEntity.java | 103 +- .../oa/dedup/graph/ConnectedComponent.java | 36 +- .../eu/dnetlib/dhp/oa/dedup/model/Block.java | 25 +- .../dnetlib/dhp/oa/dedup/MergeAuthorTest.java | 48 +- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 266 +++-- .../dhp/oa/dedup/jpath/JsonPathTest.java | 546 ++++----- .../java/eu/dnetlib/dedup/DatePicker.java | 84 +- .../eu/dnetlib/dedup/DedupRecordFactory.java | 296 +++-- .../java/eu/dnetlib/dedup/DedupUtility.java | 127 +- .../main/java/eu/dnetlib/dedup/Deduper.java | 205 ++-- .../java/eu/dnetlib/dedup/OafEntityType.java | 4 - .../dedup/SparkCreateConnectedComponent.java | 114 +- .../dnetlib/dedup/SparkCreateDedupRecord.java | 36 +- .../eu/dnetlib/dedup/SparkCreateSimRels.java | 82 +- .../java/eu/dnetlib/dedup/SparkReporter.java | 18 +- .../dedup/graph/ConnectedComponent.java | 36 +- .../dedup/sx/SparkPropagateRelationsJob.java | 83 +- .../dedup/sx/SparkUpdateEntityJob.java | 94 +- .../dhp/oa/graph/GraphHiveImporterJob.java | 45 +- .../raw/AbstractMdRecordToOafMapper.java | 783 ++++++------ .../raw/DispatchEntitiesApplication.java | 128 +- .../raw/GenerateEntitiesApplication.java | 258 ++-- .../oa/graph/raw/MergeClaimsApplication.java | 277 +++-- .../raw/MigrateDbEntitiesApplication.java | 946 ++++++++------- .../raw/MigrateMongoMdstoresApplication.java | 96 +- .../dhp/oa/graph/raw/OafToOafMapper.java | 406 ++++--- .../dhp/oa/graph/raw/OdfToOafMapper.java | 510 ++++---- .../common/AbstractMigrationApplication.java | 108 +- .../dhp/oa/graph/raw/common/DbClient.java | 86 +- .../oa/graph/raw/common/MdstoreClient.java | 139 ++- .../oa/graph/raw/common/OafMapperUtils.java | 334 +++--- .../dhp/oa/graph/raw/common/PacePerson.java | 270 ++--- .../dhp/sx/graph/ImportDataFromMongo.java | 148 +-- .../dhp/sx/graph/SparkExtractEntitiesJob.java | 99 +- .../sx/graph/SparkSXGeneratePidSimlarity.java | 96 +- .../SparkScholexplorerCreateRawGraphJob.java | 333 ++++-- .../SparkScholexplorerGraphImporter.java | 70 +- .../parser/AbstractScholexplorerParser.java | 189 +-- .../parser/DatasetScholexplorerParser.java | 277 +++-- .../PublicationScholexplorerParser.java | 208 ++-- .../oa/graph/GraphHiveImporterJobTest.java | 57 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 150 ++- .../raw/MigrateDbEntitiesApplicationTest.java | 482 ++++---- .../dhp/sx/graph/ScholexplorerParserTest.java | 23 +- .../SparkScholexplorerGraphImporterTest.java | 10 +- ...parkScholexplorerMergeEntitiesJobTest.java | 7 +- .../dnetlib/dhp/provision/ProvisionUtil.java | 37 +- .../dhp/provision/RelatedItemInfo.java | 11 +- .../provision/SparkExtractRelationCount.java | 53 +- .../dhp/provision/SparkGenerateScholix.java | 109 +- .../dhp/provision/SparkGenerateSummary.java | 137 ++- .../provision/SparkIndexCollectionOnES.java | 52 +- .../dhp/provision/scholix/Scholix.java | 92 +- .../scholix/ScholixCollectedFrom.java | 6 +- .../provision/scholix/ScholixEntityId.java | 3 +- .../provision/scholix/ScholixIdentifier.java | 3 +- .../scholix/ScholixRelationship.java | 3 +- .../provision/scholix/ScholixResource.java | 48 +- .../scholix/summary/CollectedFromType.java | 4 +- .../scholix/summary/SchemeValue.java | 4 +- .../scholix/summary/ScholixSummary.java | 162 ++- .../scholix/summary/TypedIdentifier.java | 5 +- .../provision/update/CrossRefParserJSON.java | 66 +- .../dhp/provision/update/CrossrefClient.java | 27 +- .../provision/update/Datacite2Scholix.java | 118 +- .../dhp/provision/update/DataciteClient.java | 20 +- .../update/DataciteClientIterator.java | 75 +- .../update/RetrieveUpdateFromDatacite.java | 32 +- .../update/SparkResolveScholixTarget.java | 225 ++-- .../dhp/provision/DataciteClientTest.java | 30 +- .../dhp/provision/ExtractInfoTest.java | 4 +- .../oa/provision/AdjacencyListBuilderJob.java | 110 +- .../CreateRelatedEntitiesJob_phase1.java | 152 ++- .../CreateRelatedEntitiesJob_phase2.java | 200 ++-- .../dhp/oa/provision/PrepareRelationsJob.java | 132 ++- .../dhp/oa/provision/XmlConverterJob.java | 219 ++-- .../dhp/oa/provision/XmlIndexingJob.java | 141 ++- .../oa/provision/model/EntityRelEntity.java | 10 +- .../dhp/oa/provision/model/JoinedEntity.java | 3 +- .../dhp/oa/provision/model/RelatedEntity.java | 76 +- .../oa/provision/model/SortableRelation.java | 3 +- .../dhp/oa/provision/model/Tuple2.java | 5 +- .../dhp/oa/provision/model/TypedRow.java | 1 - .../dhp/oa/provision/utils/ContextDef.java | 2 +- .../dhp/oa/provision/utils/ContextMapper.java | 14 +- .../oa/provision/utils/GraphMappingUtils.java | 16 +- .../oa/provision/utils/LicenseComparator.java | 2 - .../provision/utils/RelationPartitioner.java | 9 +- .../utils/StreamingInputDocumentFactory.java | 72 +- .../oa/provision/utils/TemplateFactory.java | 110 +- .../oa/provision/utils/TemplateResources.java | 6 +- .../oa/provision/utils/XmlRecordFactory.java | 1046 +++++++++++------ .../utils/XmlSerializationUtils.java | 101 +- .../dhp/oa/provision/GraphJoinerTest.java | 33 +- pom.xml | 31 + 215 files changed, 11956 insertions(+), 9207 deletions(-) diff --git a/dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojo.java b/dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojo.java index 5f94e7869d..08aa42f5b6 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojo.java +++ b/dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojo.java @@ -3,7 +3,6 @@ package eu.dnetlib.maven.plugin.properties; import java.io.File; import java.util.ArrayList; import java.util.List; - import org.apache.commons.lang.ArrayUtils; import org.apache.commons.lang.StringUtils; import org.apache.maven.plugin.AbstractMojo; @@ -12,60 +11,63 @@ import org.apache.maven.plugin.MojoFailureException; /** * Generates oozie properties which were not provided from commandline. - * @author mhorst * + * @author mhorst * @goal generate-properties */ public class GenerateOoziePropertiesMojo extends AbstractMojo { - public static final String PROPERTY_NAME_WF_SOURCE_DIR = "workflow.source.dir"; - public static final String PROPERTY_NAME_SANDBOX_NAME = "sandboxName"; - - private final String[] limiters = {"dhp", "dnetlib", "eu"}; - + public static final String PROPERTY_NAME_WF_SOURCE_DIR = "workflow.source.dir"; + public static final String PROPERTY_NAME_SANDBOX_NAME = "sandboxName"; + + private final String[] limiters = {"dhp", "dnetlib", "eu"}; + @Override public void execute() throws MojoExecutionException, MojoFailureException { - if (System.getProperties().containsKey(PROPERTY_NAME_WF_SOURCE_DIR) && - !System.getProperties().containsKey(PROPERTY_NAME_SANDBOX_NAME)) { - String generatedSandboxName = generateSandboxName(System.getProperties().getProperty( - PROPERTY_NAME_WF_SOURCE_DIR)); - if (generatedSandboxName!=null) { - System.getProperties().setProperty(PROPERTY_NAME_SANDBOX_NAME, - generatedSandboxName); - } else { - System.out.println("unable to generate sandbox name from path: " + - System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR)); - } - } + if (System.getProperties().containsKey(PROPERTY_NAME_WF_SOURCE_DIR) + && !System.getProperties().containsKey(PROPERTY_NAME_SANDBOX_NAME)) { + String generatedSandboxName = + generateSandboxName( + System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR)); + if (generatedSandboxName != null) { + System.getProperties() + .setProperty(PROPERTY_NAME_SANDBOX_NAME, generatedSandboxName); + } else { + System.out.println( + "unable to generate sandbox name from path: " + + System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR)); + } + } } - + /** * Generates sandbox name from workflow source directory. + * * @param wfSourceDir * @return generated sandbox name */ private String generateSandboxName(String wfSourceDir) { -// utilize all dir names until finding one of the limiters - List sandboxNameParts = new ArrayList(); - String[] tokens = StringUtils.split(wfSourceDir, File.separatorChar); - ArrayUtils.reverse(tokens); - if (tokens.length>0) { - for (String token : tokens) { - for (String limiter : limiters) { - if (limiter.equals(token)) { - return sandboxNameParts.size()>0? - StringUtils.join(sandboxNameParts.toArray()):null; - } - } - if (sandboxNameParts.size()>0) { - sandboxNameParts.add(0, File.separator); - } - sandboxNameParts.add(0, token); - } - return StringUtils.join(sandboxNameParts.toArray()); - } else { - return null; - } + // utilize all dir names until finding one of the limiters + List sandboxNameParts = new ArrayList(); + String[] tokens = StringUtils.split(wfSourceDir, File.separatorChar); + ArrayUtils.reverse(tokens); + if (tokens.length > 0) { + for (String token : tokens) { + for (String limiter : limiters) { + if (limiter.equals(token)) { + return sandboxNameParts.size() > 0 + ? StringUtils.join(sandboxNameParts.toArray()) + : null; + } + } + if (sandboxNameParts.size() > 0) { + sandboxNameParts.add(0, File.separator); + } + sandboxNameParts.add(0, token); + } + return StringUtils.join(sandboxNameParts.toArray()); + } else { + return null; + } } - } diff --git a/dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectProperties.java b/dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectProperties.java index 62f04761a9..acfd9a7f84 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectProperties.java +++ b/dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectProperties.java @@ -1,19 +1,17 @@ /** - * - * Licensed under the Educational Community License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at + * Licensed under the Educational Community License, Version 2.0 (the "License"); you may not use + * this file except in compliance with the License. You may obtain a copy of the License at * - * http://www.opensource.org/licenses/ecl2.php + *

http://www.opensource.org/licenses/ecl2.php * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and + *

Unless required by applicable law or agreed to in writing, software distributed under the + * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either + * express or implied. See the License for the specific language governing permissions and * limitations under the License. */ package eu.dnetlib.maven.plugin.properties; +import edu.umd.cs.findbugs.annotations.SuppressFBWarnings; import java.io.File; import java.io.FileInputStream; import java.io.IOException; @@ -26,7 +24,6 @@ import java.util.List; import java.util.Map.Entry; import java.util.Properties; import java.util.Set; - import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.commons.lang.StringUtils; @@ -38,29 +35,24 @@ import org.springframework.core.io.DefaultResourceLoader; import org.springframework.core.io.Resource; import org.springframework.core.io.ResourceLoader; -import edu.umd.cs.findbugs.annotations.SuppressFBWarnings; - /** - * Writes project properties for the keys listed in specified properties files. - * Based on: + * Writes project properties for the keys listed in specified properties files. Based on: * http://site.kuali.org/maven/plugins/properties-maven-plugin/1.3.2/write-project-properties-mojo.html - + * * @author mhorst * @goal write-project-properties */ public class WritePredefinedProjectProperties extends AbstractMojo { - - private static final String CR = "\r"; - private static final String LF = "\n"; - private static final String TAB = "\t"; + + private static final String CR = "\r"; + private static final String LF = "\n"; + private static final String TAB = "\t"; protected static final String PROPERTY_PREFIX_ENV = "env."; private static final String ENCODING_UTF8 = "utf8"; - - /** - * @parameter property="properties.includePropertyKeysFromFiles" - */ - private String[] includePropertyKeysFromFiles; - + + /** @parameter property="properties.includePropertyKeysFromFiles" */ + private String[] includePropertyKeysFromFiles; + /** * @parameter default-value="${project}" * @required @@ -70,55 +62,57 @@ public class WritePredefinedProjectProperties extends AbstractMojo { /** * The file that properties will be written to - * + * * @parameter property="properties.outputFile" - * default-value="${project.build.directory}/properties/project.properties"; + * default-value="${project.build.directory}/properties/project.properties"; * @required */ protected File outputFile; - - /** - * If true, the plugin will silently ignore any non-existent properties files, and the build will continue + + /** + * If true, the plugin will silently ignore any non-existent properties files, and the build + * will continue * * @parameter property="properties.quiet" default-value="true" */ private boolean quiet; - + /** - * Comma separated list of characters to escape when writing property values. cr=carriage return, lf=linefeed, - * tab=tab. Any other values are taken literally. - * + * Comma separated list of characters to escape when writing property values. cr=carriage + * return, lf=linefeed, tab=tab. Any other values are taken literally. + * * @parameter default-value="cr,lf,tab" property="properties.escapeChars" */ private String escapeChars; /** - * If true, the plugin will include system properties when writing the properties file. System properties override - * both environment variables and project properties. - * + * If true, the plugin will include system properties when writing the properties file. System + * properties override both environment variables and project properties. + * * @parameter default-value="false" property="properties.includeSystemProperties" */ private boolean includeSystemProperties; /** - * If true, the plugin will include environment variables when writing the properties file. Environment variables - * are prefixed with "env". Environment variables override project properties. - * + * If true, the plugin will include environment variables when writing the properties file. + * Environment variables are prefixed with "env". Environment variables override project + * properties. + * * @parameter default-value="false" property="properties.includeEnvironmentVariables" */ private boolean includeEnvironmentVariables; /** * Comma separated set of properties to exclude when writing the properties file - * + * * @parameter property="properties.exclude" */ private String exclude; /** - * Comma separated set of properties to write to the properties file. If provided, only the properties matching - * those supplied here will be written to the properties file. - * + * Comma separated set of properties to write to the properties file. If provided, only the + * properties matching those supplied here will be written to the properties file. + * * @parameter property="properties.include" */ private String include; @@ -127,7 +121,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo { * @see org.apache.maven.plugin.AbstractMojo#execute() */ @Override - @SuppressFBWarnings({"NP_UNWRITTEN_FIELD","UWF_UNWRITTEN_FIELD"}) + @SuppressFBWarnings({"NP_UNWRITTEN_FIELD", "UWF_UNWRITTEN_FIELD"}) public void execute() throws MojoExecutionException, MojoFailureException { Properties properties = new Properties(); // Add project properties @@ -149,10 +143,11 @@ public class WritePredefinedProjectProperties extends AbstractMojo { getLog().info("Creating " + outputFile); writeProperties(outputFile, comment, properties, escapeTokens); - } + } /** * Provides environment variables. + * * @return environment variables */ protected static Properties getEnvironmentVariables() { @@ -165,42 +160,45 @@ public class WritePredefinedProjectProperties extends AbstractMojo { /** * Removes properties which should not be written. + * * @param properties * @param omitCSV * @param includeCSV * @throws MojoExecutionException */ - protected void trim(Properties properties, String omitCSV, String includeCSV) throws MojoExecutionException { + protected void trim(Properties properties, String omitCSV, String includeCSV) + throws MojoExecutionException { List omitKeys = getListFromCSV(omitCSV); for (String key : omitKeys) { properties.remove(key); } - + List includeKeys = getListFromCSV(includeCSV); -// mh: including keys from predefined properties - if (includePropertyKeysFromFiles!=null && includePropertyKeysFromFiles.length>0) { - for (String currentIncludeLoc : includePropertyKeysFromFiles) { - if (validate(currentIncludeLoc)) { - Properties p = getProperties(currentIncludeLoc); - for (String key : p.stringPropertyNames()) { - includeKeys.add(key); - } - } - } + // mh: including keys from predefined properties + if (includePropertyKeysFromFiles != null && includePropertyKeysFromFiles.length > 0) { + for (String currentIncludeLoc : includePropertyKeysFromFiles) { + if (validate(currentIncludeLoc)) { + Properties p = getProperties(currentIncludeLoc); + for (String key : p.stringPropertyNames()) { + includeKeys.add(key); + } + } + } } - if (includeKeys!=null && !includeKeys.isEmpty()) { -// removing only when include keys provided - Set keys = properties.stringPropertyNames(); + if (includeKeys != null && !includeKeys.isEmpty()) { + // removing only when include keys provided + Set keys = properties.stringPropertyNames(); for (String key : keys) { if (!includeKeys.contains(key)) { properties.remove(key); } - } + } } } /** * Checks whether file exists. + * * @param location * @return true when exists, false otherwise. */ @@ -219,6 +217,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo { /** * Validates resource location. + * * @param location * @return true when valid, false otherwise * @throws MojoExecutionException @@ -238,6 +237,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo { /** * Provides input stream. + * * @param location * @return input stream * @throws IOException @@ -254,6 +254,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo { /** * Creates properties for given location. + * * @param location * @return properties for given location * @throws MojoExecutionException @@ -278,6 +279,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo { /** * Provides escape characters. + * * @param escapeChars * @return escape characters */ @@ -293,6 +295,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo { /** * Provides real token. + * * @param token * @return real token */ @@ -310,6 +313,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo { /** * Returns content. + * * @param comment * @param properties * @param escapeTokens @@ -332,13 +336,15 @@ public class WritePredefinedProjectProperties extends AbstractMojo { /** * Writes properties to given file. + * * @param file * @param comment * @param properties * @param escapeTokens * @throws MojoExecutionException */ - protected void writeProperties(File file, String comment, Properties properties, List escapeTokens) + protected void writeProperties( + File file, String comment, Properties properties, List escapeTokens) throws MojoExecutionException { try { String content = getContent(comment, properties, escapeTokens); @@ -347,15 +353,16 @@ public class WritePredefinedProjectProperties extends AbstractMojo { throw new MojoExecutionException("Error creating properties file", e); } } - + /** * Escapes characters. + * * @param s * @param escapeChars * @return */ protected String escape(String s, List escapeChars) { - String result = s; + String result = s; for (String escapeChar : escapeChars) { result = result.replace(escapeChar, getReplacementToken(escapeChar)); } @@ -364,6 +371,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo { /** * Provides replacement token. + * * @param escapeChar * @return replacement token */ @@ -380,21 +388,22 @@ public class WritePredefinedProjectProperties extends AbstractMojo { } /** - * Returns list from csv. - * @param csv - * @return list of values generated from CSV - */ - protected static final List getListFromCSV(String csv) { - if (StringUtils.isBlank(csv)) { - return new ArrayList(); - } - List list = new ArrayList(); - String[] tokens = StringUtils.split(csv, ","); - for (String token : tokens) { - list.add(token.trim()); - } - return list; - } + * Returns list from csv. + * + * @param csv + * @return list of values generated from CSV + */ + protected static final List getListFromCSV(String csv) { + if (StringUtils.isBlank(csv)) { + return new ArrayList(); + } + List list = new ArrayList(); + String[] tokens = StringUtils.split(csv, ","); + for (String token : tokens) { + list.add(token.trim()); + } + return list; + } public void setIncludeSystemProperties(boolean includeSystemProperties) { this.includeSystemProperties = includeSystemProperties; @@ -419,18 +428,17 @@ public class WritePredefinedProjectProperties extends AbstractMojo { public void setQuiet(boolean quiet) { this.quiet = quiet; } - - /** - * Sets property files for which keys properties should be included. - * @param includePropertyKeysFromFiles - */ - public void setIncludePropertyKeysFromFiles( - String[] includePropertyKeysFromFiles) { - if (includePropertyKeysFromFiles!=null) { - this.includePropertyKeysFromFiles = Arrays.copyOf( - includePropertyKeysFromFiles, - includePropertyKeysFromFiles.length); - } - } - -} \ No newline at end of file + + /** + * Sets property files for which keys properties should be included. + * + * @param includePropertyKeysFromFiles + */ + public void setIncludePropertyKeysFromFiles(String[] includePropertyKeysFromFiles) { + if (includePropertyKeysFromFiles != null) { + this.includePropertyKeysFromFiles = + Arrays.copyOf( + includePropertyKeysFromFiles, includePropertyKeysFromFiles.length); + } + } +} diff --git a/dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojoTest.java b/dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojoTest.java index a2cb8e0f1e..74da207565 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojoTest.java +++ b/dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojoTest.java @@ -1,33 +1,30 @@ package eu.dnetlib.maven.plugin.properties; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - import static eu.dnetlib.maven.plugin.properties.GenerateOoziePropertiesMojo.PROPERTY_NAME_SANDBOX_NAME; import static eu.dnetlib.maven.plugin.properties.GenerateOoziePropertiesMojo.PROPERTY_NAME_WF_SOURCE_DIR; import static org.junit.jupiter.api.Assertions.*; -/** - * @author mhorst, claudio.atzori - * - */ +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +/** @author mhorst, claudio.atzori */ public class GenerateOoziePropertiesMojoTest { private GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo(); - + @BeforeEach public void clearSystemProperties() { System.clearProperty(PROPERTY_NAME_SANDBOX_NAME); System.clearProperty(PROPERTY_NAME_WF_SOURCE_DIR); } - + @Test public void testExecuteEmpty() throws Exception { // execute mojo.execute(); - + // assert - assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME)); + assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME)); } @Test @@ -37,64 +34,63 @@ public class GenerateOoziePropertiesMojoTest { String sandboxName = "originalSandboxName"; System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir); System.setProperty(PROPERTY_NAME_SANDBOX_NAME, sandboxName); - + // execute mojo.execute(); - + // assert assertEquals(sandboxName, System.getProperty(PROPERTY_NAME_SANDBOX_NAME)); } - + @Test public void testExecuteEmptyWorkflowSourceDir() throws Exception { // given String workflowSourceDir = ""; System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir); - + // execute mojo.execute(); - + // assert assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME)); } - + @Test public void testExecuteNullSandboxNameGenerated() throws Exception { // given String workflowSourceDir = "eu/dnetlib/dhp/"; System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir); - + // execute mojo.execute(); - + // assert assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME)); } - + @Test public void testExecute() throws Exception { // given String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers"; System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir); - + // execute mojo.execute(); - + // assert assertEquals("wf/transformers", System.getProperty(PROPERTY_NAME_SANDBOX_NAME)); } - + @Test public void testExecuteWithoutRoot() throws Exception { // given String workflowSourceDir = "wf/transformers"; System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir); - + // execute mojo.execute(); - + // assert assertEquals("wf/transformers", System.getProperty(PROPERTY_NAME_SANDBOX_NAME)); } - } diff --git a/dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java b/dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java index 4b72130787..da832042f2 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java +++ b/dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java @@ -1,5 +1,12 @@ package eu.dnetlib.maven.plugin.properties; +import static eu.dnetlib.maven.plugin.properties.WritePredefinedProjectProperties.PROPERTY_PREFIX_ENV; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.doReturn; +import static org.mockito.Mockito.lenient; + +import java.io.*; +import java.util.Properties; import org.apache.maven.plugin.MojoExecutionException; import org.apache.maven.project.MavenProject; import org.junit.jupiter.api.*; @@ -9,24 +16,12 @@ import org.mockito.Mock; import org.mockito.MockitoAnnotations; import org.mockito.junit.jupiter.MockitoExtension; -import java.io.*; -import java.util.Properties; - -import static eu.dnetlib.maven.plugin.properties.WritePredefinedProjectProperties.PROPERTY_PREFIX_ENV; -import static org.junit.jupiter.api.Assertions.*; -import static org.mockito.Mockito.doReturn; -import static org.mockito.Mockito.lenient; - -/** - * @author mhorst, claudio.atzori - * - */ +/** @author mhorst, claudio.atzori */ @ExtendWith(MockitoExtension.class) public class WritePredefinedProjectPropertiesTest { - @Mock - private MavenProject mavenProject; - + @Mock private MavenProject mavenProject; + private WritePredefinedProjectProperties mojo; @BeforeEach @@ -39,18 +34,18 @@ public class WritePredefinedProjectPropertiesTest { } // ----------------------------------- TESTS --------------------------------------------- - + @Test public void testExecuteEmpty() throws Exception { // execute mojo.execute(); - + // assert assertTrue(mojo.outputFile.exists()); Properties storedProperties = getStoredProperties(mojo.outputFile.getParentFile()); assertEquals(0, storedProperties.size()); } - + @Test public void testExecuteWithProjectProperties() throws Exception { // given @@ -59,10 +54,10 @@ public class WritePredefinedProjectPropertiesTest { Properties projectProperties = new Properties(); projectProperties.setProperty(key, value); doReturn(projectProperties).when(mavenProject).getProperties(); - + // execute mojo.execute(); - + // assert assertTrue(mojo.outputFile.exists()); Properties storedProperties = getStoredProperties(mojo.outputFile.getParentFile()); @@ -70,7 +65,7 @@ public class WritePredefinedProjectPropertiesTest { assertTrue(storedProperties.containsKey(key)); assertEquals(value, storedProperties.getProperty(key)); } - + @Test() public void testExecuteWithProjectPropertiesAndInvalidOutputFile(@TempDir File testFolder) { // given @@ -80,13 +75,14 @@ public class WritePredefinedProjectPropertiesTest { projectProperties.setProperty(key, value); doReturn(projectProperties).when(mavenProject).getProperties(); mojo.outputFile = testFolder; - + // execute Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute()); } - + @Test - public void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) throws Exception { + public void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) + throws Exception { // given String key = "projectPropertyKey"; String value = "projectPropertyValue"; @@ -97,10 +93,10 @@ public class WritePredefinedProjectPropertiesTest { projectProperties.setProperty(excludedKey, excludedValue); doReturn(projectProperties).when(mavenProject).getProperties(); mojo.setExclude(excludedKey); - + // execute mojo.execute(); - + // assert assertTrue(mojo.outputFile.exists()); Properties storedProperties = getStoredProperties(testFolder); @@ -108,9 +104,10 @@ public class WritePredefinedProjectPropertiesTest { assertTrue(storedProperties.containsKey(key)); assertEquals(value, storedProperties.getProperty(key)); } - + @Test - public void testExecuteWithProjectPropertiesInclusion(@TempDir File testFolder) throws Exception { + public void testExecuteWithProjectPropertiesInclusion(@TempDir File testFolder) + throws Exception { // given String key = "projectPropertyKey"; String value = "projectPropertyValue"; @@ -121,10 +118,10 @@ public class WritePredefinedProjectPropertiesTest { projectProperties.setProperty(includedKey, includedValue); doReturn(projectProperties).when(mavenProject).getProperties(); mojo.setInclude(includedKey); - + // execute mojo.execute(); - + // assert assertTrue(mojo.outputFile.exists()); Properties storedProperties = getStoredProperties(testFolder); @@ -132,9 +129,10 @@ public class WritePredefinedProjectPropertiesTest { assertTrue(storedProperties.containsKey(includedKey)); assertEquals(includedValue, storedProperties.getProperty(includedKey)); } - + @Test - public void testExecuteIncludingPropertyKeysFromFile(@TempDir File testFolder) throws Exception { + public void testExecuteIncludingPropertyKeysFromFile(@TempDir File testFolder) + throws Exception { // given String key = "projectPropertyKey"; String value = "projectPropertyValue"; @@ -144,17 +142,18 @@ public class WritePredefinedProjectPropertiesTest { projectProperties.setProperty(key, value); projectProperties.setProperty(includedKey, includedValue); doReturn(projectProperties).when(mavenProject).getProperties(); - + File includedPropertiesFile = new File(testFolder, "included.properties"); Properties includedProperties = new Properties(); includedProperties.setProperty(includedKey, "irrelevantValue"); includedProperties.store(new FileWriter(includedPropertiesFile), null); - - mojo.setIncludePropertyKeysFromFiles(new String[] {includedPropertiesFile.getAbsolutePath()}); - + + mojo.setIncludePropertyKeysFromFiles( + new String[] {includedPropertiesFile.getAbsolutePath()}); + // execute mojo.execute(); - + // assert assertTrue(mojo.outputFile.exists()); Properties storedProperties = getStoredProperties(testFolder); @@ -162,9 +161,10 @@ public class WritePredefinedProjectPropertiesTest { assertTrue(storedProperties.containsKey(includedKey)); assertEquals(includedValue, storedProperties.getProperty(includedKey)); } - + @Test - public void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder) throws Exception { + public void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder) + throws Exception { // given String key = "projectPropertyKey"; String value = "projectPropertyValue"; @@ -174,12 +174,13 @@ public class WritePredefinedProjectPropertiesTest { projectProperties.setProperty(key, value); projectProperties.setProperty(includedKey, includedValue); doReturn(projectProperties).when(mavenProject).getProperties(); - - mojo.setIncludePropertyKeysFromFiles(new String[] {"/eu/dnetlib/maven/plugin/properties/included.properties"}); - + + mojo.setIncludePropertyKeysFromFiles( + new String[] {"/eu/dnetlib/maven/plugin/properties/included.properties"}); + // execute mojo.execute(); - + // assert assertTrue(mojo.outputFile.exists()); Properties storedProperties = getStoredProperties(testFolder); @@ -187,7 +188,7 @@ public class WritePredefinedProjectPropertiesTest { assertTrue(storedProperties.containsKey(includedKey)); assertEquals(includedValue, storedProperties.getProperty(includedKey)); } - + @Test public void testExecuteIncludingPropertyKeysFromBlankLocation() { // given @@ -199,15 +200,16 @@ public class WritePredefinedProjectPropertiesTest { projectProperties.setProperty(key, value); projectProperties.setProperty(includedKey, includedValue); doReturn(projectProperties).when(mavenProject).getProperties(); - + mojo.setIncludePropertyKeysFromFiles(new String[] {""}); - + // execute Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute()); } - + @Test - public void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder) throws Exception { + public void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder) + throws Exception { // given String key = "projectPropertyKey"; String value = "projectPropertyValue"; @@ -217,17 +219,18 @@ public class WritePredefinedProjectPropertiesTest { projectProperties.setProperty(key, value); projectProperties.setProperty(includedKey, includedValue); doReturn(projectProperties).when(mavenProject).getProperties(); - + File includedPropertiesFile = new File(testFolder, "included.xml"); Properties includedProperties = new Properties(); includedProperties.setProperty(includedKey, "irrelevantValue"); includedProperties.storeToXML(new FileOutputStream(includedPropertiesFile), null); - - mojo.setIncludePropertyKeysFromFiles(new String[] {includedPropertiesFile.getAbsolutePath()}); - + + mojo.setIncludePropertyKeysFromFiles( + new String[] {includedPropertiesFile.getAbsolutePath()}); + // execute mojo.execute(); - + // assert assertTrue(mojo.outputFile.exists()); Properties storedProperties = getStoredProperties(testFolder); @@ -235,9 +238,10 @@ public class WritePredefinedProjectPropertiesTest { assertTrue(storedProperties.containsKey(includedKey)); assertEquals(includedValue, storedProperties.getProperty(includedKey)); } - + @Test - public void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder) throws Exception { + public void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder) + throws Exception { // given String key = "projectPropertyKey"; String value = "projectPropertyValue"; @@ -247,59 +251,60 @@ public class WritePredefinedProjectPropertiesTest { projectProperties.setProperty(key, value); projectProperties.setProperty(includedKey, includedValue); doReturn(projectProperties).when(mavenProject).getProperties(); - + File includedPropertiesFile = new File(testFolder, "included.xml"); Properties includedProperties = new Properties(); includedProperties.setProperty(includedKey, "irrelevantValue"); includedProperties.store(new FileOutputStream(includedPropertiesFile), null); - - mojo.setIncludePropertyKeysFromFiles(new String[] {includedPropertiesFile.getAbsolutePath()}); - + + mojo.setIncludePropertyKeysFromFiles( + new String[] {includedPropertiesFile.getAbsolutePath()}); + // execute Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute()); } - + @Test public void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception { // given mojo.setQuiet(true); mojo.setIncludePropertyKeysFromFiles(new String[] {"invalid location"}); - + // execute mojo.execute(); - + // assert assertTrue(mojo.outputFile.exists()); Properties storedProperties = getStoredProperties(testFolder); assertEquals(0, storedProperties.size()); } - + @Test public void testExecuteIncludingPropertyKeysFromInvalidFile() { // given mojo.setIncludePropertyKeysFromFiles(new String[] {"invalid location"}); - + // execute Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute()); } - + @Test public void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception { // given mojo.setIncludeEnvironmentVariables(true); - + // execute mojo.execute(); - + // assert assertTrue(mojo.outputFile.exists()); Properties storedProperties = getStoredProperties(testFolder); assertTrue(storedProperties.size() > 0); for (Object currentKey : storedProperties.keySet()) { - assertTrue(((String)currentKey).startsWith(PROPERTY_PREFIX_ENV)); + assertTrue(((String) currentKey).startsWith(PROPERTY_PREFIX_ENV)); } } - + @Test public void testExecuteWithSystemProperties(@TempDir File testFolder) throws Exception { // given @@ -307,10 +312,10 @@ public class WritePredefinedProjectPropertiesTest { String value = "systemPropertyValue"; System.setProperty(key, value); mojo.setIncludeSystemProperties(true); - + // execute mojo.execute(); - + // assert assertTrue(mojo.outputFile.exists()); Properties storedProperties = getStoredProperties(testFolder); @@ -318,9 +323,10 @@ public class WritePredefinedProjectPropertiesTest { assertTrue(storedProperties.containsKey(key)); assertEquals(value, storedProperties.getProperty(key)); } - + @Test - public void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder) throws Exception { + public void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder) + throws Exception { // given String key = "systemPropertyKey "; String value = "systemPropertyValue"; @@ -328,10 +334,10 @@ public class WritePredefinedProjectPropertiesTest { mojo.setIncludeSystemProperties(true); String escapeChars = "cr,lf,tab,|"; mojo.setEscapeChars(escapeChars); - + // execute mojo.execute(); - + // assert assertTrue(mojo.outputFile.exists()); Properties storedProperties = getStoredProperties(testFolder); @@ -340,14 +346,15 @@ public class WritePredefinedProjectPropertiesTest { assertTrue(storedProperties.containsKey(key.trim())); assertEquals(value, storedProperties.getProperty(key.trim())); } - + // ----------------------------------- PRIVATE ------------------------------------------- - + private File getPropertiesFileLocation(File testFolder) { return new File(testFolder, "test.properties"); } - - private Properties getStoredProperties(File testFolder) throws FileNotFoundException, IOException { + + private Properties getStoredProperties(File testFolder) + throws FileNotFoundException, IOException { Properties properties = new Properties(); properties.load(new FileInputStream(getPropertiesFileLocation(testFolder))); return properties; diff --git a/dhp-common/src/main/java/eu/dnetlib/collector/worker/model/ApiDescriptor.java b/dhp-common/src/main/java/eu/dnetlib/collector/worker/model/ApiDescriptor.java index 255104eda2..a95b1267f3 100644 --- a/dhp-common/src/main/java/eu/dnetlib/collector/worker/model/ApiDescriptor.java +++ b/dhp-common/src/main/java/eu/dnetlib/collector/worker/model/ApiDescriptor.java @@ -3,47 +3,45 @@ package eu.dnetlib.collector.worker.model; import java.util.HashMap; import java.util.Map; - public class ApiDescriptor { - private String id; + private String id; - private String baseUrl; + private String baseUrl; - private String protocol; + private String protocol; - private Map params = new HashMap<>(); + private Map params = new HashMap<>(); - public String getBaseUrl() { - return baseUrl; - } + public String getBaseUrl() { + return baseUrl; + } - public void setBaseUrl(final String baseUrl) { - this.baseUrl = baseUrl; - } + public void setBaseUrl(final String baseUrl) { + this.baseUrl = baseUrl; + } - public String getId() { - return id; - } + public String getId() { + return id; + } - public void setId(final String id) { - this.id = id; - } + public void setId(final String id) { + this.id = id; + } - public Map getParams() { - return params; - } + public Map getParams() { + return params; + } - public void setParams(final HashMap params) { - this.params = params; - } + public void setParams(final HashMap params) { + this.params = params; + } - public String getProtocol() { - return protocol; - } - - public void setProtocol(final String protocol) { - this.protocol = protocol; - } + public String getProtocol() { + return protocol; + } + public void setProtocol(final String protocol) { + this.protocol = protocol; + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStore.java b/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStore.java index 478bda4402..1284e9ab6b 100644 --- a/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStore.java +++ b/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStore.java @@ -2,7 +2,6 @@ package eu.dnetlib.data.mdstore.manager.common.model; import java.io.Serializable; import java.util.UUID; - import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; @@ -12,108 +11,107 @@ import javax.persistence.Table; @Table(name = "mdstores") public class MDStore implements Serializable { - /** - * - */ - private static final long serialVersionUID = 3160530489149700055L; + /** */ + private static final long serialVersionUID = 3160530489149700055L; - @Id - @Column(name = "id") - private String id; + @Id + @Column(name = "id") + private String id; - @Column(name = "format") - private String format; + @Column(name = "format") + private String format; - @Column(name = "layout") - private String layout; + @Column(name = "layout") + private String layout; - @Column(name = "interpretation") - private String interpretation; + @Column(name = "interpretation") + private String interpretation; - @Column(name = "datasource_name") - private String datasourceName; + @Column(name = "datasource_name") + private String datasourceName; - @Column(name = "datasource_id") - private String datasourceId; + @Column(name = "datasource_id") + private String datasourceId; - @Column(name = "api_id") - private String apiId; + @Column(name = "api_id") + private String apiId; - public String getId() { - return id; - } + public String getId() { + return id; + } - public void setId(final String id) { - this.id = id; - } + public void setId(final String id) { + this.id = id; + } - public String getFormat() { - return format; - } + public String getFormat() { + return format; + } - public void setFormat(final String format) { - this.format = format; - } + public void setFormat(final String format) { + this.format = format; + } - public String getLayout() { - return layout; - } + public String getLayout() { + return layout; + } - public void setLayout(final String layout) { - this.layout = layout; - } + public void setLayout(final String layout) { + this.layout = layout; + } - public String getInterpretation() { - return interpretation; - } + public String getInterpretation() { + return interpretation; + } - public void setInterpretation(final String interpretation) { - this.interpretation = interpretation; - } + public void setInterpretation(final String interpretation) { + this.interpretation = interpretation; + } - public String getDatasourceName() { - return datasourceName; - } + public String getDatasourceName() { + return datasourceName; + } - public void setDatasourceName(final String datasourceName) { - this.datasourceName = datasourceName; - } + public void setDatasourceName(final String datasourceName) { + this.datasourceName = datasourceName; + } - public String getDatasourceId() { - return datasourceId; - } + public String getDatasourceId() { + return datasourceId; + } - public void setDatasourceId(final String datasourceId) { - this.datasourceId = datasourceId; - } + public void setDatasourceId(final String datasourceId) { + this.datasourceId = datasourceId; + } - public String getApiId() { - return apiId; - } + public String getApiId() { + return apiId; + } - public void setApiId(final String apiId) { - this.apiId = apiId; - } + public void setApiId(final String apiId) { + this.apiId = apiId; + } - public static MDStore newInstance(final String format, final String layout, final String interpretation) { - return newInstance(format, layout, interpretation, null, null, null); - } - - public static MDStore newInstance(final String format, - final String layout, - final String interpretation, - final String dsName, - final String dsId, - final String apiId) { - final MDStore md = new MDStore(); - md.setId("md-" + UUID.randomUUID()); - md.setFormat(format); - md.setLayout(layout); - md.setInterpretation(interpretation); - md.setDatasourceName(dsName); - md.setDatasourceId(dsId); - md.setApiId(apiId); - return md; - } + public static MDStore newInstance( + final String format, final String layout, final String interpretation) { + return newInstance(format, layout, interpretation, null, null, null); + } + public static MDStore newInstance( + final String format, + final String layout, + final String interpretation, + final String dsName, + final String dsId, + final String apiId) { + final MDStore md = new MDStore(); + md.setId("md-" + UUID.randomUUID()); + md.setFormat(format); + md.setLayout(layout); + md.setInterpretation(interpretation); + md.setDatasourceName(dsName); + md.setDatasourceId(dsId); + md.setApiId(apiId); + return md; + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreCurrentVersion.java b/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreCurrentVersion.java index 2a52d0d1d1..45f6c8ee15 100644 --- a/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreCurrentVersion.java +++ b/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreCurrentVersion.java @@ -1,7 +1,6 @@ package eu.dnetlib.data.mdstore.manager.common.model; import java.io.Serializable; - import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; @@ -11,42 +10,40 @@ import javax.persistence.Table; @Table(name = "mdstore_current_versions") public class MDStoreCurrentVersion implements Serializable { - /** - * - */ - private static final long serialVersionUID = -4757725888593745773L; + /** */ + private static final long serialVersionUID = -4757725888593745773L; - @Id - @Column(name = "mdstore") - private String mdstore; + @Id + @Column(name = "mdstore") + private String mdstore; - @Column(name = "current_version") - private String currentVersion; + @Column(name = "current_version") + private String currentVersion; - public String getMdstore() { - return mdstore; - } + public String getMdstore() { + return mdstore; + } - public void setMdstore(final String mdstore) { - this.mdstore = mdstore; - } + public void setMdstore(final String mdstore) { + this.mdstore = mdstore; + } - public String getCurrentVersion() { - return currentVersion; - } + public String getCurrentVersion() { + return currentVersion; + } - public void setCurrentVersion(final String currentVersion) { - this.currentVersion = currentVersion; - } + public void setCurrentVersion(final String currentVersion) { + this.currentVersion = currentVersion; + } - public static MDStoreCurrentVersion newInstance(final String mdId, final String versionId) { - final MDStoreCurrentVersion cv = new MDStoreCurrentVersion(); - cv.setMdstore(mdId); - cv.setCurrentVersion(versionId); - return cv; - } + public static MDStoreCurrentVersion newInstance(final String mdId, final String versionId) { + final MDStoreCurrentVersion cv = new MDStoreCurrentVersion(); + cv.setMdstore(mdId); + cv.setCurrentVersion(versionId); + return cv; + } - public static MDStoreCurrentVersion newInstance(final MDStoreVersion v) { - return newInstance(v.getMdstore(), v.getId()); - } + public static MDStoreCurrentVersion newInstance(final MDStoreVersion v) { + return newInstance(v.getMdstore(), v.getId()); + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreVersion.java b/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreVersion.java index 4ad6f137c1..b53d5f1185 100644 --- a/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreVersion.java +++ b/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreVersion.java @@ -2,7 +2,6 @@ package eu.dnetlib.data.mdstore.manager.common.model; import java.io.Serializable; import java.util.Date; - import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; @@ -14,88 +13,85 @@ import javax.persistence.TemporalType; @Table(name = "mdstore_versions") public class MDStoreVersion implements Serializable { - /** - * - */ - private static final long serialVersionUID = -4763494442274298339L; + /** */ + private static final long serialVersionUID = -4763494442274298339L; - @Id - @Column(name = "id") - private String id; + @Id + @Column(name = "id") + private String id; - @Column(name = "mdstore") - private String mdstore; + @Column(name = "mdstore") + private String mdstore; - @Column(name = "writing") - private boolean writing; + @Column(name = "writing") + private boolean writing; - @Column(name = "readcount") - private int readCount = 0; + @Column(name = "readcount") + private int readCount = 0; - @Column(name = "lastupdate") - @Temporal(TemporalType.TIMESTAMP) - private Date lastUpdate; + @Column(name = "lastupdate") + @Temporal(TemporalType.TIMESTAMP) + private Date lastUpdate; - @Column(name = "size") - private long size = 0; + @Column(name = "size") + private long size = 0; - public static MDStoreVersion newInstance(final String mdId, final boolean writing) { - final MDStoreVersion t = new MDStoreVersion(); - t.setId(mdId + "-" + new Date().getTime()); - t.setMdstore(mdId); - t.setLastUpdate(null); - t.setWriting(writing); - t.setReadCount(0); - t.setSize(0); - return t; - } + public static MDStoreVersion newInstance(final String mdId, final boolean writing) { + final MDStoreVersion t = new MDStoreVersion(); + t.setId(mdId + "-" + new Date().getTime()); + t.setMdstore(mdId); + t.setLastUpdate(null); + t.setWriting(writing); + t.setReadCount(0); + t.setSize(0); + return t; + } - public String getId() { - return id; - } + public String getId() { + return id; + } - public void setId(final String id) { - this.id = id; - } + public void setId(final String id) { + this.id = id; + } - public String getMdstore() { - return mdstore; - } + public String getMdstore() { + return mdstore; + } - public void setMdstore(final String mdstore) { - this.mdstore = mdstore; - } + public void setMdstore(final String mdstore) { + this.mdstore = mdstore; + } - public boolean isWriting() { - return writing; - } + public boolean isWriting() { + return writing; + } - public void setWriting(final boolean writing) { - this.writing = writing; - } + public void setWriting(final boolean writing) { + this.writing = writing; + } - public int getReadCount() { - return readCount; - } + public int getReadCount() { + return readCount; + } - public void setReadCount(final int readCount) { - this.readCount = readCount; - } + public void setReadCount(final int readCount) { + this.readCount = readCount; + } - public Date getLastUpdate() { - return lastUpdate; - } + public Date getLastUpdate() { + return lastUpdate; + } - public void setLastUpdate(final Date lastUpdate) { - this.lastUpdate = lastUpdate; - } + public void setLastUpdate(final Date lastUpdate) { + this.lastUpdate = lastUpdate; + } - public long getSize() { - return size; - } - - public void setSize(final long size) { - this.size = size; - } + public long getSize() { + return size; + } + public void setSize(final long size) { + this.size = size; + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreWithInfo.java b/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreWithInfo.java index dfe188f549..27c77a5e70 100644 --- a/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreWithInfo.java +++ b/dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreWithInfo.java @@ -2,7 +2,6 @@ package eu.dnetlib.data.mdstore.manager.common.model; import java.io.Serializable; import java.util.Date; - import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; @@ -14,132 +13,129 @@ import javax.persistence.TemporalType; @Table(name = "mdstores_with_info") public class MDStoreWithInfo implements Serializable { - /** - * - */ - private static final long serialVersionUID = -8445784770687571492L; + /** */ + private static final long serialVersionUID = -8445784770687571492L; - @Id - @Column(name = "id") - private String id; + @Id + @Column(name = "id") + private String id; - @Column(name = "format") - private String format; + @Column(name = "format") + private String format; - @Column(name = "layout") - private String layout; + @Column(name = "layout") + private String layout; - @Column(name = "interpretation") - private String interpretation; + @Column(name = "interpretation") + private String interpretation; - @Column(name = "datasource_name") - private String datasourceName; + @Column(name = "datasource_name") + private String datasourceName; - @Column(name = "datasource_id") - private String datasourceId; + @Column(name = "datasource_id") + private String datasourceId; - @Column(name = "api_id") - private String apiId; + @Column(name = "api_id") + private String apiId; - @Column(name = "current_version") - private String currentVersion; + @Column(name = "current_version") + private String currentVersion; - @Column(name = "lastupdate") - @Temporal(TemporalType.TIMESTAMP) - private Date lastUpdate; + @Column(name = "lastupdate") + @Temporal(TemporalType.TIMESTAMP) + private Date lastUpdate; - @Column(name = "size") - private long size = 0; + @Column(name = "size") + private long size = 0; - @Column(name = "n_versions") - private long numberOfVersions = 0; + @Column(name = "n_versions") + private long numberOfVersions = 0; - public String getId() { - return id; - } + public String getId() { + return id; + } - public void setId(final String id) { - this.id = id; - } + public void setId(final String id) { + this.id = id; + } - public String getFormat() { - return format; - } + public String getFormat() { + return format; + } - public void setFormat(final String format) { - this.format = format; - } + public void setFormat(final String format) { + this.format = format; + } - public String getLayout() { - return layout; - } + public String getLayout() { + return layout; + } - public void setLayout(final String layout) { - this.layout = layout; - } + public void setLayout(final String layout) { + this.layout = layout; + } - public String getInterpretation() { - return interpretation; - } + public String getInterpretation() { + return interpretation; + } - public void setInterpretation(final String interpretation) { - this.interpretation = interpretation; - } + public void setInterpretation(final String interpretation) { + this.interpretation = interpretation; + } - public String getDatasourceName() { - return datasourceName; - } + public String getDatasourceName() { + return datasourceName; + } - public void setDatasourceName(final String datasourceName) { - this.datasourceName = datasourceName; - } + public void setDatasourceName(final String datasourceName) { + this.datasourceName = datasourceName; + } - public String getDatasourceId() { - return datasourceId; - } + public String getDatasourceId() { + return datasourceId; + } - public void setDatasourceId(final String datasourceId) { - this.datasourceId = datasourceId; - } + public void setDatasourceId(final String datasourceId) { + this.datasourceId = datasourceId; + } - public String getApiId() { - return apiId; - } + public String getApiId() { + return apiId; + } - public void setApiId(final String apiId) { - this.apiId = apiId; - } + public void setApiId(final String apiId) { + this.apiId = apiId; + } - public String getCurrentVersion() { - return currentVersion; - } + public String getCurrentVersion() { + return currentVersion; + } - public void setCurrentVersion(final String currentVersion) { - this.currentVersion = currentVersion; - } + public void setCurrentVersion(final String currentVersion) { + this.currentVersion = currentVersion; + } - public Date getLastUpdate() { - return lastUpdate; - } + public Date getLastUpdate() { + return lastUpdate; + } - public void setLastUpdate(final Date lastUpdate) { - this.lastUpdate = lastUpdate; - } + public void setLastUpdate(final Date lastUpdate) { + this.lastUpdate = lastUpdate; + } - public long getSize() { - return size; - } + public long getSize() { + return size; + } - public void setSize(final long size) { - this.size = size; - } + public void setSize(final long size) { + this.size = size; + } - public long getNumberOfVersions() { - return numberOfVersions; - } - - public void setNumberOfVersions(final long numberOfVersions) { - this.numberOfVersions = numberOfVersions; - } + public long getNumberOfVersions() { + return numberOfVersions; + } + public void setNumberOfVersions(final long numberOfVersions) { + this.numberOfVersions = numberOfVersions; + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java b/dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java index cbfc5caf14..f3a2273cbb 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java @@ -1,10 +1,6 @@ package eu.dnetlib.dhp.application; import com.fasterxml.jackson.databind.ObjectMapper; -import org.apache.commons.cli.*; -import org.apache.commons.codec.binary.Base64; -import org.apache.commons.io.IOUtils; - import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; import java.io.Serializable; @@ -12,7 +8,9 @@ import java.io.StringWriter; import java.util.*; import java.util.zip.GZIPInputStream; import java.util.zip.GZIPOutputStream; -import java.util.zip.Inflater; +import org.apache.commons.cli.*; +import org.apache.commons.codec.binary.Base64; +import org.apache.commons.io.IOUtils; public class ArgumentApplicationParser implements Serializable { @@ -23,7 +21,8 @@ public class ArgumentApplicationParser implements Serializable { public ArgumentApplicationParser(final String json_configuration) throws Exception { final ObjectMapper mapper = new ObjectMapper(); - final OptionsParameter[] configuration = mapper.readValue(json_configuration, OptionsParameter[].class); + final OptionsParameter[] configuration = + mapper.readValue(json_configuration, OptionsParameter[].class); createOptionMap(configuration); } @@ -33,23 +32,26 @@ public class ArgumentApplicationParser implements Serializable { private void createOptionMap(final OptionsParameter[] configuration) { - Arrays.stream(configuration).map(conf -> { - final Option o = new Option(conf.getParamName(), true, conf.getParamDescription()); - o.setLongOpt(conf.getParamLongName()); - o.setRequired(conf.isParamRequired()); - if (conf.isCompressed()) { - compressedValues.add(conf.getParamLongName()); - } - return o; - }).forEach(options::addOption); - -// HelpFormatter formatter = new HelpFormatter(); -// formatter.printHelp("myapp", null, options, null, true); + Arrays.stream(configuration) + .map( + conf -> { + final Option o = + new Option( + conf.getParamName(), true, conf.getParamDescription()); + o.setLongOpt(conf.getParamLongName()); + o.setRequired(conf.isParamRequired()); + if (conf.isCompressed()) { + compressedValues.add(conf.getParamLongName()); + } + return o; + }) + .forEach(options::addOption); + // HelpFormatter formatter = new HelpFormatter(); + // formatter.printHelp("myapp", null, options, null, true); } - public static String decompressValue(final String abstractCompressed) { try { byte[] byteArray = Base64.decodeBase64(abstractCompressed.getBytes()); @@ -63,7 +65,7 @@ public class ArgumentApplicationParser implements Serializable { } } - public static String compressArgument(final String value) throws Exception{ + public static String compressArgument(final String value) throws Exception { ByteArrayOutputStream out = new ByteArrayOutputStream(); GZIPOutputStream gzip = new GZIPOutputStream(out); gzip.write(value.getBytes()); @@ -74,7 +76,14 @@ public class ArgumentApplicationParser implements Serializable { public void parseArgument(final String[] args) throws Exception { CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(options, args); - Arrays.stream(cmd.getOptions()).forEach(it -> objectMap.put(it.getLongOpt(), compressedValues.contains(it.getLongOpt())? decompressValue(it.getValue()): it.getValue())); + Arrays.stream(cmd.getOptions()) + .forEach( + it -> + objectMap.put( + it.getLongOpt(), + compressedValues.contains(it.getLongOpt()) + ? decompressValue(it.getValue()) + : it.getValue())); } public String get(final String key) { diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java b/dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java index 4e7c2826bb..dcc5376567 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java @@ -1,6 +1,5 @@ package eu.dnetlib.dhp.application; - public class OptionsParameter { private String paramName; @@ -9,8 +8,7 @@ public class OptionsParameter { private boolean paramRequired; private boolean compressed; - public OptionsParameter() { - } + public OptionsParameter() {} public String getParamName() { return paramName; diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/FunctionalInterfaceSupport.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/FunctionalInterfaceSupport.java index d78520f55b..17a039878f 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/FunctionalInterfaceSupport.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/FunctionalInterfaceSupport.java @@ -3,23 +3,19 @@ package eu.dnetlib.dhp.common; import java.io.Serializable; import java.util.function.Supplier; -/** - * Provides serializable and throwing extensions to standard functional interfaces. - */ +/** Provides serializable and throwing extensions to standard functional interfaces. */ public class FunctionalInterfaceSupport { - private FunctionalInterfaceSupport() { - } + private FunctionalInterfaceSupport() {} /** - * Serializable supplier of any kind of objects. To be used withing spark processing pipelines when supplying - * functions externally. + * Serializable supplier of any kind of objects. To be used withing spark processing pipelines + * when supplying functions externally. * * @param */ @FunctionalInterface - public interface SerializableSupplier extends Supplier, Serializable { - } + public interface SerializableSupplier extends Supplier, Serializable {} /** * Extension of consumer accepting functions throwing an exception. @@ -52,5 +48,4 @@ public class FunctionalInterfaceSupport { public interface ThrowingRunnable { void run() throws E; } - -} \ No newline at end of file +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java index f6b94c9211..48d6d79f64 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java @@ -1,5 +1,10 @@ package eu.dnetlib.dhp.common; +import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException; + +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileStatus; import org.apache.hadoop.fs.FileSystem; @@ -7,66 +12,60 @@ import org.apache.hadoop.fs.Path; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.Arrays; -import java.util.List; -import java.util.stream.Collectors; - -import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException; - -/** - * HDFS utility methods. - */ +/** HDFS utility methods. */ public class HdfsSupport { private static final Logger logger = LoggerFactory.getLogger(HdfsSupport.class); - private HdfsSupport() { - } + private HdfsSupport() {} /** * Checks a path (file or dir) exists on HDFS. * - * @param path Path to be checked + * @param path Path to be checked * @param configuration Configuration of hadoop env */ public static boolean exists(String path, Configuration configuration) { logger.info("Removing path: {}", path); - return rethrowAsRuntimeException(() -> { - Path f = new Path(path); - FileSystem fileSystem = FileSystem.get(configuration); - return fileSystem.exists(f); - }); + return rethrowAsRuntimeException( + () -> { + Path f = new Path(path); + FileSystem fileSystem = FileSystem.get(configuration); + return fileSystem.exists(f); + }); } /** * Removes a path (file or dir) from HDFS. * - * @param path Path to be removed + * @param path Path to be removed * @param configuration Configuration of hadoop env */ public static void remove(String path, Configuration configuration) { logger.info("Removing path: {}", path); - rethrowAsRuntimeException(() -> { - Path f = new Path(path); - FileSystem fileSystem = FileSystem.get(configuration); - if (fileSystem.exists(f)) { - fileSystem.delete(f, true); - } - }); + rethrowAsRuntimeException( + () -> { + Path f = new Path(path); + FileSystem fileSystem = FileSystem.get(configuration); + if (fileSystem.exists(f)) { + fileSystem.delete(f, true); + } + }); } /** * Lists hadoop files located below path or alternatively lists subdirs under path. * - * @param path Path to be listed for hadoop files + * @param path Path to be listed for hadoop files * @param configuration Configuration of hadoop env * @return List with string locations of hadoop files */ public static List listFiles(String path, Configuration configuration) { logger.info("Listing files in path: {}", path); - return rethrowAsRuntimeException(() -> Arrays - .stream(FileSystem.get(configuration).listStatus(new Path(path))) - .filter(FileStatus::isDirectory) - .map(x -> x.getPath().toString()) - .collect(Collectors.toList())); + return rethrowAsRuntimeException( + () -> + Arrays.stream(FileSystem.get(configuration).listStatus(new Path(path))) + .filter(FileStatus::isDirectory) + .map(x -> x.getPath().toString()) + .collect(Collectors.toList())); } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java index 43c18a9560..12e98a0562 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java @@ -1,61 +1,71 @@ package eu.dnetlib.dhp.common; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer; +import java.util.Objects; +import java.util.function.Function; import org.apache.spark.SparkConf; import org.apache.spark.sql.SparkSession; -import java.util.Objects; -import java.util.function.Function; - -/** - * SparkSession utility methods. - */ +/** SparkSession utility methods. */ public class SparkSessionSupport { - private SparkSessionSupport() { + private SparkSessionSupport() {} + + /** + * Runs a given function using SparkSession created using default builder and supplied + * SparkConf. Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession + * created externally. + * + * @param conf SparkConf instance + * @param isSparkSessionManaged When true will stop SparkSession + * @param fn Consumer to be applied to constructed SparkSession + */ + public static void runWithSparkSession( + SparkConf conf, + Boolean isSparkSessionManaged, + ThrowingConsumer fn) { + runWithSparkSession( + c -> SparkSession.builder().config(c).getOrCreate(), + conf, + isSparkSessionManaged, + fn); } /** - * Runs a given function using SparkSession created using default builder and supplied SparkConf. Stops SparkSession - * when SparkSession is managed. Allows to reuse SparkSession created externally. + * Runs a given function using SparkSession created with hive support and using default builder + * and supplied SparkConf. Stops SparkSession when SparkSession is managed. Allows to reuse + * SparkSession created externally. * - * @param conf SparkConf instance + * @param conf SparkConf instance * @param isSparkSessionManaged When true will stop SparkSession - * @param fn Consumer to be applied to constructed SparkSession + * @param fn Consumer to be applied to constructed SparkSession */ - public static void runWithSparkSession(SparkConf conf, - Boolean isSparkSessionManaged, - ThrowingConsumer fn) { - runWithSparkSession(c -> SparkSession.builder().config(c).getOrCreate(), conf, isSparkSessionManaged, fn); + public static void runWithSparkHiveSession( + SparkConf conf, + Boolean isSparkSessionManaged, + ThrowingConsumer fn) { + runWithSparkSession( + c -> SparkSession.builder().config(c).enableHiveSupport().getOrCreate(), + conf, + isSparkSessionManaged, + fn); } /** - * Runs a given function using SparkSession created with hive support and using default builder and supplied SparkConf. - * Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession created externally. + * Runs a given function using SparkSession created using supplied builder and supplied + * SparkConf. Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession + * created externally. * - * @param conf SparkConf instance + * @param sparkSessionBuilder Builder of SparkSession + * @param conf SparkConf instance * @param isSparkSessionManaged When true will stop SparkSession - * @param fn Consumer to be applied to constructed SparkSession + * @param fn Consumer to be applied to constructed SparkSession */ - public static void runWithSparkHiveSession(SparkConf conf, - Boolean isSparkSessionManaged, - ThrowingConsumer fn) { - runWithSparkSession(c -> SparkSession.builder().config(c).enableHiveSupport().getOrCreate(), conf, isSparkSessionManaged, fn); - } - - /** - * Runs a given function using SparkSession created using supplied builder and supplied SparkConf. Stops SparkSession - * when SparkSession is managed. Allows to reuse SparkSession created externally. - * - * @param sparkSessionBuilder Builder of SparkSession - * @param conf SparkConf instance - * @param isSparkSessionManaged When true will stop SparkSession - * @param fn Consumer to be applied to constructed SparkSession - */ - public static void runWithSparkSession(Function sparkSessionBuilder, - SparkConf conf, - Boolean isSparkSessionManaged, - ThrowingConsumer fn) { + public static void runWithSparkSession( + Function sparkSessionBuilder, + SparkConf conf, + Boolean isSparkSessionManaged, + ThrowingConsumer fn) { SparkSession spark = null; try { spark = sparkSessionBuilder.apply(conf); @@ -68,4 +78,4 @@ public class SparkSessionSupport { } } } -} \ No newline at end of file +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/ThrowingSupport.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/ThrowingSupport.java index b32803c378..5bc66f493b 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/ThrowingSupport.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/ThrowingSupport.java @@ -3,18 +3,15 @@ package eu.dnetlib.dhp.common; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingRunnable; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingSupplier; -/** - * Exception handling utility methods. - */ +/** Exception handling utility methods. */ public class ThrowingSupport { - private ThrowingSupport() { - } + private ThrowingSupport() {} /** * Executes given runnable and rethrows any exceptions as RuntimeException. * - * @param fn Runnable to be executed + * @param fn Runnable to be executed * @param Type of exception thrown */ public static void rethrowAsRuntimeException(ThrowingRunnable fn) { @@ -28,11 +25,12 @@ public class ThrowingSupport { /** * Executes given runnable and rethrows any exceptions as RuntimeException with custom message. * - * @param fn Runnable to be executed + * @param fn Runnable to be executed * @param msg Message to be set for rethrown exception * @param Type of exception thrown */ - public static void rethrowAsRuntimeException(ThrowingRunnable fn, String msg) { + public static void rethrowAsRuntimeException( + ThrowingRunnable fn, String msg) { try { fn.run(); } catch (Exception e) { @@ -43,7 +41,7 @@ public class ThrowingSupport { /** * Executes given supplier and rethrows any exceptions as RuntimeException. * - * @param fn Supplier to be executed + * @param fn Supplier to be executed * @param Type of returned value * @param Type of exception thrown * @return Result of supplier execution @@ -59,18 +57,18 @@ public class ThrowingSupport { /** * Executes given supplier and rethrows any exceptions as RuntimeException with custom message. * - * @param fn Supplier to be executed + * @param fn Supplier to be executed * @param msg Message to be set for rethrown exception * @param Type of returned value * @param Type of exception thrown * @return Result of supplier execution */ - public static T rethrowAsRuntimeException(ThrowingSupplier fn, String msg) { + public static T rethrowAsRuntimeException( + ThrowingSupplier fn, String msg) { try { return fn.get(); } catch (Exception e) { throw new RuntimeException(msg, e); } } - -} \ No newline at end of file +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/MetadataRecord.java b/dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/MetadataRecord.java index acbb7ffbbb..98ee80bd6c 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/MetadataRecord.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/MetadataRecord.java @@ -1,66 +1,52 @@ package eu.dnetlib.dhp.model.mdstore; import eu.dnetlib.dhp.utils.DHPUtils; - import java.io.Serializable; - -/** - * This class models a record inside the new Metadata store collection on HDFS * - * - */ +/** This class models a record inside the new Metadata store collection on HDFS * */ public class MetadataRecord implements Serializable { - /** - * The D-Net Identifier associated to the record - */ + /** The D-Net Identifier associated to the record */ private String id; - /** - * The original Identifier of the record - */ + /** The original Identifier of the record */ private String originalId; - - /** - * The encoding of the record, should be JSON or XML - */ + /** The encoding of the record, should be JSON or XML */ private String encoding; /** - * The information about the provenance of the record see @{@link Provenance} - * for the model of this information + * The information about the provenance of the record see @{@link Provenance} for the model of + * this information */ private Provenance provenance; - /** - * The content of the metadata - */ + /** The content of the metadata */ private String body; - /** - * the date when the record has been stored - */ + /** the date when the record has been stored */ private long dateOfCollection; - /** - * the date when the record has been stored - */ + /** the date when the record has been stored */ private long dateOfTransformation; - public MetadataRecord() { this.dateOfCollection = System.currentTimeMillis(); } - public MetadataRecord(String originalId, String encoding, Provenance provenance, String body, long dateOfCollection) { + public MetadataRecord( + String originalId, + String encoding, + Provenance provenance, + String body, + long dateOfCollection) { this.originalId = originalId; this.encoding = encoding; this.provenance = provenance; this.body = body; this.dateOfCollection = dateOfCollection; - this.id = DHPUtils.generateIdentifier(originalId,this.provenance.getNsPrefix()); + this.id = DHPUtils.generateIdentifier(originalId, this.provenance.getNsPrefix()); } public String getId() { @@ -71,7 +57,6 @@ public class MetadataRecord implements Serializable { this.id = id; } - public String getOriginalId() { return originalId; } @@ -96,7 +81,6 @@ public class MetadataRecord implements Serializable { this.provenance = provenance; } - public String getBody() { return body; } @@ -127,7 +111,6 @@ public class MetadataRecord implements Serializable { return false; } return ((MetadataRecord) o).getId().equalsIgnoreCase(id); - } @Override diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/Provenance.java b/dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/Provenance.java index de67281f23..dbbeb92765 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/Provenance.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/Provenance.java @@ -2,27 +2,20 @@ package eu.dnetlib.dhp.model.mdstore; import java.io.Serializable; - /** * @author Sandro La Bruzzo - * - * Provenace class models the provenance of the record in the metadataStore - * It contains the identifier and the name of the datasource that gives the - * record - * + *

Provenace class models the provenance of the record in the metadataStore It contains the + * identifier and the name of the datasource that gives the record */ public class Provenance implements Serializable { private String datasourceId; - private String datasourceName; private String nsPrefix; - public Provenance() { - - } + public Provenance() {} public Provenance(String datasourceId, String datasourceName, String nsPrefix) { this.datasourceId = datasourceId; diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdException.java b/dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdException.java index 77b28f207f..aa801acd54 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdException.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdException.java @@ -9,4 +9,4 @@ public class VtdException extends Exception { public VtdException(final Throwable e) { super(e); } -} \ No newline at end of file +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdUtilityParser.java b/dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdUtilityParser.java index 5d92e1c5fd..c7a86957af 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdUtilityParser.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdUtilityParser.java @@ -1,20 +1,17 @@ package eu.dnetlib.dhp.parser.utility; +import com.ximpleware.AutoPilot; +import com.ximpleware.VTDNav; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; - -import com.ximpleware.AutoPilot; -import com.ximpleware.VTDNav; - -/** - * Created by sandro on 9/29/16. - */ +/** Created by sandro on 9/29/16. */ public class VtdUtilityParser { - public static List getTextValuesWithAttributes(final AutoPilot ap, final VTDNav vn, final String xpath, final List attributes) + public static List getTextValuesWithAttributes( + final AutoPilot ap, final VTDNav vn, final String xpath, final List attributes) throws VtdException { final List results = new ArrayList<>(); try { @@ -35,25 +32,28 @@ public class VtdUtilityParser { } } - private static Map getAttributes(final VTDNav vn, final List attributes) { + private static Map getAttributes( + final VTDNav vn, final List attributes) { final Map currentAttributes = new HashMap<>(); if (attributes != null) { - attributes.forEach(attributeKey -> { - try { - int attr = vn.getAttrVal(attributeKey); - if (attr > -1) { - currentAttributes.put(attributeKey, vn.toNormalizedString(attr)); - } - } catch (Throwable e) { - throw new RuntimeException(e); - } - }); + attributes.forEach( + attributeKey -> { + try { + int attr = vn.getAttrVal(attributeKey); + if (attr > -1) { + currentAttributes.put(attributeKey, vn.toNormalizedString(attr)); + } + } catch (Throwable e) { + throw new RuntimeException(e); + } + }); } return currentAttributes; } - public static List getTextValue(final AutoPilot ap, final VTDNav vn, final String xpath) throws VtdException { + public static List getTextValue(final AutoPilot ap, final VTDNav vn, final String xpath) + throws VtdException { List results = new ArrayList<>(); try { ap.selectXPath(xpath); @@ -67,13 +67,13 @@ public class VtdUtilityParser { } } - public static String getSingleValue(final AutoPilot ap, final VTDNav nav, final String xpath) throws VtdException { + public static String getSingleValue(final AutoPilot ap, final VTDNav nav, final String xpath) + throws VtdException { try { ap.selectXPath(xpath); while (ap.evalXPath() != -1) { int it = nav.getText(); - if (it > -1) - return nav.toNormalizedString(it); + if (it > -1) return nav.toNormalizedString(it); } return null; } catch (Exception e) { @@ -103,5 +103,4 @@ public class VtdUtilityParser { this.attributes = attributes; } } - } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java index ea8943efd2..b2b86d8f22 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java @@ -1,18 +1,16 @@ package eu.dnetlib.dhp.utils; import com.jayway.jsonpath.JsonPath; -import net.minidev.json.JSONArray; -import org.apache.commons.codec.binary.Base64; -import org.apache.commons.codec.binary.Base64OutputStream; -import org.apache.commons.codec.binary.Hex; -import org.apache.commons.lang3.StringUtils; - import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; import java.nio.charset.StandardCharsets; import java.security.MessageDigest; import java.util.zip.GZIPInputStream; import java.util.zip.GZIPOutputStream; +import net.minidev.json.JSONArray; +import org.apache.commons.codec.binary.Base64; +import org.apache.commons.codec.binary.Base64OutputStream; +import org.apache.commons.codec.binary.Hex; public class DHPUtils { @@ -28,41 +26,40 @@ public class DHPUtils { } public static String generateIdentifier(final String originalId, final String nsPrefix) { - return String.format("%s::%s",nsPrefix, DHPUtils.md5(originalId)); + return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId)); } - public static String compressString(final String input ) { - try ( ByteArrayOutputStream out = new ByteArrayOutputStream(); Base64OutputStream b64os = new Base64OutputStream(out)) { + public static String compressString(final String input) { + try (ByteArrayOutputStream out = new ByteArrayOutputStream(); + Base64OutputStream b64os = new Base64OutputStream(out)) { GZIPOutputStream gzip = new GZIPOutputStream(b64os); gzip.write(input.getBytes(StandardCharsets.UTF_8)); gzip.close(); return out.toString(); - } catch (Throwable e ) { + } catch (Throwable e) { return null; } } - public static String decompressString(final String input) { byte[] byteArray = Base64.decodeBase64(input.getBytes()); int len; - try (GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream((byteArray))); ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length)) { + try (GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream((byteArray))); + ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length)) { byte[] buffer = new byte[1024]; - while((len = gis.read(buffer)) != -1){ + while ((len = gis.read(buffer)) != -1) { bos.write(buffer, 0, len); } return bos.toString(); } catch (Exception e) { return null; } - } public static String getJPathString(final String jsonPath, final String json) { try { Object o = JsonPath.read(json, jsonPath); - if (o instanceof String) - return (String) o; + if (o instanceof String) return (String) o; if (o instanceof JSONArray && ((JSONArray) o).size() > 0) return (String) ((JSONArray) o).get(0); return o.toString(); @@ -70,5 +67,4 @@ public class DHPUtils { return ""; } } - } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/AbstractExtensionFunction.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/AbstractExtensionFunction.java index bd39624404..494a73a754 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/AbstractExtensionFunction.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/AbstractExtensionFunction.java @@ -9,10 +9,13 @@ import net.sf.saxon.trans.XPathException; public abstract class AbstractExtensionFunction extends ExtensionFunctionDefinition { - public static String DEFAULT_SAXON_EXT_NS_URI = "http://www.d-net.research-infrastructures.eu/saxon-extension"; + public static String DEFAULT_SAXON_EXT_NS_URI = + "http://www.d-net.research-infrastructures.eu/saxon-extension"; public abstract String getName(); - public abstract Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException; + + public abstract Sequence doCall(XPathContext context, Sequence[] arguments) + throws XPathException; @Override public StructuredQName getFunctionQName() { @@ -28,5 +31,4 @@ public abstract class AbstractExtensionFunction extends ExtensionFunctionDefinit } }; } - -} \ No newline at end of file +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/ExtractYear.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/ExtractYear.java index f90e2a23e8..c027074bff 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/ExtractYear.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/ExtractYear.java @@ -1,5 +1,9 @@ package eu.dnetlib.dhp.utils.saxon; +import java.text.ParseException; +import java.text.SimpleDateFormat; +import java.util.Calendar; +import java.util.GregorianCalendar; import net.sf.saxon.expr.XPathContext; import net.sf.saxon.om.Item; import net.sf.saxon.om.Sequence; @@ -7,14 +11,9 @@ import net.sf.saxon.trans.XPathException; import net.sf.saxon.value.SequenceType; import net.sf.saxon.value.StringValue; -import java.text.ParseException; -import java.text.SimpleDateFormat; -import java.util.Calendar; -import java.util.GregorianCalendar; - public class ExtractYear extends AbstractExtensionFunction { - private static final String[] dateFormats = { "yyyy-MM-dd", "yyyy/MM/dd" }; + private static final String[] dateFormats = {"yyyy-MM-dd", "yyyy/MM/dd"}; @Override public String getName() { @@ -45,7 +44,7 @@ public class ExtractYear extends AbstractExtensionFunction { @Override public SequenceType[] getArgumentTypes() { - return new SequenceType[] { SequenceType.OPTIONAL_ITEM }; + return new SequenceType[] {SequenceType.OPTIONAL_ITEM}; } @Override @@ -60,7 +59,8 @@ public class ExtractYear extends AbstractExtensionFunction { c.setTime(new SimpleDateFormat(format).parse(s)); String year = String.valueOf(c.get(Calendar.YEAR)); return year; - } catch (ParseException e) {} + } catch (ParseException e) { + } } return ""; } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java index 634e08788b..7465c9735e 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java @@ -1,18 +1,19 @@ package eu.dnetlib.dhp.utils.saxon; +import java.text.ParseException; +import java.text.SimpleDateFormat; +import java.util.Date; import net.sf.saxon.expr.XPathContext; import net.sf.saxon.om.Sequence; import net.sf.saxon.trans.XPathException; import net.sf.saxon.value.SequenceType; import net.sf.saxon.value.StringValue; -import java.text.ParseException; -import java.text.SimpleDateFormat; -import java.util.Date; - public class NormalizeDate extends AbstractExtensionFunction { - private static final String[] normalizeDateFormats = { "yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "yyyy/MM/dd", "yyyy" }; + private static final String[] normalizeDateFormats = { + "yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "yyyy/MM/dd", "yyyy" + }; private static final String normalizeOutFormat = new String("yyyy-MM-dd'T'hh:mm:ss'Z'"); @@ -42,7 +43,7 @@ public class NormalizeDate extends AbstractExtensionFunction { @Override public SequenceType[] getArgumentTypes() { - return new SequenceType[] { SequenceType.OPTIONAL_ITEM }; + return new SequenceType[] {SequenceType.OPTIONAL_ITEM}; } @Override @@ -58,9 +59,9 @@ public class NormalizeDate extends AbstractExtensionFunction { Date parse = new SimpleDateFormat(format).parse(date); String res = new SimpleDateFormat(normalizeOutFormat).format(parse); return res; - } catch (ParseException e) {} + } catch (ParseException e) { + } } return ""; } - } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/PickFirst.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/PickFirst.java index a221e37c67..16ccaaa173 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/PickFirst.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/PickFirst.java @@ -24,7 +24,8 @@ public class PickFirst extends AbstractExtensionFunction { final String s1 = getValue(arguments[0]); final String s2 = getValue(arguments[1]); - return new StringValue(StringUtils.isNotBlank(s1) ? s1 : StringUtils.isNotBlank(s2) ? s2 : ""); + return new StringValue( + StringUtils.isNotBlank(s1) ? s1 : StringUtils.isNotBlank(s2) ? s2 : ""); } private String getValue(final Sequence arg) throws XPathException { @@ -49,12 +50,11 @@ public class PickFirst extends AbstractExtensionFunction { @Override public SequenceType[] getArgumentTypes() { - return new SequenceType[] { SequenceType.OPTIONAL_ITEM }; + return new SequenceType[] {SequenceType.OPTIONAL_ITEM}; } @Override public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) { return SequenceType.SINGLE_STRING; } - } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/SaxonTransformerFactory.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/SaxonTransformerFactory.java index 611709ff0d..0ee1cfb60e 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/SaxonTransformerFactory.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/SaxonTransformerFactory.java @@ -1,17 +1,17 @@ package eu.dnetlib.dhp.utils.saxon; -import net.sf.saxon.Configuration; -import net.sf.saxon.TransformerFactoryImpl; - +import java.io.StringReader; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerException; import javax.xml.transform.stream.StreamSource; -import java.io.StringReader; +import net.sf.saxon.Configuration; +import net.sf.saxon.TransformerFactoryImpl; public class SaxonTransformerFactory { /** * Creates the index record transformer from the given XSLT + * * @param xslt * @return * @throws TransformerException @@ -26,5 +26,4 @@ public class SaxonTransformerFactory { return factory.newTransformer(new StreamSource(new StringReader(xslt))); } - } diff --git a/dhp-common/src/main/java/eu/dnetlib/message/Message.java b/dhp-common/src/main/java/eu/dnetlib/message/Message.java index 3767bd0260..6accff806d 100644 --- a/dhp-common/src/main/java/eu/dnetlib/message/Message.java +++ b/dhp-common/src/main/java/eu/dnetlib/message/Message.java @@ -2,7 +2,6 @@ package eu.dnetlib.message; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; - import java.io.IOException; import java.util.Map; @@ -16,20 +15,12 @@ public class Message { private Map body; - public static Message fromJson(final String json) throws IOException { final ObjectMapper jsonMapper = new ObjectMapper(); return jsonMapper.readValue(json, Message.class); - - } - - public Message() { - - - - } + public Message() {} public Message(String workflowId, String jobName, MessageType type, Map body) { this.workflowId = workflowId; diff --git a/dhp-common/src/main/java/eu/dnetlib/message/MessageConsumer.java b/dhp-common/src/main/java/eu/dnetlib/message/MessageConsumer.java index af5339034d..a2f3eff3eb 100644 --- a/dhp-common/src/main/java/eu/dnetlib/message/MessageConsumer.java +++ b/dhp-common/src/main/java/eu/dnetlib/message/MessageConsumer.java @@ -4,7 +4,6 @@ import com.rabbitmq.client.AMQP; import com.rabbitmq.client.Channel; import com.rabbitmq.client.DefaultConsumer; import com.rabbitmq.client.Envelope; - import java.io.IOException; import java.nio.charset.StandardCharsets; import java.util.concurrent.LinkedBlockingQueue; @@ -13,7 +12,6 @@ public class MessageConsumer extends DefaultConsumer { final LinkedBlockingQueue queueMessages; - /** * Constructs a new instance and records its association to the passed-in channel. * @@ -25,19 +23,20 @@ public class MessageConsumer extends DefaultConsumer { this.queueMessages = queueMessages; } - @Override - public void handleDelivery(String consumerTag, Envelope envelope, AMQP.BasicProperties properties, byte[] body) throws IOException { + public void handleDelivery( + String consumerTag, Envelope envelope, AMQP.BasicProperties properties, byte[] body) + throws IOException { final String json = new String(body, StandardCharsets.UTF_8); Message message = Message.fromJson(json); try { this.queueMessages.put(message); - System.out.println("Receiving Message "+message); + System.out.println("Receiving Message " + message); } catch (InterruptedException e) { - if (message.getType()== MessageType.REPORT) + if (message.getType() == MessageType.REPORT) throw new RuntimeException("Error on sending message"); else { - //TODO LOGGING EXCEPTION + // TODO LOGGING EXCEPTION } } finally { getChannel().basicAck(envelope.getDeliveryTag(), false); diff --git a/dhp-common/src/main/java/eu/dnetlib/message/MessageManager.java b/dhp-common/src/main/java/eu/dnetlib/message/MessageManager.java index e3d90f7e0e..d226e76627 100644 --- a/dhp-common/src/main/java/eu/dnetlib/message/MessageManager.java +++ b/dhp-common/src/main/java/eu/dnetlib/message/MessageManager.java @@ -3,8 +3,6 @@ package eu.dnetlib.message; import com.rabbitmq.client.Channel; import com.rabbitmq.client.Connection; import com.rabbitmq.client.ConnectionFactory; -import sun.rmi.runtime.Log; - import java.io.IOException; import java.util.HashMap; import java.util.Map; @@ -21,23 +19,32 @@ public class MessageManager { private Connection connection; - private Map channels = new HashMap<>(); + private Map channels = new HashMap<>(); - private boolean durable; + private boolean durable; - private boolean autodelete; + private boolean autodelete; - final private LinkedBlockingQueue queueMessages; + private final LinkedBlockingQueue queueMessages; - public MessageManager(String messageHost, String username, String password, final LinkedBlockingQueue queueMessages) { + public MessageManager( + String messageHost, + String username, + String password, + final LinkedBlockingQueue queueMessages) { this.queueMessages = queueMessages; this.messageHost = messageHost; this.username = username; this.password = password; } - - public MessageManager(String messageHost, String username, String password, boolean durable, boolean autodelete, final LinkedBlockingQueue queueMessages) { + public MessageManager( + String messageHost, + String username, + String password, + boolean durable, + boolean autodelete, + final LinkedBlockingQueue queueMessages) { this.queueMessages = queueMessages; this.messageHost = messageHost; this.username = username; @@ -55,7 +62,12 @@ public class MessageManager { return factory.newConnection(); } - private Channel createChannel(final Connection connection, final String queueName, final boolean durable, final boolean autodelete ) throws Exception { + private Channel createChannel( + final Connection connection, + final String queueName, + final boolean durable, + final boolean autodelete) + throws Exception { Map args = new HashMap<>(); args.put("x-message-ttl", 10000); Channel channel = connection.createChannel(); @@ -63,9 +75,10 @@ public class MessageManager { return channel; } - private Channel getOrCreateChannel(final String queueName, boolean durable, boolean autodelete) throws Exception { + private Channel getOrCreateChannel(final String queueName, boolean durable, boolean autodelete) + throws Exception { if (channels.containsKey(queueName)) { - return channels.get(queueName); + return channels.get(queueName); } if (this.connection == null) { @@ -75,16 +88,16 @@ public class MessageManager { return channels.get(queueName); } - - public void close() throws IOException { - channels.values().forEach(ch-> { - try { - ch.close(); - } catch (Exception e) { - //TODO LOG - } - }); + channels.values() + .forEach( + ch -> { + try { + ch.close(); + } catch (Exception e) { + // TODO LOG + } + }); this.connection.close(); } @@ -92,26 +105,30 @@ public class MessageManager { public boolean sendMessage(final Message message, String queueName) throws Exception { try { Channel channel = getOrCreateChannel(queueName, this.durable, this.autodelete); - channel.basicPublish("", queueName,null, message.toString().getBytes()); + channel.basicPublish("", queueName, null, message.toString().getBytes()); return true; } catch (Throwable e) { throw new RuntimeException(e); } } - public boolean sendMessage(final Message message, String queueName, boolean durable_var, boolean autodelete_var) throws Exception { + public boolean sendMessage( + final Message message, String queueName, boolean durable_var, boolean autodelete_var) + throws Exception { try { Channel channel = getOrCreateChannel(queueName, durable_var, autodelete_var); - channel.basicPublish("", queueName,null, message.toString().getBytes()); + channel.basicPublish("", queueName, null, message.toString().getBytes()); return true; } catch (Throwable e) { throw new RuntimeException(e); } } - public void startConsumingMessage(final String queueName, final boolean durable, final boolean autodelete) throws Exception{ + public void startConsumingMessage( + final String queueName, final boolean durable, final boolean autodelete) + throws Exception { Channel channel = createChannel(createConnection(), queueName, durable, autodelete); - channel.basicConsume(queueName, false, new MessageConsumer(channel,queueMessages)); + channel.basicConsume(queueName, false, new MessageConsumer(channel, queueMessages)); } } diff --git a/dhp-common/src/main/java/eu/dnetlib/message/MessageType.java b/dhp-common/src/main/java/eu/dnetlib/message/MessageType.java index c2440c3fe7..37db1ec4fc 100644 --- a/dhp-common/src/main/java/eu/dnetlib/message/MessageType.java +++ b/dhp-common/src/main/java/eu/dnetlib/message/MessageType.java @@ -1,8 +1,6 @@ package eu.dnetlib.message; public enum MessageType { - ONGOING, REPORT - } diff --git a/dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelInfo.java b/dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelInfo.java index ff88cda4c1..0d6cd33c1a 100644 --- a/dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelInfo.java +++ b/dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelInfo.java @@ -2,7 +2,7 @@ package eu.dnetlib.scholexplorer.relation; import java.io.Serializable; -public class RelInfo implements Serializable { +public class RelInfo implements Serializable { private String original; private String inverse; diff --git a/dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelationMapper.java b/dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelationMapper.java index 647c117896..5d5659ea62 100644 --- a/dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelationMapper.java +++ b/dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelationMapper.java @@ -1,19 +1,18 @@ package eu.dnetlib.scholexplorer.relation; import com.fasterxml.jackson.databind.ObjectMapper; -import org.apache.commons.io.IOUtils; - import java.io.Serializable; import java.util.HashMap; +import org.apache.commons.io.IOUtils; -public class RelationMapper extends HashMap implements Serializable { +public class RelationMapper extends HashMap implements Serializable { public static RelationMapper load() throws Exception { - final String json = IOUtils.toString(RelationMapper.class.getResourceAsStream("relations.json")); + final String json = + IOUtils.toString(RelationMapper.class.getResourceAsStream("relations.json")); ObjectMapper mapper = new ObjectMapper(); return mapper.readValue(json, RelationMapper.class); } - } diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java index f4598ebd49..81f86657dc 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java @@ -1,30 +1,46 @@ package eu.dnetlib.dhp.application; -import org.apache.commons.io.IOUtils; -import org.junit.jupiter.api.Test; - import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertNotNull; +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.Test; + public class ArgumentApplicationParserTest { @Test public void testParseParameter() throws Exception { - final String jsonConfiguration = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/application/parameters.json")); + final String jsonConfiguration = + IOUtils.toString( + this.getClass() + .getResourceAsStream("/eu/dnetlib/application/parameters.json")); assertNotNull(jsonConfiguration); ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(new String[]{"-p", "value0", - "-a", "value1", - "-n", "value2", - "-u", "value3", - "-ru", "value4", - "-rp", "value5", - "-rh", "value6", - "-ro", "value7", - "-rr", "value8", - "-w", "value9", - "-cc", ArgumentApplicationParser.compressArgument(jsonConfiguration) - }); + parser.parseArgument( + new String[] { + "-p", + "value0", + "-a", + "value1", + "-n", + "value2", + "-u", + "value3", + "-ru", + "value4", + "-rp", + "value5", + "-rh", + "value6", + "-ro", + "value7", + "-rr", + "value8", + "-w", + "value9", + "-cc", + ArgumentApplicationParser.compressArgument(jsonConfiguration) + }); assertNotNull(parser.get("hdfsPath")); assertNotNull(parser.get("apidescriptor")); assertNotNull(parser.get("namenode")); @@ -47,10 +63,4 @@ public class ArgumentApplicationParserTest { assertEquals("value9", parser.get("workflowId")); assertEquals(jsonConfiguration, parser.get("ccCoco")); } - - - - - - } diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/common/HdfsSupportTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/common/HdfsSupportTest.java index f1e790ee7c..dac48b22d1 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/common/HdfsSupportTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/common/HdfsSupportTest.java @@ -1,9 +1,6 @@ package eu.dnetlib.dhp.common; -import org.apache.hadoop.conf.Configuration; -import org.junit.jupiter.api.Nested; -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.io.TempDir; +import static org.junit.jupiter.api.Assertions.*; import java.io.IOException; import java.nio.file.Files; @@ -11,8 +8,10 @@ import java.nio.file.Path; import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; - -import static org.junit.jupiter.api.Assertions.*; +import org.apache.hadoop.conf.Configuration; +import org.junit.jupiter.api.Nested; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.io.TempDir; public class HdfsSupportTest { @@ -22,8 +21,8 @@ public class HdfsSupportTest { @Test public void shouldThrowARuntimeExceptionOnError() { // when - assertThrows(RuntimeException.class, () -> - HdfsSupport.remove(null, new Configuration())); + assertThrows( + RuntimeException.class, () -> HdfsSupport.remove(null, new Configuration())); } @Test @@ -54,8 +53,8 @@ public class HdfsSupportTest { @Test public void shouldThrowARuntimeExceptionOnError() { // when - assertThrows(RuntimeException.class, () -> - HdfsSupport.listFiles(null, new Configuration())); + assertThrows( + RuntimeException.class, () -> HdfsSupport.listFiles(null, new Configuration())); } @Test @@ -68,11 +67,13 @@ public class HdfsSupportTest { // then assertEquals(2, paths.size()); - List expecteds = Arrays.stream(new String[]{subDir1.toString(), subDir2.toString()}) - .sorted().collect(Collectors.toList()); + List expecteds = + Arrays.stream(new String[] {subDir1.toString(), subDir2.toString()}) + .sorted() + .collect(Collectors.toList()); List actuals = paths.stream().sorted().collect(Collectors.toList()); assertTrue(actuals.get(0).contains(expecteds.get(0))); assertTrue(actuals.get(1).contains(expecteds.get(1))); } } -} \ No newline at end of file +} diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java index bc2dce3cff..17424c38a4 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java @@ -1,22 +1,22 @@ package eu.dnetlib.dhp.common; +import static org.mockito.Mockito.*; + import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer; +import java.util.function.Function; import org.apache.spark.SparkConf; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.Nested; import org.junit.jupiter.api.Test; -import java.util.function.Function; - -import static org.mockito.Mockito.*; - public class SparkSessionSupportTest { @Nested class RunWithSparkSession { @Test - public void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged() throws Exception { + public void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged() + throws Exception { // given SparkSession spark = mock(SparkSession.class); SparkConf conf = mock(SparkConf.class); @@ -34,7 +34,8 @@ public class SparkSessionSupportTest { } @Test - public void shouldExecuteFunctionAndStopSparkSessionWhenSparkSessionIsManaged() throws Exception { + public void shouldExecuteFunctionAndStopSparkSessionWhenSparkSessionIsManaged() + throws Exception { // given SparkSession spark = mock(SparkSession.class); SparkConf conf = mock(SparkConf.class); @@ -51,4 +52,4 @@ public class SparkSessionSupportTest { verify(spark, times(1)).stop(); } } -} \ No newline at end of file +} diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/model/mdstore/MetadataRecordTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/model/mdstore/MetadataRecordTest.java index a2bac54baf..0750ad03a9 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/model/mdstore/MetadataRecordTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/model/mdstore/MetadataRecordTest.java @@ -1,9 +1,9 @@ package eu.dnetlib.dhp.model.mdstore; -import org.junit.jupiter.api.Test; - import static org.junit.jupiter.api.Assertions.assertTrue; +import org.junit.jupiter.api.Test; + public class MetadataRecordTest { @Test @@ -12,4 +12,4 @@ public class MetadataRecordTest { MetadataRecord r = new MetadataRecord(); assertTrue(r.getDateOfCollection() > 0); } -} \ No newline at end of file +} diff --git a/dhp-common/src/test/java/eu/dnetlib/message/MessageTest.java b/dhp-common/src/test/java/eu/dnetlib/message/MessageTest.java index 73df63b321..9e57c286c5 100644 --- a/dhp-common/src/test/java/eu/dnetlib/message/MessageTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/message/MessageTest.java @@ -1,12 +1,11 @@ package eu.dnetlib.message; -import org.junit.jupiter.api.Test; +import static org.junit.jupiter.api.Assertions.*; import java.io.IOException; import java.util.HashMap; import java.util.Map; - -import static org.junit.jupiter.api.Assertions.*; +import org.junit.jupiter.api.Test; public class MessageTest { @@ -16,7 +15,7 @@ public class MessageTest { m.setWorkflowId("wId"); m.setType(MessageType.ONGOING); m.setJobName("Collection"); - Map body= new HashMap<>(); + Map body = new HashMap<>(); body.put("parsedItem", "300"); body.put("ExecutionTime", "30s"); @@ -28,28 +27,26 @@ public class MessageTest { assertEquals(m1.getJobName(), m.getJobName()); assertNotNull(m1.getBody()); - m1.getBody().keySet().forEach(it -> assertEquals(m1.getBody().get(it), m.getBody().get(it))); + m1.getBody() + .keySet() + .forEach(it -> assertEquals(m1.getBody().get(it), m.getBody().get(it))); assertEquals(m1.getJobName(), m.getJobName()); } @Test public void toStringTest() { - final String expectedJson= "{\"workflowId\":\"wId\",\"jobName\":\"Collection\",\"type\":\"ONGOING\",\"body\":{\"ExecutionTime\":\"30s\",\"parsedItem\":\"300\"}}"; + final String expectedJson = + "{\"workflowId\":\"wId\",\"jobName\":\"Collection\",\"type\":\"ONGOING\",\"body\":{\"ExecutionTime\":\"30s\",\"parsedItem\":\"300\"}}"; Message m = new Message(); m.setWorkflowId("wId"); m.setType(MessageType.ONGOING); m.setJobName("Collection"); - Map body= new HashMap<>(); + Map body = new HashMap<>(); body.put("parsedItem", "300"); body.put("ExecutionTime", "30s"); m.setBody(body); - assertEquals(expectedJson,m.toString()); - - + assertEquals(expectedJson, m.toString()); } - - - -} \ No newline at end of file +} diff --git a/dhp-common/src/test/java/eu/dnetlib/scholexplorer/relation/RelationMapperTest.java b/dhp-common/src/test/java/eu/dnetlib/scholexplorer/relation/RelationMapperTest.java index eb9fb172d6..40a2aaecd7 100644 --- a/dhp-common/src/test/java/eu/dnetlib/scholexplorer/relation/RelationMapperTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/scholexplorer/relation/RelationMapperTest.java @@ -2,14 +2,12 @@ package eu.dnetlib.scholexplorer.relation; import org.junit.jupiter.api.Test; - public class RelationMapperTest { @Test - public void testLoadRels() throws Exception{ + public void testLoadRels() throws Exception { RelationMapper relationMapper = RelationMapper.load(); relationMapper.keySet().forEach(System.out::println); - } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicAction.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicAction.java index 0f9aa3adbc..f7e5edc668 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicAction.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicAction.java @@ -2,7 +2,6 @@ package eu.dnetlib.dhp.schema.action; import com.fasterxml.jackson.databind.annotation.JsonDeserialize; import eu.dnetlib.dhp.schema.oaf.Oaf; - import java.io.Serializable; @JsonDeserialize(using = AtomicActionDeserializer.class) @@ -12,8 +11,7 @@ public class AtomicAction implements Serializable { private T payload; - public AtomicAction() { - } + public AtomicAction() {} public AtomicAction(Class clazz, T payload) { this.clazz = clazz; diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicActionDeserializer.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicActionDeserializer.java index e6017288fa..ad08e401c9 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicActionDeserializer.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicActionDeserializer.java @@ -7,13 +7,13 @@ import com.fasterxml.jackson.databind.JsonDeserializer; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.oaf.Oaf; - import java.io.IOException; public class AtomicActionDeserializer extends JsonDeserializer { @Override - public Object deserialize(JsonParser jp, DeserializationContext ctxt) throws IOException, JsonProcessingException { + public Object deserialize(JsonParser jp, DeserializationContext ctxt) + throws IOException, JsonProcessingException { JsonNode node = jp.getCodec().readTree(jp); String classTag = node.get("clazz").asText(); JsonNode payload = node.get("payload"); diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/EntityType.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/EntityType.java index 9e4fa7d8ac..701c83fc20 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/EntityType.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/EntityType.java @@ -2,15 +2,19 @@ package eu.dnetlib.dhp.schema.common; import eu.dnetlib.dhp.schema.oaf.OafEntity; -/** - * Actual entity types in the Graph - */ +/** Actual entity types in the Graph */ public enum EntityType { - - publication, dataset, otherresearchproduct, software, datasource, organization, project; + publication, + dataset, + otherresearchproduct, + software, + datasource, + organization, + project; /** * Resolves the EntityType, given the relative class name + * * @param clazz the given class name * @param actual OafEntity subclass * @return the EntityType associated to the given class @@ -19,5 +23,4 @@ public enum EntityType { return EntityType.valueOf(clazz.getSimpleName().toLowerCase()); } - } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/MainEntityType.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/MainEntityType.java index 7d65e39c09..c4abbfd003 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/MainEntityType.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/MainEntityType.java @@ -1,9 +1,9 @@ package eu.dnetlib.dhp.schema.common; -/** - * Main entity types in the Graph - */ +/** Main entity types in the Graph */ public enum MainEntityType { - - result, datasource, organization, project -} \ No newline at end of file + result, + datasource, + organization, + project +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java index 48f711a030..bc317a6ff6 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java @@ -2,33 +2,29 @@ package eu.dnetlib.dhp.schema.common; import com.google.common.collect.Maps; import eu.dnetlib.dhp.schema.oaf.*; - import java.util.Map; -/** - * Oaf model utility methods. - */ +/** Oaf model utility methods. */ public class ModelSupport { - /** - * Defines the mapping between the actual entity type and the main entity type - */ + /** Defines the mapping between the actual entity type and the main entity type */ private static Map entityMapping = Maps.newHashMap(); static { - entityMapping.put(EntityType.publication, MainEntityType.result); - entityMapping.put(EntityType.dataset, MainEntityType.result); - entityMapping.put(EntityType.otherresearchproduct, MainEntityType.result); - entityMapping.put(EntityType.software, MainEntityType.result); - entityMapping.put(EntityType.datasource, MainEntityType.datasource); - entityMapping.put(EntityType.organization, MainEntityType.organization); - entityMapping.put(EntityType.project, MainEntityType.project); + entityMapping.put(EntityType.publication, MainEntityType.result); + entityMapping.put(EntityType.dataset, MainEntityType.result); + entityMapping.put(EntityType.otherresearchproduct, MainEntityType.result); + entityMapping.put(EntityType.software, MainEntityType.result); + entityMapping.put(EntityType.datasource, MainEntityType.datasource); + entityMapping.put(EntityType.organization, MainEntityType.organization); + entityMapping.put(EntityType.project, MainEntityType.project); } /** - * Defines the mapping between the actual entity types and the relative classes implementing them + * Defines the mapping between the actual entity types and the relative classes implementing + * them */ - public final static Map entityTypes = Maps.newHashMap(); + public static final Map entityTypes = Maps.newHashMap(); static { entityTypes.put(EntityType.datasource, Datasource.class); @@ -40,7 +36,7 @@ public class ModelSupport { entityTypes.put(EntityType.publication, Publication.class); } - public final static Map oafTypes = Maps.newHashMap(); + public static final Map oafTypes = Maps.newHashMap(); static { oafTypes.put("datasource", Datasource.class); @@ -55,19 +51,19 @@ public class ModelSupport { private static final String schemeTemplate = "dnet:%s_%s_relations"; - private ModelSupport() { - } + private ModelSupport() {} /** * Checks subclass-superclass relationship. * - * @param subClazzObject Subclass object instance + * @param subClazzObject Subclass object instance * @param superClazzObject Superclass object instance - * @param Subclass type - * @param Superclass type + * @param Subclass type + * @param Superclass type * @return True if X is a subclass of Y */ - public static Boolean isSubClass(X subClazzObject, Y superClazzObject) { + public static Boolean isSubClass( + X subClazzObject, Y superClazzObject) { return isSubClass(subClazzObject.getClass(), superClazzObject.getClass()); } @@ -75,25 +71,27 @@ public class ModelSupport { * Checks subclass-superclass relationship. * * @param subClazzObject Subclass object instance - * @param superClazz Superclass class - * @param Subclass type - * @param Superclass type + * @param superClazz Superclass class + * @param Subclass type + * @param Superclass type * @return True if X is a subclass of Y */ - public static Boolean isSubClass(X subClazzObject, Class superClazz) { + public static Boolean isSubClass( + X subClazzObject, Class superClazz) { return isSubClass(subClazzObject.getClass(), superClazz); } /** * Checks subclass-superclass relationship. * - * @param subClazz Subclass class + * @param subClazz Subclass class * @param superClazz Superclass class - * @param Subclass type - * @param Superclass type + * @param Subclass type + * @param Superclass type * @return True if X is a subclass of Y */ - public static Boolean isSubClass(Class subClazz, Class superClazz) { + public static Boolean isSubClass( + Class subClazz, Class superClazz) { return superClazz.isAssignableFrom(subClazz); } @@ -104,33 +102,33 @@ public class ModelSupport { * @return */ public static Class[] getOafModelClasses() { - return new Class[]{ - Author.class, - Context.class, - Country.class, - DataInfo.class, - Dataset.class, - Datasource.class, - ExternalReference.class, - ExtraInfo.class, - Field.class, - GeoLocation.class, - Instance.class, - Journal.class, - KeyValue.class, - Oaf.class, - OafEntity.class, - OAIProvenance.class, - Organization.class, - OriginDescription.class, - OtherResearchProduct.class, - Project.class, - Publication.class, - Qualifier.class, - Relation.class, - Result.class, - Software.class, - StructuredProperty.class + return new Class[] { + Author.class, + Context.class, + Country.class, + DataInfo.class, + Dataset.class, + Datasource.class, + ExternalReference.class, + ExtraInfo.class, + Field.class, + GeoLocation.class, + Instance.class, + Journal.class, + KeyValue.class, + Oaf.class, + OafEntity.class, + OAIProvenance.class, + Organization.class, + OriginDescription.class, + OtherResearchProduct.class, + Project.class, + Publication.class, + Qualifier.class, + Relation.class, + Result.class, + Software.class, + StructuredProperty.class }; } @@ -143,9 +141,9 @@ public class ModelSupport { } public static String getScheme(final String sourceType, final String targetType) { - return String.format(schemeTemplate, + return String.format( + schemeTemplate, entityMapping.get(EntityType.valueOf(sourceType)).name(), entityMapping.get(EntityType.valueOf(targetType)).name()); } - -} \ No newline at end of file +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Author.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Author.java index 93ab60b05f..e8022bfc1d 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Author.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Author.java @@ -71,12 +71,12 @@ public class Author implements Serializable { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; Author author = (Author) o; - return Objects.equals(fullname, author.fullname) && - Objects.equals(name, author.name) && - Objects.equals(surname, author.surname) && - Objects.equals(rank, author.rank) && - Objects.equals(pid, author.pid) && - Objects.equals(affiliation, author.affiliation); + return Objects.equals(fullname, author.fullname) + && Objects.equals(name, author.name) + && Objects.equals(surname, author.surname) + && Objects.equals(rank, author.rank) + && Objects.equals(pid, author.pid) + && Objects.equals(affiliation, author.affiliation); } @Override diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Context.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Context.java index 8092004635..0e0d1ad32c 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Context.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Context.java @@ -26,17 +26,14 @@ public class Context implements Serializable { @Override public int hashCode() { - return id ==null? 0 : id.hashCode(); + return id == null ? 0 : id.hashCode(); } @Override public boolean equals(Object obj) { - if (this == obj) - return true; - if (obj == null) - return false; - if (getClass() != obj.getClass()) - return false; + if (this == obj) return true; + if (obj == null) return false; + if (getClass() != obj.getClass()) return false; Context other = (Context) obj; diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java index 49a1867018..0e3f366713 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; -import java.util.List; import java.util.Objects; public class DataInfo implements Serializable { @@ -13,7 +12,6 @@ public class DataInfo implements Serializable { private String inferenceprovenance; private Qualifier provenanceaction; - public Boolean getInvisible() { return invisible; } @@ -67,16 +65,22 @@ public class DataInfo implements Serializable { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; DataInfo dataInfo = (DataInfo) o; - return Objects.equals(invisible, dataInfo.invisible) && - Objects.equals(inferred, dataInfo.inferred) && - Objects.equals(deletedbyinference, dataInfo.deletedbyinference) && - Objects.equals(trust, dataInfo.trust) && - Objects.equals(inferenceprovenance, dataInfo.inferenceprovenance) && - Objects.equals(provenanceaction, dataInfo.provenanceaction); + return Objects.equals(invisible, dataInfo.invisible) + && Objects.equals(inferred, dataInfo.inferred) + && Objects.equals(deletedbyinference, dataInfo.deletedbyinference) + && Objects.equals(trust, dataInfo.trust) + && Objects.equals(inferenceprovenance, dataInfo.inferenceprovenance) + && Objects.equals(provenanceaction, dataInfo.provenanceaction); } @Override public int hashCode() { - return Objects.hash(invisible, inferred, deletedbyinference, trust, inferenceprovenance, provenanceaction); + return Objects.hash( + invisible, + inferred, + deletedbyinference, + trust, + inferenceprovenance, + provenanceaction); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java index 70a6d1f316..fef6ed748b 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java @@ -20,7 +20,7 @@ public class Dataset extends Result implements Serializable { private List geolocation; - public Field getStoragedate() { + public Field getStoragedate() { return storagedate; } @@ -80,23 +80,32 @@ public class Dataset extends Result implements Serializable { public void mergeFrom(OafEntity e) { super.mergeFrom(e); - if (!Dataset.class.isAssignableFrom(e.getClass())){ + if (!Dataset.class.isAssignableFrom(e.getClass())) { return; } final Dataset d = (Dataset) e; - storagedate = d.getStoragedate() != null && compareTrust(this, e)<0? d.getStoragedate() : storagedate; + storagedate = + d.getStoragedate() != null && compareTrust(this, e) < 0 + ? d.getStoragedate() + : storagedate; - device= d.getDevice() != null && compareTrust(this, e)<0? d.getDevice() : device; + device = d.getDevice() != null && compareTrust(this, e) < 0 ? d.getDevice() : device; - size= d.getSize() != null && compareTrust(this, e)<0? d.getSize() : size; + size = d.getSize() != null && compareTrust(this, e) < 0 ? d.getSize() : size; - version= d.getVersion() != null && compareTrust(this, e)<0? d.getVersion() : version; + version = d.getVersion() != null && compareTrust(this, e) < 0 ? d.getVersion() : version; - lastmetadataupdate= d.getLastmetadataupdate() != null && compareTrust(this, e)<0? d.getLastmetadataupdate() :lastmetadataupdate; + lastmetadataupdate = + d.getLastmetadataupdate() != null && compareTrust(this, e) < 0 + ? d.getLastmetadataupdate() + : lastmetadataupdate; - metadataversionnumber= d.getMetadataversionnumber() != null && compareTrust(this, e)<0? d.getMetadataversionnumber() : metadataversionnumber; + metadataversionnumber = + d.getMetadataversionnumber() != null && compareTrust(this, e) < 0 + ? d.getMetadataversionnumber() + : metadataversionnumber; geolocation = mergeLists(geolocation, d.getGeolocation()); @@ -109,17 +118,25 @@ public class Dataset extends Result implements Serializable { if (o == null || getClass() != o.getClass()) return false; if (!super.equals(o)) return false; Dataset dataset = (Dataset) o; - return Objects.equals(storagedate, dataset.storagedate) && - Objects.equals(device, dataset.device) && - Objects.equals(size, dataset.size) && - Objects.equals(version, dataset.version) && - Objects.equals(lastmetadataupdate, dataset.lastmetadataupdate) && - Objects.equals(metadataversionnumber, dataset.metadataversionnumber) && - Objects.equals(geolocation, dataset.geolocation); + return Objects.equals(storagedate, dataset.storagedate) + && Objects.equals(device, dataset.device) + && Objects.equals(size, dataset.size) + && Objects.equals(version, dataset.version) + && Objects.equals(lastmetadataupdate, dataset.lastmetadataupdate) + && Objects.equals(metadataversionnumber, dataset.metadataversionnumber) + && Objects.equals(geolocation, dataset.geolocation); } @Override public int hashCode() { - return Objects.hash(super.hashCode(), storagedate, device, size, version, lastmetadataupdate, metadataversionnumber, geolocation); + return Objects.hash( + super.hashCode(), + storagedate, + device, + size, + version, + lastmetadataupdate, + metadataversionnumber, + geolocation); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java index c8d9736c5a..f2755b86b6 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java @@ -72,7 +72,7 @@ public class Datasource extends OafEntity implements Serializable { private Field citationguidelineurl; - //{yes, no, uknown} + // {yes, no, uknown} private Field qualitymanagementkind; private Field pidsystems; @@ -367,65 +367,148 @@ public class Datasource extends OafEntity implements Serializable { public void mergeFrom(OafEntity e) { super.mergeFrom(e); - if (!Datasource.class.isAssignableFrom(e.getClass())){ + if (!Datasource.class.isAssignableFrom(e.getClass())) { return; } - Datasource d = (Datasource)e; + Datasource d = (Datasource) e; - datasourcetype = d.getDatasourcetype() != null && compareTrust(this, e)<0? d.getDatasourcetype() : datasourcetype; - openairecompatibility = d.getOpenairecompatibility() != null && compareTrust(this, e)<0? d.getOpenairecompatibility() : openairecompatibility; - officialname = d.getOfficialname() != null && compareTrust(this, e)<0? d.getOfficialname() : officialname; - englishname = d.getEnglishname() != null && compareTrust(this, e)<0? d.getEnglishname() : officialname; - websiteurl = d.getWebsiteurl() != null && compareTrust(this, e)<0? d.getWebsiteurl() : websiteurl; - logourl = d.getLogourl() != null && compareTrust(this, e)<0? d.getLogourl() : getLogourl(); - contactemail = d.getContactemail() != null && compareTrust(this, e)<0? d.getContactemail() : contactemail; - namespaceprefix = d.getNamespaceprefix() != null && compareTrust(this, e)<0? d.getNamespaceprefix() : namespaceprefix; - latitude = d.getLatitude() != null && compareTrust(this, e)<0? d.getLatitude() : latitude; - longitude = d.getLongitude() != null && compareTrust(this, e)<0? d.getLongitude() : longitude; - dateofvalidation = d.getDateofvalidation() != null && compareTrust(this, e)<0? d.getDateofvalidation() : dateofvalidation; - description = d.getDescription() != null && compareTrust(this, e)<0? d.getDescription() : description; + datasourcetype = + d.getDatasourcetype() != null && compareTrust(this, e) < 0 + ? d.getDatasourcetype() + : datasourcetype; + openairecompatibility = + d.getOpenairecompatibility() != null && compareTrust(this, e) < 0 + ? d.getOpenairecompatibility() + : openairecompatibility; + officialname = + d.getOfficialname() != null && compareTrust(this, e) < 0 + ? d.getOfficialname() + : officialname; + englishname = + d.getEnglishname() != null && compareTrust(this, e) < 0 + ? d.getEnglishname() + : officialname; + websiteurl = + d.getWebsiteurl() != null && compareTrust(this, e) < 0 + ? d.getWebsiteurl() + : websiteurl; + logourl = + d.getLogourl() != null && compareTrust(this, e) < 0 ? d.getLogourl() : getLogourl(); + contactemail = + d.getContactemail() != null && compareTrust(this, e) < 0 + ? d.getContactemail() + : contactemail; + namespaceprefix = + d.getNamespaceprefix() != null && compareTrust(this, e) < 0 + ? d.getNamespaceprefix() + : namespaceprefix; + latitude = + d.getLatitude() != null && compareTrust(this, e) < 0 ? d.getLatitude() : latitude; + longitude = + d.getLongitude() != null && compareTrust(this, e) < 0 + ? d.getLongitude() + : longitude; + dateofvalidation = + d.getDateofvalidation() != null && compareTrust(this, e) < 0 + ? d.getDateofvalidation() + : dateofvalidation; + description = + d.getDescription() != null && compareTrust(this, e) < 0 + ? d.getDescription() + : description; subjects = mergeLists(subjects, d.getSubjects()); // opendoar specific fields (od*) - odnumberofitems = d.getOdnumberofitems() != null && compareTrust(this, e)<0? d.getOdnumberofitems() : odnumberofitems; - odnumberofitemsdate = d.getOdnumberofitemsdate() != null && compareTrust(this, e)<0? d.getOdnumberofitemsdate() : odnumberofitemsdate; - odpolicies = d.getOdpolicies() != null && compareTrust(this, e)<0? d.getOdpolicies() : odpolicies; + odnumberofitems = + d.getOdnumberofitems() != null && compareTrust(this, e) < 0 + ? d.getOdnumberofitems() + : odnumberofitems; + odnumberofitemsdate = + d.getOdnumberofitemsdate() != null && compareTrust(this, e) < 0 + ? d.getOdnumberofitemsdate() + : odnumberofitemsdate; + odpolicies = + d.getOdpolicies() != null && compareTrust(this, e) < 0 + ? d.getOdpolicies() + : odpolicies; odlanguages = mergeLists(odlanguages, d.getOdlanguages()); odcontenttypes = mergeLists(odcontenttypes, d.getOdcontenttypes()); accessinfopackage = mergeLists(accessinfopackage, d.getAccessinfopackage()); // re3data fields - releasestartdate = d.getReleasestartdate() != null && compareTrust(this, e)<0? d.getReleasestartdate() : releasestartdate; - releaseenddate = d.getReleaseenddate() != null && compareTrust(this, e)<0? d.getReleaseenddate() : releaseenddate; - missionstatementurl = d.getMissionstatementurl() != null && compareTrust(this, e)<0? d.getMissionstatementurl() : missionstatementurl; - dataprovider = d.getDataprovider() != null && compareTrust(this, e)<0? d.getDataprovider() : dataprovider; - serviceprovider = d.getServiceprovider() != null && compareTrust(this, e)<0? d.getServiceprovider() : serviceprovider; + releasestartdate = + d.getReleasestartdate() != null && compareTrust(this, e) < 0 + ? d.getReleasestartdate() + : releasestartdate; + releaseenddate = + d.getReleaseenddate() != null && compareTrust(this, e) < 0 + ? d.getReleaseenddate() + : releaseenddate; + missionstatementurl = + d.getMissionstatementurl() != null && compareTrust(this, e) < 0 + ? d.getMissionstatementurl() + : missionstatementurl; + dataprovider = + d.getDataprovider() != null && compareTrust(this, e) < 0 + ? d.getDataprovider() + : dataprovider; + serviceprovider = + d.getServiceprovider() != null && compareTrust(this, e) < 0 + ? d.getServiceprovider() + : serviceprovider; // {open, restricted or closed} - databaseaccesstype = d.getDatabaseaccesstype() != null && compareTrust(this, e)<0? d.getDatabaseaccesstype() : databaseaccesstype; + databaseaccesstype = + d.getDatabaseaccesstype() != null && compareTrust(this, e) < 0 + ? d.getDatabaseaccesstype() + : databaseaccesstype; // {open, restricted or closed} - datauploadtype = d.getDatauploadtype() != null && compareTrust(this, e)<0? d.getDatauploadtype() : datauploadtype; + datauploadtype = + d.getDatauploadtype() != null && compareTrust(this, e) < 0 + ? d.getDatauploadtype() + : datauploadtype; // {feeRequired, registration, other} - databaseaccessrestriction = d.getDatabaseaccessrestriction() != null && compareTrust(this, e)<0? d.getDatabaseaccessrestriction() : databaseaccessrestriction; + databaseaccessrestriction = + d.getDatabaseaccessrestriction() != null && compareTrust(this, e) < 0 + ? d.getDatabaseaccessrestriction() + : databaseaccessrestriction; // {feeRequired, registration, other} - datauploadrestriction = d.getDatauploadrestriction() != null && compareTrust(this, e)<0? d.getDatauploadrestriction() : datauploadrestriction; + datauploadrestriction = + d.getDatauploadrestriction() != null && compareTrust(this, e) < 0 + ? d.getDatauploadrestriction() + : datauploadrestriction; - versioning = d.getVersioning() != null && compareTrust(this, e)<0? d.getVersioning() : versioning; - citationguidelineurl = d.getCitationguidelineurl() != null && compareTrust(this, e)<0? d.getCitationguidelineurl() : citationguidelineurl; + versioning = + d.getVersioning() != null && compareTrust(this, e) < 0 + ? d.getVersioning() + : versioning; + citationguidelineurl = + d.getCitationguidelineurl() != null && compareTrust(this, e) < 0 + ? d.getCitationguidelineurl() + : citationguidelineurl; - //{yes, no, unknown} - qualitymanagementkind = d.getQualitymanagementkind() != null && compareTrust(this, e)<0? d.getQualitymanagementkind() : qualitymanagementkind; - pidsystems = d.getPidsystems() != null && compareTrust(this, e)<0? d.getPidsystems() : pidsystems; + // {yes, no, unknown} + qualitymanagementkind = + d.getQualitymanagementkind() != null && compareTrust(this, e) < 0 + ? d.getQualitymanagementkind() + : qualitymanagementkind; + pidsystems = + d.getPidsystems() != null && compareTrust(this, e) < 0 + ? d.getPidsystems() + : pidsystems; - certificates = d.getCertificates() != null && compareTrust(this, e)<0? d.getCertificates() : certificates; + certificates = + d.getCertificates() != null && compareTrust(this, e) < 0 + ? d.getCertificates() + : certificates; policies = mergeLists(policies, d.getPolicies()); - journal = d.getJournal() != null && compareTrust(this, e)<0? d.getJournal() : journal; + journal = d.getJournal() != null && compareTrust(this, e) < 0 ? d.getJournal() : journal; mergeOAFDataInfo(e); } @@ -436,45 +519,81 @@ public class Datasource extends OafEntity implements Serializable { if (o == null || getClass() != o.getClass()) return false; if (!super.equals(o)) return false; Datasource that = (Datasource) o; - return Objects.equals(datasourcetype, that.datasourcetype) && - Objects.equals(openairecompatibility, that.openairecompatibility) && - Objects.equals(officialname, that.officialname) && - Objects.equals(englishname, that.englishname) && - Objects.equals(websiteurl, that.websiteurl) && - Objects.equals(logourl, that.logourl) && - Objects.equals(contactemail, that.contactemail) && - Objects.equals(namespaceprefix, that.namespaceprefix) && - Objects.equals(latitude, that.latitude) && - Objects.equals(longitude, that.longitude) && - Objects.equals(dateofvalidation, that.dateofvalidation) && - Objects.equals(description, that.description) && - Objects.equals(subjects, that.subjects) && - Objects.equals(odnumberofitems, that.odnumberofitems) && - Objects.equals(odnumberofitemsdate, that.odnumberofitemsdate) && - Objects.equals(odpolicies, that.odpolicies) && - Objects.equals(odlanguages, that.odlanguages) && - Objects.equals(odcontenttypes, that.odcontenttypes) && - Objects.equals(accessinfopackage, that.accessinfopackage) && - Objects.equals(releasestartdate, that.releasestartdate) && - Objects.equals(releaseenddate, that.releaseenddate) && - Objects.equals(missionstatementurl, that.missionstatementurl) && - Objects.equals(dataprovider, that.dataprovider) && - Objects.equals(serviceprovider, that.serviceprovider) && - Objects.equals(databaseaccesstype, that.databaseaccesstype) && - Objects.equals(datauploadtype, that.datauploadtype) && - Objects.equals(databaseaccessrestriction, that.databaseaccessrestriction) && - Objects.equals(datauploadrestriction, that.datauploadrestriction) && - Objects.equals(versioning, that.versioning) && - Objects.equals(citationguidelineurl, that.citationguidelineurl) && - Objects.equals(qualitymanagementkind, that.qualitymanagementkind) && - Objects.equals(pidsystems, that.pidsystems) && - Objects.equals(certificates, that.certificates) && - Objects.equals(policies, that.policies) && - Objects.equals(journal, that.journal); + return Objects.equals(datasourcetype, that.datasourcetype) + && Objects.equals(openairecompatibility, that.openairecompatibility) + && Objects.equals(officialname, that.officialname) + && Objects.equals(englishname, that.englishname) + && Objects.equals(websiteurl, that.websiteurl) + && Objects.equals(logourl, that.logourl) + && Objects.equals(contactemail, that.contactemail) + && Objects.equals(namespaceprefix, that.namespaceprefix) + && Objects.equals(latitude, that.latitude) + && Objects.equals(longitude, that.longitude) + && Objects.equals(dateofvalidation, that.dateofvalidation) + && Objects.equals(description, that.description) + && Objects.equals(subjects, that.subjects) + && Objects.equals(odnumberofitems, that.odnumberofitems) + && Objects.equals(odnumberofitemsdate, that.odnumberofitemsdate) + && Objects.equals(odpolicies, that.odpolicies) + && Objects.equals(odlanguages, that.odlanguages) + && Objects.equals(odcontenttypes, that.odcontenttypes) + && Objects.equals(accessinfopackage, that.accessinfopackage) + && Objects.equals(releasestartdate, that.releasestartdate) + && Objects.equals(releaseenddate, that.releaseenddate) + && Objects.equals(missionstatementurl, that.missionstatementurl) + && Objects.equals(dataprovider, that.dataprovider) + && Objects.equals(serviceprovider, that.serviceprovider) + && Objects.equals(databaseaccesstype, that.databaseaccesstype) + && Objects.equals(datauploadtype, that.datauploadtype) + && Objects.equals(databaseaccessrestriction, that.databaseaccessrestriction) + && Objects.equals(datauploadrestriction, that.datauploadrestriction) + && Objects.equals(versioning, that.versioning) + && Objects.equals(citationguidelineurl, that.citationguidelineurl) + && Objects.equals(qualitymanagementkind, that.qualitymanagementkind) + && Objects.equals(pidsystems, that.pidsystems) + && Objects.equals(certificates, that.certificates) + && Objects.equals(policies, that.policies) + && Objects.equals(journal, that.journal); } @Override public int hashCode() { - return Objects.hash(super.hashCode(), datasourcetype, openairecompatibility, officialname, englishname, websiteurl, logourl, contactemail, namespaceprefix, latitude, longitude, dateofvalidation, description, subjects, odnumberofitems, odnumberofitemsdate, odpolicies, odlanguages, odcontenttypes, accessinfopackage, releasestartdate, releaseenddate, missionstatementurl, dataprovider, serviceprovider, databaseaccesstype, datauploadtype, databaseaccessrestriction, datauploadrestriction, versioning, citationguidelineurl, qualitymanagementkind, pidsystems, certificates, policies, journal); + return Objects.hash( + super.hashCode(), + datasourcetype, + openairecompatibility, + officialname, + englishname, + websiteurl, + logourl, + contactemail, + namespaceprefix, + latitude, + longitude, + dateofvalidation, + description, + subjects, + odnumberofitems, + odnumberofitemsdate, + odpolicies, + odlanguages, + odcontenttypes, + accessinfopackage, + releasestartdate, + releaseenddate, + missionstatementurl, + dataprovider, + serviceprovider, + databaseaccesstype, + datauploadtype, + databaseaccessrestriction, + datauploadrestriction, + versioning, + citationguidelineurl, + qualitymanagementkind, + pidsystems, + certificates, + policies, + journal); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExternalReference.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExternalReference.java index 24c94065b5..35f84a9a7a 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExternalReference.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExternalReference.java @@ -97,18 +97,19 @@ public class ExternalReference implements Serializable { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; ExternalReference that = (ExternalReference) o; - return Objects.equals(sitename, that.sitename) && - Objects.equals(label, that.label) && - Objects.equals(url, that.url) && - Objects.equals(description, that.description) && - Objects.equals(qualifier, that.qualifier) && - Objects.equals(refidentifier, that.refidentifier) && - Objects.equals(query, that.query) && - Objects.equals(dataInfo, that.dataInfo); + return Objects.equals(sitename, that.sitename) + && Objects.equals(label, that.label) + && Objects.equals(url, that.url) + && Objects.equals(description, that.description) + && Objects.equals(qualifier, that.qualifier) + && Objects.equals(refidentifier, that.refidentifier) + && Objects.equals(query, that.query) + && Objects.equals(dataInfo, that.dataInfo); } @Override public int hashCode() { - return Objects.hash(sitename, label, url, description, qualifier, refidentifier, query, dataInfo); + return Objects.hash( + sitename, label, url, description, qualifier, refidentifier, query, dataInfo); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExtraInfo.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExtraInfo.java index 46107b214f..d01f1035c6 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExtraInfo.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExtraInfo.java @@ -60,11 +60,11 @@ public class ExtraInfo implements Serializable { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; ExtraInfo extraInfo = (ExtraInfo) o; - return Objects.equals(name, extraInfo.name) && - Objects.equals(typology, extraInfo.typology) && - Objects.equals(provenance, extraInfo.provenance) && - Objects.equals(trust, extraInfo.trust) && - Objects.equals(value, extraInfo.value); + return Objects.equals(name, extraInfo.name) + && Objects.equals(typology, extraInfo.typology) + && Objects.equals(provenance, extraInfo.provenance) + && Objects.equals(trust, extraInfo.trust) + && Objects.equals(value, extraInfo.value); } @Override diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java index 2ab0b4d3c3..ec9e1e0e78 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java @@ -31,12 +31,9 @@ public class Field implements Serializable { @Override public boolean equals(Object obj) { - if (this == obj) - return true; - if (obj == null) - return false; - if (getClass() != obj.getClass()) - return false; + if (this == obj) return true; + if (obj == null) return false; + if (getClass() != obj.getClass()) return false; Field other = (Field) obj; return getValue().equals(other.getValue()); } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java index 1839fbd53e..85a3dca951 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java @@ -1,9 +1,8 @@ package eu.dnetlib.dhp.schema.oaf; import com.fasterxml.jackson.annotation.JsonIgnore; -import org.apache.commons.lang3.StringUtils; - import java.io.Serializable; +import org.apache.commons.lang3.StringUtils; public class GeoLocation implements Serializable { @@ -39,13 +38,17 @@ public class GeoLocation implements Serializable { @JsonIgnore public boolean isBlank() { - return StringUtils.isBlank(point) && - StringUtils.isBlank(box) && - StringUtils.isBlank(place); + return StringUtils.isBlank(point) && StringUtils.isBlank(box) && StringUtils.isBlank(place); } public String toComparableString() { - return isBlank()?"":String.format("%s::%s%s", point != null ? point.toLowerCase() : "", box != null ? box.toLowerCase() : "", place != null ? place.toLowerCase() : ""); + return isBlank() + ? "" + : String.format( + "%s::%s%s", + point != null ? point.toLowerCase() : "", + box != null ? box.toLowerCase() : "", + place != null ? place.toLowerCase() : ""); } @Override @@ -55,16 +58,12 @@ public class GeoLocation implements Serializable { @Override public boolean equals(Object obj) { - if (this == obj) - return true; - if (obj == null) - return false; - if (getClass() != obj.getClass()) - return false; + if (this == obj) return true; + if (obj == null) return false; + if (getClass() != obj.getClass()) return false; GeoLocation other = (GeoLocation) obj; - return toComparableString() - .equals(other.toComparableString()); + return toComparableString().equals(other.toComparableString()); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java index f82296d8bf..a215c342ae 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java @@ -16,19 +16,21 @@ public class Instance implements Serializable { private List url; // other research products specifc - private String distributionlocation; + private String distributionlocation; private KeyValue collectedfrom; private Field dateofacceptance; - // ( article | book ) processing charges. Defined here to cope with possible wrongly typed results + // ( article | book ) processing charges. Defined here to cope with possible wrongly typed + // results private Field processingchargeamount; - // currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly typed results + // currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly + // typed results private Field processingchargecurrency; - private Field refereed; //peer-review status + private Field refereed; // peer-review status public Field getLicense() { return license; @@ -118,12 +120,19 @@ public class Instance implements Serializable { this.refereed = refereed; } - public String toComparableString(){ - return String.format("%s::%s::%s::%s", - hostedby != null && hostedby.getKey()!= null ? hostedby.getKey().toLowerCase() : "", - accessright!= null && accessright.getClassid()!= null ? accessright.getClassid() : "", - instancetype!= null && instancetype.getClassid()!= null ? instancetype.getClassid() : "", - url != null ? url:""); + public String toComparableString() { + return String.format( + "%s::%s::%s::%s", + hostedby != null && hostedby.getKey() != null + ? hostedby.getKey().toLowerCase() + : "", + accessright != null && accessright.getClassid() != null + ? accessright.getClassid() + : "", + instancetype != null && instancetype.getClassid() != null + ? instancetype.getClassid() + : "", + url != null ? url : ""); } @Override @@ -133,16 +142,12 @@ public class Instance implements Serializable { @Override public boolean equals(Object obj) { - if (this == obj) - return true; - if (obj == null) - return false; - if (getClass() != obj.getClass()) - return false; + if (this == obj) return true; + if (obj == null) return false; + if (getClass() != obj.getClass()) return false; Instance other = (Instance) obj; - return toComparableString() - .equals(other.toComparableString()); + return toComparableString().equals(other.toComparableString()); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java index e3c80b120e..c45c93af9b 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java @@ -130,22 +130,34 @@ public class Journal implements Serializable { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; Journal journal = (Journal) o; - return Objects.equals(name, journal.name) && - Objects.equals(issnPrinted, journal.issnPrinted) && - Objects.equals(issnOnline, journal.issnOnline) && - Objects.equals(issnLinking, journal.issnLinking) && - Objects.equals(ep, journal.ep) && - Objects.equals(iss, journal.iss) && - Objects.equals(sp, journal.sp) && - Objects.equals(vol, journal.vol) && - Objects.equals(edition, journal.edition) && - Objects.equals(conferenceplace, journal.conferenceplace) && - Objects.equals(conferencedate, journal.conferencedate) && - Objects.equals(dataInfo, journal.dataInfo); + return Objects.equals(name, journal.name) + && Objects.equals(issnPrinted, journal.issnPrinted) + && Objects.equals(issnOnline, journal.issnOnline) + && Objects.equals(issnLinking, journal.issnLinking) + && Objects.equals(ep, journal.ep) + && Objects.equals(iss, journal.iss) + && Objects.equals(sp, journal.sp) + && Objects.equals(vol, journal.vol) + && Objects.equals(edition, journal.edition) + && Objects.equals(conferenceplace, journal.conferenceplace) + && Objects.equals(conferencedate, journal.conferencedate) + && Objects.equals(dataInfo, journal.dataInfo); } @Override public int hashCode() { - return Objects.hash(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, conferenceplace, conferencedate, dataInfo); + return Objects.hash( + name, + issnPrinted, + issnOnline, + issnLinking, + ep, + iss, + sp, + vol, + edition, + conferenceplace, + conferencedate, + dataInfo); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java index 5a841b96f5..27b2f4a185 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java @@ -1,9 +1,8 @@ package eu.dnetlib.dhp.schema.oaf; import com.fasterxml.jackson.annotation.JsonIgnore; -import org.apache.commons.lang3.StringUtils; - import java.io.Serializable; +import org.apache.commons.lang3.StringUtils; public class KeyValue implements Serializable { @@ -38,7 +37,12 @@ public class KeyValue implements Serializable { } public String toComparableString() { - return isBlank()?"":String.format("%s::%s", key != null ? key.toLowerCase() : "", value != null ? value.toLowerCase() : ""); + return isBlank() + ? "" + : String.format( + "%s::%s", + key != null ? key.toLowerCase() : "", + value != null ? value.toLowerCase() : ""); } @JsonIgnore @@ -53,12 +57,9 @@ public class KeyValue implements Serializable { @Override public boolean equals(Object obj) { - if (this == obj) - return true; - if (obj == null) - return false; - if (getClass() != obj.getClass()) - return false; + if (this == obj) return true; + if (obj == null) return false; + if (getClass() != obj.getClass()) return false; KeyValue other = (KeyValue) obj; diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OAIProvenance.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OAIProvenance.java index 52ddf27d88..d85580a687 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OAIProvenance.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OAIProvenance.java @@ -3,7 +3,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; import java.util.Objects; -public class OAIProvenance implements Serializable { +public class OAIProvenance implements Serializable { private OriginDescription originDescription; diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index 64217e5d80..7a7a9a89cd 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -4,7 +4,7 @@ import java.io.Serializable; import java.util.Objects; public abstract class Oaf implements Serializable { - + private DataInfo dataInfo; private Long lastupdatetimestamp; @@ -25,24 +25,18 @@ public abstract class Oaf implements Serializable { this.lastupdatetimestamp = lastupdatetimestamp; } - public void mergeOAFDataInfo(Oaf e) { - if (e.getDataInfo()!= null && compareTrust(this,e)<0) - dataInfo = e.getDataInfo(); + if (e.getDataInfo() != null && compareTrust(this, e) < 0) dataInfo = e.getDataInfo(); } protected String extractTrust(Oaf e) { - if (e == null || e.getDataInfo()== null || e.getDataInfo().getTrust()== null) - return "0.0"; + if (e == null || e.getDataInfo() == null || e.getDataInfo().getTrust() == null) + return "0.0"; return e.getDataInfo().getTrust(); - - - } protected int compareTrust(Oaf a, Oaf b) { return extractTrust(a).compareTo(extractTrust(b)); - } @Override @@ -50,8 +44,8 @@ public abstract class Oaf implements Serializable { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; Oaf oaf = (Oaf) o; - return Objects.equals(dataInfo, oaf.dataInfo) && - Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp); + return Objects.equals(dataInfo, oaf.dataInfo) + && Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp); } @Override diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java index cd196243a0..86f4ff616f 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java @@ -86,11 +86,9 @@ public abstract class OafEntity extends Oaf implements Serializable { this.oaiprovenance = oaiprovenance; } - public void mergeFrom(OafEntity e) { - if (e == null) - return; + if (e == null) return; originalId = mergeLists(originalId, e.getOriginalId()); @@ -108,12 +106,15 @@ public abstract class OafEntity extends Oaf implements Serializable { if (e.getOaiprovenance() != null && compareTrust(this, e) < 0) oaiprovenance = e.getOaiprovenance(); - } protected List mergeLists(final List... lists) { - return Arrays.stream(lists).filter(Objects::nonNull).flatMap(List::stream).distinct().collect(Collectors.toList()); + return Arrays.stream(lists) + .filter(Objects::nonNull) + .flatMap(List::stream) + .distinct() + .collect(Collectors.toList()); } @Override @@ -122,18 +123,27 @@ public abstract class OafEntity extends Oaf implements Serializable { if (o == null || getClass() != o.getClass()) return false; if (!super.equals(o)) return false; OafEntity oafEntity = (OafEntity) o; - return Objects.equals(id, oafEntity.id) && - Objects.equals(originalId, oafEntity.originalId) && - Objects.equals(collectedfrom, oafEntity.collectedfrom) && - Objects.equals(pid, oafEntity.pid) && - Objects.equals(dateofcollection, oafEntity.dateofcollection) && - Objects.equals(dateoftransformation, oafEntity.dateoftransformation) && - Objects.equals(extraInfo, oafEntity.extraInfo) && - Objects.equals(oaiprovenance, oafEntity.oaiprovenance); + return Objects.equals(id, oafEntity.id) + && Objects.equals(originalId, oafEntity.originalId) + && Objects.equals(collectedfrom, oafEntity.collectedfrom) + && Objects.equals(pid, oafEntity.pid) + && Objects.equals(dateofcollection, oafEntity.dateofcollection) + && Objects.equals(dateoftransformation, oafEntity.dateoftransformation) + && Objects.equals(extraInfo, oafEntity.extraInfo) + && Objects.equals(oaiprovenance, oafEntity.oaiprovenance); } @Override public int hashCode() { - return Objects.hash(super.hashCode(), id, originalId, collectedfrom, pid, dateofcollection, dateoftransformation, extraInfo, oaiprovenance); + return Objects.hash( + super.hashCode(), + id, + originalId, + collectedfrom, + pid, + dateofcollection, + dateoftransformation, + extraInfo, + oaiprovenance); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java index a73a7f845b..7352b4847a 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java @@ -122,7 +122,8 @@ public class Organization extends OafEntity implements Serializable { return ecinternationalorganizationeurinterests; } - public void setEcinternationalorganizationeurinterests(Field ecinternationalorganizationeurinterests) { + public void setEcinternationalorganizationeurinterests( + Field ecinternationalorganizationeurinterests) { this.ecinternationalorganizationeurinterests = ecinternationalorganizationeurinterests; } @@ -166,32 +167,70 @@ public class Organization extends OafEntity implements Serializable { this.country = country; } - @Override public void mergeFrom(OafEntity e) { super.mergeFrom(e); - if (!Organization.class.isAssignableFrom(e.getClass())){ + if (!Organization.class.isAssignableFrom(e.getClass())) { return; } final Organization o = (Organization) e; - legalshortname = o.getLegalshortname() != null && compareTrust(this, e)<0? o.getLegalshortname() : legalshortname; - legalname = o.getLegalname() != null && compareTrust(this, e)<0 ? o.getLegalname() : legalname; + legalshortname = + o.getLegalshortname() != null && compareTrust(this, e) < 0 + ? o.getLegalshortname() + : legalshortname; + legalname = + o.getLegalname() != null && compareTrust(this, e) < 0 + ? o.getLegalname() + : legalname; alternativeNames = mergeLists(o.getAlternativeNames(), alternativeNames); - websiteurl = o.getWebsiteurl() != null && compareTrust(this, e)<0? o.getWebsiteurl() : websiteurl; - logourl = o.getLogourl() != null && compareTrust(this, e)<0? o.getLogourl() : logourl; - eclegalbody = o.getEclegalbody() != null && compareTrust(this, e)<0? o.getEclegalbody() : eclegalbody; - eclegalperson = o.getEclegalperson() != null && compareTrust(this, e)<0? o.getEclegalperson() : eclegalperson; - ecnonprofit = o.getEcnonprofit() != null && compareTrust(this, e)<0? o.getEcnonprofit() : ecnonprofit; - ecresearchorganization = o.getEcresearchorganization() != null && compareTrust(this, e)<0? o.getEcresearchorganization() : ecresearchorganization; - echighereducation = o.getEchighereducation() != null && compareTrust(this, e)<0? o.getEchighereducation() : echighereducation; - ecinternationalorganizationeurinterests = o.getEcinternationalorganizationeurinterests() != null && compareTrust(this, e)<0? o.getEcinternationalorganizationeurinterests() : ecinternationalorganizationeurinterests; - ecinternationalorganization = o.getEcinternationalorganization() != null && compareTrust(this, e)<0? o.getEcinternationalorganization() : ecinternationalorganization; - ecenterprise = o.getEcenterprise() != null && compareTrust(this, e)<0? o.getEcenterprise() :ecenterprise; - ecsmevalidated = o.getEcsmevalidated() != null && compareTrust(this, e)<0? o.getEcsmevalidated() :ecsmevalidated; - ecnutscode = o.getEcnutscode() != null && compareTrust(this, e)<0? o.getEcnutscode() :ecnutscode; - country = o.getCountry() != null && compareTrust(this, e)<0 ? o.getCountry() :country; + websiteurl = + o.getWebsiteurl() != null && compareTrust(this, e) < 0 + ? o.getWebsiteurl() + : websiteurl; + logourl = o.getLogourl() != null && compareTrust(this, e) < 0 ? o.getLogourl() : logourl; + eclegalbody = + o.getEclegalbody() != null && compareTrust(this, e) < 0 + ? o.getEclegalbody() + : eclegalbody; + eclegalperson = + o.getEclegalperson() != null && compareTrust(this, e) < 0 + ? o.getEclegalperson() + : eclegalperson; + ecnonprofit = + o.getEcnonprofit() != null && compareTrust(this, e) < 0 + ? o.getEcnonprofit() + : ecnonprofit; + ecresearchorganization = + o.getEcresearchorganization() != null && compareTrust(this, e) < 0 + ? o.getEcresearchorganization() + : ecresearchorganization; + echighereducation = + o.getEchighereducation() != null && compareTrust(this, e) < 0 + ? o.getEchighereducation() + : echighereducation; + ecinternationalorganizationeurinterests = + o.getEcinternationalorganizationeurinterests() != null && compareTrust(this, e) < 0 + ? o.getEcinternationalorganizationeurinterests() + : ecinternationalorganizationeurinterests; + ecinternationalorganization = + o.getEcinternationalorganization() != null && compareTrust(this, e) < 0 + ? o.getEcinternationalorganization() + : ecinternationalorganization; + ecenterprise = + o.getEcenterprise() != null && compareTrust(this, e) < 0 + ? o.getEcenterprise() + : ecenterprise; + ecsmevalidated = + o.getEcsmevalidated() != null && compareTrust(this, e) < 0 + ? o.getEcsmevalidated() + : ecsmevalidated; + ecnutscode = + o.getEcnutscode() != null && compareTrust(this, e) < 0 + ? o.getEcnutscode() + : ecnutscode; + country = o.getCountry() != null && compareTrust(this, e) < 0 ? o.getCountry() : country; mergeOAFDataInfo(o); } @@ -201,26 +240,45 @@ public class Organization extends OafEntity implements Serializable { if (o == null || getClass() != o.getClass()) return false; if (!super.equals(o)) return false; Organization that = (Organization) o; - return Objects.equals(legalshortname, that.legalshortname) && - Objects.equals(legalname, that.legalname) && - Objects.equals(alternativeNames, that.alternativeNames) && - Objects.equals(websiteurl, that.websiteurl) && - Objects.equals(logourl, that.logourl) && - Objects.equals(eclegalbody, that.eclegalbody) && - Objects.equals(eclegalperson, that.eclegalperson) && - Objects.equals(ecnonprofit, that.ecnonprofit) && - Objects.equals(ecresearchorganization, that.ecresearchorganization) && - Objects.equals(echighereducation, that.echighereducation) && - Objects.equals(ecinternationalorganizationeurinterests, that.ecinternationalorganizationeurinterests) && - Objects.equals(ecinternationalorganization, that.ecinternationalorganization) && - Objects.equals(ecenterprise, that.ecenterprise) && - Objects.equals(ecsmevalidated, that.ecsmevalidated) && - Objects.equals(ecnutscode, that.ecnutscode) && - Objects.equals(country, that.country); + return Objects.equals(legalshortname, that.legalshortname) + && Objects.equals(legalname, that.legalname) + && Objects.equals(alternativeNames, that.alternativeNames) + && Objects.equals(websiteurl, that.websiteurl) + && Objects.equals(logourl, that.logourl) + && Objects.equals(eclegalbody, that.eclegalbody) + && Objects.equals(eclegalperson, that.eclegalperson) + && Objects.equals(ecnonprofit, that.ecnonprofit) + && Objects.equals(ecresearchorganization, that.ecresearchorganization) + && Objects.equals(echighereducation, that.echighereducation) + && Objects.equals( + ecinternationalorganizationeurinterests, + that.ecinternationalorganizationeurinterests) + && Objects.equals(ecinternationalorganization, that.ecinternationalorganization) + && Objects.equals(ecenterprise, that.ecenterprise) + && Objects.equals(ecsmevalidated, that.ecsmevalidated) + && Objects.equals(ecnutscode, that.ecnutscode) + && Objects.equals(country, that.country); } @Override public int hashCode() { - return Objects.hash(super.hashCode(), legalshortname, legalname, alternativeNames, websiteurl, logourl, eclegalbody, eclegalperson, ecnonprofit, ecresearchorganization, echighereducation, ecinternationalorganizationeurinterests, ecinternationalorganization, ecenterprise, ecsmevalidated, ecnutscode, country); + return Objects.hash( + super.hashCode(), + legalshortname, + legalname, + alternativeNames, + websiteurl, + logourl, + eclegalbody, + eclegalperson, + ecnonprofit, + ecresearchorganization, + echighereducation, + ecinternationalorganizationeurinterests, + ecinternationalorganization, + ecenterprise, + ecsmevalidated, + ecnutscode, + country); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OriginDescription.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OriginDescription.java index 8038242ca3..6574ddf4ef 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OriginDescription.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OriginDescription.java @@ -70,16 +70,17 @@ public class OriginDescription implements Serializable { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; OriginDescription that = (OriginDescription) o; - return Objects.equals(harvestDate, that.harvestDate) && - Objects.equals(altered, that.altered) && - Objects.equals(baseURL, that.baseURL) && - Objects.equals(identifier, that.identifier) && - Objects.equals(datestamp, that.datestamp) && - Objects.equals(metadataNamespace, that.metadataNamespace); + return Objects.equals(harvestDate, that.harvestDate) + && Objects.equals(altered, that.altered) + && Objects.equals(baseURL, that.baseURL) + && Objects.equals(identifier, that.identifier) + && Objects.equals(datestamp, that.datestamp) + && Objects.equals(metadataNamespace, that.metadataNamespace); } @Override public int hashCode() { - return Objects.hash(harvestDate, altered, baseURL, identifier, datestamp, metadataNamespace); + return Objects.hash( + harvestDate, altered, baseURL, identifier, datestamp, metadataNamespace); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java index cc36817bbf..00b24a3740 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java @@ -40,11 +40,11 @@ public class OtherResearchProduct extends Result implements Serializable { public void mergeFrom(OafEntity e) { super.mergeFrom(e); - if (!OtherResearchProduct.class.isAssignableFrom(e.getClass())){ + if (!OtherResearchProduct.class.isAssignableFrom(e.getClass())) { return; } - OtherResearchProduct o = (OtherResearchProduct)e; + OtherResearchProduct o = (OtherResearchProduct) e; contactperson = mergeLists(contactperson, o.getContactperson()); contactgroup = mergeLists(contactgroup, o.getContactgroup()); @@ -58,9 +58,9 @@ public class OtherResearchProduct extends Result implements Serializable { if (o == null || getClass() != o.getClass()) return false; if (!super.equals(o)) return false; OtherResearchProduct that = (OtherResearchProduct) o; - return Objects.equals(contactperson, that.contactperson) && - Objects.equals(contactgroup, that.contactgroup) && - Objects.equals(tool, that.tool); + return Objects.equals(contactperson, that.contactperson) + && Objects.equals(contactgroup, that.contactgroup) + && Objects.equals(tool, that.tool); } @Override diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java index 023be8fc05..7ed816fbe3 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java @@ -266,44 +266,91 @@ public class Project extends OafEntity implements Serializable { this.fundedamount = fundedamount; } - @Override public void mergeFrom(OafEntity e) { super.mergeFrom(e); - if (!Project.class.isAssignableFrom(e.getClass())){ + if (!Project.class.isAssignableFrom(e.getClass())) { return; } - Project p = (Project)e; + Project p = (Project) e; - websiteurl= p.getWebsiteurl()!= null && compareTrust(this,e)<0?p.getWebsiteurl():websiteurl; - code= p.getCode()!=null && compareTrust(this,e)<0?p.getCode():code; - acronym= p.getAcronym()!= null && compareTrust(this,e)<0?p.getAcronym():acronym; - title= p.getTitle()!= null && compareTrust(this,e)<0?p.getTitle():title; - startdate= p.getStartdate()!=null && compareTrust(this,e)<0?p.getStartdate():startdate; - enddate= p.getEnddate()!=null && compareTrust(this,e)<0?p.getEnddate():enddate; - callidentifier= p.getCallidentifier()!=null && compareTrust(this,e)<0?p.getCallidentifier():callidentifier; - keywords= p.getKeywords()!=null && compareTrust(this,e)<0?p.getKeywords():keywords; - duration= p.getDuration()!=null && compareTrust(this,e)<0?p.getDuration():duration; - ecsc39= p.getEcsc39()!=null && compareTrust(this,e)<0?p.getEcsc39():ecsc39; - oamandatepublications= p.getOamandatepublications()!=null && compareTrust(this,e)<0?p.getOamandatepublications():oamandatepublications; - ecarticle29_3= p.getEcarticle29_3()!=null && compareTrust(this,e)<0?p.getEcarticle29_3():ecarticle29_3; - subjects= mergeLists(subjects, p.getSubjects()); - fundingtree= mergeLists(fundingtree, p.getFundingtree()); - contracttype= p.getContracttype()!=null && compareTrust(this,e)<0?p.getContracttype():contracttype; - optional1= p.getOptional1()!=null && compareTrust(this,e)<0?p.getOptional1():optional1; - optional2= p.getOptional2()!=null && compareTrust(this,e)<0?p.getOptional2():optional2; - jsonextrainfo= p.getJsonextrainfo()!=null && compareTrust(this,e)<0?p.getJsonextrainfo():jsonextrainfo; - contactfullname= p.getContactfullname()!=null && compareTrust(this,e)<0?p.getContactfullname():contactfullname; - contactfax= p.getContactfax()!=null && compareTrust(this,e)<0?p.getContactfax():contactfax; - contactphone= p.getContactphone()!=null && compareTrust(this,e)<0?p.getContactphone():contactphone; - contactemail= p.getContactemail()!=null && compareTrust(this,e)<0?p.getContactemail():contactemail; - summary= p.getSummary()!=null && compareTrust(this,e)<0?p.getSummary():summary; - currency= p.getCurrency()!=null && compareTrust(this,e)<0?p.getCurrency():currency; - totalcost= p.getTotalcost()!=null && compareTrust(this,e)<0?p.getTotalcost():totalcost; - fundedamount= p.getFundedamount()!= null && compareTrust(this,e)<0?p.getFundedamount():fundedamount; - mergeOAFDataInfo(e); + websiteurl = + p.getWebsiteurl() != null && compareTrust(this, e) < 0 + ? p.getWebsiteurl() + : websiteurl; + code = p.getCode() != null && compareTrust(this, e) < 0 ? p.getCode() : code; + acronym = p.getAcronym() != null && compareTrust(this, e) < 0 ? p.getAcronym() : acronym; + title = p.getTitle() != null && compareTrust(this, e) < 0 ? p.getTitle() : title; + startdate = + p.getStartdate() != null && compareTrust(this, e) < 0 + ? p.getStartdate() + : startdate; + enddate = p.getEnddate() != null && compareTrust(this, e) < 0 ? p.getEnddate() : enddate; + callidentifier = + p.getCallidentifier() != null && compareTrust(this, e) < 0 + ? p.getCallidentifier() + : callidentifier; + keywords = + p.getKeywords() != null && compareTrust(this, e) < 0 ? p.getKeywords() : keywords; + duration = + p.getDuration() != null && compareTrust(this, e) < 0 ? p.getDuration() : duration; + ecsc39 = p.getEcsc39() != null && compareTrust(this, e) < 0 ? p.getEcsc39() : ecsc39; + oamandatepublications = + p.getOamandatepublications() != null && compareTrust(this, e) < 0 + ? p.getOamandatepublications() + : oamandatepublications; + ecarticle29_3 = + p.getEcarticle29_3() != null && compareTrust(this, e) < 0 + ? p.getEcarticle29_3() + : ecarticle29_3; + subjects = mergeLists(subjects, p.getSubjects()); + fundingtree = mergeLists(fundingtree, p.getFundingtree()); + contracttype = + p.getContracttype() != null && compareTrust(this, e) < 0 + ? p.getContracttype() + : contracttype; + optional1 = + p.getOptional1() != null && compareTrust(this, e) < 0 + ? p.getOptional1() + : optional1; + optional2 = + p.getOptional2() != null && compareTrust(this, e) < 0 + ? p.getOptional2() + : optional2; + jsonextrainfo = + p.getJsonextrainfo() != null && compareTrust(this, e) < 0 + ? p.getJsonextrainfo() + : jsonextrainfo; + contactfullname = + p.getContactfullname() != null && compareTrust(this, e) < 0 + ? p.getContactfullname() + : contactfullname; + contactfax = + p.getContactfax() != null && compareTrust(this, e) < 0 + ? p.getContactfax() + : contactfax; + contactphone = + p.getContactphone() != null && compareTrust(this, e) < 0 + ? p.getContactphone() + : contactphone; + contactemail = + p.getContactemail() != null && compareTrust(this, e) < 0 + ? p.getContactemail() + : contactemail; + summary = p.getSummary() != null && compareTrust(this, e) < 0 ? p.getSummary() : summary; + currency = + p.getCurrency() != null && compareTrust(this, e) < 0 ? p.getCurrency() : currency; + totalcost = + p.getTotalcost() != null && compareTrust(this, e) < 0 + ? p.getTotalcost() + : totalcost; + fundedamount = + p.getFundedamount() != null && compareTrust(this, e) < 0 + ? p.getFundedamount() + : fundedamount; + mergeOAFDataInfo(e); } @Override @@ -312,36 +359,63 @@ public class Project extends OafEntity implements Serializable { if (o == null || getClass() != o.getClass()) return false; if (!super.equals(o)) return false; Project project = (Project) o; - return Objects.equals(websiteurl, project.websiteurl) && - Objects.equals(code, project.code) && - Objects.equals(acronym, project.acronym) && - Objects.equals(title, project.title) && - Objects.equals(startdate, project.startdate) && - Objects.equals(enddate, project.enddate) && - Objects.equals(callidentifier, project.callidentifier) && - Objects.equals(keywords, project.keywords) && - Objects.equals(duration, project.duration) && - Objects.equals(ecsc39, project.ecsc39) && - Objects.equals(oamandatepublications, project.oamandatepublications) && - Objects.equals(ecarticle29_3, project.ecarticle29_3) && - Objects.equals(subjects, project.subjects) && - Objects.equals(fundingtree, project.fundingtree) && - Objects.equals(contracttype, project.contracttype) && - Objects.equals(optional1, project.optional1) && - Objects.equals(optional2, project.optional2) && - Objects.equals(jsonextrainfo, project.jsonextrainfo) && - Objects.equals(contactfullname, project.contactfullname) && - Objects.equals(contactfax, project.contactfax) && - Objects.equals(contactphone, project.contactphone) && - Objects.equals(contactemail, project.contactemail) && - Objects.equals(summary, project.summary) && - Objects.equals(currency, project.currency) && - Objects.equals(totalcost, project.totalcost) && - Objects.equals(fundedamount, project.fundedamount); + return Objects.equals(websiteurl, project.websiteurl) + && Objects.equals(code, project.code) + && Objects.equals(acronym, project.acronym) + && Objects.equals(title, project.title) + && Objects.equals(startdate, project.startdate) + && Objects.equals(enddate, project.enddate) + && Objects.equals(callidentifier, project.callidentifier) + && Objects.equals(keywords, project.keywords) + && Objects.equals(duration, project.duration) + && Objects.equals(ecsc39, project.ecsc39) + && Objects.equals(oamandatepublications, project.oamandatepublications) + && Objects.equals(ecarticle29_3, project.ecarticle29_3) + && Objects.equals(subjects, project.subjects) + && Objects.equals(fundingtree, project.fundingtree) + && Objects.equals(contracttype, project.contracttype) + && Objects.equals(optional1, project.optional1) + && Objects.equals(optional2, project.optional2) + && Objects.equals(jsonextrainfo, project.jsonextrainfo) + && Objects.equals(contactfullname, project.contactfullname) + && Objects.equals(contactfax, project.contactfax) + && Objects.equals(contactphone, project.contactphone) + && Objects.equals(contactemail, project.contactemail) + && Objects.equals(summary, project.summary) + && Objects.equals(currency, project.currency) + && Objects.equals(totalcost, project.totalcost) + && Objects.equals(fundedamount, project.fundedamount); } @Override public int hashCode() { - return Objects.hash(super.hashCode(), websiteurl, code, acronym, title, startdate, enddate, callidentifier, keywords, duration, ecsc39, oamandatepublications, ecarticle29_3, subjects, fundingtree, contracttype, optional1, optional2, jsonextrainfo, contactfullname, contactfax, contactphone, contactemail, summary, currency, totalcost, fundedamount); + return Objects.hash( + super.hashCode(), + websiteurl, + code, + acronym, + title, + startdate, + enddate, + callidentifier, + keywords, + duration, + ecsc39, + oamandatepublications, + ecarticle29_3, + subjects, + fundingtree, + contracttype, + optional1, + optional2, + jsonextrainfo, + contactfullname, + contactfax, + contactphone, + contactemail, + summary, + currency, + totalcost, + fundedamount); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java index 20a0b2121a..1542b79334 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java @@ -20,14 +20,13 @@ public class Publication extends Result implements Serializable { public void mergeFrom(OafEntity e) { super.mergeFrom(e); - if (!Publication.class.isAssignableFrom(e.getClass())){ + if (!Publication.class.isAssignableFrom(e.getClass())) { return; } Publication p = (Publication) e; - if (p.getJournal() != null && compareTrust(this, e)<0) - journal = p.getJournal(); + if (p.getJournal() != null && compareTrust(this, e) < 0) journal = p.getJournal(); mergeOAFDataInfo(e); } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java index ae2bf1a602..9e42bdae36 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java @@ -1,9 +1,8 @@ package eu.dnetlib.dhp.schema.oaf; import com.fasterxml.jackson.annotation.JsonIgnore; -import org.apache.commons.lang3.StringUtils; - import java.io.Serializable; +import org.apache.commons.lang3.StringUtils; public class Qualifier implements Serializable { @@ -45,20 +44,24 @@ public class Qualifier implements Serializable { } public String toComparableString() { - return isBlank()?"": String.format("%s::%s::%s::%s", - classid != null ? classid : "", - classname != null ? classname : "", - schemeid != null ? schemeid : "", - schemename != null ? schemename : ""); + return isBlank() + ? "" + : String.format( + "%s::%s::%s::%s", + classid != null ? classid : "", + classname != null ? classname : "", + schemeid != null ? schemeid : "", + schemename != null ? schemename : ""); } @JsonIgnore public boolean isBlank() { - return StringUtils.isBlank(classid) && - StringUtils.isBlank(classname) && - StringUtils.isBlank(schemeid) && - StringUtils.isBlank(schemename); + return StringUtils.isBlank(classid) + && StringUtils.isBlank(classname) + && StringUtils.isBlank(schemeid) + && StringUtils.isBlank(schemename); } + @Override public int hashCode() { return toComparableString().hashCode(); @@ -66,16 +69,12 @@ public class Qualifier implements Serializable { @Override public boolean equals(Object obj) { - if (this == obj) - return true; - if (obj == null) - return false; - if (getClass() != obj.getClass()) - return false; + if (this == obj) return true; + if (obj == null) return false; + if (getClass() != obj.getClass()) return false; Qualifier other = (Qualifier) obj; - return toComparableString() - .equals(other.toComparableString()); + return toComparableString().equals(other.toComparableString()); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index 6871c01972..9d211d0586 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -1,104 +1,108 @@ package eu.dnetlib.dhp.schema.oaf; +import static com.google.common.base.Preconditions.checkArgument; + import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; -import static com.google.common.base.Preconditions.checkArgument; - public class Relation extends Oaf { - private String relType; + private String relType; - private String subRelType; + private String subRelType; - private String relClass; + private String relClass; - private String source; + private String source; - private String target; + private String target; - private List collectedFrom = new ArrayList<>(); + private List collectedFrom = new ArrayList<>(); - public String getRelType() { - return relType; - } + public String getRelType() { + return relType; + } - public void setRelType(final String relType) { - this.relType = relType; - } + public void setRelType(final String relType) { + this.relType = relType; + } - public String getSubRelType() { - return subRelType; - } + public String getSubRelType() { + return subRelType; + } - public void setSubRelType(final String subRelType) { - this.subRelType = subRelType; - } + public void setSubRelType(final String subRelType) { + this.subRelType = subRelType; + } - public String getRelClass() { - return relClass; - } + public String getRelClass() { + return relClass; + } - public void setRelClass(final String relClass) { - this.relClass = relClass; - } + public void setRelClass(final String relClass) { + this.relClass = relClass; + } - public String getSource() { - return source; - } + public String getSource() { + return source; + } - public void setSource(final String source) { - this.source = source; - } + public void setSource(final String source) { + this.source = source; + } - public String getTarget() { - return target; - } + public String getTarget() { + return target; + } - public void setTarget(final String target) { - this.target = target; - } + public void setTarget(final String target) { + this.target = target; + } - public List getCollectedFrom() { - return collectedFrom; - } + public List getCollectedFrom() { + return collectedFrom; + } - public void setCollectedFrom(final List collectedFrom) { - this.collectedFrom = collectedFrom; - } + public void setCollectedFrom(final List collectedFrom) { + this.collectedFrom = collectedFrom; + } - public void mergeFrom(final Relation r) { + public void mergeFrom(final Relation r) { - checkArgument(Objects.equals(getSource(), r.getSource()),"source ids must be equal"); - checkArgument(Objects.equals(getTarget(), r.getTarget()),"target ids must be equal"); - checkArgument(Objects.equals(getRelType(), r.getRelType()),"relType(s) must be equal"); - checkArgument(Objects.equals(getSubRelType(), r.getSubRelType()),"subRelType(s) must be equal"); - checkArgument(Objects.equals(getRelClass(), r.getRelClass()),"relClass(es) must be equal"); + checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal"); + checkArgument(Objects.equals(getTarget(), r.getTarget()), "target ids must be equal"); + checkArgument(Objects.equals(getRelType(), r.getRelType()), "relType(s) must be equal"); + checkArgument( + Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal"); + checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal"); - setCollectedFrom( - Stream - .concat(Optional.ofNullable(getCollectedFrom()).map(Collection::stream).orElse(Stream.empty()), - Optional.ofNullable(r.getCollectedFrom()).map(Collection::stream).orElse(Stream.empty())) - .distinct() // relies on KeyValue.equals - .collect(Collectors.toList())); - } + setCollectedFrom( + Stream.concat( + Optional.ofNullable(getCollectedFrom()) + .map(Collection::stream) + .orElse(Stream.empty()), + Optional.ofNullable(r.getCollectedFrom()) + .map(Collection::stream) + .orElse(Stream.empty())) + .distinct() // relies on KeyValue.equals + .collect(Collectors.toList())); + } - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - Relation relation = (Relation) o; - return relType.equals(relation.relType) && - subRelType.equals(relation.subRelType) && - relClass.equals(relation.relClass) && - source.equals(relation.source) && - target.equals(relation.target); - } - - @Override - public int hashCode() { - return Objects.hash(relType, subRelType, relClass, source, target, collectedFrom); - } + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Relation relation = (Relation) o; + return relType.equals(relation.relType) + && subRelType.equals(relation.subRelType) + && relClass.equals(relation.relClass) + && source.equals(relation.source) + && target.equals(relation.target); + } + @Override + public int hashCode() { + return Objects.hash(relType, subRelType, relClass, source, target, collectedFrom); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index f98bcec936..f9d9756d55 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java @@ -223,7 +223,7 @@ public class Result extends OafEntity implements Serializable { public void mergeFrom(OafEntity e) { super.mergeFrom(e); - if (!Result.class.isAssignableFrom(e.getClass())){ + if (!Result.class.isAssignableFrom(e.getClass())) { return; } @@ -231,11 +231,9 @@ public class Result extends OafEntity implements Serializable { instance = mergeLists(instance, r.getInstance()); - if (r.getResulttype() != null && compareTrust(this, r) < 0) - resulttype = r.getResulttype(); + if (r.getResulttype() != null && compareTrust(this, r) < 0) resulttype = r.getResulttype(); - if (r.getLanguage() != null && compareTrust(this, r) < 0) - language = r.getLanguage(); + if (r.getLanguage() != null && compareTrust(this, r) < 0) language = r.getLanguage(); country = mergeLists(country, r.getCountry()); @@ -247,8 +245,7 @@ public class Result extends OafEntity implements Serializable { description = longestLists(description, r.getDescription()); - if (r.getPublisher() != null && compareTrust(this, r) < 0) - publisher = r.getPublisher(); + if (r.getPublisher() != null && compareTrust(this, r) < 0) publisher = r.getPublisher(); if (r.getEmbargoenddate() != null && compareTrust(this, r) < 0) embargoenddate = r.getEmbargoenddate(); @@ -261,8 +258,7 @@ public class Result extends OafEntity implements Serializable { contributor = mergeLists(contributor, r.getContributor()); - if (r.getResourcetype() != null) - resourcetype = r.getResourcetype(); + if (r.getResourcetype() != null) resourcetype = r.getResourcetype(); coverage = mergeLists(coverage, r.getCoverage()); @@ -271,13 +267,21 @@ public class Result extends OafEntity implements Serializable { externalReference = mergeLists(externalReference, r.getExternalReference()); } - private List> longestLists(List> a, List> b) { - if (a == null || b == null) - return a == null ? b : a; + if (a == null || b == null) return a == null ? b : a; if (a.size() == b.size()) { - int msa = a.stream().filter(i -> i.getValue() != null).map(i -> i.getValue().length()).max(Comparator.naturalOrder()).orElse(0); - int msb = b.stream().filter(i -> i.getValue() != null).map(i -> i.getValue().length()).max(Comparator.naturalOrder()).orElse(0); + int msa = + a.stream() + .filter(i -> i.getValue() != null) + .map(i -> i.getValue().length()) + .max(Comparator.naturalOrder()) + .orElse(0); + int msb = + b.stream() + .filter(i -> i.getValue() != null) + .map(i -> i.getValue().length()) + .max(Comparator.naturalOrder()) + .orElse(0); return msa > msb ? a : b; } return a.size() > b.size() ? a : b; @@ -289,31 +293,53 @@ public class Result extends OafEntity implements Serializable { if (o == null || getClass() != o.getClass()) return false; if (!super.equals(o)) return false; Result result = (Result) o; - return Objects.equals(author, result.author) && - Objects.equals(resulttype, result.resulttype) && - Objects.equals(language, result.language) && - Objects.equals(country, result.country) && - Objects.equals(subject, result.subject) && - Objects.equals(title, result.title) && - Objects.equals(relevantdate, result.relevantdate) && - Objects.equals(description, result.description) && - Objects.equals(dateofacceptance, result.dateofacceptance) && - Objects.equals(publisher, result.publisher) && - Objects.equals(embargoenddate, result.embargoenddate) && - Objects.equals(source, result.source) && - Objects.equals(fulltext, result.fulltext) && - Objects.equals(format, result.format) && - Objects.equals(contributor, result.contributor) && - Objects.equals(resourcetype, result.resourcetype) && - Objects.equals(coverage, result.coverage) && - Objects.equals(bestaccessright, result.bestaccessright) && - Objects.equals(context, result.context) && - Objects.equals(externalReference, result.externalReference) && - Objects.equals(instance, result.instance); + return Objects.equals(author, result.author) + && Objects.equals(resulttype, result.resulttype) + && Objects.equals(language, result.language) + && Objects.equals(country, result.country) + && Objects.equals(subject, result.subject) + && Objects.equals(title, result.title) + && Objects.equals(relevantdate, result.relevantdate) + && Objects.equals(description, result.description) + && Objects.equals(dateofacceptance, result.dateofacceptance) + && Objects.equals(publisher, result.publisher) + && Objects.equals(embargoenddate, result.embargoenddate) + && Objects.equals(source, result.source) + && Objects.equals(fulltext, result.fulltext) + && Objects.equals(format, result.format) + && Objects.equals(contributor, result.contributor) + && Objects.equals(resourcetype, result.resourcetype) + && Objects.equals(coverage, result.coverage) + && Objects.equals(bestaccessright, result.bestaccessright) + && Objects.equals(context, result.context) + && Objects.equals(externalReference, result.externalReference) + && Objects.equals(instance, result.instance); } @Override public int hashCode() { - return Objects.hash(super.hashCode(), author, resulttype, language, country, subject, title, relevantdate, description, dateofacceptance, publisher, embargoenddate, source, fulltext, format, contributor, resourcetype, coverage, bestaccessright, context, externalReference, instance); + return Objects.hash( + super.hashCode(), + author, + resulttype, + language, + country, + subject, + title, + relevantdate, + description, + dateofacceptance, + publisher, + embargoenddate, + source, + fulltext, + format, + contributor, + resourcetype, + coverage, + bestaccessright, + context, + externalReference, + instance); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java index 6b51a6adae..a7d36638ef 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java @@ -50,7 +50,7 @@ public class Software extends Result implements Serializable { public void mergeFrom(OafEntity e) { super.mergeFrom(e); - if (!Software.class.isAssignableFrom(e.getClass())){ + if (!Software.class.isAssignableFrom(e.getClass())) { return; } @@ -59,9 +59,15 @@ public class Software extends Result implements Serializable { license = mergeLists(license, s.getLicense()); - codeRepositoryUrl = s.getCodeRepositoryUrl()!= null && compareTrust(this, s)<0?s.getCodeRepositoryUrl():codeRepositoryUrl; + codeRepositoryUrl = + s.getCodeRepositoryUrl() != null && compareTrust(this, s) < 0 + ? s.getCodeRepositoryUrl() + : codeRepositoryUrl; - programmingLanguage= s.getProgrammingLanguage()!= null && compareTrust(this, s)<0?s.getProgrammingLanguage():programmingLanguage; + programmingLanguage = + s.getProgrammingLanguage() != null && compareTrust(this, s) < 0 + ? s.getProgrammingLanguage() + : programmingLanguage; mergeOAFDataInfo(e); } @@ -72,14 +78,19 @@ public class Software extends Result implements Serializable { if (o == null || getClass() != o.getClass()) return false; if (!super.equals(o)) return false; Software software = (Software) o; - return Objects.equals(documentationUrl, software.documentationUrl) && - Objects.equals(license, software.license) && - Objects.equals(codeRepositoryUrl, software.codeRepositoryUrl) && - Objects.equals(programmingLanguage, software.programmingLanguage); + return Objects.equals(documentationUrl, software.documentationUrl) + && Objects.equals(license, software.license) + && Objects.equals(codeRepositoryUrl, software.codeRepositoryUrl) + && Objects.equals(programmingLanguage, software.programmingLanguage); } @Override public int hashCode() { - return Objects.hash(super.hashCode(), documentationUrl, license, codeRepositoryUrl, programmingLanguage); + return Objects.hash( + super.hashCode(), + documentationUrl, + license, + codeRepositoryUrl, + programmingLanguage); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/StructuredProperty.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/StructuredProperty.java index 5df6b80f39..a42071b188 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/StructuredProperty.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/StructuredProperty.java @@ -2,7 +2,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; -public class StructuredProperty implements Serializable { +public class StructuredProperty implements Serializable { private String value; @@ -34,8 +34,8 @@ public class StructuredProperty implements Serializable { this.dataInfo = dataInfo; } - public String toComparableString(){ - return value != null ? value.toLowerCase() : ""; + public String toComparableString() { + return value != null ? value.toLowerCase() : ""; } @Override @@ -45,16 +45,12 @@ public class StructuredProperty implements Serializable { @Override public boolean equals(Object obj) { - if (this == obj) - return true; - if (obj == null) - return false; - if (getClass() != obj.getClass()) - return false; + if (this == obj) return true; + if (obj == null) return false; + if (getClass() != obj.getClass()) return false; StructuredProperty other = (StructuredProperty) obj; - return toComparableString() - .equals(other.toComparableString()); + return toComparableString().equals(other.toComparableString()); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIDataset.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIDataset.java index 10aafaa4c3..b6c8f75a07 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIDataset.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIDataset.java @@ -2,12 +2,11 @@ package eu.dnetlib.dhp.schema.scholexplorer; import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.OafEntity; -import org.apache.commons.lang3.StringUtils; - import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; +import org.apache.commons.lang3.StringUtils; public class DLIDataset extends Dataset { @@ -47,33 +46,45 @@ public class DLIDataset extends Dataset { DLIDataset p = (DLIDataset) e; if (StringUtils.isBlank(completionStatus) && StringUtils.isNotBlank(p.completionStatus)) completionStatus = p.completionStatus; - if ("complete".equalsIgnoreCase(p.completionStatus)) - completionStatus = "complete"; + if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete"; dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom()); } - private List mergeProvenance(final List a, final List b) { + private List mergeProvenance( + final List a, final List b) { Map result = new HashMap<>(); if (a != null) - a.forEach(p -> { - if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) { - if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) { - result.put(p.getId(), p); - } + a.forEach( + p -> { + if (p != null + && StringUtils.isNotBlank(p.getId()) + && result.containsKey(p.getId())) { + if ("incomplete" + .equalsIgnoreCase( + result.get(p.getId()).getCompletionStatus()) + && StringUtils.isNotBlank(p.getCompletionStatus())) { + result.put(p.getId(), p); + } - } else if (p != null && p.getId() != null && !result.containsKey(p.getId())) - result.put(p.getId(), p); - }); + } else if (p != null && p.getId() != null && !result.containsKey(p.getId())) + result.put(p.getId(), p); + }); if (b != null) - b.forEach(p -> { - if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) { - if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) { - result.put(p.getId(), p); - } + b.forEach( + p -> { + if (p != null + && StringUtils.isNotBlank(p.getId()) + && result.containsKey(p.getId())) { + if ("incomplete" + .equalsIgnoreCase( + result.get(p.getId()).getCompletionStatus()) + && StringUtils.isNotBlank(p.getCompletionStatus())) { + result.put(p.getId(), p); + } - } else if (p != null && p.getId() != null && !result.containsKey(p.getId())) - result.put(p.getId(), p); - }); + } else if (p != null && p.getId() != null && !result.containsKey(p.getId())) + result.put(p.getId(), p); + }); return new ArrayList<>(result.values()); } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIPublication.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIPublication.java index ebd56eaa91..6b2d440bc6 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIPublication.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIPublication.java @@ -2,9 +2,9 @@ package eu.dnetlib.dhp.schema.scholexplorer; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Publication; -import org.apache.commons.lang3.StringUtils; import java.io.Serializable; import java.util.*; +import org.apache.commons.lang3.StringUtils; public class DLIPublication extends Publication implements Serializable { @@ -44,33 +44,45 @@ public class DLIPublication extends Publication implements Serializable { DLIPublication p = (DLIPublication) e; if (StringUtils.isBlank(completionStatus) && StringUtils.isNotBlank(p.completionStatus)) completionStatus = p.completionStatus; - if ("complete".equalsIgnoreCase(p.completionStatus)) - completionStatus = "complete"; + if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete"; dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom()); } - private List mergeProvenance(final List a, final List b) { + private List mergeProvenance( + final List a, final List b) { Map result = new HashMap<>(); if (a != null) - a.forEach(p -> { - if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) { - if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) { - result.put(p.getId(), p); - } + a.forEach( + p -> { + if (p != null + && StringUtils.isNotBlank(p.getId()) + && result.containsKey(p.getId())) { + if ("incomplete" + .equalsIgnoreCase( + result.get(p.getId()).getCompletionStatus()) + && StringUtils.isNotBlank(p.getCompletionStatus())) { + result.put(p.getId(), p); + } - } else if (p != null && p.getId() != null && !result.containsKey(p.getId())) - result.put(p.getId(), p); - }); + } else if (p != null && p.getId() != null && !result.containsKey(p.getId())) + result.put(p.getId(), p); + }); if (b != null) - b.forEach(p -> { - if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) { - if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) { - result.put(p.getId(), p); - } + b.forEach( + p -> { + if (p != null + && StringUtils.isNotBlank(p.getId()) + && result.containsKey(p.getId())) { + if ("incomplete" + .equalsIgnoreCase( + result.get(p.getId()).getCompletionStatus()) + && StringUtils.isNotBlank(p.getCompletionStatus())) { + result.put(p.getId(), p); + } - } else if (p != null && p.getId() != null && !result.containsKey(p.getId())) - result.put(p.getId(), p); - }); + } else if (p != null && p.getId() != null && !result.containsKey(p.getId())) + result.put(p.getId(), p); + }); return new ArrayList<>(result.values()); } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIUnknown.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIUnknown.java index c7e6dda276..155a0f6088 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIUnknown.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIUnknown.java @@ -1,15 +1,13 @@ package eu.dnetlib.dhp.schema.scholexplorer; import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import org.apache.commons.lang3.StringUtils; - import java.io.Serializable; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; +import org.apache.commons.lang3.StringUtils; public class DLIUnknown extends Oaf implements Serializable { @@ -49,7 +47,6 @@ public class DLIUnknown extends Oaf implements Serializable { this.id = id; } - public List getPid() { return pid; } @@ -75,33 +72,45 @@ public class DLIUnknown extends Oaf implements Serializable { } public void mergeFrom(DLIUnknown p) { - if ("complete".equalsIgnoreCase(p.completionStatus)) - completionStatus = "complete"; + if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete"; dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom()); } - private List mergeProvenance(final List a, final List b) { + private List mergeProvenance( + final List a, final List b) { Map result = new HashMap<>(); if (a != null) - a.forEach(p -> { - if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) { - if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) { - result.put(p.getId(), p); - } + a.forEach( + p -> { + if (p != null + && StringUtils.isNotBlank(p.getId()) + && result.containsKey(p.getId())) { + if ("incomplete" + .equalsIgnoreCase( + result.get(p.getId()).getCompletionStatus()) + && StringUtils.isNotBlank(p.getCompletionStatus())) { + result.put(p.getId(), p); + } - } else if (p != null && p.getId() != null && !result.containsKey(p.getId())) - result.put(p.getId(), p); - }); + } else if (p != null && p.getId() != null && !result.containsKey(p.getId())) + result.put(p.getId(), p); + }); if (b != null) - b.forEach(p -> { - if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) { - if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) { - result.put(p.getId(), p); - } + b.forEach( + p -> { + if (p != null + && StringUtils.isNotBlank(p.getId()) + && result.containsKey(p.getId())) { + if ("incomplete" + .equalsIgnoreCase( + result.get(p.getId()).getCompletionStatus()) + && StringUtils.isNotBlank(p.getCompletionStatus())) { + result.put(p.getId(), p); + } - } else if (p != null && p.getId() != null && !result.containsKey(p.getId())) - result.put(p.getId(), p); - }); + } else if (p != null && p.getId() != null && !result.containsKey(p.getId())) + result.put(p.getId(), p); + }); return new ArrayList<>(result.values()); } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/ProvenaceInfo.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/ProvenaceInfo.java index 3fe069b032..73384378c4 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/ProvenaceInfo.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/ProvenaceInfo.java @@ -10,7 +10,7 @@ public class ProvenaceInfo implements Serializable { private String completionStatus; - private String collectionMode ="collected"; + private String collectionMode = "collected"; public String getId() { return id; diff --git a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/action/AtomicActionTest.java b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/action/AtomicActionTest.java index d216c05d5f..30fbe551c5 100644 --- a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/action/AtomicActionTest.java +++ b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/action/AtomicActionTest.java @@ -1,18 +1,14 @@ package eu.dnetlib.dhp.schema.action; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.Relation; -import org.apache.commons.lang3.StringUtils; - -import org.junit.jupiter.api.Test; - -import java.io.IOException; - import static org.junit.jupiter.api.Assertions.*; -/** - * @author claudio.atzori - */ +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.schema.oaf.Relation; +import java.io.IOException; +import org.apache.commons.lang3.StringUtils; +import org.junit.jupiter.api.Test; + +/** @author claudio.atzori */ public class AtomicActionTest { @Test @@ -36,7 +32,5 @@ public class AtomicActionTest { assertEquals(aa1.getClazz(), aa2.getClazz()); assertEquals(aa1.getPayload(), aa2.getPayload()); - } - } diff --git a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java index 21583cd445..65b65ebebf 100644 --- a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java +++ b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java @@ -1,14 +1,14 @@ package eu.dnetlib.dhp.schema.common; +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertTrue; + import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; import org.junit.jupiter.api.Nested; import org.junit.jupiter.api.Test; -import static org.junit.jupiter.api.Assertions.assertFalse; -import static org.junit.jupiter.api.Assertions.assertTrue; - public class ModelSupportTest { @Nested @@ -32,4 +32,4 @@ public class ModelSupportTest { assertTrue(result); } } -} \ No newline at end of file +} diff --git a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java index ac4bd5d27d..58ff670bc8 100644 --- a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java +++ b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java @@ -1,11 +1,11 @@ package eu.dnetlib.dhp.schema.oaf; import static org.junit.jupiter.api.Assertions.*; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; import java.util.Arrays; import java.util.List; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class MergeTest { @@ -19,7 +19,7 @@ public class MergeTest { @Test public void mergeListsTest() { - //string list merge test + // string list merge test List a = Arrays.asList("a", "b", "c", "e"); List b = Arrays.asList("a", "b", "c", "d"); List c = null; @@ -44,7 +44,6 @@ public class MergeTest { assertNotNull(a.getCollectedfrom()); assertEquals(3, a.getCollectedfrom().size()); - } @Test @@ -60,7 +59,6 @@ public class MergeTest { assertNotNull(a.getSubject()); assertEquals(3, a.getSubject().size()); - } private KeyValue setKV(final String key, final String value) { @@ -73,7 +71,8 @@ public class MergeTest { return k; } - private StructuredProperty setSP(final String value, final String schema, final String classname) { + private StructuredProperty setSP( + final String value, final String schema, final String classname) { StructuredProperty s = new StructuredProperty(); s.setValue(value); Qualifier q = new Qualifier(); diff --git a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/scholexplorer/DLItest.java b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/scholexplorer/DLItest.java index 6a88151c95..63d3135dbc 100644 --- a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/scholexplorer/DLItest.java +++ b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/scholexplorer/DLItest.java @@ -6,48 +6,44 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.SerializationFeature; import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import org.junit.jupiter.api.Test; - import java.io.IOException; import java.util.Arrays; import java.util.Collections; +import org.junit.jupiter.api.Test; public class DLItest { - @Test public void testMergePublication() throws JsonProcessingException { DLIPublication a1 = new DLIPublication(); - a1.setPid(Arrays.asList( createSP("123456","pdb","dnet:pid_types"))); + a1.setPid(Arrays.asList(createSP("123456", "pdb", "dnet:pid_types"))); a1.setTitle(Collections.singletonList(createSP("Un Titolo", "title", "dnetTitle"))); - a1.setDlicollectedfrom(Arrays.asList(createCollectedFrom("znd","Zenodo","complete"))); + a1.setDlicollectedfrom(Arrays.asList(createCollectedFrom("znd", "Zenodo", "complete"))); a1.setCompletionStatus("complete"); DLIPublication a = new DLIPublication(); - a.setPid(Arrays.asList(createSP("10.11","doi","dnet:pid_types"), createSP("123456","pdb","dnet:pid_types"))); + a.setPid( + Arrays.asList( + createSP("10.11", "doi", "dnet:pid_types"), + createSP("123456", "pdb", "dnet:pid_types"))); a.setTitle(Collections.singletonList(createSP("A Title", "title", "dnetTitle"))); - a.setDlicollectedfrom(Arrays.asList(createCollectedFrom("dct","datacite","complete"),createCollectedFrom("dct","datacite","incomplete"))); + a.setDlicollectedfrom( + Arrays.asList( + createCollectedFrom("dct", "datacite", "complete"), + createCollectedFrom("dct", "datacite", "incomplete"))); a.setCompletionStatus("incomplete"); a.mergeFrom(a1); ObjectMapper mapper = new ObjectMapper(); System.out.println(mapper.writeValueAsString(a)); - - - - - - - } - - @Test public void testDeserialization() throws IOException { - final String json ="{\"dataInfo\":{\"invisible\":false,\"inferred\":null,\"deletedbyinference\":false,\"trust\":\"0.9\",\"inferenceprovenance\":null,\"provenanceaction\":null},\"lastupdatetimestamp\":null,\"id\":\"60|bd9352547098929a394655ad1a44a479\",\"originalId\":[\"bd9352547098929a394655ad1a44a479\"],\"collectedfrom\":[{\"key\":\"dli_________::datacite\",\"value\":\"Datasets in Datacite\",\"dataInfo\":null,\"blank\":false}],\"pid\":[{\"value\":\"10.7925/DRS1.DUCHAS_5078760\",\"qualifier\":{\"classid\":\"doi\",\"classname\":\"doi\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\",\"blank\":false},\"dataInfo\":null}],\"dateofcollection\":\"2020-01-09T08:29:31.885Z\",\"dateoftransformation\":null,\"extraInfo\":null,\"oaiprovenance\":null,\"author\":[{\"fullname\":\"Cathail, S. Ó\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Donnell, Breda Mc\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Ireland. Department of Arts, Culture, and the Gaeltacht\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"University College Dublin\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"National Folklore Foundation\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Cathail, S. Ó\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Donnell, Breda Mc\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null}],\"resulttype\":null,\"language\":null,\"country\":null,\"subject\":[{\"value\":\"Recreation\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null},{\"value\":\"Entertainments and recreational activities\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null},{\"value\":\"Siamsaíocht agus caitheamh aimsire\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null}],\"title\":[{\"value\":\"Games We Play\",\"qualifier\":null,\"dataInfo\":null}],\"relevantdate\":[{\"value\":\"1938-09-28\",\"qualifier\":{\"classid\":\"date\",\"classname\":\"date\",\"schemeid\":\"dnet::date\",\"schemename\":\"dnet::date\",\"blank\":false},\"dataInfo\":null}],\"description\":[{\"value\":\"Story collected by Breda Mc Donnell, a student at Tenure school (Tinure, Co. Louth) (no informant identified).\",\"dataInfo\":null}],\"dateofacceptance\":null,\"publisher\":{\"value\":\"University College Dublin\",\"dataInfo\":null},\"embargoenddate\":null,\"source\":null,\"fulltext\":null,\"format\":null,\"contributor\":null,\"resourcetype\":null,\"coverage\":null,\"refereed\":null,\"context\":null,\"processingchargeamount\":null,\"processingchargecurrency\":null,\"externalReference\":null,\"instance\":[],\"storagedate\":null,\"device\":null,\"size\":null,\"version\":null,\"lastmetadataupdate\":null,\"metadataversionnumber\":null,\"geolocation\":null,\"dlicollectedfrom\":[{\"id\":\"dli_________::datacite\",\"name\":\"Datasets in Datacite\",\"completionStatus\":\"complete\",\"collectionMode\":\"resolved\"}],\"completionStatus\":\"complete\"}"; + final String json = + "{\"dataInfo\":{\"invisible\":false,\"inferred\":null,\"deletedbyinference\":false,\"trust\":\"0.9\",\"inferenceprovenance\":null,\"provenanceaction\":null},\"lastupdatetimestamp\":null,\"id\":\"60|bd9352547098929a394655ad1a44a479\",\"originalId\":[\"bd9352547098929a394655ad1a44a479\"],\"collectedfrom\":[{\"key\":\"dli_________::datacite\",\"value\":\"Datasets in Datacite\",\"dataInfo\":null,\"blank\":false}],\"pid\":[{\"value\":\"10.7925/DRS1.DUCHAS_5078760\",\"qualifier\":{\"classid\":\"doi\",\"classname\":\"doi\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\",\"blank\":false},\"dataInfo\":null}],\"dateofcollection\":\"2020-01-09T08:29:31.885Z\",\"dateoftransformation\":null,\"extraInfo\":null,\"oaiprovenance\":null,\"author\":[{\"fullname\":\"Cathail, S. Ó\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Donnell, Breda Mc\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Ireland. Department of Arts, Culture, and the Gaeltacht\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"University College Dublin\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"National Folklore Foundation\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Cathail, S. Ó\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Donnell, Breda Mc\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null}],\"resulttype\":null,\"language\":null,\"country\":null,\"subject\":[{\"value\":\"Recreation\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null},{\"value\":\"Entertainments and recreational activities\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null},{\"value\":\"Siamsaíocht agus caitheamh aimsire\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null}],\"title\":[{\"value\":\"Games We Play\",\"qualifier\":null,\"dataInfo\":null}],\"relevantdate\":[{\"value\":\"1938-09-28\",\"qualifier\":{\"classid\":\"date\",\"classname\":\"date\",\"schemeid\":\"dnet::date\",\"schemename\":\"dnet::date\",\"blank\":false},\"dataInfo\":null}],\"description\":[{\"value\":\"Story collected by Breda Mc Donnell, a student at Tenure school (Tinure, Co. Louth) (no informant identified).\",\"dataInfo\":null}],\"dateofacceptance\":null,\"publisher\":{\"value\":\"University College Dublin\",\"dataInfo\":null},\"embargoenddate\":null,\"source\":null,\"fulltext\":null,\"format\":null,\"contributor\":null,\"resourcetype\":null,\"coverage\":null,\"refereed\":null,\"context\":null,\"processingchargeamount\":null,\"processingchargecurrency\":null,\"externalReference\":null,\"instance\":[],\"storagedate\":null,\"device\":null,\"size\":null,\"version\":null,\"lastmetadataupdate\":null,\"metadataversionnumber\":null,\"geolocation\":null,\"dlicollectedfrom\":[{\"id\":\"dli_________::datacite\",\"name\":\"Datasets in Datacite\",\"completionStatus\":\"complete\",\"collectionMode\":\"resolved\"}],\"completionStatus\":\"complete\"}"; ObjectMapper mapper = new ObjectMapper(); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); @@ -56,7 +52,8 @@ public class DLItest { System.out.println(mapper.writeValueAsString(dliDataset)); } - private ProvenaceInfo createCollectedFrom(final String id, final String name, final String completionStatus) { + private ProvenaceInfo createCollectedFrom( + final String id, final String name, final String completionStatus) { ProvenaceInfo p = new ProvenaceInfo(); p.setId(id); p.setName(name); @@ -64,8 +61,8 @@ public class DLItest { return p; } - - private StructuredProperty createSP(final String value, final String className, final String schemeName) { + private StructuredProperty createSP( + final String value, final String className, final String schemeName) { StructuredProperty p = new StructuredProperty(); p.setValue(value); Qualifier schema = new Qualifier(); @@ -76,6 +73,4 @@ public class DLItest { p.setQualifier(schema); return p; } - - } diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java index 994108b1cb..f3a8763886 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java @@ -10,117 +10,130 @@ import eu.dnetlib.dhp.actionmanager.partition.PartitionActionSetsByPayloadTypeJo import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import org.dom4j.Document; -import org.dom4j.Element; -import org.dom4j.io.SAXReader; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - import java.io.Serializable; import java.io.StringReader; import java.util.ArrayList; import java.util.List; import java.util.NoSuchElementException; import java.util.stream.Collectors; +import org.dom4j.Document; +import org.dom4j.Element; +import org.dom4j.io.SAXReader; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; public class ISClient implements Serializable { - private static final Logger log = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class); + private static final Logger log = + LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class); - private static final String INPUT_ACTION_SET_ID_SEPARATOR = ","; + private static final String INPUT_ACTION_SET_ID_SEPARATOR = ","; - private ISLookUpService isLookup; + private ISLookUpService isLookup; - public ISClient(String isLookupUrl) { - isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl); - } + public ISClient(String isLookupUrl) { + isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl); + } - public List getLatestRawsetPaths(String setIds) { + public List getLatestRawsetPaths(String setIds) { - List ids = Lists.newArrayList(Splitter.on(INPUT_ACTION_SET_ID_SEPARATOR) - .omitEmptyStrings() - .trimResults() - .split(setIds)); + List ids = + Lists.newArrayList( + Splitter.on(INPUT_ACTION_SET_ID_SEPARATOR) + .omitEmptyStrings() + .trimResults() + .split(setIds)); - return ids.stream() - .map(id -> getSet(isLookup, id)) - .map(as -> as.getPathToLatest()) - .collect(Collectors.toCollection(ArrayList::new)); - } + return ids.stream() + .map(id -> getSet(isLookup, id)) + .map(as -> as.getPathToLatest()) + .collect(Collectors.toCollection(ArrayList::new)); + } - private ActionManagerSet getSet(ISLookUpService isLookup, final String setId) { + private ActionManagerSet getSet(ISLookUpService isLookup, final String setId) { - final String q = "for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') " - + "where $x//SET/@id = '" + setId + "' return $x"; + final String q = + "for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') " + + "where $x//SET/@id = '" + + setId + + "' return $x"; - try { - final String basePath = getBasePathHDFS(isLookup); - final String setProfile = isLookup.getResourceProfileByQuery(q); - return getActionManagerSet(basePath, setProfile); - } catch (ISLookUpException | ActionManagerException e) { - throw new RuntimeException("Error accessing Sets, using query: " + q); - } - } + try { + final String basePath = getBasePathHDFS(isLookup); + final String setProfile = isLookup.getResourceProfileByQuery(q); + return getActionManagerSet(basePath, setProfile); + } catch (ISLookUpException | ActionManagerException e) { + throw new RuntimeException("Error accessing Sets, using query: " + q); + } + } - private ActionManagerSet getActionManagerSet(final String basePath, final String profile) throws ActionManagerException { - final SAXReader reader = new SAXReader(); - final ActionManagerSet set = new ActionManagerSet(); + private ActionManagerSet getActionManagerSet(final String basePath, final String profile) + throws ActionManagerException { + final SAXReader reader = new SAXReader(); + final ActionManagerSet set = new ActionManagerSet(); - try { - final Document doc = reader.read(new StringReader(profile)); + try { + final Document doc = reader.read(new StringReader(profile)); - set.setId(doc.valueOf("//SET/@id").trim()); - set.setName(doc.valueOf("//SET").trim()); - set.setImpact(ImpactTypes.valueOf(doc.valueOf("//IMPACT").trim())); - set.setLatest(doc.valueOf("//RAW_SETS/LATEST/@id"), doc.valueOf("//RAW_SETS/LATEST/@creationDate"), doc.valueOf("//RAW_SETS/LATEST/@lastUpdate")); - set.setDirectory(doc.valueOf("//SET/@directory")); - final List expiredNodes = doc.selectNodes("//RAW_SETS/EXPIRED"); - if (expiredNodes != null) { - for (int i = 0; i < expiredNodes.size(); i++) { - Element ex = (Element) expiredNodes.get(i); - set.addExpired(ex.attributeValue("id"), ex.attributeValue("creationDate"), ex.attributeValue("lastUpdate")); - } - } + set.setId(doc.valueOf("//SET/@id").trim()); + set.setName(doc.valueOf("//SET").trim()); + set.setImpact(ImpactTypes.valueOf(doc.valueOf("//IMPACT").trim())); + set.setLatest( + doc.valueOf("//RAW_SETS/LATEST/@id"), + doc.valueOf("//RAW_SETS/LATEST/@creationDate"), + doc.valueOf("//RAW_SETS/LATEST/@lastUpdate")); + set.setDirectory(doc.valueOf("//SET/@directory")); + final List expiredNodes = doc.selectNodes("//RAW_SETS/EXPIRED"); + if (expiredNodes != null) { + for (int i = 0; i < expiredNodes.size(); i++) { + Element ex = (Element) expiredNodes.get(i); + set.addExpired( + ex.attributeValue("id"), + ex.attributeValue("creationDate"), + ex.attributeValue("lastUpdate")); + } + } - final StringBuilder sb = new StringBuilder(); - sb.append(basePath); - sb.append("/"); - sb.append(doc.valueOf("//SET/@directory")); - sb.append("/"); - sb.append(doc.valueOf("//RAW_SETS/LATEST/@id")); - set.setPathToLatest(sb.toString()); + final StringBuilder sb = new StringBuilder(); + sb.append(basePath); + sb.append("/"); + sb.append(doc.valueOf("//SET/@directory")); + sb.append("/"); + sb.append(doc.valueOf("//RAW_SETS/LATEST/@id")); + set.setPathToLatest(sb.toString()); - return set; - } catch (Exception e) { - throw new ActionManagerException("Error creating set from profile: " + profile, e); - } - } - - private String getBasePathHDFS(ISLookUpService isLookup) throws ActionManagerException { - return queryServiceProperty(isLookup, "basePath"); - } - - private String queryServiceProperty(ISLookUpService isLookup, final String propertyName) throws ActionManagerException { - final String q = "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='" - + propertyName + "']/@value/string()"; - log.debug("quering for service property: " + q); - try { - final List value = isLookup.quickSearchProfile(q); - return Iterables.getOnlyElement(value); - } catch (ISLookUpException e) { - String msg = "Error accessing service profile, using query: " + q; - log.error(msg, e); - throw new ActionManagerException(msg, e); - } catch (NoSuchElementException e) { - String msg = "missing service property: " + propertyName; - log.error(msg, e); - throw new ActionManagerException(msg, e); - } catch (IllegalArgumentException e) { - String msg = "found more than one service property: " + propertyName; - log.error(msg, e); - throw new ActionManagerException(msg, e); - } - } + return set; + } catch (Exception e) { + throw new ActionManagerException("Error creating set from profile: " + profile, e); + } + } + private String getBasePathHDFS(ISLookUpService isLookup) throws ActionManagerException { + return queryServiceProperty(isLookup, "basePath"); + } + private String queryServiceProperty(ISLookUpService isLookup, final String propertyName) + throws ActionManagerException { + final String q = + "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='" + + propertyName + + "']/@value/string()"; + log.debug("quering for service property: " + q); + try { + final List value = isLookup.quickSearchProfile(q); + return Iterables.getOnlyElement(value); + } catch (ISLookUpException e) { + String msg = "Error accessing service profile, using query: " + q; + log.error(msg, e); + throw new ActionManagerException(msg, e); + } catch (NoSuchElementException e) { + String msg = "missing service property: " + propertyName; + log.error(msg, e); + throw new ActionManagerException(msg, e); + } catch (IllegalArgumentException e) { + String msg = "found more than one service property: " + propertyName; + log.error(msg, e); + throw new ActionManagerException(msg, e); + } + } } diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java index 7c4d0616cb..9ead5411f5 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java @@ -1,9 +1,15 @@ package eu.dnetlib.dhp.actionmanager.partition; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static org.apache.spark.sql.functions.*; + import eu.dnetlib.dhp.actionmanager.ISClient; -import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import java.util.Arrays; +import java.util.List; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.spark.SparkConf; @@ -14,32 +20,27 @@ import org.apache.spark.sql.types.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static org.apache.spark.sql.functions.*; - -/** - * Partitions given set of action sets by payload type. - */ +/** Partitions given set of action sets by payload type. */ public class PartitionActionSetsByPayloadTypeJob { - private static final Logger logger = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class); + private static final Logger logger = + LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class); - private static final StructType KV_SCHEMA = StructType$.MODULE$.apply( - Arrays.asList( - StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()), - StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty()) - )); + private static final StructType KV_SCHEMA = + StructType$.MODULE$.apply( + Arrays.asList( + StructField$.MODULE$.apply( + "key", DataTypes.StringType, false, Metadata.empty()), + StructField$.MODULE$.apply( + "value", DataTypes.StringType, false, Metadata.empty()))); - private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$.apply( - Arrays.asList( - StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()), - StructField$.MODULE$.apply("payload", DataTypes.StringType, false, Metadata.empty()) - )); + private static final StructType ATOMIC_ACTION_SCHEMA = + StructType$.MODULE$.apply( + Arrays.asList( + StructField$.MODULE$.apply( + "clazz", DataTypes.StringType, false, Metadata.empty()), + StructField$.MODULE$.apply( + "payload", DataTypes.StringType, false, Metadata.empty()))); private ISClient isClient; @@ -47,20 +48,20 @@ public class PartitionActionSetsByPayloadTypeJob { this.isClient = new ISClient(isLookupUrl); } - public PartitionActionSetsByPayloadTypeJob() { - } + public PartitionActionSetsByPayloadTypeJob() {} public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils.toString( - PromoteActionPayloadForGraphTableJob.class - .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json")); + String jsonConfiguration = + IOUtils.toString( + PromoteActionPayloadForGraphTableJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); String inputActionSetIds = parser.get("inputActionSetIds"); @@ -72,7 +73,8 @@ public class PartitionActionSetsByPayloadTypeJob { String isLookupUrl = parser.get("isLookupUrl"); logger.info("isLookupUrl: {}", isLookupUrl); - new PartitionActionSetsByPayloadTypeJob(isLookupUrl).run(isSparkSessionManaged, inputActionSetIds, outputPath); + new PartitionActionSetsByPayloadTypeJob(isLookupUrl) + .run(isSparkSessionManaged, inputActionSetIds, outputPath); } protected void run(Boolean isSparkSessionManaged, String inputActionSetIds, String outputPath) { @@ -83,53 +85,51 @@ public class PartitionActionSetsByPayloadTypeJob { SparkConf conf = new SparkConf(); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - runWithSparkSession(conf, isSparkSessionManaged, + runWithSparkSession( + conf, + isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); readAndWriteActionSetsFromPaths(spark, inputActionSetPaths, outputPath); }); } - private static void removeOutputDir(SparkSession spark, - String path) { + private static void removeOutputDir(SparkSession spark, String path) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } - private static void readAndWriteActionSetsFromPaths(SparkSession spark, - List inputActionSetPaths, - String outputPath) { - inputActionSetPaths - .stream() - .filter(path -> HdfsSupport.exists(path, spark.sparkContext().hadoopConfiguration())) - .forEach(inputActionSetPath -> { - Dataset actionDS = readActionSetFromPath(spark, inputActionSetPath); - saveActions(actionDS, outputPath); - }); + private static void readAndWriteActionSetsFromPaths( + SparkSession spark, List inputActionSetPaths, String outputPath) { + inputActionSetPaths.stream() + .filter( + path -> + HdfsSupport.exists( + path, spark.sparkContext().hadoopConfiguration())) + .forEach( + inputActionSetPath -> { + Dataset actionDS = + readActionSetFromPath(spark, inputActionSetPath); + saveActions(actionDS, outputPath); + }); } - private static Dataset readActionSetFromPath(SparkSession spark, - String path) { + private static Dataset readActionSetFromPath(SparkSession spark, String path) { logger.info("Reading actions from path: {}", path); JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD rdd = sc - .sequenceFile(path, Text.class, Text.class) - .map(x -> RowFactory.create(x._1().toString(), x._2().toString())); + JavaRDD rdd = + sc.sequenceFile(path, Text.class, Text.class) + .map(x -> RowFactory.create(x._1().toString(), x._2().toString())); return spark.createDataFrame(rdd, KV_SCHEMA) .withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA)) .select(expr("atomic_action.*")); } - private static void saveActions(Dataset actionDS, - String path) { + private static void saveActions(Dataset actionDS, String path) { logger.info("Saving actions to path: {}", path); - actionDS - .write() - .partitionBy("clazz") - .mode(SaveMode.Append) - .parquet(path); + actionDS.write().partitionBy("clazz").mode(SaveMode.Append).parquet(path); } public ISClient getIsClient() { diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java index 19b2104bcd..eb839245b5 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java @@ -1,41 +1,39 @@ package eu.dnetlib.dhp.actionmanager.promote; +import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; + import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Relation; - import java.util.function.BiFunction; -import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; - -/** - * OAF model merging support. - */ +/** OAF model merging support. */ public class MergeAndGet { - private MergeAndGet() { - } + private MergeAndGet() {} /** * Strategy for merging OAF model objects. - *

- * MERGE_FROM_AND_GET: use OAF 'mergeFrom' method - * SELECT_NEWER_AND_GET: use last update timestamp to return newer instance + * + *

MERGE_FROM_AND_GET: use OAF 'mergeFrom' method SELECT_NEWER_AND_GET: use last update + * timestamp to return newer instance */ public enum Strategy { - MERGE_FROM_AND_GET, SELECT_NEWER_AND_GET + MERGE_FROM_AND_GET, + SELECT_NEWER_AND_GET } /** * Returns a function for merging OAF model objects. * * @param strategy Strategy to be used to merge objects - * @param Graph table type - * @param Action payload type + * @param Graph table type + * @param Action payload type * @return BiFunction to be used to merge OAF objects */ - public static SerializableSupplier> functionFor(Strategy strategy) { + public static + SerializableSupplier> functionFor(Strategy strategy) { switch (strategy) { case MERGE_FROM_AND_GET: return () -> MergeAndGet::mergeFromAndGet; @@ -49,26 +47,36 @@ public class MergeAndGet { if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) { ((Relation) x).mergeFrom((Relation) y); return x; - } else if (isSubClass(x, OafEntity.class) && isSubClass(y, OafEntity.class) && isSubClass(x, y)) { + } else if (isSubClass(x, OafEntity.class) + && isSubClass(y, OafEntity.class) + && isSubClass(x, y)) { ((OafEntity) x).mergeFrom((OafEntity) y); return x; } - throw new RuntimeException(String.format("MERGE_FROM_AND_GET incompatible types: %s, %s", - x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); + throw new RuntimeException( + String.format( + "MERGE_FROM_AND_GET incompatible types: %s, %s", + x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); } private static G selectNewerAndGet(G x, A y) { - if (x.getClass().equals(y.getClass()) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) { + if (x.getClass().equals(y.getClass()) + && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) { return x; - } else if (x.getClass().equals(y.getClass()) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) { + } else if (x.getClass().equals(y.getClass()) + && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) { return (G) y; } else if (isSubClass(x, y) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) { return x; } else if (isSubClass(x, y) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) { - throw new RuntimeException(String.format("SELECT_NEWER_AND_GET cannot return right type when it is not the same as left type: %s, %s", - x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); + throw new RuntimeException( + String.format( + "SELECT_NEWER_AND_GET cannot return right type when it is not the same as left type: %s, %s", + x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); } - throw new RuntimeException(String.format("SELECT_NEWER_AND_GET cannot be used when left is not subtype of right: %s, %s", - x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); + throw new RuntimeException( + String.format( + "SELECT_NEWER_AND_GET cannot be used when left is not subtype of right: %s, %s", + x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); } } diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java index 20b75842c5..1fa173e9c9 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java @@ -1,14 +1,20 @@ package eu.dnetlib.dhp.actionmanager.promote; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; + import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; +import java.util.Objects; +import java.util.Optional; +import java.util.function.BiFunction; +import java.util.function.Function; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -17,33 +23,25 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.Objects; -import java.util.Optional; -import java.util.function.BiFunction; -import java.util.function.Function; - -import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -/** - * Applies a given action payload file to graph table of compatible type. - */ +/** Applies a given action payload file to graph table of compatible type. */ public class PromoteActionPayloadForGraphTableJob { - private static final Logger logger = LoggerFactory.getLogger(PromoteActionPayloadForGraphTableJob.class); + private static final Logger logger = + LoggerFactory.getLogger(PromoteActionPayloadForGraphTableJob.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils.toString( - PromoteActionPayloadForGraphTableJob.class - .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json")); + String jsonConfiguration = + IOUtils.toString( + PromoteActionPayloadForGraphTableJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); String inputGraphTablePath = parser.get("inputGraphTablePath"); @@ -61,11 +59,13 @@ public class PromoteActionPayloadForGraphTableJob { String outputGraphTablePath = parser.get("outputGraphTablePath"); logger.info("outputGraphTablePath: {}", outputGraphTablePath); - MergeAndGet.Strategy strategy = MergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase()); + MergeAndGet.Strategy strategy = + MergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase()); logger.info("strategy: {}", strategy); Class rowClazz = (Class) Class.forName(graphTableClassName); - Class actionPayloadClazz = (Class) Class.forName(actionPayloadClassName); + Class actionPayloadClazz = + (Class) Class.forName(actionPayloadClassName); throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(rowClazz, actionPayloadClazz); @@ -73,10 +73,13 @@ public class PromoteActionPayloadForGraphTableJob { conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - runWithSparkSession(conf, isSparkSessionManaged, + runWithSparkSession( + conf, + isSparkSessionManaged, spark -> { removeOutputDir(spark, outputGraphTablePath); - promoteActionPayloadForGraphTable(spark, + promoteActionPayloadForGraphTable( + spark, inputGraphTablePath, inputActionPayloadPath, outputGraphTablePath, @@ -86,44 +89,50 @@ public class PromoteActionPayloadForGraphTableJob { }); } - private static void throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(Class rowClazz, - Class actionPayloadClazz) { + private static void throwIfGraphTableClassIsNotSubClassOfActionPayloadClass( + Class rowClazz, Class actionPayloadClazz) { if (!isSubClass(rowClazz, actionPayloadClazz)) { - String msg = String.format("graph table class is not a subclass of action payload class: graph=%s, action=%s", - rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName()); + String msg = + String.format( + "graph table class is not a subclass of action payload class: graph=%s, action=%s", + rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName()); throw new RuntimeException(msg); } } - private static void removeOutputDir(SparkSession spark, - String path) { + private static void removeOutputDir(SparkSession spark, String path) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } - private static void promoteActionPayloadForGraphTable(SparkSession spark, - String inputGraphTablePath, - String inputActionPayloadPath, - String outputGraphTablePath, - MergeAndGet.Strategy strategy, - Class rowClazz, - Class actionPayloadClazz) { + private static void promoteActionPayloadForGraphTable( + SparkSession spark, + String inputGraphTablePath, + String inputActionPayloadPath, + String outputGraphTablePath, + MergeAndGet.Strategy strategy, + Class rowClazz, + Class actionPayloadClazz) { Dataset rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz); - Dataset actionPayloadDS = readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz); + Dataset actionPayloadDS = + readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz); - Dataset result = promoteActionPayloadForGraphTable(rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz) - .map((MapFunction) value -> value, Encoders.bean(rowClazz)); + Dataset result = + promoteActionPayloadForGraphTable( + rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz) + .map((MapFunction) value -> value, Encoders.bean(rowClazz)); saveGraphTable(result, outputGraphTablePath); } - private static Dataset readGraphTable(SparkSession spark, - String path, - Class rowClazz) { + private static Dataset readGraphTable( + SparkSession spark, String path, Class rowClazz) { logger.info("Reading graph table from path: {}", path); return spark.read() .textFile(path) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, rowClazz), Encoders.bean(rowClazz)); + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, rowClazz), + Encoders.bean(rowClazz)); /* return spark @@ -133,33 +142,44 @@ public class PromoteActionPayloadForGraphTableJob { */ } - private static Dataset readActionPayload(SparkSession spark, - String path, - Class actionPayloadClazz) { + private static Dataset readActionPayload( + SparkSession spark, String path, Class actionPayloadClazz) { logger.info("Reading action payload from path: {}", path); - return spark - .read() + return spark.read() .parquet(path) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value.getAs("payload"), - actionPayloadClazz), Encoders.bean(actionPayloadClazz)); + .map( + (MapFunction) + value -> + OBJECT_MAPPER.readValue( + value.getAs("payload"), actionPayloadClazz), + Encoders.bean(actionPayloadClazz)); } - private static Dataset promoteActionPayloadForGraphTable(Dataset rowDS, - Dataset actionPayloadDS, - MergeAndGet.Strategy strategy, - Class rowClazz, - Class actionPayloadClazz) { - logger.info("Promoting action payload for graph table: payload={}, table={}", actionPayloadClazz.getSimpleName(), rowClazz.getSimpleName()); + private static Dataset promoteActionPayloadForGraphTable( + Dataset rowDS, + Dataset actionPayloadDS, + MergeAndGet.Strategy strategy, + Class rowClazz, + Class actionPayloadClazz) { + logger.info( + "Promoting action payload for graph table: payload={}, table={}", + actionPayloadClazz.getSimpleName(), + rowClazz.getSimpleName()); - SerializableSupplier> rowIdFn = PromoteActionPayloadForGraphTableJob::idFn; - SerializableSupplier> actionPayloadIdFn = PromoteActionPayloadForGraphTableJob::idFn; - SerializableSupplier> mergeRowWithActionPayloadAndGetFn = MergeAndGet.functionFor(strategy); - SerializableSupplier> mergeRowsAndGetFn = MergeAndGet.functionFor(strategy); + SerializableSupplier> rowIdFn = + PromoteActionPayloadForGraphTableJob::idFn; + SerializableSupplier> actionPayloadIdFn = + PromoteActionPayloadForGraphTableJob::idFn; + SerializableSupplier> mergeRowWithActionPayloadAndGetFn = + MergeAndGet.functionFor(strategy); + SerializableSupplier> mergeRowsAndGetFn = + MergeAndGet.functionFor(strategy); SerializableSupplier zeroFn = zeroFn(rowClazz); - SerializableSupplier> isNotZeroFn = PromoteActionPayloadForGraphTableJob::isNotZeroFnUsingIdOrSource; + SerializableSupplier> isNotZeroFn = + PromoteActionPayloadForGraphTableJob::isNotZeroFnUsingIdOrSource; - Dataset joinedAndMerged = PromoteActionPayloadFunctions - .joinGraphTableWithActionPayloadAndMerge( + Dataset joinedAndMerged = + PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge( rowDS, actionPayloadDS, rowIdFn, @@ -168,14 +188,8 @@ public class PromoteActionPayloadForGraphTableJob { rowClazz, actionPayloadClazz); - return PromoteActionPayloadFunctions - .groupGraphTableByIdAndMerge( - joinedAndMerged, - rowIdFn, - mergeRowsAndGetFn, - zeroFn, - isNotZeroFn, - rowClazz); + return PromoteActionPayloadFunctions.groupGraphTableByIdAndMerge( + joinedAndMerged, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, rowClazz); } private static Function idFn() { @@ -190,19 +204,49 @@ public class PromoteActionPayloadForGraphTableJob { private static String idFnForRelation(T t) { Relation r = (Relation) t; return Optional.ofNullable(r.getSource()) - .map(source -> Optional.ofNullable(r.getTarget()) - .map(target -> Optional.ofNullable(r.getRelType()) - .map(relType -> Optional.ofNullable(r.getSubRelType()) - .map(subRelType -> Optional.ofNullable(r.getRelClass()) - .map(relClass -> String.join(source, target, relType, subRelType, relClass)) - .orElse(String.join(source, target, relType, subRelType)) - ) - .orElse(String.join(source, target, relType)) - ) - .orElse(String.join(source, target)) - ) - .orElse(source) - ) + .map( + source -> + Optional.ofNullable(r.getTarget()) + .map( + target -> + Optional.ofNullable(r.getRelType()) + .map( + relType -> + Optional.ofNullable( + r + .getSubRelType()) + .map( + subRelType -> + Optional + .ofNullable( + r + .getRelClass()) + .map( + relClass -> + String + .join( + source, + target, + relType, + subRelType, + relClass)) + .orElse( + String + .join( + source, + target, + relType, + subRelType))) + .orElse( + String + .join( + source, + target, + relType))) + .orElse( + String.join( + source, target))) + .orElse(source)) .orElse(null); } @@ -242,13 +286,8 @@ public class PromoteActionPayloadForGraphTableJob { }; } - private static void saveGraphTable(Dataset result, - String path) { + private static void saveGraphTable(Dataset result, String path) { logger.info("Saving graph table to path: {}", path); - result - .toJSON() - .write() - .option("compression", "gzip") - .text(path); + result.toJSON().write().option("compression", "gzip").text(path); } } diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java index fda86cb194..c783740293 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java @@ -1,7 +1,13 @@ package eu.dnetlib.dhp.actionmanager.promote; +import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; + import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; import eu.dnetlib.dhp.schema.oaf.Oaf; +import java.util.Objects; +import java.util.Optional; +import java.util.function.BiFunction; +import java.util.function.Function; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; @@ -11,95 +17,113 @@ import org.apache.spark.sql.TypedColumn; import org.apache.spark.sql.expressions.Aggregator; import scala.Tuple2; -import java.util.Objects; -import java.util.Optional; -import java.util.function.BiFunction; -import java.util.function.Function; - -import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; - -/** - * Promote action payload functions. - */ +/** Promote action payload functions. */ public class PromoteActionPayloadFunctions { - private PromoteActionPayloadFunctions() { - } + private PromoteActionPayloadFunctions() {} /** - * Joins dataset representing graph table with dataset representing action payload using supplied functions. + * Joins dataset representing graph table with dataset representing action payload using + * supplied functions. * - * @param rowDS Dataset representing graph table - * @param actionPayloadDS Dataset representing action payload - * @param rowIdFn Function used to get the id of graph table row - * @param actionPayloadIdFn Function used to get id of action payload instance - * @param mergeAndGetFn Function used to merge graph table row and action payload instance - * @param rowClazz Class of graph table + * @param rowDS Dataset representing graph table + * @param actionPayloadDS Dataset representing action payload + * @param rowIdFn Function used to get the id of graph table row + * @param actionPayloadIdFn Function used to get id of action payload instance + * @param mergeAndGetFn Function used to merge graph table row and action payload instance + * @param rowClazz Class of graph table * @param actionPayloadClazz Class of action payload - * @param Type of graph table row - * @param Type of action payload instance + * @param Type of graph table row + * @param Type of action payload instance * @return Dataset of merged graph table rows and action payload instances */ - public static Dataset joinGraphTableWithActionPayloadAndMerge(Dataset rowDS, - Dataset actionPayloadDS, - SerializableSupplier> rowIdFn, - SerializableSupplier> actionPayloadIdFn, - SerializableSupplier> mergeAndGetFn, - Class rowClazz, - Class actionPayloadClazz) { + public static Dataset joinGraphTableWithActionPayloadAndMerge( + Dataset rowDS, + Dataset actionPayloadDS, + SerializableSupplier> rowIdFn, + SerializableSupplier> actionPayloadIdFn, + SerializableSupplier> mergeAndGetFn, + Class rowClazz, + Class actionPayloadClazz) { if (!isSubClass(rowClazz, actionPayloadClazz)) { - throw new RuntimeException("action payload type must be the same or be a super type of table row type"); + throw new RuntimeException( + "action payload type must be the same or be a super type of table row type"); } Dataset> rowWithIdDS = mapToTupleWithId(rowDS, rowIdFn, rowClazz); - Dataset> actionPayloadWithIdDS = mapToTupleWithId(actionPayloadDS, actionPayloadIdFn, actionPayloadClazz); + Dataset> actionPayloadWithIdDS = + mapToTupleWithId(actionPayloadDS, actionPayloadIdFn, actionPayloadClazz); return rowWithIdDS - .joinWith(actionPayloadWithIdDS, rowWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")), "full_outer") - .map((MapFunction, Tuple2>, G>) value -> { - Optional rowOpt = Optional.ofNullable(value._1()).map(Tuple2::_2); - Optional actionPayloadOpt = Optional.ofNullable(value._2()).map(Tuple2::_2); - return rowOpt - .map(row -> actionPayloadOpt - .map(actionPayload -> mergeAndGetFn.get().apply(row, actionPayload)) - .orElse(row)) - .orElseGet(() -> actionPayloadOpt - .filter(actionPayload -> actionPayload.getClass().equals(rowClazz)) - .map(rowClazz::cast) - .orElse(null)); - }, Encoders.kryo(rowClazz)) + .joinWith( + actionPayloadWithIdDS, + rowWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")), + "full_outer") + .map( + (MapFunction, Tuple2>, G>) + value -> { + Optional rowOpt = + Optional.ofNullable(value._1()).map(Tuple2::_2); + Optional actionPayloadOpt = + Optional.ofNullable(value._2()).map(Tuple2::_2); + return rowOpt.map( + row -> + actionPayloadOpt + .map( + actionPayload -> + mergeAndGetFn + .get() + .apply( + row, + actionPayload)) + .orElse(row)) + .orElseGet( + () -> + actionPayloadOpt + .filter( + actionPayload -> + actionPayload + .getClass() + .equals( + rowClazz)) + .map(rowClazz::cast) + .orElse(null)); + }, + Encoders.kryo(rowClazz)) .filter((FilterFunction) Objects::nonNull); } - private static Dataset> mapToTupleWithId(Dataset ds, - SerializableSupplier> idFn, - Class clazz) { - return ds - .map((MapFunction>) value -> new Tuple2<>(idFn.get().apply(value), value), - Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); + private static Dataset> mapToTupleWithId( + Dataset ds, SerializableSupplier> idFn, Class clazz) { + return ds.map( + (MapFunction>) + value -> new Tuple2<>(idFn.get().apply(value), value), + Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); } /** * Groups graph table by id and aggregates using supplied functions. * - * @param rowDS Dataset representing graph table - * @param rowIdFn Function used to get the id of graph table row + * @param rowDS Dataset representing graph table + * @param rowIdFn Function used to get the id of graph table row * @param mergeAndGetFn Function used to merge graph table rows - * @param zeroFn Function to create a zero/empty instance of graph table row - * @param isNotZeroFn Function to check if graph table row is not zero/empty - * @param rowClazz Class of graph table - * @param Type of graph table row + * @param zeroFn Function to create a zero/empty instance of graph table row + * @param isNotZeroFn Function to check if graph table row is not zero/empty + * @param rowClazz Class of graph table + * @param Type of graph table row * @return Dataset of aggregated graph table rows */ - public static Dataset groupGraphTableByIdAndMerge(Dataset rowDS, - SerializableSupplier> rowIdFn, - SerializableSupplier> mergeAndGetFn, - SerializableSupplier zeroFn, - SerializableSupplier> isNotZeroFn, - Class rowClazz) { - TypedColumn aggregator = new TableAggregator<>(zeroFn, mergeAndGetFn, isNotZeroFn, rowClazz).toColumn(); - return rowDS - .groupByKey((MapFunction) x -> rowIdFn.get().apply(x), Encoders.STRING()) + public static Dataset groupGraphTableByIdAndMerge( + Dataset rowDS, + SerializableSupplier> rowIdFn, + SerializableSupplier> mergeAndGetFn, + SerializableSupplier zeroFn, + SerializableSupplier> isNotZeroFn, + Class rowClazz) { + TypedColumn aggregator = + new TableAggregator<>(zeroFn, mergeAndGetFn, isNotZeroFn, rowClazz).toColumn(); + return rowDS.groupByKey( + (MapFunction) x -> rowIdFn.get().apply(x), Encoders.STRING()) .agg(aggregator) .map((MapFunction, G>) Tuple2::_2, Encoders.kryo(rowClazz)); } @@ -115,10 +139,11 @@ public class PromoteActionPayloadFunctions { private SerializableSupplier> isNotZeroFn; private Class rowClazz; - public TableAggregator(SerializableSupplier zeroFn, - SerializableSupplier> mergeAndGetFn, - SerializableSupplier> isNotZeroFn, - Class rowClazz) { + public TableAggregator( + SerializableSupplier zeroFn, + SerializableSupplier> mergeAndGetFn, + SerializableSupplier> isNotZeroFn, + Class rowClazz) { this.zeroFn = zeroFn; this.mergeAndGetFn = mergeAndGetFn; this.isNotZeroFn = isNotZeroFn; @@ -149,7 +174,8 @@ public class PromoteActionPayloadFunctions { } else if (!isNotZero.apply(left) && isNotZero.apply(right)) { return right; } - throw new RuntimeException("internal aggregation error: left and right objects are zero"); + throw new RuntimeException( + "internal aggregation error: left and right objects are zero"); } @Override @@ -167,4 +193,4 @@ public class PromoteActionPayloadFunctions { return Encoders.kryo(rowClazz); } } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java index bd5dc9a5df..7f605d92d1 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java @@ -1,10 +1,20 @@ package eu.dnetlib.dhp.actionmanager.partition; +import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException; +import static org.apache.spark.sql.functions.*; +import static org.junit.jupiter.api.Assertions.assertIterableEquals; +import static scala.collection.JavaConversions.mutableSeqAsJavaList; + import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.common.collect.Lists; import eu.dnetlib.dhp.actionmanager.ISClient; import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest; import eu.dnetlib.dhp.schema.oaf.*; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.*; +import java.util.stream.Collectors; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapreduce.Job; @@ -25,32 +35,23 @@ import org.mockito.junit.jupiter.MockitoExtension; import scala.Tuple2; import scala.collection.mutable.Seq; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.*; -import java.util.stream.Collectors; - -import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException; -import static org.apache.spark.sql.functions.*; -import static org.junit.jupiter.api.Assertions.assertIterableEquals; -import static scala.collection.JavaConversions.mutableSeqAsJavaList; - @ExtendWith(MockitoExtension.class) public class PartitionActionSetsByPayloadTypeJobTest { - private static final ClassLoader cl = PartitionActionSetsByPayloadTypeJobTest.class.getClassLoader(); + private static final ClassLoader cl = + PartitionActionSetsByPayloadTypeJobTest.class.getClassLoader(); private static Configuration configuration; private static SparkSession spark; private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$.apply( - Arrays.asList( - StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()), - StructField$.MODULE$.apply("payload", DataTypes.StringType, false, Metadata.empty()) - )); + private static final StructType ATOMIC_ACTION_SCHEMA = + StructType$.MODULE$.apply( + Arrays.asList( + StructField$.MODULE$.apply( + "clazz", DataTypes.StringType, false, Metadata.empty()), + StructField$.MODULE$.apply( + "payload", DataTypes.StringType, false, Metadata.empty()))); @BeforeAll public static void beforeAll() throws IOException { @@ -71,11 +72,11 @@ public class PartitionActionSetsByPayloadTypeJobTest { @Nested class Main { - @Mock - private ISClient isClient; + @Mock private ISClient isClient; @Test - public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception { + public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) + throws Exception { // given Path inputActionSetsBaseDir = workingDir.resolve("input").resolve("action_sets"); Path outputDir = workingDir.resolve("output"); @@ -85,15 +86,16 @@ public class PartitionActionSetsByPayloadTypeJobTest { List inputActionSetsPaths = resolveInputActionSetPaths(inputActionSetsBaseDir); // when - Mockito.when(isClient.getLatestRawsetPaths(Mockito.anyString())).thenReturn(inputActionSetsPaths); + Mockito.when(isClient.getLatestRawsetPaths(Mockito.anyString())) + .thenReturn(inputActionSetsPaths); PartitionActionSetsByPayloadTypeJob job = new PartitionActionSetsByPayloadTypeJob(); job.setIsClient(isClient); job.run( Boolean.FALSE, - "", // it can be empty we're mocking the response from isClient to resolve the paths - outputDir.toString() - ); + "", // it can be empty we're mocking the response from isClient to resolve the + // paths + outputDir.toString()); // then Files.exists(outputDir); @@ -110,112 +112,134 @@ public class PartitionActionSetsByPayloadTypeJobTest { } } - private List resolveInputActionSetPaths(Path inputActionSetsBaseDir) throws IOException { + private List resolveInputActionSetPaths(Path inputActionSetsBaseDir) + throws IOException { Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir(); - return Files - .list(inputActionSetJsonDumpsDir) - .map(path -> { - String inputActionSetId = path.getFileName().toString(); - return inputActionSetsBaseDir.resolve(inputActionSetId).toString(); - }) + return Files.list(inputActionSetJsonDumpsDir) + .map( + path -> { + String inputActionSetId = path.getFileName().toString(); + return inputActionSetsBaseDir.resolve(inputActionSetId).toString(); + }) .collect(Collectors.toCollection(ArrayList::new)); } - private static Map> createActionSets(Path inputActionSetsDir) throws IOException { + private static Map> createActionSets(Path inputActionSetsDir) + throws IOException { Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir(); Map> oafsByType = new HashMap<>(); - Files - .list(inputActionSetJsonDumpsDir) - .forEach(inputActionSetJsonDumpFile -> { - String inputActionSetId = inputActionSetJsonDumpFile.getFileName().toString(); - Path inputActionSetDir = inputActionSetsDir.resolve(inputActionSetId); + Files.list(inputActionSetJsonDumpsDir) + .forEach( + inputActionSetJsonDumpFile -> { + String inputActionSetId = + inputActionSetJsonDumpFile.getFileName().toString(); + Path inputActionSetDir = inputActionSetsDir.resolve(inputActionSetId); - Dataset actionDS = readActionsFromJsonDump(inputActionSetJsonDumpFile.toString()) - .cache(); + Dataset actionDS = + readActionsFromJsonDump(inputActionSetJsonDumpFile.toString()) + .cache(); - writeActionsAsJobInput(actionDS, inputActionSetId, inputActionSetDir.toString()); + writeActionsAsJobInput( + actionDS, inputActionSetId, inputActionSetDir.toString()); - Map> actionSetOafsByType = actionDS - .withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA)) - .select(expr("atomic_action.*")) - .groupBy(col("clazz")) - .agg(collect_list(col("payload")).as("payload_list")) - .collectAsList() - .stream() - .map(row -> new AbstractMap.SimpleEntry<>(row.getAs("clazz"), - mutableSeqAsJavaList(row.>getAs("payload_list")))) - .collect(Collectors.toMap(AbstractMap.SimpleEntry::getKey, AbstractMap.SimpleEntry::getValue)); + Map> actionSetOafsByType = + actionDS + .withColumn( + "atomic_action", + from_json(col("value"), ATOMIC_ACTION_SCHEMA)) + .select(expr("atomic_action.*")).groupBy(col("clazz")) + .agg(collect_list(col("payload")).as("payload_list")) + .collectAsList().stream() + .map( + row -> + new AbstractMap.SimpleEntry<>( + row.getAs("clazz"), + mutableSeqAsJavaList( + row.>getAs( + "payload_list")))) + .collect( + Collectors.toMap( + AbstractMap.SimpleEntry::getKey, + AbstractMap.SimpleEntry::getValue)); - actionSetOafsByType.keySet() - .forEach(x -> { - if (oafsByType.containsKey(x)) { - List collected = new ArrayList<>(); - collected.addAll(oafsByType.get(x)); - collected.addAll(actionSetOafsByType.get(x)); - oafsByType.put(x, collected); - } else { - oafsByType.put(x, actionSetOafsByType.get(x)); - } - }); - }); + actionSetOafsByType + .keySet() + .forEach( + x -> { + if (oafsByType.containsKey(x)) { + List collected = new ArrayList<>(); + collected.addAll(oafsByType.get(x)); + collected.addAll(actionSetOafsByType.get(x)); + oafsByType.put(x, collected); + } else { + oafsByType.put(x, actionSetOafsByType.get(x)); + } + }); + }); return oafsByType; } private static Path getInputActionSetJsonDumpsDir() { - return Paths - .get(Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/partition/input/")) + return Paths.get( + Objects.requireNonNull( + cl.getResource("eu/dnetlib/dhp/actionmanager/partition/input/")) .getFile()); } private static Dataset readActionsFromJsonDump(String path) { - return spark - .read() - .textFile(path); + return spark.read().textFile(path); } - private static void writeActionsAsJobInput(Dataset actionDS, - String inputActionSetId, - String path) { - actionDS - .javaRDD() + private static void writeActionsAsJobInput( + Dataset actionDS, String inputActionSetId, String path) { + actionDS.javaRDD() .mapToPair(json -> new Tuple2<>(new Text(inputActionSetId), new Text(json))) - .saveAsNewAPIHadoopFile(path, + .saveAsNewAPIHadoopFile( + path, Text.class, Text.class, SequenceFileOutputFormat.class, configuration); } - private static void assertForOafType(Path outputDir, Map> oafsByClassName, Class clazz) { - Path outputDatasetDir = outputDir.resolve(String.format("clazz=%s", clazz.getCanonicalName())); + private static void assertForOafType( + Path outputDir, Map> oafsByClassName, Class clazz) { + Path outputDatasetDir = + outputDir.resolve(String.format("clazz=%s", clazz.getCanonicalName())); Files.exists(outputDatasetDir); - List actuals = readActionPayloadFromJobOutput(outputDatasetDir.toString(), clazz).collectAsList(); + List actuals = + readActionPayloadFromJobOutput(outputDatasetDir.toString(), clazz).collectAsList(); actuals.sort(Comparator.comparingInt(Object::hashCode)); - List expecteds = oafsByClassName.get(clazz.getCanonicalName()).stream() - .map(json -> mapToOaf(json, clazz)) - .sorted(Comparator.comparingInt(Object::hashCode)) - .collect(Collectors.toList()); + List expecteds = + oafsByClassName.get(clazz.getCanonicalName()).stream() + .map(json -> mapToOaf(json, clazz)) + .sorted(Comparator.comparingInt(Object::hashCode)) + .collect(Collectors.toList()); assertIterableEquals(expecteds, actuals); } - private static Dataset readActionPayloadFromJobOutput(String path, - Class clazz) { - return spark - .read() + private static Dataset readActionPayloadFromJobOutput( + String path, Class clazz) { + return spark.read() .parquet(path) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value.getAs("payload"), clazz), + .map( + (MapFunction) + value -> + OBJECT_MAPPER.readValue( + value.getAs("payload"), clazz), Encoders.bean(clazz)); } private static T mapToOaf(String json, Class clazz) { return rethrowAsRuntimeException( () -> OBJECT_MAPPER.readValue(json, clazz), - String.format("failed to map json to class: json=%s, class=%s", json, clazz.getCanonicalName()) - ); + String.format( + "failed to map json to class: json=%s, class=%s", + json, clazz.getCanonicalName())); } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java index 154e0a3311..6a46170c0a 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java @@ -1,17 +1,16 @@ package eu.dnetlib.dhp.actionmanager.promote; -import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; -import eu.dnetlib.dhp.schema.oaf.*; -import org.junit.jupiter.api.Nested; -import org.junit.jupiter.api.Test; - -import java.util.function.BiFunction; - import static eu.dnetlib.dhp.actionmanager.promote.MergeAndGet.Strategy; import static eu.dnetlib.dhp.actionmanager.promote.MergeAndGet.functionFor; import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.*; +import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; +import eu.dnetlib.dhp.schema.oaf.*; +import java.util.function.BiFunction; +import org.junit.jupiter.api.Nested; +import org.junit.jupiter.api.Test; + public class MergeAndGetTest { @Nested @@ -24,11 +23,11 @@ public class MergeAndGetTest { Oaf b = mock(Oaf.class); // when - SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.MERGE_FROM_AND_GET); // then - assertThrows(RuntimeException.class, () -> - fn.get().apply(a, b)); + assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); } @Test @@ -38,11 +37,11 @@ public class MergeAndGetTest { Relation b = mock(Relation.class); // when - SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.MERGE_FROM_AND_GET); // then - assertThrows(RuntimeException.class, () -> - fn.get().apply(a, b)); + assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); } @Test @@ -52,11 +51,11 @@ public class MergeAndGetTest { OafEntity b = mock(OafEntity.class); // when - SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.MERGE_FROM_AND_GET); // then - assertThrows(RuntimeException.class, () -> - fn.get().apply(a, b)); + assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); } @Test @@ -66,11 +65,11 @@ public class MergeAndGetTest { Oaf b = mock(Oaf.class); // when - SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.MERGE_FROM_AND_GET); // then - assertThrows(RuntimeException.class, () -> - fn.get().apply(a, b)); + assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); } @Test @@ -80,11 +79,11 @@ public class MergeAndGetTest { OafEntity b = mock(OafEntity.class); // when - SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.MERGE_FROM_AND_GET); // then - assertThrows(RuntimeException.class, () -> - fn.get().apply(a, b)); + assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); } @Test @@ -94,7 +93,8 @@ public class MergeAndGetTest { Relation b = mock(Relation.class); // when - SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.MERGE_FROM_AND_GET); // then Oaf x = fn.get().apply(a, b); @@ -110,11 +110,11 @@ public class MergeAndGetTest { Oaf b = mock(Oaf.class); // when - SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.MERGE_FROM_AND_GET); // then - assertThrows(RuntimeException.class, () -> - fn.get().apply(a, b)); + assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); } @Test @@ -124,30 +124,28 @@ public class MergeAndGetTest { Relation b = mock(Relation.class); // when - SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.MERGE_FROM_AND_GET); // then - assertThrows(RuntimeException.class, () -> - fn.get().apply(a, b)); + assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); } @Test public void shouldThrowForOafEntityAndOafEntityButNotSubclasses() { // given - class OafEntitySub1 extends OafEntity { - } - class OafEntitySub2 extends OafEntity { - } + class OafEntitySub1 extends OafEntity {} + class OafEntitySub2 extends OafEntity {} OafEntitySub1 a = mock(OafEntitySub1.class); OafEntitySub2 b = mock(OafEntitySub2.class); // when - SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.MERGE_FROM_AND_GET); // then - assertThrows(RuntimeException.class, () -> - fn.get().apply(a, b)); + assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); } @Test @@ -157,7 +155,8 @@ public class MergeAndGetTest { OafEntity b = mock(OafEntity.class); // when - SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.MERGE_FROM_AND_GET); // then Oaf x = fn.get().apply(a, b); @@ -177,11 +176,11 @@ public class MergeAndGetTest { Relation b = mock(Relation.class); // when - SerializableSupplier> fn = functionFor(Strategy.SELECT_NEWER_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.SELECT_NEWER_AND_GET); // then - assertThrows(RuntimeException.class, () -> - fn.get().apply(a, b)); + assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); } @Test @@ -191,11 +190,11 @@ public class MergeAndGetTest { OafEntity b = mock(OafEntity.class); // when - SerializableSupplier> fn = functionFor(Strategy.SELECT_NEWER_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.SELECT_NEWER_AND_GET); // then - assertThrows(RuntimeException.class, () -> - fn.get().apply(a, b)); + assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); } @Test @@ -205,28 +204,29 @@ public class MergeAndGetTest { Result b = mock(Result.class); // when - SerializableSupplier> fn = functionFor(Strategy.SELECT_NEWER_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.SELECT_NEWER_AND_GET); // then - assertThrows(RuntimeException.class, () -> - fn.get().apply(a, b)); + assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); } @Test public void shouldThrowWhenSuperTypeIsNewerForResultAndOafEntity() { // given - // real types must be used because subclass-superclass resolution does not work for mocks + // real types must be used because subclass-superclass resolution does not work for + // mocks Dataset a = new Dataset(); a.setLastupdatetimestamp(1L); Result b = new Result(); b.setLastupdatetimestamp(2L); // when - SerializableSupplier> fn = functionFor(Strategy.SELECT_NEWER_AND_GET); + SerializableSupplier> fn = + functionFor(Strategy.SELECT_NEWER_AND_GET); // then - assertThrows(RuntimeException.class, () -> - fn.get().apply(a, b)); + assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); } @Test @@ -265,4 +265,4 @@ public class MergeAndGetTest { assertEquals(a, x); } } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java index 6f53fbec25..29592bb491 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java @@ -1,8 +1,20 @@ package eu.dnetlib.dhp.actionmanager.promote; +import static org.junit.jupiter.api.Assertions.*; +import static org.junit.jupiter.params.provider.Arguments.arguments; + import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.Comparator; +import java.util.List; +import java.util.Objects; +import java.util.stream.Collectors; +import java.util.stream.Stream; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -14,21 +26,9 @@ import org.junit.jupiter.params.ParameterizedTest; import org.junit.jupiter.params.provider.Arguments; import org.junit.jupiter.params.provider.MethodSource; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.Comparator; -import java.util.List; -import java.util.Objects; -import java.util.stream.Collectors; -import java.util.stream.Stream; - -import static org.junit.jupiter.api.Assertions.*; -import static org.junit.jupiter.params.provider.Arguments.arguments; - public class PromoteActionPayloadForGraphTableJobTest { - private static final ClassLoader cl = PromoteActionPayloadForGraphTableJobTest.class.getClassLoader(); + private static final ClassLoader cl = + PromoteActionPayloadForGraphTableJobTest.class.getClassLoader(); private static SparkSession spark; @@ -52,7 +52,9 @@ public class PromoteActionPayloadForGraphTableJobTest { @BeforeEach public void beforeEach() throws IOException { - workingDir = Files.createTempDirectory(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName()); + workingDir = + Files.createTempDirectory( + PromoteActionPayloadForGraphTableJobTest.class.getSimpleName()); inputDir = workingDir.resolve("input"); inputGraphRootDir = inputDir.resolve("graph"); inputActionPayloadRootDir = inputDir.resolve("action_payload"); @@ -80,87 +82,130 @@ public class PromoteActionPayloadForGraphTableJobTest { Class actionPayloadClazz = OafEntity.class; // when - RuntimeException exception = assertThrows(RuntimeException.class, () -> - PromoteActionPayloadForGraphTableJob.main(new String[]{ - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-inputGraphTablePath", "", - "-graphTableClassName", rowClazz.getCanonicalName(), - "-inputActionPayloadPath", "", - "-actionPayloadClassName", actionPayloadClazz.getCanonicalName(), - "-outputGraphTablePath", "", - "-mergeAndGetStrategy", MergeAndGet.Strategy.SELECT_NEWER_AND_GET.name() - })); + RuntimeException exception = + assertThrows( + RuntimeException.class, + () -> + PromoteActionPayloadForGraphTableJob.main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-inputGraphTablePath", "", + "-graphTableClassName", rowClazz.getCanonicalName(), + "-inputActionPayloadPath", "", + "-actionPayloadClassName", + actionPayloadClazz.getCanonicalName(), + "-outputGraphTablePath", "", + "-mergeAndGetStrategy", + MergeAndGet.Strategy.SELECT_NEWER_AND_GET + .name() + })); // then - String msg = String.format("graph table class is not a subclass of action payload class: graph=%s, action=%s", - rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName()); + String msg = + String.format( + "graph table class is not a subclass of action payload class: graph=%s, action=%s", + rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName()); assertTrue(exception.getMessage().contains(msg)); } @ParameterizedTest(name = "strategy: {0}, graph table: {1}, action payload: {2}") - @MethodSource("eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest#promoteJobTestParams") - public void shouldPromoteActionPayloadForGraphTable(MergeAndGet.Strategy strategy, - Class rowClazz, - Class actionPayloadClazz) throws Exception { + @MethodSource( + "eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest#promoteJobTestParams") + public void shouldPromoteActionPayloadForGraphTable( + MergeAndGet.Strategy strategy, + Class rowClazz, + Class actionPayloadClazz) + throws Exception { // given Path inputGraphTableDir = createGraphTable(inputGraphRootDir, rowClazz); - Path inputActionPayloadDir = createActionPayload(inputActionPayloadRootDir, rowClazz, actionPayloadClazz); - Path outputGraphTableDir = outputDir.resolve("graph").resolve(rowClazz.getSimpleName().toLowerCase()); + Path inputActionPayloadDir = + createActionPayload(inputActionPayloadRootDir, rowClazz, actionPayloadClazz); + Path outputGraphTableDir = + outputDir.resolve("graph").resolve(rowClazz.getSimpleName().toLowerCase()); // when - PromoteActionPayloadForGraphTableJob.main(new String[]{ - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-inputGraphTablePath", inputGraphTableDir.toString(), - "-graphTableClassName", rowClazz.getCanonicalName(), - "-inputActionPayloadPath", inputActionPayloadDir.toString(), - "-actionPayloadClassName", actionPayloadClazz.getCanonicalName(), - "-outputGraphTablePath", outputGraphTableDir.toString(), - "-mergeAndGetStrategy", strategy.name() - }); + PromoteActionPayloadForGraphTableJob.main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-inputGraphTablePath", inputGraphTableDir.toString(), + "-graphTableClassName", rowClazz.getCanonicalName(), + "-inputActionPayloadPath", inputActionPayloadDir.toString(), + "-actionPayloadClassName", actionPayloadClazz.getCanonicalName(), + "-outputGraphTablePath", outputGraphTableDir.toString(), + "-mergeAndGetStrategy", strategy.name() + }); // then assertTrue(Files.exists(outputGraphTableDir)); - List actualOutputRows = readGraphTableFromJobOutput(outputGraphTableDir.toString(), rowClazz) - .collectAsList() - .stream() - .sorted(Comparator.comparingInt(Object::hashCode)) - .collect(Collectors.toList()); - String expectedOutputGraphTableJsonDumpPath = resultFileLocation(strategy, rowClazz, actionPayloadClazz); - Path expectedOutputGraphTableJsonDumpFile = Paths - .get(Objects.requireNonNull(cl.getResource(expectedOutputGraphTableJsonDumpPath)).getFile()); - List expectedOutputRows = readGraphTableFromJsonDump(expectedOutputGraphTableJsonDumpFile.toString(), rowClazz) - .collectAsList() - .stream() - .sorted(Comparator.comparingInt(Object::hashCode)) - .collect(Collectors.toList()); + List actualOutputRows = + readGraphTableFromJobOutput(outputGraphTableDir.toString(), rowClazz) + .collectAsList().stream() + .sorted(Comparator.comparingInt(Object::hashCode)) + .collect(Collectors.toList()); + String expectedOutputGraphTableJsonDumpPath = + resultFileLocation(strategy, rowClazz, actionPayloadClazz); + Path expectedOutputGraphTableJsonDumpFile = + Paths.get( + Objects.requireNonNull( + cl.getResource(expectedOutputGraphTableJsonDumpPath)) + .getFile()); + List expectedOutputRows = + readGraphTableFromJsonDump( + expectedOutputGraphTableJsonDumpFile.toString(), rowClazz) + .collectAsList().stream() + .sorted(Comparator.comparingInt(Object::hashCode)) + .collect(Collectors.toList()); assertIterableEquals(expectedOutputRows, actualOutputRows); } } public static Stream promoteJobTestParams() { return Stream.of( - arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, eu.dnetlib.dhp.schema.oaf.Dataset.class, eu.dnetlib.dhp.schema.oaf.Dataset.class), - arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, eu.dnetlib.dhp.schema.oaf.Dataset.class, eu.dnetlib.dhp.schema.oaf.Result.class), - arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Datasource.class, Datasource.class), - arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Organization.class, Organization.class), - arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, OtherResearchProduct.class, OtherResearchProduct.class), - arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, OtherResearchProduct.class, Result.class), + arguments( + MergeAndGet.Strategy.MERGE_FROM_AND_GET, + eu.dnetlib.dhp.schema.oaf.Dataset.class, + eu.dnetlib.dhp.schema.oaf.Dataset.class), + arguments( + MergeAndGet.Strategy.MERGE_FROM_AND_GET, + eu.dnetlib.dhp.schema.oaf.Dataset.class, + eu.dnetlib.dhp.schema.oaf.Result.class), + arguments( + MergeAndGet.Strategy.MERGE_FROM_AND_GET, + Datasource.class, + Datasource.class), + arguments( + MergeAndGet.Strategy.MERGE_FROM_AND_GET, + Organization.class, + Organization.class), + arguments( + MergeAndGet.Strategy.MERGE_FROM_AND_GET, + OtherResearchProduct.class, + OtherResearchProduct.class), + arguments( + MergeAndGet.Strategy.MERGE_FROM_AND_GET, + OtherResearchProduct.class, + Result.class), arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Project.class, Project.class), - arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Publication.class, Publication.class), + arguments( + MergeAndGet.Strategy.MERGE_FROM_AND_GET, + Publication.class, + Publication.class), arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Publication.class, Result.class), arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Relation.class, Relation.class), arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Software.class, Software.class), - arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Software.class, Result.class) - ); + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Software.class, Result.class)); } - private static Path createGraphTable(Path inputGraphRootDir, - Class rowClazz) { + private static Path createGraphTable( + Path inputGraphRootDir, Class rowClazz) { String inputGraphTableJsonDumpPath = inputGraphTableJsonDumpLocation(rowClazz); - Path inputGraphTableJsonDumpFile = Paths - .get(Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)).getFile()); - Dataset rowDS = readGraphTableFromJsonDump(inputGraphTableJsonDumpFile.toString(), rowClazz); + Path inputGraphTableJsonDumpFile = + Paths.get( + Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)) + .getFile()); + Dataset rowDS = + readGraphTableFromJsonDump(inputGraphTableJsonDumpFile.toString(), rowClazz); String inputGraphTableName = rowClazz.getSimpleName().toLowerCase(); Path inputGraphTableDir = inputGraphRootDir.resolve(inputGraphTableName); writeGraphTableAaJobInput(rowDS, inputGraphTableDir.toString()); @@ -169,71 +214,74 @@ public class PromoteActionPayloadForGraphTableJobTest { private static String inputGraphTableJsonDumpLocation(Class rowClazz) { return String.format( - "%s/%s.json", "eu/dnetlib/dhp/actionmanager/promote/input/graph", rowClazz.getSimpleName().toLowerCase()); + "%s/%s.json", + "eu/dnetlib/dhp/actionmanager/promote/input/graph", + rowClazz.getSimpleName().toLowerCase()); } - private static Dataset readGraphTableFromJsonDump(String path, - Class rowClazz) { - return spark - .read() + private static Dataset readGraphTableFromJsonDump( + String path, Class rowClazz) { + return spark.read() .textFile(path) - .map((MapFunction) json -> OBJECT_MAPPER.readValue(json, rowClazz), Encoders.bean(rowClazz)); + .map( + (MapFunction) json -> OBJECT_MAPPER.readValue(json, rowClazz), + Encoders.bean(rowClazz)); } - private static void writeGraphTableAaJobInput(Dataset rowDS, - String path) { - rowDS - .write() - .option("compression", "gzip") - .json(path); + private static void writeGraphTableAaJobInput(Dataset rowDS, String path) { + rowDS.write().option("compression", "gzip").json(path); } - private static Path createActionPayload(Path inputActionPayloadRootDir, - Class rowClazz, - Class actionPayloadClazz) { - String inputActionPayloadJsonDumpPath = inputActionPayloadJsonDumpLocation(rowClazz, actionPayloadClazz); - Path inputActionPayloadJsonDumpFile = Paths - .get(Objects.requireNonNull(cl.getResource(inputActionPayloadJsonDumpPath)).getFile()); - Dataset actionPayloadDS = readActionPayloadFromJsonDump(inputActionPayloadJsonDumpFile.toString()); - Path inputActionPayloadDir = inputActionPayloadRootDir.resolve(actionPayloadClazz.getSimpleName().toLowerCase()); + private static Path createActionPayload( + Path inputActionPayloadRootDir, Class rowClazz, Class actionPayloadClazz) { + String inputActionPayloadJsonDumpPath = + inputActionPayloadJsonDumpLocation(rowClazz, actionPayloadClazz); + Path inputActionPayloadJsonDumpFile = + Paths.get( + Objects.requireNonNull(cl.getResource(inputActionPayloadJsonDumpPath)) + .getFile()); + Dataset actionPayloadDS = + readActionPayloadFromJsonDump(inputActionPayloadJsonDumpFile.toString()); + Path inputActionPayloadDir = + inputActionPayloadRootDir.resolve(actionPayloadClazz.getSimpleName().toLowerCase()); writeActionPayloadAsJobInput(actionPayloadDS, inputActionPayloadDir.toString()); return inputActionPayloadDir; } - private static String inputActionPayloadJsonDumpLocation(Class rowClazz, - Class actionPayloadClazz) { + private static String inputActionPayloadJsonDumpLocation( + Class rowClazz, Class actionPayloadClazz) { - return String.format("eu/dnetlib/dhp/actionmanager/promote/input/action_payload/%s_table/%s.json", - rowClazz.getSimpleName().toLowerCase(), actionPayloadClazz.getSimpleName().toLowerCase()); + return String.format( + "eu/dnetlib/dhp/actionmanager/promote/input/action_payload/%s_table/%s.json", + rowClazz.getSimpleName().toLowerCase(), + actionPayloadClazz.getSimpleName().toLowerCase()); } private static Dataset readActionPayloadFromJsonDump(String path) { - return spark - .read() - .textFile(path); + return spark.read().textFile(path); } - private static void writeActionPayloadAsJobInput(Dataset actionPayloadDS, - String path) { - actionPayloadDS - .withColumnRenamed("value", "payload") - .write() - .parquet(path); + private static void writeActionPayloadAsJobInput(Dataset actionPayloadDS, String path) { + actionPayloadDS.withColumnRenamed("value", "payload").write().parquet(path); } - private static Dataset readGraphTableFromJobOutput(String path, - Class rowClazz) { - return spark - .read() + private static Dataset readGraphTableFromJobOutput( + String path, Class rowClazz) { + return spark.read() .textFile(path) - .map((MapFunction) json -> OBJECT_MAPPER.readValue(json, rowClazz), Encoders.bean(rowClazz)); + .map( + (MapFunction) json -> OBJECT_MAPPER.readValue(json, rowClazz), + Encoders.bean(rowClazz)); } - private static String resultFileLocation(MergeAndGet.Strategy strategy, - Class rowClazz, - Class actionPayloadClazz) { - return String - .format("eu/dnetlib/dhp/actionmanager/promote/output/graph/%s/%s/%s_action_payload/result.json", - strategy.name().toLowerCase(), rowClazz.getSimpleName().toLowerCase(), actionPayloadClazz.getSimpleName().toLowerCase()); + private static String resultFileLocation( + MergeAndGet.Strategy strategy, + Class rowClazz, + Class actionPayloadClazz) { + return String.format( + "eu/dnetlib/dhp/actionmanager/promote/output/graph/%s/%s/%s_action_payload/result.json", + strategy.name().toLowerCase(), + rowClazz.getSimpleName().toLowerCase(), + actionPayloadClazz.getSimpleName().toLowerCase()); } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java index e3fc7db485..5c69e32e3c 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java @@ -1,7 +1,15 @@ package eu.dnetlib.dhp.actionmanager.promote; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertThrows; + import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; import eu.dnetlib.dhp.schema.oaf.Oaf; +import java.util.Arrays; +import java.util.List; +import java.util.Objects; +import java.util.function.BiFunction; +import java.util.function.Function; import org.apache.spark.SparkConf; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -11,15 +19,6 @@ import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Nested; import org.junit.jupiter.api.Test; -import java.util.Arrays; -import java.util.List; -import java.util.Objects; -import java.util.function.BiFunction; -import java.util.function.Function; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertThrows; - public class PromoteActionPayloadFunctionsTest { private static SparkSession spark; @@ -44,20 +43,20 @@ public class PromoteActionPayloadFunctionsTest { @Test public void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() { // given - class OafImpl extends Oaf { - } + class OafImpl extends Oaf {} // when - assertThrows(RuntimeException.class, () -> - PromoteActionPayloadFunctions - .joinGraphTableWithActionPayloadAndMerge(null, + assertThrows( + RuntimeException.class, + () -> + PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge( + null, null, null, null, null, OafImplSubSub.class, - OafImpl.class - )); + OafImpl.class)); } @Test @@ -68,40 +67,53 @@ public class PromoteActionPayloadFunctionsTest { String id2 = "id2"; String id3 = "id3"; String id4 = "id4"; - List rowData = Arrays.asList( - createOafImplSubSub(id0), - createOafImplSubSub(id1), - createOafImplSubSub(id2), - createOafImplSubSub(id3) - ); - Dataset rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class)); + List rowData = + Arrays.asList( + createOafImplSubSub(id0), + createOafImplSubSub(id1), + createOafImplSubSub(id2), + createOafImplSubSub(id3)); + Dataset rowDS = + spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class)); - List actionPayloadData = Arrays.asList( - createOafImplSubSub(id1), - createOafImplSubSub(id2), createOafImplSubSub(id2), - createOafImplSubSub(id3), createOafImplSubSub(id3), createOafImplSubSub(id3), - createOafImplSubSub(id4), createOafImplSubSub(id4), createOafImplSubSub(id4), createOafImplSubSub(id4) - ); - Dataset actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.bean(OafImplSubSub.class)); + List actionPayloadData = + Arrays.asList( + createOafImplSubSub(id1), + createOafImplSubSub(id2), + createOafImplSubSub(id2), + createOafImplSubSub(id3), + createOafImplSubSub(id3), + createOafImplSubSub(id3), + createOafImplSubSub(id4), + createOafImplSubSub(id4), + createOafImplSubSub(id4), + createOafImplSubSub(id4)); + Dataset actionPayloadDS = + spark.createDataset(actionPayloadData, Encoders.bean(OafImplSubSub.class)); - SerializableSupplier> rowIdFn = () -> OafImplRoot::getId; - SerializableSupplier> actionPayloadIdFn = () -> OafImplRoot::getId; - SerializableSupplier> mergeAndGetFn = () -> (x, y) -> { - x.merge(y); - return x; - }; + SerializableSupplier> rowIdFn = + () -> OafImplRoot::getId; + SerializableSupplier> actionPayloadIdFn = + () -> OafImplRoot::getId; + SerializableSupplier> + mergeAndGetFn = + () -> + (x, y) -> { + x.merge(y); + return x; + }; // when - List results = PromoteActionPayloadFunctions - .joinGraphTableWithActionPayloadAndMerge(rowDS, - actionPayloadDS, - rowIdFn, - actionPayloadIdFn, - mergeAndGetFn, - OafImplSubSub.class, - OafImplSubSub.class - ) - .collectAsList(); + List results = + PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge( + rowDS, + actionPayloadDS, + rowIdFn, + actionPayloadIdFn, + mergeAndGetFn, + OafImplSubSub.class, + OafImplSubSub.class) + .collectAsList(); // then assertEquals(11, results.size()); @@ -111,23 +123,24 @@ public class PromoteActionPayloadFunctionsTest { assertEquals(3, results.stream().filter(x -> x.getId().equals(id3)).count()); assertEquals(4, results.stream().filter(x -> x.getId().equals(id4)).count()); - results.forEach(result -> { - switch (result.getId()) { - case "id0": - assertEquals(1, result.getMerged()); - break; - case "id1": - case "id2": - case "id3": - assertEquals(2, result.getMerged()); - break; - case "id4": - assertEquals(1, result.getMerged()); - break; - default: - throw new RuntimeException(); - } - }); + results.forEach( + result -> { + switch (result.getId()) { + case "id0": + assertEquals(1, result.getMerged()); + break; + case "id1": + case "id2": + case "id3": + assertEquals(2, result.getMerged()); + break; + case "id4": + assertEquals(1, result.getMerged()); + break; + default: + throw new RuntimeException(); + } + }); } @Test @@ -138,40 +151,53 @@ public class PromoteActionPayloadFunctionsTest { String id2 = "id2"; String id3 = "id3"; String id4 = "id4"; - List rowData = Arrays.asList( - createOafImplSubSub(id0), - createOafImplSubSub(id1), - createOafImplSubSub(id2), - createOafImplSubSub(id3) - ); - Dataset rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class)); + List rowData = + Arrays.asList( + createOafImplSubSub(id0), + createOafImplSubSub(id1), + createOafImplSubSub(id2), + createOafImplSubSub(id3)); + Dataset rowDS = + spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class)); - List actionPayloadData = Arrays.asList( - createOafImplSub(id1), - createOafImplSub(id2), createOafImplSub(id2), - createOafImplSub(id3), createOafImplSub(id3), createOafImplSub(id3), - createOafImplSub(id4), createOafImplSub(id4), createOafImplSub(id4), createOafImplSub(id4) - ); - Dataset actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.bean(OafImplSub.class)); + List actionPayloadData = + Arrays.asList( + createOafImplSub(id1), + createOafImplSub(id2), + createOafImplSub(id2), + createOafImplSub(id3), + createOafImplSub(id3), + createOafImplSub(id3), + createOafImplSub(id4), + createOafImplSub(id4), + createOafImplSub(id4), + createOafImplSub(id4)); + Dataset actionPayloadDS = + spark.createDataset(actionPayloadData, Encoders.bean(OafImplSub.class)); - SerializableSupplier> rowIdFn = () -> OafImplRoot::getId; - SerializableSupplier> actionPayloadIdFn = () -> OafImplRoot::getId; - SerializableSupplier> mergeAndGetFn = () -> (x, y) -> { - x.merge(y); - return x; - }; + SerializableSupplier> rowIdFn = + () -> OafImplRoot::getId; + SerializableSupplier> actionPayloadIdFn = + () -> OafImplRoot::getId; + SerializableSupplier> + mergeAndGetFn = + () -> + (x, y) -> { + x.merge(y); + return x; + }; // when - List results = PromoteActionPayloadFunctions - .joinGraphTableWithActionPayloadAndMerge(rowDS, - actionPayloadDS, - rowIdFn, - actionPayloadIdFn, - mergeAndGetFn, - OafImplSubSub.class, - OafImplSub.class - ) - .collectAsList(); + List results = + PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge( + rowDS, + actionPayloadDS, + rowIdFn, + actionPayloadIdFn, + mergeAndGetFn, + OafImplSubSub.class, + OafImplSub.class) + .collectAsList(); // then assertEquals(7, results.size()); @@ -181,22 +207,22 @@ public class PromoteActionPayloadFunctionsTest { assertEquals(3, results.stream().filter(x -> x.getId().equals(id3)).count()); assertEquals(0, results.stream().filter(x -> x.getId().equals(id4)).count()); - results.forEach(result -> { - switch (result.getId()) { - case "id0": - assertEquals(1, result.getMerged()); - break; - case "id1": - case "id2": - case "id3": - assertEquals(2, result.getMerged()); - break; - default: - throw new RuntimeException(); - } - }); + results.forEach( + result -> { + switch (result.getId()) { + case "id0": + assertEquals(1, result.getMerged()); + break; + case "id1": + case "id2": + case "id3": + assertEquals(2, result.getMerged()); + break; + default: + throw new RuntimeException(); + } + }); } - } @Nested @@ -208,30 +234,40 @@ public class PromoteActionPayloadFunctionsTest { String id1 = "id1"; String id2 = "id2"; String id3 = "id3"; - List rowData = Arrays.asList( - createOafImplSubSub(id1), - createOafImplSubSub(id2), createOafImplSubSub(id2), - createOafImplSubSub(id3), createOafImplSubSub(id3), createOafImplSubSub(id3) - ); - Dataset rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class)); + List rowData = + Arrays.asList( + createOafImplSubSub(id1), + createOafImplSubSub(id2), + createOafImplSubSub(id2), + createOafImplSubSub(id3), + createOafImplSubSub(id3), + createOafImplSubSub(id3)); + Dataset rowDS = + spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class)); - SerializableSupplier> rowIdFn = () -> OafImplRoot::getId; - SerializableSupplier> mergeAndGetFn = () -> (x, y) -> { - x.merge(y); - return x; - }; + SerializableSupplier> rowIdFn = + () -> OafImplRoot::getId; + SerializableSupplier> + mergeAndGetFn = + () -> + (x, y) -> { + x.merge(y); + return x; + }; SerializableSupplier zeroFn = OafImplSubSub::new; - SerializableSupplier> isNotZeroFn = () -> x -> Objects.nonNull(x.getId()); + SerializableSupplier> isNotZeroFn = + () -> x -> Objects.nonNull(x.getId()); // when - List results = PromoteActionPayloadFunctions - .groupGraphTableByIdAndMerge(rowDS, - rowIdFn, - mergeAndGetFn, - zeroFn, - isNotZeroFn, - OafImplSubSub.class) - .collectAsList(); + List results = + PromoteActionPayloadFunctions.groupGraphTableByIdAndMerge( + rowDS, + rowIdFn, + mergeAndGetFn, + zeroFn, + isNotZeroFn, + OafImplSubSub.class) + .collectAsList(); // then assertEquals(3, results.size()); @@ -239,23 +275,23 @@ public class PromoteActionPayloadFunctionsTest { assertEquals(1, results.stream().filter(x -> x.getId().equals(id2)).count()); assertEquals(1, results.stream().filter(x -> x.getId().equals(id3)).count()); - results.forEach(result -> { - switch (result.getId()) { - case "id1": - assertEquals(1, result.getMerged()); - break; - case "id2": - assertEquals(2, result.getMerged()); - break; - case "id3": - assertEquals(3, result.getMerged()); - break; - default: - throw new RuntimeException(); - } - }); + results.forEach( + result -> { + switch (result.getId()) { + case "id1": + assertEquals(1, result.getMerged()); + break; + case "id2": + assertEquals(2, result.getMerged()); + break; + case "id3": + assertEquals(3, result.getMerged()); + break; + default: + throw new RuntimeException(); + } + }); } - } public static class OafImplRoot extends Oaf { @@ -310,5 +346,4 @@ public class PromoteActionPayloadFunctionsTest { x.setId(id); return x; } - } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java index f4da193a1c..494d3d5c1e 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java @@ -7,6 +7,11 @@ import eu.dnetlib.dhp.model.mdstore.Provenance; import eu.dnetlib.message.Message; import eu.dnetlib.message.MessageManager; import eu.dnetlib.message.MessageType; +import java.io.ByteArrayInputStream; +import java.nio.charset.StandardCharsets; +import java.util.HashMap; +import java.util.Map; +import java.util.Objects; import org.apache.commons.cli.*; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; @@ -24,94 +29,135 @@ import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; -import java.io.ByteArrayInputStream; -import java.nio.charset.StandardCharsets; -import java.util.HashMap; -import java.util.Map; -import java.util.Objects; - public class GenerateNativeStoreSparkJob { + public static MetadataRecord parseRecord( + final String input, + final String xpath, + final String encoding, + final Provenance provenance, + final Long dateOfCollection, + final LongAccumulator totalItems, + final LongAccumulator invalidRecords) { - public static MetadataRecord parseRecord (final String input, final String xpath, final String encoding, final Provenance provenance, final Long dateOfCollection, final LongAccumulator totalItems, final LongAccumulator invalidRecords) { - - if(totalItems != null) - totalItems.add(1); + if (totalItems != null) totalItems.add(1); try { SAXReader reader = new SAXReader(); - Document document = reader.read(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8))); + Document document = + reader.read(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8))); Node node = document.selectSingleNode(xpath); final String originalIdentifier = node.getText(); if (StringUtils.isBlank(originalIdentifier)) { - if (invalidRecords!= null) - invalidRecords.add(1); + if (invalidRecords != null) invalidRecords.add(1); return null; } - return new MetadataRecord(originalIdentifier, encoding, provenance, input, dateOfCollection); + return new MetadataRecord( + originalIdentifier, encoding, provenance, input, dateOfCollection); } catch (Throwable e) { - if (invalidRecords!= null) - invalidRecords.add(1); + if (invalidRecords != null) invalidRecords.add(1); e.printStackTrace(); return null; - } } public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(GenerateNativeStoreSparkJob.class.getResourceAsStream("/eu/dnetlib/dhp/collection/collection_input_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + GenerateNativeStoreSparkJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/collection/collection_input_parameters.json"))); parser.parseArgument(args); - final ObjectMapper jsonMapper = new ObjectMapper(); - final Provenance provenance = jsonMapper.readValue(parser.get("provenance"), Provenance.class); - final long dateOfCollection = new Long(parser.get("dateOfCollection")); + final ObjectMapper jsonMapper = new ObjectMapper(); + final Provenance provenance = + jsonMapper.readValue(parser.get("provenance"), Provenance.class); + final long dateOfCollection = new Long(parser.get("dateOfCollection")); - final SparkSession spark = SparkSession - .builder() - .appName("GenerateNativeStoreSparkJob") - .master(parser.get("master")) - .getOrCreate(); + final SparkSession spark = + SparkSession.builder() + .appName("GenerateNativeStoreSparkJob") + .master(parser.get("master")) + .getOrCreate(); final Map ongoingMap = new HashMap<>(); final Map reportMap = new HashMap<>(); - final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest")); + final boolean test = + parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest")); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - final JavaPairRDD inputRDD = sc.sequenceFile(parser.get("input"), IntWritable.class, Text.class); + final JavaPairRDD inputRDD = + sc.sequenceFile(parser.get("input"), IntWritable.class, Text.class); final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems"); final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords"); - final MessageManager manager = new MessageManager(parser.get("rabbitHost"), parser.get("rabbitUser"), parser.get("rabbitPassword"), false, false, null); + final MessageManager manager = + new MessageManager( + parser.get("rabbitHost"), + parser.get("rabbitUser"), + parser.get("rabbitPassword"), + false, + false, + null); - final JavaRDD mappeRDD = inputRDD.map(item -> parseRecord(item._2().toString(), parser.get("xpath"), parser.get("encoding"), provenance, dateOfCollection, totalItems, invalidRecords)) - .filter(Objects::nonNull).distinct(); + final JavaRDD mappeRDD = + inputRDD.map( + item -> + parseRecord( + item._2().toString(), + parser.get("xpath"), + parser.get("encoding"), + provenance, + dateOfCollection, + totalItems, + invalidRecords)) + .filter(Objects::nonNull) + .distinct(); ongoingMap.put("ongoing", "0"); if (!test) { - manager.sendMessage(new Message(parser.get("workflowId"),"DataFrameCreation", MessageType.ONGOING, ongoingMap ), parser.get("rabbitOngoingQueue"), true, false); + manager.sendMessage( + new Message( + parser.get("workflowId"), + "DataFrameCreation", + MessageType.ONGOING, + ongoingMap), + parser.get("rabbitOngoingQueue"), + true, + false); } - final Encoder encoder = Encoders.bean(MetadataRecord.class); final Dataset mdstore = spark.createDataset(mappeRDD.rdd(), encoder); final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords"); mdStoreRecords.add(mdstore.count()); - ongoingMap.put("ongoing", ""+ totalItems.value()); + ongoingMap.put("ongoing", "" + totalItems.value()); if (!test) { - manager.sendMessage(new Message(parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap), parser.get("rabbitOngoingQueue"), true, false); - + manager.sendMessage( + new Message( + parser.get("workflowId"), + "DataFrameCreation", + MessageType.ONGOING, + ongoingMap), + parser.get("rabbitOngoingQueue"), + true, + false); } mdstore.write().format("parquet").save(parser.get("output")); - reportMap.put("inputItem" , ""+ totalItems.value()); + reportMap.put("inputItem", "" + totalItems.value()); reportMap.put("invalidRecords", "" + invalidRecords.value()); reportMap.put("mdStoreSize", "" + mdStoreRecords.value()); if (!test) { - manager.sendMessage(new Message(parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap), parser.get("rabbitReportQueue"), true, false); + manager.sendMessage( + new Message( + parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap), + parser.get("rabbitReportQueue"), + true, + false); manager.close(); } - } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java index cfa0e417b4..fa628ac9e1 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java @@ -2,10 +2,9 @@ package eu.dnetlib.dhp.collection.plugin; import eu.dnetlib.collector.worker.model.ApiDescriptor; import eu.dnetlib.dhp.collection.worker.DnetCollectorException; - import java.util.stream.Stream; public interface CollectorPlugin { - Stream collect(ApiDescriptor api) throws DnetCollectorException; + Stream collect(ApiDescriptor api) throws DnetCollectorException; } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java index ad893ce528..a089a57504 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java @@ -1,5 +1,11 @@ package eu.dnetlib.dhp.collection.plugin.oai; +import com.google.common.base.Splitter; +import com.google.common.collect.Iterators; +import com.google.common.collect.Lists; +import eu.dnetlib.collector.worker.model.ApiDescriptor; +import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; +import eu.dnetlib.dhp.collection.worker.DnetCollectorException; import java.util.ArrayList; import java.util.Iterator; import java.util.List; @@ -7,62 +13,70 @@ import java.util.Spliterator; import java.util.Spliterators; import java.util.stream.Stream; import java.util.stream.StreamSupport; -import com.google.common.base.Splitter; -import com.google.common.collect.Iterators; -import com.google.common.collect.Lists; - - -import eu.dnetlib.collector.worker.model.ApiDescriptor; -import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; -import eu.dnetlib.dhp.collection.worker.DnetCollectorException; - public class OaiCollectorPlugin implements CollectorPlugin { - private static final String FORMAT_PARAM = "format"; - private static final String OAI_SET_PARAM = "set"; - private static final Object OAI_FROM_DATE_PARAM = "fromDate"; - private static final Object OAI_UNTIL_DATE_PARAM = "untilDate"; + private static final String FORMAT_PARAM = "format"; + private static final String OAI_SET_PARAM = "set"; + private static final Object OAI_FROM_DATE_PARAM = "fromDate"; + private static final Object OAI_UNTIL_DATE_PARAM = "untilDate"; + private OaiIteratorFactory oaiIteratorFactory; - private OaiIteratorFactory oaiIteratorFactory; + @Override + public Stream collect(final ApiDescriptor api) throws DnetCollectorException { + final String baseUrl = api.getBaseUrl(); + final String mdFormat = api.getParams().get(FORMAT_PARAM); + final String setParam = api.getParams().get(OAI_SET_PARAM); + final String fromDate = api.getParams().get(OAI_FROM_DATE_PARAM); + final String untilDate = api.getParams().get(OAI_UNTIL_DATE_PARAM); - @Override - public Stream collect(final ApiDescriptor api) throws DnetCollectorException { - final String baseUrl = api.getBaseUrl(); - final String mdFormat = api.getParams().get(FORMAT_PARAM); - final String setParam = api.getParams().get(OAI_SET_PARAM); - final String fromDate = api.getParams().get(OAI_FROM_DATE_PARAM); - final String untilDate = api.getParams().get(OAI_UNTIL_DATE_PARAM); + final List sets = new ArrayList<>(); + if (setParam != null) { + sets.addAll( + Lists.newArrayList( + Splitter.on(",").omitEmptyStrings().trimResults().split(setParam))); + } + if (sets.isEmpty()) { + // If no set is defined, ALL the sets must be harvested + sets.add(""); + } - final List sets = new ArrayList<>(); - if (setParam != null) { - sets.addAll(Lists.newArrayList(Splitter.on(",").omitEmptyStrings().trimResults().split(setParam))); - } - if (sets.isEmpty()) { - // If no set is defined, ALL the sets must be harvested - sets.add(""); - } + if (baseUrl == null || baseUrl.isEmpty()) { + throw new DnetCollectorException("Param 'baseurl' is null or empty"); + } - if (baseUrl == null || baseUrl.isEmpty()) { throw new DnetCollectorException("Param 'baseurl' is null or empty"); } + if (mdFormat == null || mdFormat.isEmpty()) { + throw new DnetCollectorException("Param 'mdFormat' is null or empty"); + } - if (mdFormat == null || mdFormat.isEmpty()) { throw new DnetCollectorException("Param 'mdFormat' is null or empty"); } + if (fromDate != null && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) { + throw new DnetCollectorException("Invalid date (YYYY-MM-DD): " + fromDate); + } - if (fromDate != null && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) { throw new DnetCollectorException("Invalid date (YYYY-MM-DD): " + fromDate); } + if (untilDate != null && !untilDate.matches("\\d{4}-\\d{2}-\\d{2}")) { + throw new DnetCollectorException("Invalid date (YYYY-MM-DD): " + untilDate); + } - if (untilDate != null && !untilDate.matches("\\d{4}-\\d{2}-\\d{2}")) { throw new DnetCollectorException("Invalid date (YYYY-MM-DD): " + untilDate); } + final Iterator> iters = + sets.stream() + .map( + set -> + getOaiIteratorFactory() + .newIterator( + baseUrl, mdFormat, set, fromDate, + untilDate)) + .iterator(); - final Iterator> iters = sets.stream() - .map(set -> getOaiIteratorFactory().newIterator(baseUrl, mdFormat, set, fromDate, untilDate)) - .iterator(); + return StreamSupport.stream( + Spliterators.spliteratorUnknownSize(Iterators.concat(iters), Spliterator.ORDERED), + false); + } - return StreamSupport.stream(Spliterators.spliteratorUnknownSize(Iterators.concat(iters), Spliterator.ORDERED), false); - } - - public OaiIteratorFactory getOaiIteratorFactory() { - if (oaiIteratorFactory == null){ - oaiIteratorFactory = new OaiIteratorFactory(); - } - return oaiIteratorFactory; - } + public OaiIteratorFactory getOaiIteratorFactory() { + if (oaiIteratorFactory == null) { + oaiIteratorFactory = new OaiIteratorFactory(); + } + return oaiIteratorFactory; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java index cd093ed2d1..013e837221 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java @@ -1,15 +1,14 @@ package eu.dnetlib.dhp.collection.plugin.oai; +import eu.dnetlib.dhp.collection.worker.DnetCollectorException; +import eu.dnetlib.dhp.collection.worker.utils.HttpConnector; +import eu.dnetlib.dhp.collection.worker.utils.XmlCleaner; import java.io.StringReader; import java.io.UnsupportedEncodingException; import java.net.URLEncoder; import java.util.Iterator; import java.util.Queue; import java.util.concurrent.PriorityBlockingQueue; - -import eu.dnetlib.dhp.collection.worker.DnetCollectorException; -import eu.dnetlib.dhp.collection.worker.utils.HttpConnector; -import eu.dnetlib.dhp.collection.worker.utils.XmlCleaner; import org.apache.commons.lang.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -18,146 +17,163 @@ import org.dom4j.DocumentException; import org.dom4j.Node; import org.dom4j.io.SAXReader; - public class OaiIterator implements Iterator { - private static final Log log = LogFactory.getLog(OaiIterator.class); // NOPMD by marko on 11/24/08 5:02 PM + private static final Log log = + LogFactory.getLog(OaiIterator.class); // NOPMD by marko on 11/24/08 5:02 PM - private final Queue queue = new PriorityBlockingQueue<>(); - private final SAXReader reader = new SAXReader(); + private final Queue queue = new PriorityBlockingQueue<>(); + private final SAXReader reader = new SAXReader(); - private final String baseUrl; - private final String set; - private final String mdFormat; - private final String fromDate; - private final String untilDate; - private String token; - private boolean started; - private final HttpConnector httpConnector; + private final String baseUrl; + private final String set; + private final String mdFormat; + private final String fromDate; + private final String untilDate; + private String token; + private boolean started; + private final HttpConnector httpConnector; - public OaiIterator(final String baseUrl, final String mdFormat, final String set, final String fromDate, final String untilDate, - final HttpConnector httpConnector) { - this.baseUrl = baseUrl; - this.mdFormat = mdFormat; - this.set = set; - this.fromDate = fromDate; - this.untilDate = untilDate; - this.started = false; - this.httpConnector = httpConnector; - } + public OaiIterator( + final String baseUrl, + final String mdFormat, + final String set, + final String fromDate, + final String untilDate, + final HttpConnector httpConnector) { + this.baseUrl = baseUrl; + this.mdFormat = mdFormat; + this.set = set; + this.fromDate = fromDate; + this.untilDate = untilDate; + this.started = false; + this.httpConnector = httpConnector; + } - private void verifyStarted() { - if (!this.started) { - this.started = true; - try { - this.token = firstPage(); - } catch (final DnetCollectorException e) { - throw new RuntimeException(e); - } - } - } + private void verifyStarted() { + if (!this.started) { + this.started = true; + try { + this.token = firstPage(); + } catch (final DnetCollectorException e) { + throw new RuntimeException(e); + } + } + } - @Override - public boolean hasNext() { - synchronized (queue) { - verifyStarted(); - return !queue.isEmpty(); - } - } + @Override + public boolean hasNext() { + synchronized (queue) { + verifyStarted(); + return !queue.isEmpty(); + } + } - @Override - public String next() { - synchronized (queue) { - verifyStarted(); - final String res = queue.poll(); - while (queue.isEmpty() && token != null && !token.isEmpty()) { - try { - token = otherPages(token); - } catch (final DnetCollectorException e) { - throw new RuntimeException(e); - } - } - return res; - } - } + @Override + public String next() { + synchronized (queue) { + verifyStarted(); + final String res = queue.poll(); + while (queue.isEmpty() && token != null && !token.isEmpty()) { + try { + token = otherPages(token); + } catch (final DnetCollectorException e) { + throw new RuntimeException(e); + } + } + return res; + } + } - @Override - public void remove() {} + @Override + public void remove() {} - private String firstPage() throws DnetCollectorException { - try { - String url = baseUrl + "?verb=ListRecords&metadataPrefix=" + URLEncoder.encode(mdFormat, "UTF-8"); - if (set != null && !set.isEmpty()) { - url += "&set=" + URLEncoder.encode(set, "UTF-8"); - } - if (fromDate != null && fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) { - url += "&from=" + URLEncoder.encode(fromDate, "UTF-8"); - } - if (untilDate != null && untilDate.matches("\\d{4}-\\d{2}-\\d{2}")) { - url += "&until=" + URLEncoder.encode(untilDate, "UTF-8"); - } - log.info("Start harvesting using url: " + url); + private String firstPage() throws DnetCollectorException { + try { + String url = + baseUrl + + "?verb=ListRecords&metadataPrefix=" + + URLEncoder.encode(mdFormat, "UTF-8"); + if (set != null && !set.isEmpty()) { + url += "&set=" + URLEncoder.encode(set, "UTF-8"); + } + if (fromDate != null && fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) { + url += "&from=" + URLEncoder.encode(fromDate, "UTF-8"); + } + if (untilDate != null && untilDate.matches("\\d{4}-\\d{2}-\\d{2}")) { + url += "&until=" + URLEncoder.encode(untilDate, "UTF-8"); + } + log.info("Start harvesting using url: " + url); - return downloadPage(url); - } catch (final UnsupportedEncodingException e) { - throw new DnetCollectorException(e); - } - } + return downloadPage(url); + } catch (final UnsupportedEncodingException e) { + throw new DnetCollectorException(e); + } + } - private String extractResumptionToken(final String xml) { + private String extractResumptionToken(final String xml) { - final String s = StringUtils.substringAfter(xml, "", "", " newIterator(final String baseUrl, final String mdFormat, final String set, final String fromDate, final String untilDate) { - return new OaiIterator(baseUrl, mdFormat, set, fromDate, untilDate, getHttpConnector()); - } - - private HttpConnector getHttpConnector() { - if (httpConnector== null) - httpConnector = new HttpConnector(); - return httpConnector; - } - - + public Iterator newIterator( + final String baseUrl, + final String mdFormat, + final String set, + final String fromDate, + final String untilDate) { + return new OaiIterator(baseUrl, mdFormat, set, fromDate, untilDate, getHttpConnector()); + } + private HttpConnector getHttpConnector() { + if (httpConnector == null) httpConnector = new HttpConnector(); + return httpConnector; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorException.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorException.java index 75ccc4d91c..2b9921922f 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorException.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorException.java @@ -2,29 +2,30 @@ package eu.dnetlib.dhp.collection.worker; public class DnetCollectorException extends Exception { - /** - * - */ - private static final long serialVersionUID = -290723075076039757L; + /** */ + private static final long serialVersionUID = -290723075076039757L; - public DnetCollectorException() { - super(); - } + public DnetCollectorException() { + super(); + } - public DnetCollectorException(final String message, final Throwable cause, final boolean enableSuppression, final boolean writableStackTrace) { - super(message, cause, enableSuppression, writableStackTrace); - } + public DnetCollectorException( + final String message, + final Throwable cause, + final boolean enableSuppression, + final boolean writableStackTrace) { + super(message, cause, enableSuppression, writableStackTrace); + } - public DnetCollectorException(final String message, final Throwable cause) { - super(message, cause); - } + public DnetCollectorException(final String message, final Throwable cause) { + super(message, cause); + } - public DnetCollectorException(final String message) { - super(message); - } - - public DnetCollectorException(final Throwable cause) { - super(cause); - } + public DnetCollectorException(final String message) { + super(message); + } + public DnetCollectorException(final Throwable cause) { + super(cause); + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorker.java index c76536b3a9..5a08525017 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorker.java @@ -2,13 +2,17 @@ package eu.dnetlib.dhp.collection.worker; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.collector.worker.model.ApiDescriptor; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory; import eu.dnetlib.message.Message; import eu.dnetlib.message.MessageManager; import eu.dnetlib.message.MessageType; +import java.io.IOException; +import java.net.URI; +import java.util.HashMap; +import java.util.Map; +import java.util.concurrent.atomic.AtomicInteger; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; @@ -18,37 +22,34 @@ import org.apache.hadoop.io.Text; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.net.URI; -import java.util.HashMap; -import java.util.Map; -import java.util.concurrent.atomic.AtomicInteger; - public class DnetCollectorWorker { private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorker.class); - private final CollectorPluginFactory collectorPluginFactory; private final ArgumentApplicationParser argumentParser; private final MessageManager manager; - - public DnetCollectorWorker(final CollectorPluginFactory collectorPluginFactory, final ArgumentApplicationParser argumentParser, final MessageManager manager) throws DnetCollectorException { + public DnetCollectorWorker( + final CollectorPluginFactory collectorPluginFactory, + final ArgumentApplicationParser argumentParser, + final MessageManager manager) + throws DnetCollectorException { this.collectorPluginFactory = collectorPluginFactory; this.argumentParser = argumentParser; this.manager = manager; } - public void collect() throws DnetCollectorException { try { final ObjectMapper jsonMapper = new ObjectMapper(); - final ApiDescriptor api = jsonMapper.readValue(argumentParser.get("apidescriptor"), ApiDescriptor.class); + final ApiDescriptor api = + jsonMapper.readValue(argumentParser.get("apidescriptor"), ApiDescriptor.class); - final CollectorPlugin plugin = collectorPluginFactory.getPluginByProtocol(api.getProtocol()); + final CollectorPlugin plugin = + collectorPluginFactory.getPluginByProtocol(api.getProtocol()); final String hdfsuri = argumentParser.get("namenode"); @@ -62,7 +63,7 @@ public class DnetCollectorWorker { System.setProperty("HADOOP_USER_NAME", argumentParser.get("userHDFS")); System.setProperty("hadoop.home.dir", "/"); - //Get the filesystem - HDFS + // Get the filesystem - HDFS FileSystem.get(URI.create(hdfsuri), conf); Path hdfswritepath = new Path(argumentParser.get("hdfsPath")); @@ -71,43 +72,69 @@ public class DnetCollectorWorker { final Map ongoingMap = new HashMap<>(); final Map reportMap = new HashMap<>(); final AtomicInteger counter = new AtomicInteger(0); - try (SequenceFile.Writer writer = SequenceFile.createWriter(conf, - SequenceFile.Writer.file(hdfswritepath), SequenceFile.Writer.keyClass(IntWritable.class), - SequenceFile.Writer.valueClass(Text.class))) { + try (SequenceFile.Writer writer = + SequenceFile.createWriter( + conf, + SequenceFile.Writer.file(hdfswritepath), + SequenceFile.Writer.keyClass(IntWritable.class), + SequenceFile.Writer.valueClass(Text.class))) { final IntWritable key = new IntWritable(counter.get()); final Text value = new Text(); - plugin.collect(api).forEach(content -> { - - key.set(counter.getAndIncrement()); - value.set(content); - if (counter.get() % 10 == 0) { - try { - ongoingMap.put("ongoing", "" + counter.get()); - log.debug("Sending message: "+ manager.sendMessage(new Message(argumentParser.get("workflowId"), "Collection", MessageType.ONGOING, ongoingMap), argumentParser.get("rabbitOngoingQueue"), true, false)); - } catch (Exception e) { - log.error("Error on sending message ", e); - } - } - try { - writer.append(key, value); - } catch (IOException e) { - throw new RuntimeException(e); - } - - }); + plugin.collect(api) + .forEach( + content -> { + key.set(counter.getAndIncrement()); + value.set(content); + if (counter.get() % 10 == 0) { + try { + ongoingMap.put("ongoing", "" + counter.get()); + log.debug( + "Sending message: " + + manager.sendMessage( + new Message( + argumentParser.get( + "workflowId"), + "Collection", + MessageType.ONGOING, + ongoingMap), + argumentParser.get( + "rabbitOngoingQueue"), + true, + false)); + } catch (Exception e) { + log.error("Error on sending message ", e); + } + } + try { + writer.append(key, value); + } catch (IOException e) { + throw new RuntimeException(e); + } + }); } ongoingMap.put("ongoing", "" + counter.get()); - manager.sendMessage(new Message(argumentParser.get("workflowId"), "Collection", MessageType.ONGOING, ongoingMap), argumentParser.get("rabbitOngoingQueue"), true, false); + manager.sendMessage( + new Message( + argumentParser.get("workflowId"), + "Collection", + MessageType.ONGOING, + ongoingMap), + argumentParser.get("rabbitOngoingQueue"), + true, + false); reportMap.put("collected", "" + counter.get()); - manager.sendMessage(new Message(argumentParser.get("workflowId"), "Collection", MessageType.REPORT, reportMap), argumentParser.get("rabbitOngoingQueue"), true, false); + manager.sendMessage( + new Message( + argumentParser.get("workflowId"), + "Collection", + MessageType.REPORT, + reportMap), + argumentParser.get("rabbitOngoingQueue"), + true, + false); manager.close(); } catch (Throwable e) { - throw new DnetCollectorException("Error on collecting ",e); + throw new DnetCollectorException("Error on collecting ", e); } } - - - - - } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorkerApplication.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorkerApplication.java index d4bd22817c..9c19383bb3 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorkerApplication.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorkerApplication.java @@ -1,6 +1,5 @@ package eu.dnetlib.dhp.collection.worker; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory; import eu.dnetlib.message.MessageManager; @@ -8,16 +7,13 @@ import org.apache.commons.io.IOUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; - /** - * DnetCollectortWorkerApplication is the main class responsible to start - * the Dnet Collection into HDFS. - * This module will be executed on the hadoop cluster and taking in input some parameters - * that tells it which is the right collector plugin to use and where store the data into HDFS path + * DnetCollectortWorkerApplication is the main class responsible to start the Dnet Collection into + * HDFS. This module will be executed on the hadoop cluster and taking in input some parameters that + * tells it which is the right collector plugin to use and where store the data into HDFS path * * @author Sandro La Bruzzo */ - public class DnetCollectorWorkerApplication { private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorkerApplication.class); @@ -26,22 +22,27 @@ public class DnetCollectorWorkerApplication { private static ArgumentApplicationParser argumentParser; - - /** - * @param args - */ + /** @param args */ public static void main(final String[] args) throws Exception { - argumentParser= new ArgumentApplicationParser(IOUtils.toString(DnetCollectorWorker.class.getResourceAsStream("/eu/dnetlib/collector/worker/collector_parameter.json"))); + argumentParser = + new ArgumentApplicationParser( + IOUtils.toString( + DnetCollectorWorker.class.getResourceAsStream( + "/eu/dnetlib/collector/worker/collector_parameter.json"))); argumentParser.parseArgument(args); log.info("hdfsPath =" + argumentParser.get("hdfsPath")); log.info("json = " + argumentParser.get("apidescriptor")); - final MessageManager manager = new MessageManager(argumentParser.get("rabbitHost"), argumentParser.get("rabbitUser"), argumentParser.get("rabbitPassword"), false, false, null); - final DnetCollectorWorker worker = new DnetCollectorWorker(collectorPluginFactory, argumentParser, manager); + final MessageManager manager = + new MessageManager( + argumentParser.get("rabbitHost"), + argumentParser.get("rabbitUser"), + argumentParser.get("rabbitPassword"), + false, + false, + null); + final DnetCollectorWorker worker = + new DnetCollectorWorker(collectorPluginFactory, argumentParser, manager); worker.collect(); - - } - - } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginErrorLogList.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginErrorLogList.java index 807479c5da..27d8fa5fb5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginErrorLogList.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginErrorLogList.java @@ -4,16 +4,15 @@ import java.util.LinkedList; public class CollectorPluginErrorLogList extends LinkedList { - private static final long serialVersionUID = -6925786561303289704L; - - @Override - public String toString() { - String log = new String(); - int index = 0; - for (final String errorMessage : this) { - log += String.format("Retry #%s: %s / ", index++, errorMessage); - } - return log; - } + private static final long serialVersionUID = -6925786561303289704L; + @Override + public String toString() { + String log = new String(); + int index = 0; + for (final String errorMessage : this) { + log += String.format("Retry #%s: %s / ", index++, errorMessage); + } + return log; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginFactory.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginFactory.java index cc2eaaddc8..2dd0f1a6f5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginFactory.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginFactory.java @@ -4,19 +4,16 @@ import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin; import eu.dnetlib.dhp.collection.worker.DnetCollectorException; -; - - public class CollectorPluginFactory { - public CollectorPlugin getPluginByProtocol(final String protocol) throws DnetCollectorException { - if (protocol==null) throw new DnetCollectorException("protocol cannot be null"); - switch (protocol.toLowerCase().trim()){ + public CollectorPlugin getPluginByProtocol(final String protocol) + throws DnetCollectorException { + if (protocol == null) throw new DnetCollectorException("protocol cannot be null"); + switch (protocol.toLowerCase().trim()) { case "oai": return new OaiCollectorPlugin(); default: - throw new DnetCollectorException("UNknown protocol"); + throw new DnetCollectorException("UNknown protocol"); } - } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/HttpConnector.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/HttpConnector.java index 24e9f1ac15..816ebbd806 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/HttpConnector.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/HttpConnector.java @@ -1,15 +1,6 @@ package eu.dnetlib.dhp.collection.worker.utils; import eu.dnetlib.dhp.collection.worker.DnetCollectorException; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang.math.NumberUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -import javax.net.ssl.HttpsURLConnection; -import javax.net.ssl.SSLContext; -import javax.net.ssl.TrustManager; -import javax.net.ssl.X509TrustManager; import java.io.IOException; import java.io.InputStream; import java.net.*; @@ -17,203 +8,243 @@ import java.security.GeneralSecurityException; import java.security.cert.X509Certificate; import java.util.List; import java.util.Map; - +import javax.net.ssl.HttpsURLConnection; +import javax.net.ssl.SSLContext; +import javax.net.ssl.TrustManager; +import javax.net.ssl.X509TrustManager; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang.math.NumberUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; public class HttpConnector { - private static final Log log = LogFactory.getLog(HttpConnector.class); + private static final Log log = LogFactory.getLog(HttpConnector.class); - private int maxNumberOfRetry = 6; - private int defaultDelay = 120; // seconds - private int readTimeOut = 120; // seconds + private int maxNumberOfRetry = 6; + private int defaultDelay = 120; // seconds + private int readTimeOut = 120; // seconds - private String responseType = null; + private String responseType = null; - private final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)"; + private final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)"; - public HttpConnector() { - CookieHandler.setDefault(new CookieManager(null, CookiePolicy.ACCEPT_ALL)); - } + public HttpConnector() { + CookieHandler.setDefault(new CookieManager(null, CookiePolicy.ACCEPT_ALL)); + } - /** - * Given the URL returns the content via HTTP GET - * - * @param requestUrl - * the URL - * @return the content of the downloaded resource - * @throws DnetCollectorException - * when retrying more than maxNumberOfRetry times - */ - public String getInputSource(final String requestUrl) throws DnetCollectorException { - return attemptDownlaodAsString(requestUrl, 1, new CollectorPluginErrorLogList()); - } + /** + * Given the URL returns the content via HTTP GET + * + * @param requestUrl the URL + * @return the content of the downloaded resource + * @throws DnetCollectorException when retrying more than maxNumberOfRetry times + */ + public String getInputSource(final String requestUrl) throws DnetCollectorException { + return attemptDownlaodAsString(requestUrl, 1, new CollectorPluginErrorLogList()); + } - /** - * Given the URL returns the content as a stream via HTTP GET - * - * @param requestUrl - * the URL - * @return the content of the downloaded resource as InputStream - * @throws DnetCollectorException - * when retrying more than maxNumberOfRetry times - */ - public InputStream getInputSourceAsStream(final String requestUrl) throws DnetCollectorException { - return attemptDownload(requestUrl, 1, new CollectorPluginErrorLogList()); - } + /** + * Given the URL returns the content as a stream via HTTP GET + * + * @param requestUrl the URL + * @return the content of the downloaded resource as InputStream + * @throws DnetCollectorException when retrying more than maxNumberOfRetry times + */ + public InputStream getInputSourceAsStream(final String requestUrl) + throws DnetCollectorException { + return attemptDownload(requestUrl, 1, new CollectorPluginErrorLogList()); + } - private String attemptDownlaodAsString(final String requestUrl, final int retryNumber, final CollectorPluginErrorLogList errorList) - throws DnetCollectorException { - try { - final InputStream s = attemptDownload(requestUrl, 1, new CollectorPluginErrorLogList()); - try { - return IOUtils.toString(s); - } catch (final IOException e) { - log.error("error while retrieving from http-connection occured: " + requestUrl, e); - Thread.sleep(defaultDelay * 1000); - errorList.add(e.getMessage()); - return attemptDownlaodAsString(requestUrl, retryNumber + 1, errorList); - } finally { - IOUtils.closeQuietly(s); - } - } catch (final InterruptedException e) { - throw new DnetCollectorException(e); - } - } + private String attemptDownlaodAsString( + final String requestUrl, + final int retryNumber, + final CollectorPluginErrorLogList errorList) + throws DnetCollectorException { + try { + final InputStream s = attemptDownload(requestUrl, 1, new CollectorPluginErrorLogList()); + try { + return IOUtils.toString(s); + } catch (final IOException e) { + log.error("error while retrieving from http-connection occured: " + requestUrl, e); + Thread.sleep(defaultDelay * 1000); + errorList.add(e.getMessage()); + return attemptDownlaodAsString(requestUrl, retryNumber + 1, errorList); + } finally { + IOUtils.closeQuietly(s); + } + } catch (final InterruptedException e) { + throw new DnetCollectorException(e); + } + } - private InputStream attemptDownload(final String requestUrl, final int retryNumber, final CollectorPluginErrorLogList errorList) - throws DnetCollectorException { + private InputStream attemptDownload( + final String requestUrl, + final int retryNumber, + final CollectorPluginErrorLogList errorList) + throws DnetCollectorException { - if (retryNumber > maxNumberOfRetry) { throw new DnetCollectorException("Max number of retries exceeded. Cause: \n " + errorList); } + if (retryNumber > maxNumberOfRetry) { + throw new DnetCollectorException( + "Max number of retries exceeded. Cause: \n " + errorList); + } - log.debug("Downloading " + requestUrl + " - try: " + retryNumber); - try { - InputStream input = null; + log.debug("Downloading " + requestUrl + " - try: " + retryNumber); + try { + InputStream input = null; - try { - final HttpURLConnection urlConn = (HttpURLConnection) new URL(requestUrl).openConnection(); - urlConn.setInstanceFollowRedirects(false); - urlConn.setReadTimeout(readTimeOut * 1000); - urlConn.addRequestProperty("User-Agent", userAgent); + try { + final HttpURLConnection urlConn = + (HttpURLConnection) new URL(requestUrl).openConnection(); + urlConn.setInstanceFollowRedirects(false); + urlConn.setReadTimeout(readTimeOut * 1000); + urlConn.addRequestProperty("User-Agent", userAgent); - if (log.isDebugEnabled()) { - logHeaderFields(urlConn); - } + if (log.isDebugEnabled()) { + logHeaderFields(urlConn); + } - final int retryAfter = obtainRetryAfter(urlConn.getHeaderFields()); - if (retryAfter > 0 && urlConn.getResponseCode() == HttpURLConnection.HTTP_UNAVAILABLE) { - log.warn("waiting and repeating request after " + retryAfter + " sec."); - Thread.sleep(retryAfter * 1000); - errorList.add("503 Service Unavailable"); - urlConn.disconnect(); - return attemptDownload(requestUrl, retryNumber + 1, errorList); - } else if (urlConn.getResponseCode() == HttpURLConnection.HTTP_MOVED_PERM || urlConn.getResponseCode() == HttpURLConnection.HTTP_MOVED_TEMP) { - final String newUrl = obtainNewLocation(urlConn.getHeaderFields()); - log.debug("The requested url has been moved to " + newUrl); - errorList.add(String.format("%s %s. Moved to: %s", urlConn.getResponseCode(), urlConn.getResponseMessage(), newUrl)); - urlConn.disconnect(); - return attemptDownload(newUrl, retryNumber + 1, errorList); - } else if (urlConn.getResponseCode() != HttpURLConnection.HTTP_OK) { - log.error(String.format("HTTP error: %s %s", urlConn.getResponseCode(), urlConn.getResponseMessage())); - Thread.sleep(defaultDelay * 1000); - errorList.add(String.format("%s %s", urlConn.getResponseCode(), urlConn.getResponseMessage())); - urlConn.disconnect(); - return attemptDownload(requestUrl, retryNumber + 1, errorList); - } else { - input = urlConn.getInputStream(); - responseType = urlConn.getContentType(); - return input; - } - } catch (final IOException e) { - log.error("error while retrieving from http-connection occured: " + requestUrl, e); - Thread.sleep(defaultDelay * 1000); - errorList.add(e.getMessage()); - return attemptDownload(requestUrl, retryNumber + 1, errorList); - } - } catch (final InterruptedException e) { - throw new DnetCollectorException(e); - } - } + final int retryAfter = obtainRetryAfter(urlConn.getHeaderFields()); + if (retryAfter > 0 + && urlConn.getResponseCode() == HttpURLConnection.HTTP_UNAVAILABLE) { + log.warn("waiting and repeating request after " + retryAfter + " sec."); + Thread.sleep(retryAfter * 1000); + errorList.add("503 Service Unavailable"); + urlConn.disconnect(); + return attemptDownload(requestUrl, retryNumber + 1, errorList); + } else if (urlConn.getResponseCode() == HttpURLConnection.HTTP_MOVED_PERM + || urlConn.getResponseCode() == HttpURLConnection.HTTP_MOVED_TEMP) { + final String newUrl = obtainNewLocation(urlConn.getHeaderFields()); + log.debug("The requested url has been moved to " + newUrl); + errorList.add( + String.format( + "%s %s. Moved to: %s", + urlConn.getResponseCode(), + urlConn.getResponseMessage(), + newUrl)); + urlConn.disconnect(); + return attemptDownload(newUrl, retryNumber + 1, errorList); + } else if (urlConn.getResponseCode() != HttpURLConnection.HTTP_OK) { + log.error( + String.format( + "HTTP error: %s %s", + urlConn.getResponseCode(), urlConn.getResponseMessage())); + Thread.sleep(defaultDelay * 1000); + errorList.add( + String.format( + "%s %s", + urlConn.getResponseCode(), urlConn.getResponseMessage())); + urlConn.disconnect(); + return attemptDownload(requestUrl, retryNumber + 1, errorList); + } else { + input = urlConn.getInputStream(); + responseType = urlConn.getContentType(); + return input; + } + } catch (final IOException e) { + log.error("error while retrieving from http-connection occured: " + requestUrl, e); + Thread.sleep(defaultDelay * 1000); + errorList.add(e.getMessage()); + return attemptDownload(requestUrl, retryNumber + 1, errorList); + } + } catch (final InterruptedException e) { + throw new DnetCollectorException(e); + } + } - private void logHeaderFields(final HttpURLConnection urlConn) throws IOException { - log.debug("StatusCode: " + urlConn.getResponseMessage()); + private void logHeaderFields(final HttpURLConnection urlConn) throws IOException { + log.debug("StatusCode: " + urlConn.getResponseMessage()); - for (final Map.Entry> e : urlConn.getHeaderFields().entrySet()) { - if (e.getKey() != null) { - for (final String v : e.getValue()) { - log.debug(" key: " + e.getKey() + " - value: " + v); - } - } - } - } + for (final Map.Entry> e : urlConn.getHeaderFields().entrySet()) { + if (e.getKey() != null) { + for (final String v : e.getValue()) { + log.debug(" key: " + e.getKey() + " - value: " + v); + } + } + } + } - private int obtainRetryAfter(final Map> headerMap) { - for (final String key : headerMap.keySet()) { - if (key != null && key.toLowerCase().equals("retry-after") && headerMap.get(key).size() > 0 - && NumberUtils.isNumber(headerMap.get(key).get(0))) { return Integer.parseInt(headerMap.get(key).get(0)) + 10; } - } - return -1; - } + private int obtainRetryAfter(final Map> headerMap) { + for (final String key : headerMap.keySet()) { + if (key != null + && key.toLowerCase().equals("retry-after") + && headerMap.get(key).size() > 0 + && NumberUtils.isNumber(headerMap.get(key).get(0))) { + return Integer.parseInt(headerMap.get(key).get(0)) + 10; + } + } + return -1; + } - private String obtainNewLocation(final Map> headerMap) throws DnetCollectorException { - for (final String key : headerMap.keySet()) { - if (key != null && key.toLowerCase().equals("location") && headerMap.get(key).size() > 0) { return headerMap.get(key).get(0); } - } - throw new DnetCollectorException("The requested url has been MOVED, but 'location' param is MISSING"); - } + private String obtainNewLocation(final Map> headerMap) + throws DnetCollectorException { + for (final String key : headerMap.keySet()) { + if (key != null + && key.toLowerCase().equals("location") + && headerMap.get(key).size() > 0) { + return headerMap.get(key).get(0); + } + } + throw new DnetCollectorException( + "The requested url has been MOVED, but 'location' param is MISSING"); + } - /** - * register for https scheme; this is a workaround and not intended for the use in trusted environments - */ - public void initTrustManager() { - final X509TrustManager tm = new X509TrustManager() { + /** + * register for https scheme; this is a workaround and not intended for the use in trusted + * environments + */ + public void initTrustManager() { + final X509TrustManager tm = + new X509TrustManager() { - @Override - public void checkClientTrusted(final X509Certificate[] xcs, final String string) {} + @Override + public void checkClientTrusted( + final X509Certificate[] xcs, final String string) {} - @Override - public void checkServerTrusted(final X509Certificate[] xcs, final String string) {} + @Override + public void checkServerTrusted( + final X509Certificate[] xcs, final String string) {} - @Override - public X509Certificate[] getAcceptedIssuers() { - return null; - } - }; - try { - final SSLContext ctx = SSLContext.getInstance("TLS"); - ctx.init(null, new TrustManager[] { tm }, null); - HttpsURLConnection.setDefaultSSLSocketFactory(ctx.getSocketFactory()); - } catch (final GeneralSecurityException e) { - log.fatal(e); - throw new IllegalStateException(e); - } - } + @Override + public X509Certificate[] getAcceptedIssuers() { + return null; + } + }; + try { + final SSLContext ctx = SSLContext.getInstance("TLS"); + ctx.init(null, new TrustManager[] {tm}, null); + HttpsURLConnection.setDefaultSSLSocketFactory(ctx.getSocketFactory()); + } catch (final GeneralSecurityException e) { + log.fatal(e); + throw new IllegalStateException(e); + } + } - public int getMaxNumberOfRetry() { - return maxNumberOfRetry; - } + public int getMaxNumberOfRetry() { + return maxNumberOfRetry; + } - public void setMaxNumberOfRetry(final int maxNumberOfRetry) { - this.maxNumberOfRetry = maxNumberOfRetry; - } + public void setMaxNumberOfRetry(final int maxNumberOfRetry) { + this.maxNumberOfRetry = maxNumberOfRetry; + } - public int getDefaultDelay() { - return defaultDelay; - } + public int getDefaultDelay() { + return defaultDelay; + } - public void setDefaultDelay(final int defaultDelay) { - this.defaultDelay = defaultDelay; - } + public void setDefaultDelay(final int defaultDelay) { + this.defaultDelay = defaultDelay; + } - public int getReadTimeOut() { - return readTimeOut; - } + public int getReadTimeOut() { + return readTimeOut; + } - public void setReadTimeOut(final int readTimeOut) { - this.readTimeOut = readTimeOut; - } - - public String getResponseType() { - return responseType; - } + public void setReadTimeOut(final int readTimeOut) { + this.readTimeOut = readTimeOut; + } + public String getResponseType() { + return responseType; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/XmlCleaner.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/XmlCleaner.java index 8c8ee629f3..911b65cc05 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/XmlCleaner.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/XmlCleaner.java @@ -6,254 +6,392 @@ import java.util.Map; import java.util.Set; import java.util.regex.Pattern; -/** - * @author jochen, Andreas Czerniak - * - */ +/** @author jochen, Andreas Czerniak */ public class XmlCleaner { - /** - * Pattern for numeric entities. - */ - private static Pattern validCharacterEntityPattern = Pattern.compile("^&#x?\\d{2,4};"); //$NON-NLS-1$ - // private static Pattern validCharacterEntityPattern = Pattern.compile("^&#?\\d{2,4};"); //$NON-NLS-1$ + /** Pattern for numeric entities. */ + private static Pattern validCharacterEntityPattern = + Pattern.compile("^&#x?\\d{2,4};"); // $NON-NLS-1$ + // private static Pattern validCharacterEntityPattern = Pattern.compile("^&#?\\d{2,4};"); + // //$NON-NLS-1$ - // see https://www.w3.org/TR/REC-xml/#charsets , not only limited to - private static Pattern invalidControlCharPattern = Pattern.compile("&#x?1[0-9a-fA-F];"); + // see https://www.w3.org/TR/REC-xml/#charsets , not only limited to + private static Pattern invalidControlCharPattern = Pattern.compile("&#x?1[0-9a-fA-F];"); - /** - * Pattern that negates the allowable XML 4 byte unicode characters. Valid are: #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] | - * [#x10000-#x10FFFF] - */ - private static Pattern invalidCharacterPattern = Pattern.compile("[^\t\r\n\u0020-\uD7FF\uE000-\uFFFD]"); //$NON-NLS-1$ + /** + * Pattern that negates the allowable XML 4 byte unicode characters. Valid are: #x9 | #xA | #xD + * | [#x20-#xD7FF] | [#xE000-#xFFFD] | [#x10000-#x10FFFF] + */ + private static Pattern invalidCharacterPattern = + Pattern.compile("[^\t\r\n\u0020-\uD7FF\uE000-\uFFFD]"); // $NON-NLS-1$ - // Map entities to their unicode equivalent - private static Set goodEntities = new HashSet<>(); - private static Map badEntities = new HashMap<>(); + // Map entities to their unicode equivalent + private static Set goodEntities = new HashSet<>(); + private static Map badEntities = new HashMap<>(); - static { - // pre-defined XML entities - goodEntities.add("""); //$NON-NLS-1$ // quotation mark - goodEntities.add("&"); //$NON-NLS-1$ // ampersand - goodEntities.add("<"); //$NON-NLS-1$ // less-than sign - goodEntities.add(">"); //$NON-NLS-1$ // greater-than sign - // control entities - // badEntities.put(" ", ""); - badEntities.put("", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("€", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("‚", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("ƒ", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("„", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("…", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("†", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("‡", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("ˆ", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("‰", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("Š", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("‹", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("Œ", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("Ž", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("‘", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("’", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("“", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("”", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("•", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("–", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("—", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("˜", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("™", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("š", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("›", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("œ", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("ž", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - badEntities.put("Ÿ", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character - // misc entities - badEntities.put("€", "\u20AC"); //$NON-NLS-1$ //$NON-NLS-2$ // euro - badEntities.put("‘", "\u2018"); //$NON-NLS-1$ //$NON-NLS-2$ // left single quotation mark - badEntities.put("’", "\u2019"); //$NON-NLS-1$ //$NON-NLS-2$ // right single quotation mark - // Latin 1 entities - badEntities.put(" ", "\u00A0"); //$NON-NLS-1$ //$NON-NLS-2$ // no-break space - badEntities.put("¡", "\u00A1"); //$NON-NLS-1$ //$NON-NLS-2$ // inverted exclamation mark - badEntities.put("¢", "\u00A2"); //$NON-NLS-1$ //$NON-NLS-2$ // cent sign - badEntities.put("£", "\u00A3"); //$NON-NLS-1$ //$NON-NLS-2$ // pound sign - badEntities.put("¤", "\u00A4"); //$NON-NLS-1$ //$NON-NLS-2$ // currency sign - badEntities.put("¥", "\u00A5"); //$NON-NLS-1$ //$NON-NLS-2$ // yen sign - badEntities.put("¦", "\u00A6"); //$NON-NLS-1$ //$NON-NLS-2$ // broken vertical bar - badEntities.put("§", "\u00A7"); //$NON-NLS-1$ //$NON-NLS-2$ // section sign - badEntities.put("¨", "\u00A8"); //$NON-NLS-1$ //$NON-NLS-2$ // diaeresis - badEntities.put("©", "\u00A9"); //$NON-NLS-1$ //$NON-NLS-2$ // copyright sign - badEntities.put("ª", "\u00AA"); //$NON-NLS-1$ //$NON-NLS-2$ // feminine ordinal indicator - badEntities.put("«", "\u00AB"); //$NON-NLS-1$ //$NON-NLS-2$ // left-pointing double angle quotation mark - badEntities.put("¬", "\u00AC"); //$NON-NLS-1$ //$NON-NLS-2$ // not sign - badEntities.put("­", "\u00AD"); //$NON-NLS-1$ //$NON-NLS-2$ // soft hyphen - badEntities.put("®", "\u00AE"); //$NON-NLS-1$ //$NON-NLS-2$ // registered sign - badEntities.put("¯", "\u00AF"); //$NON-NLS-1$ //$NON-NLS-2$ // macron - badEntities.put("°", "\u00B0"); //$NON-NLS-1$ //$NON-NLS-2$ // degree sign - badEntities.put("±", "\u00B1"); //$NON-NLS-1$ //$NON-NLS-2$ // plus-minus sign - badEntities.put("²", "\u00B2"); //$NON-NLS-1$ //$NON-NLS-2$ // superscript two - badEntities.put("³", "\u00B3"); //$NON-NLS-1$ //$NON-NLS-2$ // superscript three - badEntities.put("´", "\u00B4"); //$NON-NLS-1$ //$NON-NLS-2$ // acute accent - badEntities.put("µ", "\u00B5"); //$NON-NLS-1$ //$NON-NLS-2$ // micro sign - badEntities.put("¶", "\u00B6"); //$NON-NLS-1$ //$NON-NLS-2$ // pilcrow sign - badEntities.put("·", "\u00B7"); //$NON-NLS-1$ //$NON-NLS-2$ // middle dot - badEntities.put("¸", "\u00B8"); //$NON-NLS-1$ //$NON-NLS-2$ // cedilla - badEntities.put("¹", "\u00B9"); //$NON-NLS-1$ //$NON-NLS-2$ // superscript one - badEntities.put("º", "\u00BA"); //$NON-NLS-1$ //$NON-NLS-2$ // masculine ordinal indicator - badEntities.put("»", "\u00BB"); //$NON-NLS-1$ //$NON-NLS-2$ // right-pointing double angle quotation mark - badEntities.put("¼", "\u00BC"); //$NON-NLS-1$ //$NON-NLS-2$ // vulgar fraction one quarter - badEntities.put("½", "\u00BD"); //$NON-NLS-1$ //$NON-NLS-2$ // vulgar fraction one half - badEntities.put("¾", "\u00BE"); //$NON-NLS-1$ //$NON-NLS-2$ // vulgar fraction three quarters - badEntities.put("¿", "\u00BF"); //$NON-NLS-1$ //$NON-NLS-2$ // inverted question mark - badEntities.put("À", "\u00C0"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with grave - badEntities.put("Á", "\u00C1"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with acute - badEntities.put("Â", "\u00C2"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with circumflex - badEntities.put("Ã", "\u00C3"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with tilde - badEntities.put("Ä", "\u00C4"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with diaeresis - badEntities.put("Å", "\u00C5"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with ring above - badEntities.put("Æ", "\u00C6"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter AE - badEntities.put("Ç", "\u00C7"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter C with cedilla - badEntities.put("È", "\u00C8"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter E with grave - badEntities.put("É", "\u00C9"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter E with acute - badEntities.put("Ê", "\u00CA"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter E with circumflex - badEntities.put("Ë", "\u00CB"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter E with diaeresis - badEntities.put("Ì", "\u00CC"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter I with grave - badEntities.put("Í", "\u00CD"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter I with acute - badEntities.put("Î", "\u00CE"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter I with circumflex - badEntities.put("Ï", "\u00CF"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter I with diaeresis - badEntities.put("Ð", "\u00D0"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter ETH - badEntities.put("Ñ", "\u00D1"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter N with tilde - badEntities.put("Ò", "\u00D2"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with grave - badEntities.put("Ó", "\u00D3"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with acute - badEntities.put("Ô", "\u00D4"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with circumflex - badEntities.put("Õ", "\u00D5"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with tilde - badEntities.put("Ö", "\u00D6"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with diaeresis - badEntities.put("×", "\u00D7"); //$NON-NLS-1$ //$NON-NLS-2$ // multiplication sign - badEntities.put("Ø", "\u00D8"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with stroke - badEntities.put("Ù", "\u00D9"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter U with grave - badEntities.put("Ú", "\u00DA"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter U with acute - badEntities.put("Û", "\u00DB"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter U with circumflex - badEntities.put("Ü", "\u00DC"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter U with diaeresis - badEntities.put("Ý", "\u00DD"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter Y with acute - badEntities.put("Þ", "\u00DE"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter THORN - badEntities.put("ß", "\u00DF"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter sharp s - badEntities.put("à", "\u00E0"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with grave - badEntities.put("á", "\u00E1"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with acute - badEntities.put("â", "\u00E2"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with circumflex - badEntities.put("ã", "\u00E3"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with tilde - badEntities.put("ä", "\u00E4"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with diaeresis - badEntities.put("å", "\u00E5"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with ring above - badEntities.put("æ", "\u00E6"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter ae - badEntities.put("ç", "\u00E7"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter c with cedilla - badEntities.put("è", "\u00E8"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter e with grave - badEntities.put("é", "\u00E9"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter e with acute - badEntities.put("ê", "\u00EA"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter e with circumflex - badEntities.put("ë", "\u00EB"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter e with diaeresis - badEntities.put("ì", "\u00EC"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter i with grave - badEntities.put("í", "\u00ED"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter i with acute - badEntities.put("î", "\u00EE"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter i with circumflex - badEntities.put("ï", "\u00EF"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter i with diaeresis - badEntities.put("ð", "\u00F0"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter eth - badEntities.put("ñ", "\u00F1"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter n with tilde - badEntities.put("ò", "\u00F2"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with grave - badEntities.put("ó", "\u00F3"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with acute - badEntities.put("ô", "\u00F4"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with circumflex - badEntities.put("õ", "\u00F5"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with tilde - badEntities.put("ö", "\u00F6"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with diaeresis - badEntities.put("÷", "\u00F7"); //$NON-NLS-1$ //$NON-NLS-2$ // division sign - badEntities.put("ø", "\u00F8"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with stroke - badEntities.put("ù", "\u00F9"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter u with grave - badEntities.put("ú", "\u00FA"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter u with acute - badEntities.put("û", "\u00FB"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter u with circumflex - badEntities.put("ü", "\u00FC"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter u with diaeresis - badEntities.put("ý", "\u00FD"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter y with acute - badEntities.put("þ", "\u00FE"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter thorn - badEntities.put("ÿ", "\u00FF"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter y with diaeresis - } + static { + // pre-defined XML entities + goodEntities.add("""); // $NON-NLS-1$ // quotation mark + goodEntities.add("&"); // $NON-NLS-1$ // ampersand + goodEntities.add("<"); // $NON-NLS-1$ // less-than sign + goodEntities.add(">"); // $NON-NLS-1$ // greater-than sign + // control entities + // badEntities.put(" ", ""); + badEntities.put("", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("€", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("‚", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("ƒ", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("„", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("…", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("†", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("‡", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("ˆ", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("‰", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("Š", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("‹", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("Œ", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("Ž", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("‘", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("’", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("“", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("”", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("•", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("–", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("—", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("˜", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("™", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("š", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("›", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("œ", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("ž", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + badEntities.put("Ÿ", " "); // $NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character + // misc entities + badEntities.put("€", "\u20AC"); // $NON-NLS-1$ //$NON-NLS-2$ // euro + badEntities.put( + "‘", "\u2018"); // $NON-NLS-1$ //$NON-NLS-2$ // left single quotation mark + badEntities.put( + "’", "\u2019"); // $NON-NLS-1$ //$NON-NLS-2$ // right single quotation mark + // Latin 1 entities + badEntities.put(" ", "\u00A0"); // $NON-NLS-1$ //$NON-NLS-2$ // no-break space + badEntities.put( + "¡", "\u00A1"); // $NON-NLS-1$ //$NON-NLS-2$ // inverted exclamation mark + badEntities.put("¢", "\u00A2"); // $NON-NLS-1$ //$NON-NLS-2$ // cent sign + badEntities.put("£", "\u00A3"); // $NON-NLS-1$ //$NON-NLS-2$ // pound sign + badEntities.put("¤", "\u00A4"); // $NON-NLS-1$ //$NON-NLS-2$ // currency sign + badEntities.put("¥", "\u00A5"); // $NON-NLS-1$ //$NON-NLS-2$ // yen sign + badEntities.put("¦", "\u00A6"); // $NON-NLS-1$ //$NON-NLS-2$ // broken vertical bar + badEntities.put("§", "\u00A7"); // $NON-NLS-1$ //$NON-NLS-2$ // section sign + badEntities.put("¨", "\u00A8"); // $NON-NLS-1$ //$NON-NLS-2$ // diaeresis + badEntities.put("©", "\u00A9"); // $NON-NLS-1$ //$NON-NLS-2$ // copyright sign + badEntities.put( + "ª", "\u00AA"); // $NON-NLS-1$ //$NON-NLS-2$ // feminine ordinal indicator + badEntities.put( + "«", + "\u00AB"); //$NON-NLS-1$ //$NON-NLS-2$ // left-pointing double angle quotation mark + badEntities.put("¬", "\u00AC"); // $NON-NLS-1$ //$NON-NLS-2$ // not sign + badEntities.put("­", "\u00AD"); // $NON-NLS-1$ //$NON-NLS-2$ // soft hyphen + badEntities.put("®", "\u00AE"); // $NON-NLS-1$ //$NON-NLS-2$ // registered sign + badEntities.put("¯", "\u00AF"); // $NON-NLS-1$ //$NON-NLS-2$ // macron + badEntities.put("°", "\u00B0"); // $NON-NLS-1$ //$NON-NLS-2$ // degree sign + badEntities.put("±", "\u00B1"); // $NON-NLS-1$ //$NON-NLS-2$ // plus-minus sign + badEntities.put("²", "\u00B2"); // $NON-NLS-1$ //$NON-NLS-2$ // superscript two + badEntities.put("³", "\u00B3"); // $NON-NLS-1$ //$NON-NLS-2$ // superscript three + badEntities.put("´", "\u00B4"); // $NON-NLS-1$ //$NON-NLS-2$ // acute accent + badEntities.put("µ", "\u00B5"); // $NON-NLS-1$ //$NON-NLS-2$ // micro sign + badEntities.put("¶", "\u00B6"); // $NON-NLS-1$ //$NON-NLS-2$ // pilcrow sign + badEntities.put("·", "\u00B7"); // $NON-NLS-1$ //$NON-NLS-2$ // middle dot + badEntities.put("¸", "\u00B8"); // $NON-NLS-1$ //$NON-NLS-2$ // cedilla + badEntities.put("¹", "\u00B9"); // $NON-NLS-1$ //$NON-NLS-2$ // superscript one + badEntities.put( + "º", "\u00BA"); // $NON-NLS-1$ //$NON-NLS-2$ // masculine ordinal indicator + badEntities.put( + "»", + "\u00BB"); //$NON-NLS-1$ //$NON-NLS-2$ // right-pointing double angle quotation mark + badEntities.put( + "¼", "\u00BC"); // $NON-NLS-1$ //$NON-NLS-2$ // vulgar fraction one quarter + badEntities.put( + "½", "\u00BD"); // $NON-NLS-1$ //$NON-NLS-2$ // vulgar fraction one half + badEntities.put( + "¾", + "\u00BE"); // $NON-NLS-1$ //$NON-NLS-2$ // vulgar fraction three quarters + badEntities.put( + "¿", "\u00BF"); // $NON-NLS-1$ //$NON-NLS-2$ // inverted question mark + badEntities.put( + "À", + "\u00C0"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with grave + badEntities.put( + "Á", + "\u00C1"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with acute + badEntities.put( + "Â", + "\u00C2"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with circumflex + badEntities.put( + "Ã", + "\u00C3"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with tilde + badEntities.put( + "Ä", + "\u00C4"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with diaeresis + badEntities.put( + "Å", + "\u00C5"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with ring above + badEntities.put( + "Æ", "\u00C6"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter AE + badEntities.put( + "Ç", + "\u00C7"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter C with cedilla + badEntities.put( + "È", + "\u00C8"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter E with grave + badEntities.put( + "É", + "\u00C9"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter E with acute + badEntities.put( + "Ê", + "\u00CA"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter E with circumflex + badEntities.put( + "Ë", + "\u00CB"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter E with diaeresis + badEntities.put( + "Ì", + "\u00CC"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter I with grave + badEntities.put( + "Í", + "\u00CD"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter I with acute + badEntities.put( + "Î", + "\u00CE"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter I with circumflex + badEntities.put( + "Ï", + "\u00CF"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter I with diaeresis + badEntities.put("Ð", "\u00D0"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter ETH + badEntities.put( + "Ñ", + "\u00D1"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter N with tilde + badEntities.put( + "Ò", + "\u00D2"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with grave + badEntities.put( + "Ó", + "\u00D3"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with acute + badEntities.put( + "Ô", + "\u00D4"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with circumflex + badEntities.put( + "Õ", + "\u00D5"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with tilde + badEntities.put( + "Ö", + "\u00D6"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with diaeresis + badEntities.put("×", "\u00D7"); // $NON-NLS-1$ //$NON-NLS-2$ // multiplication sign + badEntities.put( + "Ø", + "\u00D8"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with stroke + badEntities.put( + "Ù", + "\u00D9"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter U with grave + badEntities.put( + "Ú", + "\u00DA"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter U with acute + badEntities.put( + "Û", + "\u00DB"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter U with circumflex + badEntities.put( + "Ü", + "\u00DC"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter U with diaeresis + badEntities.put( + "Ý", + "\u00DD"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter Y with acute + badEntities.put( + "Þ", "\u00DE"); // $NON-NLS-1$ //$NON-NLS-2$ // latin capital letter THORN + badEntities.put( + "ß", "\u00DF"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter sharp s + badEntities.put( + "à", + "\u00E0"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with grave + badEntities.put( + "á", + "\u00E1"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with acute + badEntities.put( + "â", + "\u00E2"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with circumflex + badEntities.put( + "ã", + "\u00E3"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with tilde + badEntities.put( + "ä", + "\u00E4"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with diaeresis + badEntities.put( + "å", + "\u00E5"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with ring above + badEntities.put("æ", "\u00E6"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter ae + badEntities.put( + "ç", + "\u00E7"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter c with cedilla + badEntities.put( + "è", + "\u00E8"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter e with grave + badEntities.put( + "é", + "\u00E9"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter e with acute + badEntities.put( + "ê", + "\u00EA"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter e with circumflex + badEntities.put( + "ë", + "\u00EB"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter e with diaeresis + badEntities.put( + "ì", + "\u00EC"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter i with grave + badEntities.put( + "í", + "\u00ED"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter i with acute + badEntities.put( + "î", + "\u00EE"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter i with circumflex + badEntities.put( + "ï", + "\u00EF"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter i with diaeresis + badEntities.put("ð", "\u00F0"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter eth + badEntities.put( + "ñ", + "\u00F1"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter n with tilde + badEntities.put( + "ò", + "\u00F2"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with grave + badEntities.put( + "ó", + "\u00F3"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with acute + badEntities.put( + "ô", + "\u00F4"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with circumflex + badEntities.put( + "õ", + "\u00F5"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with tilde + badEntities.put( + "ö", + "\u00F6"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with diaeresis + badEntities.put("÷", "\u00F7"); // $NON-NLS-1$ //$NON-NLS-2$ // division sign + badEntities.put( + "ø", + "\u00F8"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with stroke + badEntities.put( + "ù", + "\u00F9"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter u with grave + badEntities.put( + "ú", + "\u00FA"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter u with acute + badEntities.put( + "û", + "\u00FB"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter u with circumflex + badEntities.put( + "ü", + "\u00FC"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter u with diaeresis + badEntities.put( + "ý", + "\u00FD"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter y with acute + badEntities.put( + "þ", "\u00FE"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter thorn + badEntities.put( + "ÿ", + "\u00FF"); // $NON-NLS-1$ //$NON-NLS-2$ // latin small letter y with diaeresis + } - /** - * For each entity in the input that is not allowed in XML, replace the entity with its unicode equivalent or remove it. For each - * instance of a bare {@literal &}, replace it with {@literal &
- * } XML only allows 4 entities: {@literal &amp;}, {@literal &quot;}, {@literal &lt;} and {@literal &gt;}. - * - * @param broken - * the string to handle entities - * @return the string with entities appropriately fixed up - */ - static public String cleanAllEntities(final String broken) { - if (broken == null) { return null; } + /** + * For each entity in the input that is not allowed in XML, replace the entity with its unicode + * equivalent or remove it. For each instance of a bare {@literal &}, replace it with {@literal + * &
} XML only allows 4 entities: {@literal &amp;}, {@literal &quot;}, + * {@literal &lt;} and {@literal &gt;}. + * + * @param broken the string to handle entities + * @return the string with entities appropriately fixed up + */ + public static String cleanAllEntities(final String broken) { + if (broken == null) { + return null; + } - String working = invalidControlCharPattern.matcher(broken).replaceAll(""); - working = invalidCharacterPattern.matcher(working).replaceAll(""); + String working = invalidControlCharPattern.matcher(broken).replaceAll(""); + working = invalidCharacterPattern.matcher(working).replaceAll(""); - int cleanfrom = 0; + int cleanfrom = 0; - while (true) { - int amp = working.indexOf('&', cleanfrom); - // If there are no more amps then we are done - if (amp == -1) { - break; - } - // Skip references of the kind &#ddd; - if (validCharacterEntityPattern.matcher(working.substring(amp)).find()) { - cleanfrom = working.indexOf(';', amp) + 1; - continue; - } - int i = amp + 1; - while (true) { - // if we are at the end of the string then just escape the '&'; - if (i >= working.length()) { return working.substring(0, amp) + "&" + working.substring(amp + 1); //$NON-NLS-1$ - } - // if we have come to a ; then we have an entity - // If it is something that xml can't handle then replace it. - final char c = working.charAt(i); - if (c == ';') { - final String entity = working.substring(amp, i + 1); - final String replace = handleEntity(entity); - working = working.substring(0, amp) + replace + working.substring(i + 1); - break; - } - // Did we end an entity without finding a closing ; - // Then treat it as an '&' that needs to be replaced with & - if (!Character.isLetterOrDigit(c)) { - working = working.substring(0, amp) + "&" + working.substring(amp + 1); //$NON-NLS-1$ - amp = i + 4; // account for the 4 extra characters - break; - } - i++; - } - cleanfrom = amp + 1; - } + while (true) { + int amp = working.indexOf('&', cleanfrom); + // If there are no more amps then we are done + if (amp == -1) { + break; + } + // Skip references of the kind &#ddd; + if (validCharacterEntityPattern.matcher(working.substring(amp)).find()) { + cleanfrom = working.indexOf(';', amp) + 1; + continue; + } + int i = amp + 1; + while (true) { + // if we are at the end of the string then just escape the '&'; + if (i >= working.length()) { + return working.substring(0, amp) + + "&" + + working.substring(amp + 1); // $NON-NLS-1$ + } + // if we have come to a ; then we have an entity + // If it is something that xml can't handle then replace it. + final char c = working.charAt(i); + if (c == ';') { + final String entity = working.substring(amp, i + 1); + final String replace = handleEntity(entity); + working = working.substring(0, amp) + replace + working.substring(i + 1); + break; + } + // Did we end an entity without finding a closing ; + // Then treat it as an '&' that needs to be replaced with & + if (!Character.isLetterOrDigit(c)) { + working = + working.substring(0, amp) + + "&" + + working.substring(amp + 1); // $NON-NLS-1$ + amp = i + 4; // account for the 4 extra characters + break; + } + i++; + } + cleanfrom = amp + 1; + } - if (Pattern.compile("<<").matcher(working).find()) { - working = working.replaceAll("<<", "<<"); - } + if (Pattern.compile("<<").matcher(working).find()) { + working = working.replaceAll("<<", "<<"); + } - if (Pattern.compile(">>").matcher(working).find()) { - working = working.replaceAll(">>", ">>"); - } + if (Pattern.compile(">>").matcher(working).find()) { + working = working.replaceAll(">>", ">>"); + } - return working; - } + return working; + } - /** - * Replace entity with its unicode equivalent, if it is not a valid XML entity. Otherwise strip it out. XML only allows 4 entities: - * &amp;, &quot;, &lt; and &gt;. - * - * @param entity - * the entity to be replaced - * @return the substitution for the entity, either itself, the unicode equivalent or an empty string. - */ - private static String handleEntity(final String entity) { - if (goodEntities.contains(entity)) { return entity; } + /** + * Replace entity with its unicode equivalent, if it is not a valid XML entity. Otherwise strip + * it out. XML only allows 4 entities: &amp;, &quot;, &lt; and &gt;. + * + * @param entity the entity to be replaced + * @return the substitution for the entity, either itself, the unicode equivalent or an empty + * string. + */ + private static String handleEntity(final String entity) { + if (goodEntities.contains(entity)) { + return entity; + } - final String replace = badEntities.get(entity); - if (replace != null) { return replace; } + final String replace = badEntities.get(entity); + if (replace != null) { + return replace; + } - return replace != null ? replace : ""; - } + return replace != null ? replace : ""; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/LicenseComparator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/LicenseComparator.java index 9d0e82aca9..126a97e399 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/LicenseComparator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/LicenseComparator.java @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.migration.actions; import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier; - import java.util.Comparator; public class LicenseComparator implements Comparator { @@ -45,5 +44,4 @@ public class LicenseComparator implements Comparator { // Else (but unlikely), lexicographical ordering will do. return lClass.compareTo(rClass); } - } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/MigrateActionSet.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/MigrateActionSet.java index 487fac359c..680f7759c1 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/MigrateActionSet.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/MigrateActionSet.java @@ -6,6 +6,11 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import java.io.File; +import java.io.FileOutputStream; +import java.io.OutputStream; +import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; @@ -17,12 +22,6 @@ import org.apache.hadoop.tools.DistCp; import org.apache.hadoop.tools.DistCpOptions; import org.apache.hadoop.util.ToolRunner; -import java.io.File; -import java.io.FileOutputStream; -import java.io.OutputStream; -import java.util.*; -import java.util.stream.Collectors; - public class MigrateActionSet { private static final Log log = LogFactory.getLog(MigrateActionSet.class); @@ -34,9 +33,11 @@ public class MigrateActionSet { private static Boolean DEFAULT_TRANSFORM_ONLY = false; public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(MigrateActionSet.class.getResourceAsStream( - "/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + MigrateActionSet.class.getResourceAsStream( + "/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json"))); parser.parseArgument(args); new MigrateActionSet().run(parser); @@ -47,7 +48,7 @@ public class MigrateActionSet { final String isLookupUrl = parser.get("isLookupUrl"); final String sourceNN = parser.get("sourceNameNode"); final String targetNN = parser.get("targetNameNode"); - final String workDir = parser.get("workingDirectory"); + final String workDir = parser.get("workingDirectory"); final Integer distcp_num_maps = Integer.parseInt(parser.get("distcp_num_maps")); final String distcp_memory_mb = parser.get("distcp_memory_mb"); @@ -63,10 +64,12 @@ public class MigrateActionSet { ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); - Configuration conf = getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps); + Configuration conf = + getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps); FileSystem targetFS = FileSystem.get(conf); - Configuration sourceConf = getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps); + Configuration sourceConf = + getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps); sourceConf.set(FileSystem.FS_DEFAULT_NAME_KEY, sourceNN); FileSystem sourceFS = FileSystem.get(sourceConf); @@ -75,14 +78,20 @@ public class MigrateActionSet { List targetPaths = new ArrayList<>(); final List sourcePaths = getSourcePaths(sourceNN, isLookUp); - log.info(String.format("paths to process:\n%s", sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n")))); - for(Path source : sourcePaths) { + log.info( + String.format( + "paths to process:\n%s", + sourcePaths.stream() + .map(p -> p.toString()) + .collect(Collectors.joining("\n")))); + for (Path source : sourcePaths) { if (!sourceFS.exists(source)) { log.warn(String.format("skipping unexisting path: %s", source)); } else { - LinkedList pathQ = Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath())); + LinkedList pathQ = + Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath())); final String rawSet = pathQ.pollLast(); log.info(String.format("got RAWSET: %s", rawSet)); @@ -91,7 +100,14 @@ public class MigrateActionSet { final String actionSetDirectory = pathQ.pollLast(); - final Path targetPath = new Path(targetNN + workDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawSet); + final Path targetPath = + new Path( + targetNN + + workDir + + SEPARATOR + + actionSetDirectory + + SEPARATOR + + rawSet); log.info(String.format("using TARGET PATH: %s", targetPath)); @@ -99,7 +115,13 @@ public class MigrateActionSet { if (targetFS.exists(targetPath)) { targetFS.delete(targetPath, true); } - runDistcp(distcp_num_maps, distcp_memory_mb, distcp_task_timeout, conf, source, targetPath); + runDistcp( + distcp_num_maps, + distcp_memory_mb, + distcp_task_timeout, + conf, + source, + targetPath); } targetPaths.add(targetPath); @@ -107,19 +129,25 @@ public class MigrateActionSet { } } - props.setProperty(TARGET_PATHS, targetPaths - .stream() - .map(p -> p.toString()) - .collect(Collectors.joining(","))); + props.setProperty( + TARGET_PATHS, + targetPaths.stream().map(p -> p.toString()).collect(Collectors.joining(","))); File file = new File(System.getProperty("oozie.action.output.properties")); - try(OutputStream os = new FileOutputStream(file)) { + try (OutputStream os = new FileOutputStream(file)) { props.store(os, ""); } System.out.println(file.getAbsolutePath()); } - private void runDistcp(Integer distcp_num_maps, String distcp_memory_mb, String distcp_task_timeout, Configuration conf, Path source, Path targetPath) throws Exception { + private void runDistcp( + Integer distcp_num_maps, + String distcp_memory_mb, + String distcp_task_timeout, + Configuration conf, + Path source, + Path targetPath) + throws Exception { final DistCpOptions op = new DistCpOptions(source, targetPath); op.setMaxMaps(distcp_num_maps); @@ -127,20 +155,25 @@ public class MigrateActionSet { op.preserve(DistCpOptions.FileAttribute.REPLICATION); op.preserve(DistCpOptions.FileAttribute.CHECKSUMTYPE); - int res = ToolRunner.run(new DistCp(conf, op), new String[]{ - "-Dmapred.task.timeout=" + distcp_task_timeout, - "-Dmapreduce.map.memory.mb=" + distcp_memory_mb, - "-pb", - "-m " + distcp_num_maps, - source.toString(), - targetPath.toString()}); + int res = + ToolRunner.run( + new DistCp(conf, op), + new String[] { + "-Dmapred.task.timeout=" + distcp_task_timeout, + "-Dmapreduce.map.memory.mb=" + distcp_memory_mb, + "-pb", + "-m " + distcp_num_maps, + source.toString(), + targetPath.toString() + }); if (res != 0) { throw new RuntimeException(String.format("distcp exited with code %s", res)); } } - private Configuration getConfiguration(String distcp_task_timeout, String distcp_memory_mb, Integer distcp_num_maps) { + private Configuration getConfiguration( + String distcp_task_timeout, String distcp_memory_mb, Integer distcp_num_maps) { final Configuration conf = new Configuration(); conf.set("dfs.webhdfs.socket.connect-timeout", distcp_task_timeout); conf.set("dfs.webhdfs.socket.read-timeout", distcp_task_timeout); @@ -151,20 +184,20 @@ public class MigrateActionSet { return conf; } - private List getSourcePaths(String sourceNN, ISLookUpService isLookUp) throws ISLookUpException { - String XQUERY = "distinct-values(\n" + - "let $basePath := collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()\n" + - "for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') \n" + - "let $setDir := $x//SET/@directory/string()\n" + - "let $rawSet := $x//RAW_SETS/LATEST/@id/string()\n" + - "return concat($basePath, '/', $setDir, '/', $rawSet))"; + private List getSourcePaths(String sourceNN, ISLookUpService isLookUp) + throws ISLookUpException { + String XQUERY = + "distinct-values(\n" + + "let $basePath := collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()\n" + + "for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') \n" + + "let $setDir := $x//SET/@directory/string()\n" + + "let $rawSet := $x//RAW_SETS/LATEST/@id/string()\n" + + "return concat($basePath, '/', $setDir, '/', $rawSet))"; log.info(String.format("running xquery:\n%s", XQUERY)); - return isLookUp.quickSearchProfile(XQUERY) - .stream() + return isLookUp.quickSearchProfile(XQUERY).stream() .map(p -> sourceNN + p) .map(Path::new) .collect(Collectors.toList()); } - } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java index a7e70ee813..b5d027c03a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java @@ -4,12 +4,11 @@ import com.google.common.collect.Lists; import com.googlecode.protobuf.format.JsonFormat; import eu.dnetlib.data.proto.*; import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.commons.lang3.StringUtils; - import java.io.Serializable; import java.util.List; import java.util.Optional; import java.util.stream.Collectors; +import org.apache.commons.lang3.StringUtils; public class ProtoConverter implements Serializable { @@ -42,10 +41,12 @@ public class ProtoConverter implements Serializable { rel.setRelType(r.getRelType().toString()); rel.setSubRelType(r.getSubRelType().toString()); rel.setRelClass(r.getRelClass()); - rel.setCollectedFrom(r.getCollectedfromCount() > 0 ? - r.getCollectedfromList().stream() - .map(kv -> mapKV(kv)) - .collect(Collectors.toList()) : null); + rel.setCollectedFrom( + r.getCollectedfromCount() > 0 + ? r.getCollectedfromList().stream() + .map(kv -> mapKV(kv)) + .collect(Collectors.toList()) + : null); return rel; } @@ -71,8 +72,7 @@ public class ProtoConverter implements Serializable { final ResultProtos.Result r = oaf.getEntity().getResult(); if (r.getInstanceCount() > 0) { - return r.getInstanceList() - .stream() + return r.getInstanceList().stream() .map(i -> convertInstance(i)) .collect(Collectors.toList()); } @@ -96,15 +96,16 @@ public class ProtoConverter implements Serializable { } private static Organization convertOrganization(OafProtos.Oaf oaf) { - final OrganizationProtos.Organization.Metadata m = oaf.getEntity().getOrganization().getMetadata(); + final OrganizationProtos.Organization.Metadata m = + oaf.getEntity().getOrganization().getMetadata(); final Organization org = setOaf(new Organization(), oaf); setEntity(org, oaf); org.setLegalshortname(mapStringField(m.getLegalshortname())); org.setLegalname(mapStringField(m.getLegalname())); - org.setAlternativeNames(m.getAlternativeNamesList(). - stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); + org.setAlternativeNames( + m.getAlternativeNamesList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); org.setWebsiteurl(mapStringField(m.getWebsiteurl())); org.setLogourl(mapStringField(m.getLogourl())); org.setEclegalbody(mapStringField(m.getEclegalbody())); @@ -112,7 +113,8 @@ public class ProtoConverter implements Serializable { org.setEcnonprofit(mapStringField(m.getEcnonprofit())); org.setEcresearchorganization(mapStringField(m.getEcresearchorganization())); org.setEchighereducation(mapStringField(m.getEchighereducation())); - org.setEcinternationalorganizationeurinterests(mapStringField(m.getEcinternationalorganizationeurinterests())); + org.setEcinternationalorganizationeurinterests( + mapStringField(m.getEcinternationalorganizationeurinterests())); org.setEcinternationalorganization(mapStringField(m.getEcinternationalorganization())); org.setEcenterprise(mapStringField(m.getEcenterprise())); org.setEcsmevalidated(mapStringField(m.getEcsmevalidated())); @@ -123,13 +125,14 @@ public class ProtoConverter implements Serializable { } private static Datasource convertDataSource(OafProtos.Oaf oaf) { - final DatasourceProtos.Datasource.Metadata m = oaf.getEntity().getDatasource().getMetadata(); + final DatasourceProtos.Datasource.Metadata m = + oaf.getEntity().getDatasource().getMetadata(); final Datasource datasource = setOaf(new Datasource(), oaf); setEntity(datasource, oaf); - datasource.setAccessinfopackage(m.getAccessinfopackageList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); + datasource.setAccessinfopackage( + m.getAccessinfopackageList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); datasource.setCertificates(mapStringField(m.getCertificates())); datasource.setCitationguidelineurl(mapStringField(m.getCitationguidelineurl())); datasource.setContactemail(mapStringField(m.getContactemail())); @@ -148,37 +151,36 @@ public class ProtoConverter implements Serializable { datasource.setLogourl(mapStringField(m.getLogourl())); datasource.setMissionstatementurl(mapStringField(m.getMissionstatementurl())); datasource.setNamespaceprefix(mapStringField(m.getNamespaceprefix())); - datasource.setOdcontenttypes(m.getOdcontenttypesList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); - datasource.setOdlanguages(m.getOdlanguagesList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); + datasource.setOdcontenttypes( + m.getOdcontenttypesList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); + datasource.setOdlanguages( + m.getOdlanguagesList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); datasource.setOdnumberofitems(mapStringField(m.getOdnumberofitems())); datasource.setOdnumberofitemsdate(mapStringField(m.getOdnumberofitemsdate())); datasource.setOdpolicies(mapStringField(m.getOdpolicies())); datasource.setOfficialname(mapStringField(m.getOfficialname())); datasource.setOpenairecompatibility(mapQualifier(m.getOpenairecompatibility())); datasource.setPidsystems(mapStringField(m.getPidsystems())); - datasource.setPolicies(m.getPoliciesList() - .stream() - .map(ProtoConverter::mapKV) - .collect(Collectors.toList())); + datasource.setPolicies( + m.getPoliciesList().stream() + .map(ProtoConverter::mapKV) + .collect(Collectors.toList())); datasource.setQualitymanagementkind(mapStringField(m.getQualitymanagementkind())); datasource.setReleaseenddate(mapStringField(m.getReleaseenddate())); datasource.setServiceprovider(mapBoolField(m.getServiceprovider())); datasource.setReleasestartdate(mapStringField(m.getReleasestartdate())); - datasource.setSubjects(m.getSubjectsList() - .stream() - .map(ProtoConverter::mapStructuredProperty) - .collect(Collectors.toList())); + datasource.setSubjects( + m.getSubjectsList().stream() + .map(ProtoConverter::mapStructuredProperty) + .collect(Collectors.toList())); datasource.setVersioning(mapBoolField(m.getVersioning())); datasource.setWebsiteurl(mapStringField(m.getWebsiteurl())); datasource.setJournal(mapJournal(m.getJournal())); - return datasource; } @@ -204,14 +206,16 @@ public class ProtoConverter implements Serializable { project.setFundedamount(m.getFundedamount()); project.setTotalcost(m.getTotalcost()); project.setKeywords(mapStringField(m.getKeywords())); - project.setSubjects(m.getSubjectsList().stream() - .map(sp -> mapStructuredProperty(sp)) - .collect(Collectors.toList())); + project.setSubjects( + m.getSubjectsList().stream() + .map(sp -> mapStructuredProperty(sp)) + .collect(Collectors.toList())); project.setTitle(mapStringField(m.getTitle())); project.setWebsiteurl(mapStringField(m.getWebsiteurl())); - project.setFundingtree(m.getFundingtreeList().stream() - .map(f -> mapStringField(f)) - .collect(Collectors.toList())); + project.setFundingtree( + m.getFundingtreeList().stream() + .map(f -> mapStringField(f)) + .collect(Collectors.toList())); project.setJsonextrainfo(mapStringField(m.getJsonextrainfo())); project.setSummary(mapStringField(m.getSummary())); project.setOptional1(mapStringField(m.getOptional1())); @@ -242,14 +246,14 @@ public class ProtoConverter implements Serializable { setEntity(software, oaf); setResult(software, oaf); - software.setDocumentationUrl(m.getDocumentationUrlList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); - software.setLicense(m.getLicenseList() - .stream() - .map(ProtoConverter::mapStructuredProperty) - .collect(Collectors.toList())); + software.setDocumentationUrl( + m.getDocumentationUrlList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); + software.setLicense( + m.getLicenseList().stream() + .map(ProtoConverter::mapStructuredProperty) + .collect(Collectors.toList())); software.setCodeRepositoryUrl(mapStringField(m.getCodeRepositoryUrl())); software.setProgrammingLanguage(mapQualifier(m.getProgrammingLanguage())); return software; @@ -260,18 +264,18 @@ public class ProtoConverter implements Serializable { OtherResearchProduct otherResearchProducts = setOaf(new OtherResearchProduct(), oaf); setEntity(otherResearchProducts, oaf); setResult(otherResearchProducts, oaf); - otherResearchProducts.setContactperson(m.getContactpersonList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); - otherResearchProducts.setContactgroup(m.getContactgroupList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); - otherResearchProducts.setTool(m.getToolList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); + otherResearchProducts.setContactperson( + m.getContactpersonList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); + otherResearchProducts.setContactgroup( + m.getContactgroupList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); + otherResearchProducts.setTool( + m.getToolList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); return otherResearchProducts; } @@ -298,12 +302,11 @@ public class ProtoConverter implements Serializable { dataset.setVersion(mapStringField(m.getVersion())); dataset.setLastmetadataupdate(mapStringField(m.getLastmetadataupdate())); dataset.setMetadataversionnumber(mapStringField(m.getMetadataversionnumber())); - dataset.setGeolocation(m.getGeolocationList() - .stream() - .map(ProtoConverter::mapGeolocation) - .collect(Collectors.toList())); + dataset.setGeolocation( + m.getGeolocationList().stream() + .map(ProtoConverter::mapGeolocation) + .collect(Collectors.toList())); return dataset; - } public static T setOaf(T oaf, OafProtos.Oaf o) { @@ -313,100 +316,103 @@ public class ProtoConverter implements Serializable { } public static T setEntity(T entity, OafProtos.Oaf oaf) { - //setting Entity fields + // setting Entity fields final OafProtos.OafEntity e = oaf.getEntity(); entity.setId(e.getId()); entity.setOriginalId(e.getOriginalIdList()); - entity.setCollectedfrom(e.getCollectedfromList() - .stream() - .map(ProtoConverter::mapKV) - .collect(Collectors.toList())); - entity.setPid(e.getPidList().stream() - .map(ProtoConverter::mapStructuredProperty) - .collect(Collectors.toList())); + entity.setCollectedfrom( + e.getCollectedfromList().stream() + .map(ProtoConverter::mapKV) + .collect(Collectors.toList())); + entity.setPid( + e.getPidList().stream() + .map(ProtoConverter::mapStructuredProperty) + .collect(Collectors.toList())); entity.setDateofcollection(e.getDateofcollection()); entity.setDateoftransformation(e.getDateoftransformation()); - entity.setExtraInfo(e.getExtraInfoList() - .stream() - .map(ProtoConverter::mapExtraInfo) - .collect(Collectors.toList())); + entity.setExtraInfo( + e.getExtraInfoList().stream() + .map(ProtoConverter::mapExtraInfo) + .collect(Collectors.toList())); return entity; } public static T setResult(T entity, OafProtos.Oaf oaf) { - //setting Entity fields + // setting Entity fields final ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata(); - entity.setAuthor(m.getAuthorList() - .stream() - .map(ProtoConverter::mapAuthor) - .collect(Collectors.toList())); + entity.setAuthor( + m.getAuthorList().stream() + .map(ProtoConverter::mapAuthor) + .collect(Collectors.toList())); entity.setResulttype(mapQualifier(m.getResulttype())); entity.setLanguage(mapQualifier(m.getLanguage())); - entity.setCountry(m.getCountryList() - .stream() - .map(ProtoConverter::mapQualifierAsCountry) - .collect(Collectors.toList())); - entity.setSubject(m.getSubjectList() - .stream() - .map(ProtoConverter::mapStructuredProperty) - .collect(Collectors.toList())); - entity.setTitle(m.getTitleList() - .stream() - .map(ProtoConverter::mapStructuredProperty) - .collect(Collectors.toList())); - entity.setRelevantdate(m.getRelevantdateList() - .stream() - .map(ProtoConverter::mapStructuredProperty) - .collect(Collectors.toList())); - entity.setDescription(m.getDescriptionList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); + entity.setCountry( + m.getCountryList().stream() + .map(ProtoConverter::mapQualifierAsCountry) + .collect(Collectors.toList())); + entity.setSubject( + m.getSubjectList().stream() + .map(ProtoConverter::mapStructuredProperty) + .collect(Collectors.toList())); + entity.setTitle( + m.getTitleList().stream() + .map(ProtoConverter::mapStructuredProperty) + .collect(Collectors.toList())); + entity.setRelevantdate( + m.getRelevantdateList().stream() + .map(ProtoConverter::mapStructuredProperty) + .collect(Collectors.toList())); + entity.setDescription( + m.getDescriptionList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); entity.setDateofacceptance(mapStringField(m.getDateofacceptance())); entity.setPublisher(mapStringField(m.getPublisher())); entity.setEmbargoenddate(mapStringField(m.getEmbargoenddate())); - entity.setSource(m.getSourceList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); - entity.setFulltext(m.getFulltextList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); - entity.setFormat(m.getFormatList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); - entity.setContributor(m.getContributorList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); + entity.setSource( + m.getSourceList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); + entity.setFulltext( + m.getFulltextList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); + entity.setFormat( + m.getFormatList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); + entity.setContributor( + m.getContributorList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); entity.setResourcetype(mapQualifier(m.getResourcetype())); - entity.setCoverage(m.getCoverageList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); - entity.setContext(m.getContextList() - .stream() - .map(ProtoConverter::mapContext) - .collect(Collectors.toList())); + entity.setCoverage( + m.getCoverageList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); + entity.setContext( + m.getContextList().stream() + .map(ProtoConverter::mapContext) + .collect(Collectors.toList())); - entity.setBestaccessright(getBestAccessRights(oaf.getEntity().getResult().getInstanceList())); + entity.setBestaccessright( + getBestAccessRights(oaf.getEntity().getResult().getInstanceList())); return entity; } private static Qualifier getBestAccessRights(List instanceList) { if (instanceList != null) { - final Optional min = instanceList.stream() - .map(i -> i.getAccessright()).min(new LicenseComparator()); + final Optional min = + instanceList.stream().map(i -> i.getAccessright()).min(new LicenseComparator()); final Qualifier rights = min.isPresent() ? mapQualifier(min.get()) : new Qualifier(); if (StringUtils.isBlank(rights.getClassid())) { rights.setClassid(UNKNOWN); } - if (StringUtils.isBlank(rights.getClassname()) || UNKNOWN.equalsIgnoreCase(rights.getClassname())) { + if (StringUtils.isBlank(rights.getClassname()) + || UNKNOWN.equalsIgnoreCase(rights.getClassname())) { rights.setClassname(NOT_AVAILABLE); } if (StringUtils.isBlank(rights.getSchemeid())) { @@ -425,14 +431,13 @@ public class ProtoConverter implements Serializable { final Context entity = new Context(); entity.setId(context.getId()); - entity.setDataInfo(context.getDataInfoList() - .stream() - .map(ProtoConverter::mapDataInfo) - .collect(Collectors.toList())); + entity.setDataInfo( + context.getDataInfoList().stream() + .map(ProtoConverter::mapDataInfo) + .collect(Collectors.toList())); return entity; } - public static KeyValue mapKV(FieldTypeProtos.KeyValue kv) { final KeyValue keyValue = new KeyValue(); keyValue.setKey(kv.getKey()); @@ -495,7 +500,8 @@ public class ProtoConverter implements Serializable { return entity; } - public static OriginDescription mapOriginalDescription(FieldTypeProtos.OAIProvenance.OriginDescription originDescription) { + public static OriginDescription mapOriginalDescription( + FieldTypeProtos.OAIProvenance.OriginDescription originDescription) { final OriginDescription originDescriptionResult = new OriginDescription(); originDescriptionResult.setHarvestDate(originDescription.getHarvestDate()); originDescriptionResult.setAltered(originDescription.getAltered()); @@ -550,24 +556,24 @@ public class ProtoConverter implements Serializable { entity.setName(author.getName()); entity.setSurname(author.getSurname()); entity.setRank(author.getRank()); - entity.setPid(author.getPidList() - .stream() - .map(kv -> { - final StructuredProperty sp = new StructuredProperty(); - sp.setValue(kv.getValue()); - final Qualifier q = new Qualifier(); - q.setClassid(kv.getKey()); - q.setClassname(kv.getKey()); - sp.setQualifier(q); - return sp; - }) - .collect(Collectors.toList())); - entity.setAffiliation(author.getAffiliationList() - .stream() - .map(ProtoConverter::mapStringField) - .collect(Collectors.toList())); + entity.setPid( + author.getPidList().stream() + .map( + kv -> { + final StructuredProperty sp = new StructuredProperty(); + sp.setValue(kv.getValue()); + final Qualifier q = new Qualifier(); + q.setClassid(kv.getKey()); + q.setClassname(kv.getKey()); + sp.setQualifier(q); + return sp; + }) + .collect(Collectors.toList())); + entity.setAffiliation( + author.getAffiliationList().stream() + .map(ProtoConverter::mapStringField) + .collect(Collectors.toList())); return entity; - } public static GeoLocation mapGeolocation(ResultProtos.Result.GeoLocation geoLocation) { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/TransformActions.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/TransformActions.java index 65dec7b7f6..81c2e77059 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/TransformActions.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/TransformActions.java @@ -5,14 +5,17 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.base.Splitter; import com.google.common.collect.Lists; import com.google.protobuf.InvalidProtocolBufferException; -import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.data.proto.OafProtos; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - +import java.io.IOException; +import java.io.Serializable; +import java.util.LinkedList; +import java.util.Objects; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; @@ -21,16 +24,9 @@ import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.GzipCodec; -import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.sql.SparkSession; -import scala.Tuple2; - -import java.io.IOException; -import java.io.Serializable; -import java.util.LinkedList; -import java.util.Objects; public class TransformActions implements Serializable { @@ -38,9 +34,11 @@ public class TransformActions implements Serializable { private static final String SEPARATOR = "/"; public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(MigrateActionSet.class.getResourceAsStream( - "/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + MigrateActionSet.class.getResourceAsStream( + "/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json"))); parser.parseArgument(args); new TransformActions().run(parser); @@ -51,7 +49,7 @@ public class TransformActions implements Serializable { final String isLookupUrl = parser.get("isLookupUrl"); log.info("isLookupUrl: " + isLookupUrl); - final String inputPaths = parser.get("inputPaths"); + final String inputPaths = parser.get("inputPaths"); if (StringUtils.isBlank(inputPaths)) { throw new RuntimeException("empty inputPaths"); @@ -60,18 +58,25 @@ public class TransformActions implements Serializable { final String targetBaseDir = getTargetBaseDir(isLookupUrl); - try(SparkSession spark = getSparkSession(parser)) { + try (SparkSession spark = getSparkSession(parser)) { final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration()); - for(String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) { + for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) { - LinkedList pathQ = Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath)); + LinkedList pathQ = + Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath)); final String rawset = pathQ.pollLast(); final String actionSetDirectory = pathQ.pollLast(); - final Path targetDirectory = new Path(targetBaseDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawset); + final Path targetDirectory = + new Path( + targetBaseDir + + SEPARATOR + + actionSetDirectory + + SEPARATOR + + rawset); if (fs.exists(targetDirectory)) { log.info(String.format("found target directory '%s", targetDirectory)); @@ -79,20 +84,27 @@ public class TransformActions implements Serializable { log.info(String.format("deleted target directory '%s", targetDirectory)); } - log.info(String.format("transforming actions from '%s' to '%s'", sourcePath, targetDirectory)); + log.info( + String.format( + "transforming actions from '%s' to '%s'", + sourcePath, targetDirectory)); sc.sequenceFile(sourcePath, Text.class, Text.class) - .map(a -> eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON(a._2().toString())) - .map(a -> doTransform(a)) - .filter(Objects::isNull) - .filter(a -> a.getPayload() == null) - .map(a -> new ObjectMapper().writeValueAsString(a)) - .saveAsTextFile(targetDirectory.toString(), GzipCodec.class); + .map( + a -> + eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON( + a._2().toString())) + .map(a -> doTransform(a)) + .filter(Objects::isNull) + .filter(a -> a.getPayload() == null) + .map(a -> new ObjectMapper().writeValueAsString(a)) + .saveAsTextFile(targetDirectory.toString(), GzipCodec.class); } } } - private Text transformAction(eu.dnetlib.actionmanager.actions.AtomicAction aa) throws InvalidProtocolBufferException, JsonProcessingException { + private Text transformAction(eu.dnetlib.actionmanager.actions.AtomicAction aa) + throws InvalidProtocolBufferException, JsonProcessingException { final Text out = new Text(); final ObjectMapper mapper = new ObjectMapper(); if (aa.getTargetValue() != null && aa.getTargetValue().length > 0) { @@ -135,7 +147,8 @@ public class TransformActions implements Serializable { return new AtomicAction<>(Relation.class, rel); } - private AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa) throws InvalidProtocolBufferException { + private AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa) + throws InvalidProtocolBufferException { final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue()); final Oaf oaf = ProtoConverter.convert(proto_oaf); switch (proto_oaf.getKind()) { @@ -148,14 +161,21 @@ public class TransformActions implements Serializable { case project: return new AtomicAction<>(Project.class, (Project) oaf); case result: - final String resulttypeid = proto_oaf.getEntity().getResult().getMetadata().getResulttype().getClassid(); + final String resulttypeid = + proto_oaf + .getEntity() + .getResult() + .getMetadata() + .getResulttype() + .getClassid(); switch (resulttypeid) { case "publication": return new AtomicAction<>(Publication.class, (Publication) oaf); case "software": return new AtomicAction<>(Software.class, (Software) oaf); case "other": - return new AtomicAction<>(OtherResearchProduct.class, (OtherResearchProduct) oaf); + return new AtomicAction<>( + OtherResearchProduct.class, (OtherResearchProduct) oaf); case "dataset": return new AtomicAction<>(Dataset.class, (Dataset) oaf); default: @@ -163,7 +183,8 @@ public class TransformActions implements Serializable { return new AtomicAction<>(Result.class, (Result) oaf); } default: - throw new IllegalArgumentException("invalid entity type: " + proto_oaf.getEntity().getType()); + throw new IllegalArgumentException( + "invalid entity type: " + proto_oaf.getEntity().getType()); } case relation: return new AtomicAction<>(Relation.class, (Relation) oaf); @@ -174,15 +195,15 @@ public class TransformActions implements Serializable { private String getTargetBaseDir(String isLookupUrl) throws ISLookUpException { ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); - String XQUERY = "collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()"; + String XQUERY = + "collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()"; return isLookUp.getResourceProfileByQuery(XQUERY); } private static SparkSession getSparkSession(ArgumentApplicationParser parser) { SparkConf conf = new SparkConf(); - return SparkSession - .builder() + return SparkSession.builder() .appName(TransformActions.class.getSimpleName()) .master(parser.get("master")) .config(conf) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformFunction.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformFunction.java index 5cd78491b8..9e07a2d47a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformFunction.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformFunction.java @@ -3,30 +3,33 @@ package eu.dnetlib.dhp.transformation; import eu.dnetlib.dhp.model.mdstore.MetadataRecord; import eu.dnetlib.dhp.transformation.functions.Cleaner; import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary; +import java.io.ByteArrayInputStream; +import java.io.StringWriter; +import java.util.Map; +import javax.xml.transform.stream.StreamSource; import net.sf.saxon.s9api.*; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.util.LongAccumulator; -import javax.xml.transform.stream.StreamSource; -import java.io.ByteArrayInputStream; -import java.io.StringWriter; -import java.util.Map; - public class TransformFunction implements MapFunction { - private final LongAccumulator totalItems; private final LongAccumulator errorItems; private final LongAccumulator transformedItems; private final String transformationRule; private final Cleaner cleanFunction; - private final long dateOfTransformation; - - public TransformFunction(LongAccumulator totalItems, LongAccumulator errorItems, LongAccumulator transformedItems, final String transformationRule, long dateOfTransformation, final Map vocabularies) throws Exception { - this.totalItems= totalItems; + public TransformFunction( + LongAccumulator totalItems, + LongAccumulator errorItems, + LongAccumulator transformedItems, + final String transformationRule, + long dateOfTransformation, + final Map vocabularies) + throws Exception { + this.totalItems = totalItems; this.errorItems = errorItems; this.transformedItems = transformedItems; this.transformationRule = transformationRule; @@ -41,13 +44,21 @@ public class TransformFunction implements MapFunction encoder = Encoders.bean(MetadataRecord.class); - final Dataset mdstoreInput = spark.read().format("parquet").load(inputPath).as(encoder); + final Dataset mdstoreInput = + spark.read().format("parquet").load(inputPath).as(encoder); final LongAccumulator totalItems = spark.sparkContext().longAccumulator("TotalItems"); final LongAccumulator errorItems = spark.sparkContext().longAccumulator("errorItems"); - final LongAccumulator transformedItems = spark.sparkContext().longAccumulator("transformedItems"); + final LongAccumulator transformedItems = + spark.sparkContext().longAccumulator("transformedItems"); final Map vocabularies = new HashMap<>(); vocabularies.put("dnet:languages", VocabularyHelper.getVocabularyFromAPI("dnet:languages")); - final TransformFunction transformFunction = new TransformFunction(totalItems, errorItems, transformedItems, trasformationRule, dateOfCollection, vocabularies) ; + final TransformFunction transformFunction = + new TransformFunction( + totalItems, + errorItems, + transformedItems, + trasformationRule, + dateOfCollection, + vocabularies); mdstoreInput.map(transformFunction, encoder).write().format("parquet").save(outputPath); if (rabbitHost != null) { System.out.println("SEND FINAL REPORT"); final Map reportMap = new HashMap<>(); - reportMap.put("inputItem" , ""+ totalItems.value()); + reportMap.put("inputItem", "" + totalItems.value()); reportMap.put("invalidRecords", "" + errorItems.value()); reportMap.put("mdStoreSize", "" + transformedItems.value()); System.out.println(new Message(workflowId, "Transform", MessageType.REPORT, reportMap)); if (!test) { - final MessageManager manager = new MessageManager(rabbitHost, rabbitUser, rabbitPassword, false, false, null); - manager.sendMessage(new Message(workflowId, "Transform", MessageType.REPORT, reportMap), rabbitReportQueue, true, false); + final MessageManager manager = + new MessageManager( + rabbitHost, rabbitUser, rabbitPassword, false, false, null); + manager.sendMessage( + new Message(workflowId, "Transform", MessageType.REPORT, reportMap), + rabbitReportQueue, + true, + false); manager.close(); } } } - private static String extractXSLTFromTR(final String tr) throws DocumentException { SAXReader reader = new SAXReader(); Document document = reader.read(new ByteArrayInputStream(tr.getBytes())); Node node = document.selectSingleNode("//CODE/*[local-name()='stylesheet']"); return node.asXML(); } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/functions/Cleaner.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/functions/Cleaner.java index 47f33a342a..a15e05864f 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/functions/Cleaner.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/functions/Cleaner.java @@ -2,17 +2,14 @@ package eu.dnetlib.dhp.transformation.functions; import eu.dnetlib.dhp.transformation.vocabulary.Term; import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary; +import java.util.Map; +import java.util.Optional; import net.sf.saxon.s9api.*; import scala.Serializable; -import java.util.Map; -import java.util.Optional; - public class Cleaner implements ExtensionFunction, Serializable { - - private final Map vocabularies; - + private final Map vocabularies; public Cleaner(Map vocabularies) { this.vocabularies = vocabularies; @@ -30,20 +27,22 @@ public class Cleaner implements ExtensionFunction, Serializable { @Override public SequenceType[] getArgumentTypes() { - return new SequenceType[] - { - SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ONE), - SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ONE) - - }; + return new SequenceType[] { + SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ONE), + SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ONE) + }; } @Override public XdmValue call(XdmValue[] xdmValues) throws SaxonApiException { final String currentValue = xdmValues[0].itemAt(0).getStringValue(); - final String vocabularyName =xdmValues[1].itemAt(0).getStringValue(); - Optional cleanedValue = vocabularies.get(vocabularyName).getTerms().stream().filter(it -> it.getNativeName().equalsIgnoreCase(currentValue)).findAny(); + final String vocabularyName = xdmValues[1].itemAt(0).getStringValue(); + Optional cleanedValue = + vocabularies.get(vocabularyName).getTerms().stream() + .filter(it -> it.getNativeName().equalsIgnoreCase(currentValue)) + .findAny(); - return new XdmAtomicValue(cleanedValue.isPresent()?cleanedValue.get().getCode():currentValue); + return new XdmAtomicValue( + cleanedValue.isPresent() ? cleanedValue.get().getCode() : currentValue); } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/Term.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/Term.java index f93c2a1207..3f02098b19 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/Term.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/Term.java @@ -10,7 +10,6 @@ public class Term implements Serializable { private String code; private String synonyms; - public String getEnglishName() { return englishName; } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/Vocabulary.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/Vocabulary.java index 58e9cb95c8..1268924efb 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/Vocabulary.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/Vocabulary.java @@ -2,7 +2,6 @@ package eu.dnetlib.dhp.transformation.vocabulary; import java.io.Serializable; import java.util.List; -import java.util.Map; public class Vocabulary implements Serializable { @@ -51,7 +50,4 @@ public class Vocabulary implements Serializable { public void setTerms(List terms) { this.terms = terms; } - - - } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/VocabularyHelper.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/VocabularyHelper.java index b6ecf795c8..455777b31b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/VocabularyHelper.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/VocabularyHelper.java @@ -1,23 +1,21 @@ package eu.dnetlib.dhp.transformation.vocabulary; import com.fasterxml.jackson.databind.ObjectMapper; -import org.apache.commons.io.IOUtils; - import java.io.Serializable; import java.net.URL; import java.nio.charset.Charset; +import org.apache.commons.io.IOUtils; public class VocabularyHelper implements Serializable { - private final static String OPENAIRE_URL ="http://api.openaire.eu/vocabularies/%s.json"; + private static final String OPENAIRE_URL = "http://api.openaire.eu/vocabularies/%s.json"; public static Vocabulary getVocabularyFromAPI(final String vocabularyName) throws Exception { final URL url = new URL(String.format(OPENAIRE_URL, vocabularyName)); final String response = IOUtils.toString(url, Charset.defaultCharset()); - final ObjectMapper jsonMapper = new ObjectMapper(); - final Vocabulary vocabulary = jsonMapper.readValue(response, Vocabulary.class); + final ObjectMapper jsonMapper = new ObjectMapper(); + final Vocabulary vocabulary = jsonMapper.readValue(response, Vocabulary.class); return vocabulary; } - } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/CollectionJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/CollectionJobTest.java index fde928a8b6..88fdd4b9ca 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/CollectionJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/CollectionJobTest.java @@ -1,89 +1,106 @@ package eu.dnetlib.dhp.collection; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; -import org.junit.jupiter.api.AfterEach; - -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.model.mdstore.MetadataRecord; -import eu.dnetlib.dhp.model.mdstore.Provenance; - import static org.junit.jupiter.api.Assertions.*; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.model.mdstore.MetadataRecord; +import eu.dnetlib.dhp.model.mdstore.Provenance; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + public class CollectionJobTest { - private Path testDir; + private Path testDir; - @BeforeEach - public void setup() throws IOException { - testDir = Files.createTempDirectory("dhp-collection"); - } + @BeforeEach + public void setup() throws IOException { + testDir = Files.createTempDirectory("dhp-collection"); + } - @AfterEach - public void teadDown() throws IOException { - FileUtils.deleteDirectory(testDir.toFile()); - } + @AfterEach + public void teadDown() throws IOException { + FileUtils.deleteDirectory(testDir.toFile()); + } - @Test - public void tesCollection() throws Exception { - final Provenance provenance = new Provenance("pippo", "puppa", "ns_prefix"); - GenerateNativeStoreSparkJob.main(new String[] { - "-mt", "local", - "-w", "wid", - "-e", "XML", - "-d", "" + System.currentTimeMillis(), - "-p", new ObjectMapper().writeValueAsString(provenance), - "-x", "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", - "-i", this.getClass().getResource("/eu/dnetlib/dhp/collection/native.seq").toString(), - "-o", testDir.toString() + "/store", - "-t", "true", - "-ru", "", - "-rp", "", - "-rh", "", - "-ro", "", - "-rr", "" }); - System.out.println(new ObjectMapper().writeValueAsString(provenance)); - } + @Test + public void tesCollection() throws Exception { + final Provenance provenance = new Provenance("pippo", "puppa", "ns_prefix"); + GenerateNativeStoreSparkJob.main( + new String[] { + "-mt", "local", + "-w", "wid", + "-e", "XML", + "-d", "" + System.currentTimeMillis(), + "-p", new ObjectMapper().writeValueAsString(provenance), + "-x", + "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", + "-i", + this.getClass() + .getResource("/eu/dnetlib/dhp/collection/native.seq") + .toString(), + "-o", testDir.toString() + "/store", + "-t", "true", + "-ru", "", + "-rp", "", + "-rh", "", + "-ro", "", + "-rr", "" + }); + System.out.println(new ObjectMapper().writeValueAsString(provenance)); + } - @Test - public void testGenerationMetadataRecord() throws Exception { + @Test + public void testGenerationMetadataRecord() throws Exception { - final String xml = IOUtils.toString(this.getClass().getResourceAsStream("./record.xml")); + final String xml = IOUtils.toString(this.getClass().getResourceAsStream("./record.xml")); - final MetadataRecord record = GenerateNativeStoreSparkJob - .parseRecord(xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar", - "ns_prefix"), System.currentTimeMillis(), null, null); + final MetadataRecord record = + GenerateNativeStoreSparkJob.parseRecord( + xml, + "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", + "XML", + new Provenance("foo", "bar", "ns_prefix"), + System.currentTimeMillis(), + null, + null); - assert record != null; - System.out.println(record.getId()); - System.out.println(record.getOriginalId()); + assert record != null; + System.out.println(record.getId()); + System.out.println(record.getOriginalId()); + } - } - - @Test - public void TestEquals() throws IOException { - - final String xml = IOUtils.toString(this.getClass().getResourceAsStream("./record.xml")); - final MetadataRecord record = GenerateNativeStoreSparkJob - .parseRecord(xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar", - "ns_prefix"), System.currentTimeMillis(), null, null); - final MetadataRecord record1 = GenerateNativeStoreSparkJob - .parseRecord(xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar", - "ns_prefix"), System.currentTimeMillis(), null, null); - assert record != null; - record.setBody("ciao"); - assert record1 != null; - record1.setBody("mondo"); - assertEquals(record, record1); - - } + @Test + public void TestEquals() throws IOException { + final String xml = IOUtils.toString(this.getClass().getResourceAsStream("./record.xml")); + final MetadataRecord record = + GenerateNativeStoreSparkJob.parseRecord( + xml, + "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", + "XML", + new Provenance("foo", "bar", "ns_prefix"), + System.currentTimeMillis(), + null, + null); + final MetadataRecord record1 = + GenerateNativeStoreSparkJob.parseRecord( + xml, + "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", + "XML", + new Provenance("foo", "bar", "ns_prefix"), + System.currentTimeMillis(), + null, + null); + assert record != null; + record.setBody("ciao"); + assert record1 != null; + record1.setBody("mondo"); + assertEquals(record, record1); + } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java index 665e989d83..7957d90416 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java @@ -1,5 +1,8 @@ package eu.dnetlib.dhp.collector.worker; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.mockito.Mockito.*; + import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.collector.worker.model.ApiDescriptor; import eu.dnetlib.dhp.application.ArgumentApplicationParser; @@ -7,23 +10,18 @@ import eu.dnetlib.dhp.collection.worker.DnetCollectorWorker; import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory; import eu.dnetlib.message.Message; import eu.dnetlib.message.MessageManager; +import java.io.File; import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; -import java.io.File; - -import static org.junit.jupiter.api.Assertions.assertNotNull; -import static org.mockito.Mockito.*; - - public class DnetCollectorWorkerApplicationTests { - private ArgumentApplicationParser argumentParser = mock(ArgumentApplicationParser.class); private MessageManager messageManager = mock(MessageManager.class); private DnetCollectorWorker worker; + @BeforeEach public void setup() throws Exception { ObjectMapper mapper = new ObjectMapper(); @@ -35,25 +33,30 @@ public class DnetCollectorWorkerApplicationTests { when(argumentParser.get("workflowId")).thenReturn("sandro"); when(argumentParser.get("rabbitOngoingQueue")).thenReturn("sandro"); - when(messageManager.sendMessage(any(Message.class), anyString(), anyBoolean(),anyBoolean())).thenAnswer(a -> { - System.out.println("sent message: "+a.getArguments()[0]); - return true; - }); - when(messageManager.sendMessage(any(Message.class), anyString())).thenAnswer(a -> { - System.out.println("Called"); - return true; - }); - worker = new DnetCollectorWorker(new CollectorPluginFactory(), argumentParser, messageManager); + when(messageManager.sendMessage( + any(Message.class), anyString(), anyBoolean(), anyBoolean())) + .thenAnswer( + a -> { + System.out.println("sent message: " + a.getArguments()[0]); + return true; + }); + when(messageManager.sendMessage(any(Message.class), anyString())) + .thenAnswer( + a -> { + System.out.println("Called"); + return true; + }); + worker = + new DnetCollectorWorker( + new CollectorPluginFactory(), argumentParser, messageManager); } - @AfterEach - public void dropDown(){ + public void dropDown() { File f = new File("/tmp/file.seq"); f.delete(); } - @Test public void testFindPlugin() throws Exception { final CollectorPluginFactory collectorPluginEnumerator = new CollectorPluginFactory(); @@ -61,7 +64,6 @@ public class DnetCollectorWorkerApplicationTests { assertNotNull(collectorPluginEnumerator.getPluginByProtocol("OAI")); } - @Test public void testCollectionOAI() throws Exception { final ApiDescriptor api = new ApiDescriptor(); @@ -86,5 +88,4 @@ public class DnetCollectorWorkerApplicationTests { api.getParams().put("format", "oai_dc"); return api; } - } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index dfa0c37203..5bc9434cb1 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -1,10 +1,18 @@ package eu.dnetlib.dhp.transformation; +import static org.junit.jupiter.api.Assertions.assertNotNull; + import eu.dnetlib.dhp.model.mdstore.MetadataRecord; import eu.dnetlib.dhp.transformation.functions.Cleaner; import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary; import eu.dnetlib.dhp.transformation.vocabulary.VocabularyHelper; import eu.dnetlib.dhp.utils.DHPUtils; +import java.io.StringWriter; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; +import java.util.Map; +import javax.xml.transform.stream.StreamSource; import net.sf.saxon.s9api.*; import org.apache.commons.io.IOUtils; import org.apache.spark.util.LongAccumulator; @@ -18,20 +26,10 @@ import org.junit.jupiter.api.io.TempDir; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -import javax.xml.transform.stream.StreamSource; -import java.io.StringWriter; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; -import java.util.Map; - -import static org.junit.jupiter.api.Assertions.assertNotNull; - @ExtendWith(MockitoExtension.class) public class TransformationJobTest { - @Mock - private LongAccumulator accumulator; + @Mock private LongAccumulator accumulator; @Test public void testTransformSaxonHE() throws Exception { @@ -42,13 +40,24 @@ public class TransformationJobTest { Processor proc = new Processor(false); proc.registerExtensionFunction(cleanFunction); final XsltCompiler comp = proc.newXsltCompiler(); - XsltExecutable exp = comp.compile(new StreamSource(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/ext_simple.xsl"))); - XdmNode source = proc.newDocumentBuilder().build(new StreamSource(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input.xml"))); + XsltExecutable exp = + comp.compile( + new StreamSource( + this.getClass() + .getResourceAsStream( + "/eu/dnetlib/dhp/transform/ext_simple.xsl"))); + XdmNode source = + proc.newDocumentBuilder() + .build( + new StreamSource( + this.getClass() + .getResourceAsStream( + "/eu/dnetlib/dhp/transform/input.xml"))); XsltTransformer trans = exp.load(); trans.setInitialContextNode(source); final StringWriter output = new StringWriter(); Serializer out = proc.newSerializer(output); - out.setOutputProperty(Serializer.Property.METHOD,"xml"); + out.setOutputProperty(Serializer.Property.METHOD, "xml"); out.setOutputProperty(Serializer.Property.INDENT, "yes"); trans.setDestination(out); trans.transform(); @@ -58,27 +67,35 @@ public class TransformationJobTest { @DisplayName("Test TransformSparkJobNode.main") @Test public void transformTest(@TempDir Path testDir) throws Exception { - final String mdstore_input = this.getClass().getResource("/eu/dnetlib/dhp/transform/mdstorenative").getFile(); - final String mdstore_output = testDir.toString()+"/version"; - final String xslt = DHPUtils.compressString(IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/tr.xml"))); - TransformSparkJobNode.main(new String[]{ - "-mt", "local", - "-i", mdstore_input, - "-o", mdstore_output, - "-d", "1", - "-w", "1", - "-tr", xslt, - "-t", "true", - "-ru", "", - "-rp", "", - "-rh", "", - "-ro", "", - "-rr", ""}); + final String mdstore_input = + this.getClass().getResource("/eu/dnetlib/dhp/transform/mdstorenative").getFile(); + final String mdstore_output = testDir.toString() + "/version"; + final String xslt = + DHPUtils.compressString( + IOUtils.toString( + this.getClass() + .getResourceAsStream("/eu/dnetlib/dhp/transform/tr.xml"))); + TransformSparkJobNode.main( + new String[] { + "-mt", "local", + "-i", mdstore_input, + "-o", mdstore_output, + "-d", "1", + "-w", "1", + "-tr", xslt, + "-t", "true", + "-ru", "", + "-rp", "", + "-rh", "", + "-ro", "", + "-rr", "" + }); } @Test public void tryLoadFolderOnCP() throws Exception { - final String path = this.getClass().getResource("/eu/dnetlib/dhp/transform/mdstorenative").getFile(); + final String path = + this.getClass().getResource("/eu/dnetlib/dhp/transform/mdstorenative").getFile(); System.out.println("path = " + path); Path tempDirWithPrefix = Files.createTempDirectory("mdstore_output"); @@ -88,20 +105,25 @@ public class TransformationJobTest { Files.deleteIfExists(tempDirWithPrefix); } - @Test public void testTransformFunction() throws Exception { SAXReader reader = new SAXReader(); - Document document = reader.read(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/tr.xml")); + Document document = + reader.read( + this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/tr.xml")); Node node = document.selectSingleNode("//CODE/*[local-name()='stylesheet']"); final String xslt = node.asXML(); Map vocabularies = new HashMap<>(); vocabularies.put("dnet:languages", VocabularyHelper.getVocabularyFromAPI("dnet:languages")); - TransformFunction tf = new TransformFunction(accumulator, accumulator, accumulator, xslt, 1, vocabularies); + TransformFunction tf = + new TransformFunction(accumulator, accumulator, accumulator, xslt, 1, vocabularies); MetadataRecord record = new MetadataRecord(); - record.setBody(IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input.xml"))); + record.setBody( + IOUtils.toString( + this.getClass() + .getResourceAsStream("/eu/dnetlib/dhp/transform/input.xml"))); final MetadataRecord result = tf.call(record); assertNotNull(result.getBody()); @@ -109,17 +131,19 @@ public class TransformationJobTest { System.out.println(result.getBody()); } - @Test public void extractTr() throws Exception { - final String xmlTr = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/tr.xml")); + final String xmlTr = + IOUtils.toString( + this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/tr.xml")); SAXReader reader = new SAXReader(); - Document document = reader.read(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/tr.xml")); + Document document = + reader.read( + this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/tr.xml")); Node node = document.selectSingleNode("//CODE/*[local-name()='stylesheet']"); System.out.println(node.asXML()); } - } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/vocabulary/VocabularyTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/vocabulary/VocabularyTest.java index c2db17a9d7..04b933fb52 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/vocabulary/VocabularyTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/vocabulary/VocabularyTest.java @@ -1,17 +1,15 @@ package eu.dnetlib.dhp.transformation.vocabulary; -import org.junit.jupiter.api.Test; import static org.junit.jupiter.api.Assertions.*; + +import org.junit.jupiter.api.Test; + public class VocabularyTest { - - @Test public void testLoadVocabulary() throws Exception { final Vocabulary vocabulary = VocabularyHelper.getVocabularyFromAPI("dnet:languages"); - assertEquals("dnet:languages",vocabulary.getName()); - - + assertEquals("dnet:languages", vocabulary.getName()); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java index f52e4bb39a..bb310050ce 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java @@ -4,11 +4,15 @@ import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; +import java.io.IOException; +import java.io.Serializable; +import java.io.StringReader; +import java.util.ArrayList; +import java.util.List; import org.apache.spark.SparkConf; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.SaveMode; @@ -18,19 +22,13 @@ import org.dom4j.DocumentException; import org.dom4j.Element; import org.dom4j.io.SAXReader; -import java.io.IOException; -import java.io.Serializable; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.List; - abstract class AbstractSparkAction implements Serializable { - protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() - .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + protected static final ObjectMapper OBJECT_MAPPER = + new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - public ArgumentApplicationParser parser; //parameters for the spark action - public SparkSession spark; //the spark session + public ArgumentApplicationParser parser; // parameters for the spark action + public SparkSession spark; // the spark session public AbstractSparkAction(ArgumentApplicationParser parser, SparkSession spark) { @@ -38,9 +36,12 @@ abstract class AbstractSparkAction implements Serializable { this.spark = spark; } - public List getConfigurations(ISLookUpService isLookUpService, String orchestrator) throws ISLookUpException, DocumentException, IOException { + public List getConfigurations(ISLookUpService isLookUpService, String orchestrator) + throws ISLookUpException, DocumentException, IOException { - final String xquery = String.format("/RESOURCE_PROFILE[.//DEDUPLICATION/ACTION_SET/@id = '%s']", orchestrator); + final String xquery = + String.format( + "/RESOURCE_PROFILE[.//DEDUPLICATION/ACTION_SET/@id = '%s']", orchestrator); String orchestratorProfile = isLookUpService.getResourceProfileByQuery(xquery); @@ -57,14 +58,16 @@ abstract class AbstractSparkAction implements Serializable { return configurations; } - private DedupConfig loadConfig(final ISLookUpService isLookUpService, final String actionSetId, final Object o) + private DedupConfig loadConfig( + final ISLookUpService isLookUpService, final String actionSetId, final Object o) throws ISLookUpException, IOException { final Element s = (Element) o; final String configProfileId = s.attributeValue("id"); final String conf = - isLookUpService.getResourceProfileByQuery(String.format( - "for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", - configProfileId)); + isLookUpService.getResourceProfileByQuery( + String.format( + "for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", + configProfileId)); DedupConfig dedupConfig = new ObjectMapper().readValue(conf, DedupConfig.class); dedupConfig.getPace().initModel(); @@ -74,21 +77,15 @@ abstract class AbstractSparkAction implements Serializable { return dedupConfig; } - abstract void run(ISLookUpService isLookUpService) throws DocumentException, IOException, ISLookUpException; + abstract void run(ISLookUpService isLookUpService) + throws DocumentException, IOException, ISLookUpException; protected static SparkSession getSparkSession(SparkConf conf) { - return SparkSession - .builder() - .config(conf) - .getOrCreate(); + return SparkSession.builder().config(conf).getOrCreate(); } protected static void save(Dataset dataset, String outPath, SaveMode mode) { - dataset - .write() - .option("compression", "gzip") - .mode(mode) - .json(outPath); + dataset.write().option("compression", "gzip").mode(mode).json(outPath); } protected static void removeOutputDir(SparkSession spark, String path) { diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java index b4d0e268a7..905fbace69 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java @@ -1,18 +1,17 @@ package eu.dnetlib.dhp.oa.dedup; -import eu.dnetlib.dhp.schema.oaf.Field; -import org.apache.commons.lang.StringUtils; - -import java.time.Year; -import java.util.*; -import java.util.stream.Collectors; - import static java.util.Collections.reverseOrder; import static java.util.Map.Entry.comparingByValue; import static java.util.stream.Collectors.toMap; import static org.apache.commons.lang.StringUtils.endsWith; import static org.apache.commons.lang.StringUtils.substringBefore; +import eu.dnetlib.dhp.schema.oaf.Field; +import java.time.Year; +import java.util.*; +import java.util.stream.Collectors; +import org.apache.commons.lang.StringUtils; + public class DatePicker { private static final String DATE_PATTERN = "\\d{4}-\\d{2}-\\d{2}"; @@ -22,33 +21,32 @@ public class DatePicker { public static Field pick(final Collection dateofacceptance) { - final Map frequencies = dateofacceptance - .parallelStream() - .filter(StringUtils::isNotBlank) - .collect( - Collectors.toConcurrentMap( - w -> w, w -> 1, Integer::sum)); + final Map frequencies = + dateofacceptance + .parallelStream() + .filter(StringUtils::isNotBlank) + .collect(Collectors.toConcurrentMap(w -> w, w -> 1, Integer::sum)); if (frequencies.isEmpty()) { return new Field<>(); } final Field date = new Field<>(); - date.setValue(frequencies.keySet().iterator().next()); + date.setValue(frequencies.keySet().iterator().next()); // let's sort this map by values first, filtering out invalid dates - final Map sorted = frequencies - .entrySet() - .stream() - .filter(d -> StringUtils.isNotBlank(d.getKey())) - .filter(d -> d.getKey().matches(DATE_PATTERN)) - .filter(d -> inRange(d.getKey())) - .sorted(reverseOrder(comparingByValue())) - .collect( - toMap( - Map.Entry::getKey, - Map.Entry::getValue, (e1, e2) -> e2, - LinkedHashMap::new)); + final Map sorted = + frequencies.entrySet().stream() + .filter(d -> StringUtils.isNotBlank(d.getKey())) + .filter(d -> d.getKey().matches(DATE_PATTERN)) + .filter(d -> inRange(d.getKey())) + .sorted(reverseOrder(comparingByValue())) + .collect( + toMap( + Map.Entry::getKey, + Map.Entry::getValue, + (e1, e2) -> e2, + LinkedHashMap::new)); // shortcut if (sorted.size() == 0) { @@ -58,18 +56,24 @@ public class DatePicker { // voting method (1/3 + 1) wins if (sorted.size() >= 3) { final int acceptThreshold = (sorted.size() / 3) + 1; - final List accepted = sorted.entrySet().stream() - .filter(e -> e.getValue() >= acceptThreshold) - .map(e -> e.getKey()) - .collect(Collectors.toList()); + final List accepted = + sorted.entrySet().stream() + .filter(e -> e.getValue() >= acceptThreshold) + .map(e -> e.getKey()) + .collect(Collectors.toList()); // cannot find strong majority if (accepted.isEmpty()) { final int max = sorted.values().iterator().next(); - Optional first = sorted.entrySet().stream() - .filter(e -> e.getValue() == max && !endsWith(e.getKey(), DATE_DEFAULT_SUFFIX)) - .map(Map.Entry::getKey) - .findFirst(); + Optional first = + sorted.entrySet().stream() + .filter( + e -> + e.getValue() == max + && !endsWith( + e.getKey(), DATE_DEFAULT_SUFFIX)) + .map(Map.Entry::getKey) + .findFirst(); if (first.isPresent()) { date.setValue(first.get()); return date; @@ -83,9 +87,10 @@ public class DatePicker { date.setValue(accepted.get(0)); return date; } else { - final Optional first = accepted.stream() - .filter(d -> !endsWith(d, DATE_DEFAULT_SUFFIX)) - .findFirst(); + final Optional first = + accepted.stream() + .filter(d -> !endsWith(d, DATE_DEFAULT_SUFFIX)) + .findFirst(); if (first.isPresent()) { date.setValue(first.get()); return date; @@ -94,7 +99,7 @@ public class DatePicker { return date; } - //1st non YYYY-01-01 is returned + // 1st non YYYY-01-01 is returned } else { if (sorted.size() == 2) { for (Map.Entry e : sorted.entrySet()) { @@ -115,5 +120,4 @@ public class DatePicker { final int year = Integer.parseInt(substringBefore(date, "-")); return year >= YEAR_LB && year <= YEAR_UB; } - -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index da16e6dffe..1cb04d02f7 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -3,63 +3,76 @@ package eu.dnetlib.dhp.oa.dedup; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; -import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.pace.config.DedupConfig; -import org.apache.spark.api.java.JavaPairRDD; +import java.util.Collection; +import java.util.Iterator; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; - import scala.Tuple2; -import java.util.Collection; -import java.util.Iterator; - public class DedupRecordFactory { - protected static final ObjectMapper OBJECT_MAPPER = new com.fasterxml.jackson.databind.ObjectMapper() - .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + protected static final ObjectMapper OBJECT_MAPPER = + new com.fasterxml.jackson.databind.ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); public static Dataset createDedupRecord( - final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, final Class clazz, final DedupConfig dedupConf) { + final SparkSession spark, + final String mergeRelsInputPath, + final String entitiesInputPath, + final Class clazz, + final DedupConfig dedupConf) { long ts = System.currentTimeMillis(); - // - Dataset> entities = spark.read() - .textFile(entitiesInputPath) - .map((MapFunction>) it -> { - T entity = OBJECT_MAPPER.readValue(it, clazz); - return new Tuple2<>(entity.getId(), entity); - }, Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); + // + Dataset> entities = + spark.read() + .textFile(entitiesInputPath) + .map( + (MapFunction>) + it -> { + T entity = OBJECT_MAPPER.readValue(it, clazz); + return new Tuple2<>(entity.getId(), entity); + }, + Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); + // : source is the dedup_id, target is the id of the mergedIn + Dataset> mergeRels = + spark.read() + .load(mergeRelsInputPath) + .as(Encoders.bean(Relation.class)) + .where("relClass == 'merges'") + .map( + (MapFunction>) + r -> new Tuple2<>(r.getSource(), r.getTarget()), + Encoders.tuple(Encoders.STRING(), Encoders.STRING())); - //: source is the dedup_id, target is the id of the mergedIn - Dataset> mergeRels = spark - .read() - .load(mergeRelsInputPath) - .as(Encoders.bean(Relation.class)) - .where("relClass == 'merges'") - .map((MapFunction>) - r -> new Tuple2<>(r.getSource(), r.getTarget()), Encoders.tuple(Encoders.STRING(), Encoders.STRING())); - - // - return mergeRels.joinWith(entities, mergeRels.col("_1").equalTo(entities.col("_1")), "left_outer") - .filter((FilterFunction, Tuple2>>) value -> value._2() != null) - .map((MapFunction, Tuple2>, T>) - value -> value._2()._2(), Encoders.kryo(clazz)) + // + return mergeRels + .joinWith(entities, mergeRels.col("_1").equalTo(entities.col("_1")), "left_outer") + .filter( + (FilterFunction, Tuple2>>) + value -> value._2() != null) + .map( + (MapFunction, Tuple2>, T>) + value -> value._2()._2(), + Encoders.kryo(clazz)) .groupByKey((MapFunction) value -> value.getId(), Encoders.STRING()) - .mapGroups((MapGroupsFunction) - (key, values) -> entityMerger(key, values, ts, clazz), Encoders.bean(clazz)); + .mapGroups( + (MapGroupsFunction) + (key, values) -> entityMerger(key, values, ts, clazz), + Encoders.bean(clazz)); } - private static T entityMerger(String id, Iterator entities, final long ts, Class clazz) { + private static T entityMerger( + String id, Iterator entities, final long ts, Class clazz) { try { T entity = clazz.newInstance(); entity.setId(id); @@ -70,18 +83,19 @@ public class DedupRecordFactory { entity.setLastupdatetimestamp(ts); final Collection dates = Lists.newArrayList(); - entities.forEachRemaining(e -> { - entity.mergeFrom(e); - if (ModelSupport.isSubClass(e, Result.class)) { - Result r1 = (Result) e; - Result er = (Result) entity; - er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor())); + entities.forEachRemaining( + e -> { + entity.mergeFrom(e); + if (ModelSupport.isSubClass(e, Result.class)) { + Result r1 = (Result) e; + Result er = (Result) entity; + er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor())); - if (er.getDateofacceptance() != null) { - dates.add(r1.getDateofacceptance().getValue()); - } - } - }); + if (er.getDateofacceptance() != null) { + dates.add(r1.getDateofacceptance().getValue()); + } + } + }); if (ModelSupport.isSubClass(entity, Result.class)) { ((Result) entity).setDateofacceptance(DatePicker.pick(dates)); @@ -91,5 +105,4 @@ public class DedupRecordFactory { throw new RuntimeException(e); } } - } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java index 39f52151ab..a832a58687 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java @@ -9,9 +9,13 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.clustering.BlacklistAwareClusteringCombiner; import eu.dnetlib.pace.config.DedupConfig; - import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.model.Person; +import java.io.StringReader; +import java.security.MessageDigest; +import java.text.Normalizer; +import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.codec.binary.Hex; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkContext; @@ -22,30 +26,43 @@ import org.dom4j.Element; import org.dom4j.io.SAXReader; import scala.Tuple2; -import java.io.StringReader; -import java.security.MessageDigest; -import java.text.Normalizer; -import java.util.*; -import java.util.stream.Collectors; - public class DedupUtility { private static final Double THRESHOLD = 0.95; - public static Map constructAccumulator(final DedupConfig dedupConf, final SparkContext context) { + public static Map constructAccumulator( + final DedupConfig dedupConf, final SparkContext context) { Map accumulators = new HashMap<>(); - String acc1 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "records per hash key = 1"); + String acc1 = + String.format( + "%s::%s", dedupConf.getWf().getEntityType(), "records per hash key = 1"); accumulators.put(acc1, context.longAccumulator(acc1)); - String acc2 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "missing " + dedupConf.getWf().getOrderField()); + String acc2 = + String.format( + "%s::%s", + dedupConf.getWf().getEntityType(), + "missing " + dedupConf.getWf().getOrderField()); accumulators.put(acc2, context.longAccumulator(acc2)); - String acc3 = String.format("%s::%s", dedupConf.getWf().getEntityType(), String.format("Skipped records for count(%s) >= %s", dedupConf.getWf().getOrderField(), dedupConf.getWf().getGroupMaxSize())); + String acc3 = + String.format( + "%s::%s", + dedupConf.getWf().getEntityType(), + String.format( + "Skipped records for count(%s) >= %s", + dedupConf.getWf().getOrderField(), + dedupConf.getWf().getGroupMaxSize())); accumulators.put(acc3, context.longAccumulator(acc3)); String acc4 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "skip list"); accumulators.put(acc4, context.longAccumulator(acc4)); - String acc5 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "dedupSimilarity (x2)"); + String acc5 = + String.format("%s::%s", dedupConf.getWf().getEntityType(), "dedupSimilarity (x2)"); accumulators.put(acc5, context.longAccumulator(acc5)); - String acc6 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "d < " + dedupConf.getWf().getThreshold()); + String acc6 = + String.format( + "%s::%s", + dedupConf.getWf().getEntityType(), + "d < " + dedupConf.getWf().getThreshold()); accumulators.put(acc6, context.longAccumulator(acc6)); return accumulators; @@ -66,7 +83,6 @@ public class DedupUtility { } } - public static List mergeAuthor(final List a, final List b) { int pa = countAuthorsPids(a); int pb = countAuthorsPids(b); @@ -86,32 +102,44 @@ public class DedupUtility { } private static void enrichPidFromList(List base, List enrich) { - if (base == null || enrich == null) - return; - final Map basePidAuthorMap = base.stream() - .filter(a -> a.getPid() != null && a.getPid().size() > 0) - .flatMap(a -> a.getPid() - .stream() - .map(p -> new Tuple2<>(p.toComparableString(), a)) - ).collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); + if (base == null || enrich == null) return; + final Map basePidAuthorMap = + base.stream() + .filter(a -> a.getPid() != null && a.getPid().size() > 0) + .flatMap( + a -> + a.getPid().stream() + .map(p -> new Tuple2<>(p.toComparableString(), a))) + .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); - final List> pidToEnrich = enrich - .stream() - .filter(a -> a.getPid() != null && a.getPid().size() > 0) - .flatMap(a -> a.getPid().stream().filter(p -> !basePidAuthorMap.containsKey(p.toComparableString())).map(p -> new Tuple2<>(p, a))) - .collect(Collectors.toList()); + final List> pidToEnrich = + enrich.stream() + .filter(a -> a.getPid() != null && a.getPid().size() > 0) + .flatMap( + a -> + a.getPid().stream() + .filter( + p -> + !basePidAuthorMap.containsKey( + p.toComparableString())) + .map(p -> new Tuple2<>(p, a))) + .collect(Collectors.toList()); - - pidToEnrich.forEach(a -> { - Optional> simAuhtor = base.stream().map(ba -> new Tuple2<>(sim(ba, a._2()), ba)).max(Comparator.comparing(Tuple2::_1)); - if (simAuhtor.isPresent() && simAuhtor.get()._1() > THRESHOLD) { - Author r = simAuhtor.get()._2(); - r.getPid().add(a._1()); - } - }); + pidToEnrich.forEach( + a -> { + Optional> simAuhtor = + base.stream() + .map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) + .max(Comparator.comparing(Tuple2::_1)); + if (simAuhtor.isPresent() && simAuhtor.get()._1() > THRESHOLD) { + Author r = simAuhtor.get()._2(); + r.getPid().add(a._1()); + } + }); } - public static String createDedupRecordPath(final String basePath, final String actionSetId, final String entityType) { + public static String createDedupRecordPath( + final String basePath, final String actionSetId, final String entityType) { return String.format("%s/%s/%s_deduprecord", basePath, actionSetId, entityType); } @@ -119,11 +147,13 @@ public class DedupUtility { return String.format("%s/%s", basePath, entityType); } - public static String createSimRelPath(final String basePath, final String actionSetId,final String entityType) { + public static String createSimRelPath( + final String basePath, final String actionSetId, final String entityType) { return String.format("%s/%s/%s_simrel", basePath, actionSetId, entityType); } - public static String createMergeRelPath(final String basePath, final String actionSetId, final String entityType) { + public static String createMergeRelPath( + final String basePath, final String actionSetId, final String entityType) { return String.format("%s/%s/%s_mergerel", basePath, actionSetId, entityType); } @@ -133,19 +163,21 @@ public class DedupUtility { final Person pb = parse(b); if (pa.isAccurate() & pb.isAccurate()) { - return new JaroWinkler().score( - normalize(pa.getSurnameString()), - normalize(pb.getSurnameString())); + return new JaroWinkler() + .score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())); } else { - return new JaroWinkler().score( - normalize(pa.getNormalisedFullname()), - normalize(pb.getNormalisedFullname())); + return new JaroWinkler() + .score( + normalize(pa.getNormalisedFullname()), + normalize(pb.getNormalisedFullname())); } } private static String normalize(final String s) { return nfd(s).toLowerCase() - // do not compact the regexes in a single expression, would cause StackOverflowError in case of large input strings + // do not compact the regexes in a single expression, would cause StackOverflowError + // in case + // of large input strings .replaceAll("(\\W)+", " ") .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") .replaceAll("(\\p{Punct})+", " ") @@ -166,30 +198,29 @@ public class DedupUtility { } } - private static int countAuthorsPids(List authors) { - if (authors == null) - return 0; + if (authors == null) return 0; return (int) authors.stream().filter(DedupUtility::hasPid).count(); } private static int authorsSize(List authors) { - if (authors == null) - return 0; + if (authors == null) return 0; return authors.size(); } private static boolean hasPid(Author a) { - if (a == null || a.getPid() == null || a.getPid().size() == 0) - return false; + if (a == null || a.getPid() == null || a.getPid().size() == 0) return false; return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue())); } - public static List getConfigurations(String isLookUpUrl, String orchestrator) throws ISLookUpException, DocumentException { + public static List getConfigurations(String isLookUpUrl, String orchestrator) + throws ISLookUpException, DocumentException { final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookUpUrl); - final String xquery = String.format("/RESOURCE_PROFILE[.//DEDUPLICATION/ACTION_SET/@id = '%s']", orchestrator); + final String xquery = + String.format( + "/RESOURCE_PROFILE[.//DEDUPLICATION/ACTION_SET/@id = '%s']", orchestrator); String orchestratorProfile = isLookUpService.getResourceProfileByQuery(xquery); @@ -203,17 +234,18 @@ public class DedupUtility { } return configurations; - } - private static DedupConfig loadConfig(final ISLookUpService isLookUpService, final String actionSetId, final Object o) + private static DedupConfig loadConfig( + final ISLookUpService isLookUpService, final String actionSetId, final Object o) throws ISLookUpException { final Element s = (Element) o; final String configProfileId = s.attributeValue("id"); final String conf = - isLookUpService.getResourceProfileByQuery(String.format( - "for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", - configProfileId)); + isLookUpService.getResourceProfileByQuery( + String.format( + "for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", + configProfileId)); final DedupConfig dedupConfig = DedupConfig.load(conf); dedupConfig.getWf().setConfigurationId(actionSetId); return dedupConfig; diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java index 28b85853f8..a7554ebe11 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java @@ -4,47 +4,50 @@ import eu.dnetlib.dhp.oa.dedup.model.Block; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.BlockProcessor; +import java.util.Map; +import java.util.stream.Collectors; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.util.LongAccumulator; import scala.Serializable; import scala.Tuple2; -import java.util.Map; -import java.util.stream.Collectors; - public class Deduper implements Serializable { - public static JavaPairRDD computeRelations(JavaSparkContext context, JavaPairRDD blocks, DedupConfig config) { - Map accumulators = DedupUtility.constructAccumulator(config, context.sc()); + public static JavaPairRDD computeRelations( + JavaSparkContext context, JavaPairRDD blocks, DedupConfig config) { + Map accumulators = + DedupUtility.constructAccumulator(config, context.sc()); - return blocks - .flatMapToPair(it -> { - final SparkReporter reporter = new SparkReporter(accumulators); - new BlockProcessor(config).processSortedBlock(it._1(), it._2().getDocuments(), reporter); - return reporter.getRelations().iterator(); - }) + return blocks.flatMapToPair( + it -> { + final SparkReporter reporter = new SparkReporter(accumulators); + new BlockProcessor(config) + .processSortedBlock(it._1(), it._2().getDocuments(), reporter); + return reporter.getRelations().iterator(); + }) .mapToPair(it -> new Tuple2<>(it._1() + it._2(), it)) .reduceByKey((a, b) -> a) .mapToPair(Tuple2::_2); } - public static JavaPairRDD createSortedBlocks(JavaPairRDD mapDocs, DedupConfig config) { + public static JavaPairRDD createSortedBlocks( + JavaPairRDD mapDocs, DedupConfig config) { final String of = config.getWf().getOrderField(); final int maxQueueSize = config.getWf().getGroupMaxSize(); return mapDocs - //the reduce is just to be sure that we haven't document with same id + // the reduce is just to be sure that we haven't document with same id .reduceByKey((a, b) -> a) .map(Tuple2::_2) - //Clustering: from to List - .flatMap(a -> DedupUtility.getGroupingKeys(config, a) - .stream() - .map(it -> Block.from(it, a)) - .collect(Collectors.toList()) - .iterator()) + // Clustering: from to List + .flatMap( + a -> + DedupUtility.getGroupingKeys(config, a).stream() + .map(it -> Block.from(it, a)) + .collect(Collectors.toList()) + .iterator()) .mapToPair(block -> new Tuple2<>(block.getKey(), block)) .reduceByKey((b1, b2) -> Block.from(b1, b2, of, maxQueueSize)); } - -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java index c2b1fc9c24..127a19139e 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java @@ -8,12 +8,10 @@ import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; +import java.io.IOException; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; @@ -21,8 +19,6 @@ import org.dom4j.DocumentException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; - public class SparkCreateDedupRecord extends AbstractSparkAction { private static final Logger log = LoggerFactory.getLogger(SparkCreateDedupRecord.class); @@ -32,9 +28,11 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { } public static void main(String[] args) throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateSimRels.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); parser.parseArgument(args); SparkConf conf = new SparkConf(); @@ -46,7 +44,8 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { } @Override - public void run(ISLookUpService isLookUpService) throws ISLookUpException, DocumentException, IOException { + public void run(ISLookUpService isLookUpService) + throws ISLookUpException, DocumentException, IOException { final String graphBasePath = parser.get("graphBasePath"); final String isLookUpUrl = parser.get("isLookUpUrl"); @@ -58,25 +57,28 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { log.info("actionSetId: '{}'", actionSetId); log.info("workingPath: '{}'", workingPath); - for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { + for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) { String subEntity = dedupConf.getWf().getSubEntityValue(); log.info("Creating deduprecords for: '{}'", subEntity); - final String outputPath = DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity); + final String outputPath = + DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity); removeOutputDir(spark, outputPath); - final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity); + final String mergeRelPath = + DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity); final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity); Class clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz, dedupConf) - .map((MapFunction) value -> OBJECT_MAPPER.writeValueAsString(value), Encoders.STRING()) - .write() - .mode(SaveMode.Overwrite) - .json(outputPath); + .map( + (MapFunction) + value -> OBJECT_MAPPER.writeValueAsString(value), + Encoders.STRING()) + .write() + .mode(SaveMode.Overwrite) + .json(outputPath); } - } - } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java index 9c46404b7b..ca6d04d496 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java @@ -1,8 +1,8 @@ package eu.dnetlib.dhp.oa.dedup; import com.google.common.hash.Hashing; -import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent; import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.DataInfo; @@ -13,6 +13,10 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.util.MapDocumentUtil; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; @@ -25,14 +29,9 @@ import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; -import scala.Tuple2; import org.slf4j.Logger; import org.slf4j.LoggerFactory; - -import java.io.IOException; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; +import scala.Tuple2; public class SparkCreateMergeRels extends AbstractSparkAction { @@ -45,9 +44,11 @@ public class SparkCreateMergeRels extends AbstractSparkAction { } public static void main(String[] args) throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateSimRels.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); parser.parseArgument(args); final String isLookUpUrl = parser.get("isLookUpUrl"); @@ -57,11 +58,13 @@ public class SparkCreateMergeRels extends AbstractSparkAction { conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - new SparkCreateMergeRels(parser, getSparkSession(conf)).run(ISLookupClientFactory.getLookUpService(isLookUpUrl)); + new SparkCreateMergeRels(parser, getSparkSession(conf)) + .run(ISLookupClientFactory.getLookUpService(isLookUpUrl)); } @Override - public void run(ISLookUpService isLookUpService) throws ISLookUpException, DocumentException, IOException { + public void run(ISLookUpService isLookUpService) + throws ISLookUpException, DocumentException, IOException { final String graphBasePath = parser.get("graphBasePath"); final String workingPath = parser.get("workingPath"); @@ -75,7 +78,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction { final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { + for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) { final String subEntity = dedupConf.getWf().getSubEntityValue(); log.info("Creating mergerels for: '{}'", subEntity); @@ -83,46 +86,59 @@ public class SparkCreateMergeRels extends AbstractSparkAction { final int maxIterations = dedupConf.getWf().getMaxIterations(); log.info("Max iterations {}", maxIterations); - final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity); + final String mergeRelPath = + DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity); - final JavaPairRDD vertexes = sc.textFile(graphBasePath + "/" + subEntity) - .map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s)) - .mapToPair((PairFunction) s -> new Tuple2<>(hash(s), s)); + final JavaPairRDD vertexes = + sc.textFile(graphBasePath + "/" + subEntity) + .map( + s -> + MapDocumentUtil.getJPathString( + dedupConf.getWf().getIdPath(), s)) + .mapToPair( + (PairFunction) + s -> new Tuple2<>(hash(s), s)); - final RDD> edgeRdd = spark - .read() - .load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)) - .as(Encoders.bean(Relation.class)) - .javaRDD() - .map(it -> new Edge<>(hash(it.getSource()), hash(it.getTarget()), it.getRelClass())) - .rdd(); + final RDD> edgeRdd = + spark.read() + .load( + DedupUtility.createSimRelPath( + workingPath, actionSetId, subEntity)) + .as(Encoders.bean(Relation.class)) + .javaRDD() + .map( + it -> + new Edge<>( + hash(it.getSource()), + hash(it.getTarget()), + it.getRelClass())) + .rdd(); - final Dataset mergeRels = spark - .createDataset(GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, maxIterations) - .toJavaRDD() - .filter(k -> k.getDocIds().size() > 1) - .flatMap(cc -> ccToMergeRel(cc, dedupConf)) - .rdd(), Encoders.bean(Relation.class)); + final Dataset mergeRels = + spark.createDataset( + GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, maxIterations) + .toJavaRDD() + .filter(k -> k.getDocIds().size() > 1) + .flatMap(cc -> ccToMergeRel(cc, dedupConf)) + .rdd(), + Encoders.bean(Relation.class)); - mergeRels - .write() - .mode(SaveMode.Append) - .parquet(mergeRelPath); + mergeRels.write().mode(SaveMode.Append).parquet(mergeRelPath); } - } - public Iterator ccToMergeRel(ConnectedComponent cc, DedupConfig dedupConf){ - return cc.getDocIds() - .stream() - .flatMap(id -> { - List tmp = new ArrayList<>(); + public Iterator ccToMergeRel(ConnectedComponent cc, DedupConfig dedupConf) { + return cc.getDocIds().stream() + .flatMap( + id -> { + List tmp = new ArrayList<>(); - tmp.add(rel(cc.getCcId(), id, "merges", dedupConf)); - tmp.add(rel(id, cc.getCcId(), "isMergedIn", dedupConf)); + tmp.add(rel(cc.getCcId(), id, "merges", dedupConf)); + tmp.add(rel(id, cc.getCcId(), "isMergedIn", dedupConf)); - return tmp.stream(); - }).iterator(); + return tmp.stream(); + }) + .iterator(); } private Relation rel(String source, String target, String relClass, DedupConfig dedupConf) { @@ -144,8 +160,8 @@ public class SparkCreateMergeRels extends AbstractSparkAction { provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS); info.setProvenanceaction(provenanceAction); - //TODO calculate the trust value based on the similarity score of the elements in the CC - //info.setTrust(); + // TODO calculate the trust value based on the similarity score of the elements in the CC + // info.setTrust(); r.setDataInfo(info); return r; @@ -154,5 +170,4 @@ public class SparkCreateMergeRels extends AbstractSparkAction { public static long hash(final String id) { return Hashing.murmur3_128().hashString(id).asLong(); } - } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java index d02aef64cb..2fd807ccb2 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java @@ -2,7 +2,6 @@ package eu.dnetlib.dhp.oa.dedup; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.dedup.model.Block; -import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; @@ -13,14 +12,13 @@ import eu.dnetlib.pace.model.FieldListImpl; import eu.dnetlib.pace.model.FieldValueImpl; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.MapDocumentUtil; +import java.io.IOException; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.PairFunction; -import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; @@ -29,8 +27,6 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import scala.Tuple2; -import java.io.IOException; - public class SparkCreateSimRels extends AbstractSparkAction { private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class); @@ -40,28 +36,29 @@ public class SparkCreateSimRels extends AbstractSparkAction { } public static void main(String[] args) throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateSimRels.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); parser.parseArgument(args); SparkConf conf = new SparkConf(); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - conf.registerKryoClasses(new Class[] { - MapDocument.class, - FieldListImpl.class, - FieldValueImpl.class, - Block.class - }); + conf.registerKryoClasses( + new Class[] { + MapDocument.class, FieldListImpl.class, FieldValueImpl.class, Block.class + }); new SparkCreateSimRels(parser, getSparkSession(conf)) .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } @Override - public void run(ISLookUpService isLookUpService) throws DocumentException, IOException, ISLookUpException { + public void run(ISLookUpService isLookUpService) + throws DocumentException, IOException, ISLookUpException { - //read oozie parameters + // read oozie parameters final String graphBasePath = parser.get("graphBasePath"); final String isLookUpUrl = parser.get("isLookUpUrl"); final String actionSetId = parser.get("actionSetId"); @@ -72,32 +69,39 @@ public class SparkCreateSimRels extends AbstractSparkAction { log.info("actionSetId: '{}'", actionSetId); log.info("workingPath: '{}'", workingPath); - //for each dedup configuration - for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { + // for each dedup configuration + for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) { final String entity = dedupConf.getWf().getEntityType(); final String subEntity = dedupConf.getWf().getSubEntityValue(); log.info("Creating simrels for: '{}'", subEntity); - final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity); + final String outputPath = + DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity); removeOutputDir(spark, outputPath); JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaPairRDD mapDocuments = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) - .mapToPair((PairFunction) s -> { - MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); - return new Tuple2<>(d.getIdentifier(), d); - }); + JavaPairRDD mapDocuments = + sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) + .mapToPair( + (PairFunction) + s -> { + MapDocument d = + MapDocumentUtil.asMapDocumentWithJPath( + dedupConf, s); + return new Tuple2<>(d.getIdentifier(), d); + }); - //create blocks for deduplication + // create blocks for deduplication JavaPairRDD blocks = Deduper.createSortedBlocks(mapDocuments, dedupConf); - //create relations by comparing only elements in the same group - JavaRDD relations = Deduper.computeRelations(sc, blocks, dedupConf) - .map(t -> createSimRel(t._1(), t._2(), entity)); + // create relations by comparing only elements in the same group + JavaRDD relations = + Deduper.computeRelations(sc, blocks, dedupConf) + .map(t -> createSimRel(t._1(), t._2(), entity)); - //save the simrel in the workingdir + // save the simrel in the workingdir spark.createDataset(relations.rdd(), Encoders.bean(Relation.class)) .write() .mode(SaveMode.Append) @@ -113,7 +117,7 @@ public class SparkCreateSimRels extends AbstractSparkAction { r.setRelClass("isSimilarTo"); r.setDataInfo(new DataInfo()); - switch(entity) { + switch (entity) { case "result": r.setRelType("resultResult"); break; @@ -125,5 +129,4 @@ public class SparkCreateSimRels extends AbstractSparkAction { } return r; } - } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index 86d19d96d4..17c99c0023 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -1,7 +1,7 @@ package eu.dnetlib.dhp.oa.dedup; -import com.fasterxml.jackson.databind.DeserializationFeature; -import com.fasterxml.jackson.databind.ObjectMapper; +import static org.apache.spark.sql.functions.col; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.DataInfo; @@ -9,8 +9,6 @@ import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.IOUtils; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; @@ -18,10 +16,6 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import scala.Tuple2; -import java.io.IOException; - -import static org.apache.spark.sql.functions.col; - public class SparkPropagateRelation extends AbstractSparkAction { private static final Logger log = LoggerFactory.getLogger(SparkPropagateRelation.class); @@ -31,14 +25,17 @@ public class SparkPropagateRelation extends AbstractSparkAction { TARGET } - public SparkPropagateRelation(ArgumentApplicationParser parser, SparkSession spark) throws Exception { + public SparkPropagateRelation(ArgumentApplicationParser parser, SparkSession spark) + throws Exception { super(parser, spark); } public static void main(String[] args) throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateSimRels.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); parser.parseArgument(args); @@ -64,47 +61,63 @@ public class SparkPropagateRelation extends AbstractSparkAction { final String outputRelationPath = DedupUtility.createEntityPath(dedupGraphPath, "relation"); removeOutputDir(spark, outputRelationPath); - Dataset mergeRels = spark.read() - .load(DedupUtility.createMergeRelPath(workingPath, "*", "*")) - .as(Encoders.bean(Relation.class)); + Dataset mergeRels = + spark.read() + .load(DedupUtility.createMergeRelPath(workingPath, "*", "*")) + .as(Encoders.bean(Relation.class)); - Dataset> mergedIds = mergeRels - .where(col("relClass").equalTo("merges")) - .select(col("source"), col("target")) - .distinct() - .map((MapFunction>) - r -> new Tuple2<>(r.getString(1), r.getString(0)), - Encoders.tuple(Encoders.STRING(), Encoders.STRING())) - .cache(); + Dataset> mergedIds = + mergeRels + .where(col("relClass").equalTo("merges")) + .select(col("source"), col("target")) + .distinct() + .map( + (MapFunction>) + r -> new Tuple2<>(r.getString(1), r.getString(0)), + Encoders.tuple(Encoders.STRING(), Encoders.STRING())) + .cache(); final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation"); - Dataset rels = spark.read() - .textFile(relationPath) - .map(patchRelFn(), Encoders.bean(Relation.class)); + Dataset rels = + spark.read() + .textFile(relationPath) + .map(patchRelFn(), Encoders.bean(Relation.class)); Dataset newRels = processDataset( - processDataset(rels, mergedIds, FieldType.SOURCE, getFixRelFn(FieldType.SOURCE)), - mergedIds, FieldType.TARGET, getFixRelFn(FieldType.TARGET)) - .filter(SparkPropagateRelation::containsDedup); + processDataset( + rels, + mergedIds, + FieldType.SOURCE, + getFixRelFn(FieldType.SOURCE)), + mergedIds, + FieldType.TARGET, + getFixRelFn(FieldType.TARGET)) + .filter(SparkPropagateRelation::containsDedup); - Dataset updated = processDataset( - processDataset(rels, mergedIds, FieldType.SOURCE, getDeletedFn()), - mergedIds, FieldType.TARGET, getDeletedFn()); + Dataset updated = + processDataset( + processDataset(rels, mergedIds, FieldType.SOURCE, getDeletedFn()), + mergedIds, + FieldType.TARGET, + getDeletedFn()); save(newRels.union(updated), outputRelationPath, SaveMode.Overwrite); - } - private static Dataset processDataset(Dataset rels, Dataset> mergedIds, FieldType type, - MapFunction, Tuple2>, Relation> mapFn) { - final Dataset> mapped = rels - .map((MapFunction>) + private static Dataset processDataset( + Dataset rels, + Dataset> mergedIds, + FieldType type, + MapFunction, Tuple2>, Relation> mapFn) { + final Dataset> mapped = + rels.map( + (MapFunction>) r -> new Tuple2<>(getId(r, type), r), Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class))); - return mapped - .joinWith(mergedIds, mapped.col("_1").equalTo(mergedIds.col("_1")), "left_outer") + return mapped.joinWith( + mergedIds, mapped.col("_1").equalTo(mergedIds.col("_1")), "left_outer") .map(mapFn, Encoders.bean(Relation.class)); } @@ -129,7 +142,8 @@ public class SparkPropagateRelation extends AbstractSparkAction { } } - private static MapFunction, Tuple2>, Relation> getFixRelFn(FieldType type) { + private static MapFunction, Tuple2>, Relation> + getFixRelFn(FieldType type) { return value -> { if (value._2() != null) { Relation r = value._1()._2(); @@ -153,7 +167,8 @@ public class SparkPropagateRelation extends AbstractSparkAction { }; } - private static MapFunction, Tuple2>, Relation> getDeletedFn() { + private static MapFunction, Tuple2>, Relation> + getDeletedFn() { return value -> { if (value._2() != null) { Relation r = value._1()._2(); @@ -168,7 +183,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { } private static boolean containsDedup(final Relation r) { - return r.getSource().toLowerCase().contains("dedup") || r.getTarget().toLowerCase().contains("dedup"); + return r.getSource().toLowerCase().contains("dedup") + || r.getTarget().toLowerCase().contains("dedup"); } - -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkReporter.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkReporter.java index 98ee37e14f..99c3b73f3f 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkReporter.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkReporter.java @@ -1,15 +1,12 @@ package eu.dnetlib.dhp.oa.dedup; import eu.dnetlib.pace.util.Reporter; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.spark.util.LongAccumulator; -import scala.Serializable; -import scala.Tuple2; - import java.util.ArrayList; import java.util.List; import java.util.Map; +import org.apache.spark.util.LongAccumulator; +import scala.Serializable; +import scala.Tuple2; public class SparkReporter implements Serializable, Reporter { @@ -17,17 +14,20 @@ public class SparkReporter implements Serializable, Reporter { private Map accumulators; - public SparkReporter(Map accumulators){ + public SparkReporter(Map accumulators) { this.accumulators = accumulators; } - public void incrementCounter(String counterGroup, String counterName, long delta, Map accumulators) { + public void incrementCounter( + String counterGroup, + String counterName, + long delta, + Map accumulators) { final String accumulatorName = String.format("%s::%s", counterGroup, counterName); - if (accumulators.containsKey(accumulatorName)){ + if (accumulators.containsKey(accumulatorName)) { accumulators.get(accumulatorName).add(delta); } - } @Override diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java index ea0a06bbe9..fde5dd75f8 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.oa.dedup; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.dedup.model.Block; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Oaf; @@ -9,10 +8,8 @@ import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import eu.dnetlib.pace.model.FieldListImpl; -import eu.dnetlib.pace.model.FieldValueImpl; -import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.MapDocumentUtil; +import java.io.IOException; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileStatus; @@ -32,8 +29,6 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import scala.Tuple2; -import java.io.IOException; - public class SparkUpdateEntity extends AbstractSparkAction { private static final Logger log = LoggerFactory.getLogger(SparkUpdateEntity.class); @@ -45,10 +40,11 @@ public class SparkUpdateEntity extends AbstractSparkAction { } public static void main(String[] args) throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkUpdateEntity.class.getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkUpdateEntity.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); parser.parseArgument(args); SparkConf conf = new SparkConf(); @@ -71,43 +67,62 @@ public class SparkUpdateEntity extends AbstractSparkAction { final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - //for each entity - ModelSupport.entityTypes.forEach((entity, clazz) -> { - final String outputPath = dedupGraphPath + "/" + entity; - removeOutputDir(spark, outputPath); + // for each entity + ModelSupport.entityTypes.forEach( + (entity, clazz) -> { + final String outputPath = dedupGraphPath + "/" + entity; + removeOutputDir(spark, outputPath); - JavaRDD sourceEntity = sc.textFile(DedupUtility.createEntityPath(graphBasePath, entity.toString())); + JavaRDD sourceEntity = + sc.textFile( + DedupUtility.createEntityPath( + graphBasePath, entity.toString())); - if (mergeRelExists(workingPath, entity.toString())) { + if (mergeRelExists(workingPath, entity.toString())) { - final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, "*", entity.toString()); - final String dedupRecordPath = DedupUtility.createDedupRecordPath(workingPath, "*", entity.toString()); + final String mergeRelPath = + DedupUtility.createMergeRelPath( + workingPath, "*", entity.toString()); + final String dedupRecordPath = + DedupUtility.createDedupRecordPath( + workingPath, "*", entity.toString()); - final Dataset rel = spark.read() - .load(mergeRelPath) - .as(Encoders.bean(Relation.class)); + final Dataset rel = + spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class)); - final JavaPairRDD mergedIds = rel - .where("relClass == 'merges'") - .select(rel.col("target")) - .distinct() - .toJavaRDD() - .mapToPair((PairFunction) r -> new Tuple2<>(r.getString(0), "d")); + final JavaPairRDD mergedIds = + rel.where("relClass == 'merges'") + .select(rel.col("target")) + .distinct() + .toJavaRDD() + .mapToPair( + (PairFunction) + r -> new Tuple2<>(r.getString(0), "d")); - JavaPairRDD entitiesWithId = sourceEntity - .mapToPair((PairFunction) s -> new Tuple2<>(MapDocumentUtil.getJPathString(IDJSONPATH, s), s)); + JavaPairRDD entitiesWithId = + sourceEntity.mapToPair( + (PairFunction) + s -> + new Tuple2<>( + MapDocumentUtil.getJPathString( + IDJSONPATH, s), + s)); - JavaRDD map = entitiesWithId - .leftOuterJoin(mergedIds) - .map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), clazz) : k._2()._1()); + JavaRDD map = + entitiesWithId + .leftOuterJoin(mergedIds) + .map( + k -> + k._2()._2().isPresent() + ? updateDeletedByInference( + k._2()._1(), clazz) + : k._2()._1()); - sourceEntity = map.union(sc.textFile(dedupRecordPath)); - } - - sourceEntity.saveAsTextFile(outputPath, GzipCodec.class); - - }); + sourceEntity = map.union(sc.textFile(dedupRecordPath)); + } + sourceEntity.saveAsTextFile(outputPath, GzipCodec.class); + }); } public boolean mergeRelExists(String basePath, String entity) { @@ -120,7 +135,10 @@ public class SparkUpdateEntity extends AbstractSparkAction { for (FileStatus fs : fileStatuses) { if (fs.isDirectory()) - if (fileSystem.exists(new Path(DedupUtility.createMergeRelPath(basePath, fs.getPath().getName(), entity)))) + if (fileSystem.exists( + new Path( + DedupUtility.createMergeRelPath( + basePath, fs.getPath().getName(), entity)))) result = true; } @@ -130,16 +148,15 @@ public class SparkUpdateEntity extends AbstractSparkAction { } } - private static String updateDeletedByInference(final String json, final Class clazz) { + private static String updateDeletedByInference( + final String json, final Class clazz) { try { Oaf entity = OBJECT_MAPPER.readValue(json, clazz); - if (entity.getDataInfo()== null) - entity.setDataInfo(new DataInfo()); + if (entity.getDataInfo() == null) entity.setDataInfo(new DataInfo()); entity.getDataInfo().setDeletedbyinference(true); return OBJECT_MAPPER.writeValueAsString(entity); } catch (IOException e) { throw new RuntimeException("Unable to convert json", e); } } - } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java index 7bfa5dc3dc..4baac02295 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java @@ -3,21 +3,18 @@ package eu.dnetlib.dhp.oa.dedup.graph; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.dedup.DedupUtility; import eu.dnetlib.pace.util.PaceException; -import org.apache.commons.lang.StringUtils; -import org.codehaus.jackson.annotate.JsonIgnore; - import java.io.IOException; import java.io.Serializable; import java.util.Set; +import org.apache.commons.lang.StringUtils; +import org.codehaus.jackson.annotate.JsonIgnore; public class ConnectedComponent implements Serializable { private Set docIds; private String ccId; - - public ConnectedComponent() { - } + public ConnectedComponent() {} public ConnectedComponent(Set docIds) { this.docIds = docIds; @@ -28,7 +25,7 @@ public class ConnectedComponent implements Serializable { if (docIds.size() > 1) { final String s = getMin(); String prefix = s.split("\\|")[0]; - ccId =prefix + "|dedup_______::" + DedupUtility.md5(s); + ccId = prefix + "|dedup_______::" + DedupUtility.md5(s); return ccId; } else { return docIds.iterator().next(); @@ -36,24 +33,25 @@ public class ConnectedComponent implements Serializable { } @JsonIgnore - public String getMin(){ + public String getMin() { final StringBuilder min = new StringBuilder(); - docIds.forEach(i -> { - if (StringUtils.isBlank(min.toString())) { - min.append(i); - } else { - if (min.toString().compareTo(i) > 0) { - min.setLength(0); - min.append(i); - } - } - }); + docIds.forEach( + i -> { + if (StringUtils.isBlank(min.toString())) { + min.append(i); + } else { + if (min.toString().compareTo(i) > 0) { + min.setLength(0); + min.append(i); + } + } + }); return min.toString(); } @Override - public String toString(){ + public String toString() { ObjectMapper mapper = new ObjectMapper(); try { return mapper.writeValueAsString(this); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Block.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Block.java index e1ccf143c9..8f3d3ffa4e 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Block.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Block.java @@ -2,7 +2,6 @@ package eu.dnetlib.dhp.oa.dedup.model; import com.google.common.collect.Lists; import eu.dnetlib.pace.model.MapDocument; - import java.io.Serializable; import java.util.ArrayList; import java.util.Comparator; @@ -36,11 +35,13 @@ public class Block implements Serializable { Iterable it = () -> blocks; block.setDocuments( - StreamSupport.stream(it.spliterator(), false) - .flatMap(b -> b.getDocuments().stream()) - .sorted(Comparator.comparing(a -> a.getFieldMap().get(orderField).stringValue())) - .limit(maxSize) - .collect(Collectors.toCollection(ArrayList::new))); + StreamSupport.stream(it.spliterator(), false) + .flatMap(b -> b.getDocuments().stream()) + .sorted( + Comparator.comparing( + a -> a.getFieldMap().get(orderField).stringValue())) + .limit(maxSize) + .collect(Collectors.toCollection(ArrayList::new))); return block; } @@ -48,12 +49,12 @@ public class Block implements Serializable { Block block = new Block(); block.setKey(b1.getKey()); block.setDocuments( - Stream.concat( - b1.getDocuments().stream(), - b2.getDocuments().stream()) - .sorted(Comparator.comparing(a -> a.getFieldMap().get(orderField).stringValue())) - .limit(maxSize) - .collect(Collectors.toCollection(ArrayList::new))); + Stream.concat(b1.getDocuments().stream(), b2.getDocuments().stream()) + .sorted( + Comparator.comparing( + a -> a.getFieldMap().get(orderField).stringValue())) + .limit(maxSize) + .collect(Collectors.toCollection(ArrayList::new))); return block; } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java index 970fc0ddbd..29e010cbd0 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java @@ -1,15 +1,13 @@ package eu.dnetlib.dhp.oa.dedup; -import eu.dnetlib.dhp.oa.dedup.DedupUtility; import eu.dnetlib.dhp.schema.oaf.Publication; -import org.apache.commons.io.IOUtils; -import org.codehaus.jackson.map.ObjectMapper; -import org.junit.jupiter.api.BeforeEach; - import java.io.IOException; import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; +import org.apache.commons.io.IOUtils; +import org.codehaus.jackson.map.ObjectMapper; +import org.junit.jupiter.api.BeforeEach; public class MergeAuthorTest { @@ -18,28 +16,36 @@ public class MergeAuthorTest { @BeforeEach public void setUp() throws Exception { - final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/json/authors_merge.json")); + final String json = + IOUtils.toString( + this.getClass() + .getResourceAsStream( + "/eu/dnetlib/dhp/dedup/json/authors_merge.json")); - publicationsToMerge = Arrays.asList(json.split("\n")).stream().map(s-> { - try { - return mapper.readValue(s, Publication.class); - } catch (IOException e) { - throw new RuntimeException(e); - } - }).collect(Collectors.toList()); + publicationsToMerge = + Arrays.asList(json.split("\n")).stream() + .map( + s -> { + try { + return mapper.readValue(s, Publication.class); + } catch (IOException e) { + throw new RuntimeException(e); + } + }) + .collect(Collectors.toList()); } - //FIX ME Michele DB this tests doesn't work - //@Test - public void test() throws Exception { + // FIX ME Michele DB this tests doesn't work + // @Test + public void test() throws Exception { Publication dedup = new Publication(); - publicationsToMerge.forEach(p-> { - dedup.mergeFrom(p); - dedup.setAuthor(DedupUtility.mergeAuthor(dedup.getAuthor(),p.getAuthor())); - }); + publicationsToMerge.forEach( + p -> { + dedup.mergeFrom(p); + dedup.setAuthor(DedupUtility.mergeAuthor(dedup.getAuthor(), p.getAuthor())); + }); System.out.println(mapper.writeValueAsString(dedup)); } - } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 880e917ce7..7ad2f6d17a 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -1,9 +1,18 @@ package eu.dnetlib.dhp.oa.dedup; +import static java.nio.file.Files.createTempDirectory; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.mockito.Mockito.lenient; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import java.io.File; +import java.io.IOException; +import java.io.Serializable; +import java.net.URISyntaxException; +import java.nio.file.Paths; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -16,16 +25,6 @@ import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; -import java.io.File; -import java.io.IOException; -import java.io.Serializable; -import java.net.URISyntaxException; -import java.nio.file.Paths; - -import static java.nio.file.Files.createTempDirectory; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.mockito.Mockito.lenient; - @ExtendWith(MockitoExtension.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class) public class SparkDedupTest implements Serializable { @@ -39,61 +38,94 @@ public class SparkDedupTest implements Serializable { private static String testGraphBasePath; private static String testOutputBasePath; private static String testDedupGraphBasePath; - private final static String testActionSetId = "test-orchestrator"; + private static final String testActionSetId = "test-orchestrator"; @BeforeAll private static void cleanUp() throws IOException, URISyntaxException { - testGraphBasePath = Paths.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath(); + testGraphBasePath = + Paths.get( + SparkDedupTest.class + .getResource("/eu/dnetlib/dhp/dedup/entities") + .toURI()) + .toFile() + .getAbsolutePath(); - testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString(); - testDedupGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString(); + testOutputBasePath = + createTempDirectory(SparkDedupTest.class.getSimpleName() + "-") + .toAbsolutePath() + .toString(); + testDedupGraphBasePath = + createTempDirectory(SparkDedupTest.class.getSimpleName() + "-") + .toAbsolutePath() + .toString(); FileUtils.deleteDirectory(new File(testOutputBasePath)); FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); - spark = SparkSession - .builder() - .appName(SparkCreateSimRels.class.getSimpleName()) - .master("local[*]") - .config(new SparkConf()) - .getOrCreate(); + spark = + SparkSession.builder() + .appName(SparkCreateSimRels.class.getSimpleName()) + .master("local[*]") + .config(new SparkConf()) + .getOrCreate(); jsc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - } @BeforeEach private void setUp() throws IOException, ISLookUpException { - lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) - .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) + .thenReturn( + IOUtils.toString( + SparkDedupTest.class.getResourceAsStream( + "/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); - lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) - .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) + .thenReturn( + IOUtils.toString( + SparkDedupTest.class.getResourceAsStream( + "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); - lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) - .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) + .thenReturn( + IOUtils.toString( + SparkDedupTest.class.getResourceAsStream( + "/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); } @Test @Order(1) public void createSimRelsTest() throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); - parser.parseArgument(new String[]{ - "-mt", "local[*]", - "-i", testGraphBasePath, - "-asi", testActionSetId, - "-la", "lookupurl", - "-w", testOutputBasePath}); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateSimRels.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); + parser.parseArgument( + new String[] { + "-mt", "local[*]", + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath + }); new SparkCreateSimRels(parser, spark).run(isLookUpService); - long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel").count(); - long pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count(); + long orgs_simrel = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel") + .count(); + long pubs_simrel = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel") + .count(); assertEquals(3288, orgs_simrel); assertEquals(7260, pubs_simrel); @@ -103,44 +135,69 @@ public class SparkDedupTest implements Serializable { @Order(2) public void createMergeRelsTest() throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateMergeRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); - parser.parseArgument(new String[]{ - "-mt", "local[*]", - "-i", testGraphBasePath, - "-asi", testActionSetId, - "-la", "lookupurl", - "-w", testOutputBasePath}); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateMergeRels.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + parser.parseArgument( + new String[] { + "-mt", "local[*]", + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath + }); new SparkCreateMergeRels(parser, spark).run(isLookUpService); - long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count(); - long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count(); + long orgs_mergerel = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") + .count(); + long pubs_mergerel = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .count(); assertEquals(1244, orgs_mergerel); assertEquals(1460, pubs_mergerel); - } @Test @Order(3) public void createDedupRecordTest() throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); - parser.parseArgument(new String[]{ - "-mt", "local[*]", - "-i", testGraphBasePath, - "-asi", testActionSetId, - "-la", "lookupurl", - "-w", testOutputBasePath}); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateDedupRecord.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); + parser.parseArgument( + new String[] { + "-mt", "local[*]", + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath + }); new SparkCreateDedupRecord(parser, spark).run(isLookUpService); - long orgs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count(); - long pubs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count(); + long orgs_deduprecord = + jsc.textFile( + testOutputBasePath + + "/" + + testActionSetId + + "/organization_deduprecord") + .count(); + long pubs_deduprecord = + jsc.textFile( + testOutputBasePath + + "/" + + testActionSetId + + "/publication_deduprecord") + .count(); assertEquals(82, orgs_deduprecord); assertEquals(66, pubs_deduprecord); @@ -150,42 +207,55 @@ public class SparkDedupTest implements Serializable { @Order(4) public void updateEntityTest() throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkUpdateEntity.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); - parser.parseArgument(new String[]{ - "-mt", "local[*]", - "-i", testGraphBasePath, - "-w", testOutputBasePath, - "-o", testDedupGraphBasePath - }); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkUpdateEntity.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); + parser.parseArgument( + new String[] { + "-mt", "local[*]", + "-i", testGraphBasePath, + "-w", testOutputBasePath, + "-o", testDedupGraphBasePath + }); new SparkUpdateEntity(parser, spark).run(isLookUpService); long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count(); long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count(); - long mergedOrgs = spark - .read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .map(Relation::getTarget) - .distinct().count(); + long mergedOrgs = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct() + .count(); - long mergedPubs = spark - .read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .map(Relation::getTarget) - .distinct().count(); + long mergedPubs = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct() + .count(); assertEquals(897, publications); assertEquals(835, organizations); - long deletedOrgs = jsc.textFile(testDedupGraphBasePath + "/organization") - .filter(this::isDeletedByInference).count(); - long deletedPubs = jsc.textFile(testDedupGraphBasePath + "/publication") - .filter(this::isDeletedByInference).count(); + long deletedOrgs = + jsc.textFile(testDedupGraphBasePath + "/organization") + .filter(this::isDeletedByInference) + .count(); + long deletedPubs = + jsc.textFile(testDedupGraphBasePath + "/publication") + .filter(this::isDeletedByInference) + .count(); assertEquals(mergedOrgs, deletedOrgs); assertEquals(mergedPubs, deletedPubs); @@ -195,22 +265,24 @@ public class SparkDedupTest implements Serializable { @Order(5) public void propagateRelationTest() throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkPropagateRelation.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); - parser.parseArgument(new String[]{ - "-mt", "local[*]", - "-i", testGraphBasePath, - "-w", testOutputBasePath, - "-o", testDedupGraphBasePath - }); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkPropagateRelation.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); + parser.parseArgument( + new String[] { + "-mt", "local[*]", + "-i", testGraphBasePath, + "-w", testOutputBasePath, + "-o", testDedupGraphBasePath + }); new SparkPropagateRelation(parser, spark).run(isLookUpService); long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); assertEquals(826, relations); - } @AfterAll @@ -220,6 +292,6 @@ public class SparkDedupTest implements Serializable { } public boolean isDeletedByInference(String s) { - return s.contains("\"deletedbyinference\":true"); + return s.contains("\"deletedbyinference\":true"); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java index d72734ed5a..b8b83b7580 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java @@ -7,283 +7,285 @@ import org.junit.jupiter.api.Test; public class JsonPathTest { - String json = "{\t\"dataInfo\":{\t\t\"invisible\":false,\t\t\"inferred\":false,\t\t\"deletedbyinference\":false,\t\t\"trust\":\"0.810000002384185791\",\t\t\"inferenceprovenance\":\"\",\t\t\"provenanceaction\":{\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t}\t},\t\"lastupdatetimestamp\":1584960968152,\t\"id\":\"20|corda__h2020::9faf23721249f26ac2c16eb857ea1fb9\",\t\"originalId\":[\t\t\"corda__h2020::927957582\"\t],\t\"collectedfrom\":[\t\t{\t\t\t\"key\":\"openaire____::corda_h2020\",\t\t\t\"value\":\"CORDA - COmmon Research DAta Warehouse - Horizon 2020\",\t\t\t\"dataInfo\":null\t\t}\t],\t\"pid\":[\t],\t\"dateofcollection\":\"2016-06-05\",\t\"dateoftransformation\":\"2019-11-19\",\t\"extraInfo\":[\t],\t\"oaiprovenance\":null,\t\"legalshortname\":{\t\t\"value\":\"Comentor AB\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"legalname\":{\t\t\"value\":\"Comentor AB\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"alternativeNames\":[\t],\t\"websiteurl\":{\t\t\"value\":\"http://www.comentor.se\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"logourl\":null,\t\"eclegalbody\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"eclegalperson\":{\t\t\"value\":\"true\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecnonprofit\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecresearchorganization\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"echighereducation\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecinternationalorganizationeurinterests\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecinternationalorganization\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecenterprise\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecsmevalidated\":{\t\t\"value\":\"true\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecnutscode\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"country\":null}"; - DedupConfig conf = DedupConfig.load("{\n" + - " \"wf\" : {\n" + - " \"threshold\" : \"0.99\",\n" + - " \"dedupRun\" : \"001\",\n" + - " \"entityType\" : \"organization\",\n" + - " \"subEntityValue\": \"organization\",\n" + - " \"orderField\" : \"legalname\",\n" + - " \"queueMaxSize\" : \"2000\",\n" + - " \"groupMaxSize\" : \"50\",\n" + - " \"slidingWindowSize\" : \"200\",\n" + - " \"idPath\":\"$.id\",\n" + - " \"rootBuilder\" : [ \"organization\", \"projectOrganization_participation_isParticipant\", \"datasourceOrganization_provision_isProvidedBy\" ],\n" + - " \"includeChildren\" : \"true\",\n" + - " \"maxIterations\": \"20\"\n" + - " },\n" + - " \"pace\" : {\n" + - " \"clustering\" : [\n" + - " { \"name\" : \"sortedngrampairs\", \"fields\" : [ \"legalname\" ], \"params\" : { \"max\" : 2, \"ngramLen\" : \"3\"} },\n" + - " { \"name\" : \"suffixprefix\", \"fields\" : [ \"legalname\" ], \"params\" : { \"max\" : 1, \"len\" : \"3\" } },\n" + - " { \"name\" : \"urlclustering\", \"fields\" : [ \"websiteurl\" ], \"params\" : { } },\n" + - " { \"name\" : \"keywordsclustering\", \"fields\" : [ \"legalname\" ], \"params\" : { \"max\": 2, \"windowSize\": 4} }\n" + - " ],\n" + - " \"decisionTree\" : {\n" + - " \"start\": {\n" + - " \"fields\": [\n" + - " {\n" + - " \"field\": \"gridid\",\n" + - " \"comparator\": \"exactMatch\",\n" + - " \"weight\": 1,\n" + - " \"countIfUndefined\": \"false\",\n" + - " \"params\": {}\n" + - " }\n" + - " ],\n" + - " \"threshold\": 1,\n" + - " \"aggregation\": \"AVG\",\n" + - " \"positive\": \"MATCH\",\n" + - " \"negative\": \"NO_MATCH\",\n" + - " \"undefined\": \"layer2\",\n" + - " \"ignoreUndefined\": \"false\"\n" + - " },\n" + - " \"layer2\": {\n" + - " \"fields\": [\n" + - " {\n" + - " \"field\": \"websiteurl\",\n" + - " \"comparator\": \"domainExactMatch\",\n" + - " \"weight\": 1,\n" + - " \"countIfUndefined\": \"false\",\n" + - " \"params\": {}\n" + - " },\n" + - " {\n" + - " \"field\": \"country\",\n" + - " \"comparator\": \"exactMatch\",\n" + - " \"weight\": 1,\n" + - " \"countIfUndefined\": \"true\",\n" + - " \"params\": {}\n" + - " },\n" + - " {\n" + - " \"field\": \"legalname\",\n" + - " \"comparator\": \"numbersMatch\",\n" + - " \"weight\": 1,\n" + - " \"countIfUndefined\": \"true\",\n" + - " \"params\": {}\n" + - " },\n" + - " {\n" + - " \"field\": \"legalname\",\n" + - " \"comparator\": \"romansMatch\",\n" + - " \"weight\": 1,\n" + - " \"countIfUndefined\": \"true\",\n" + - " \"params\": {}\n" + - " }\n" + - " ],\n" + - " \"threshold\": 1,\n" + - " \"aggregation\": \"AND\",\n" + - " \"positive\": \"layer3\",\n" + - " \"negative\": \"NO_MATCH\",\n" + - " \"undefined\": \"layer3\",\n" + - " \"ignoreUndefined\": \"true\"\n" + - " },\n" + - " \"layer3\": {\n" + - " \"fields\": [\n" + - " {\n" + - " \"field\": \"legalname\",\n" + - " \"comparator\": \"cityMatch\",\n" + - " \"weight\": 1.0,\n" + - " \"countIfUndefined\": \"true\",\n" + - " \"params\": {\n" + - " \"windowSize\": \"4\"\n" + - " }\n" + - " }\n" + - " ],\n" + - " \"threshold\": 0.1,\n" + - " \"aggregation\": \"AVG\",\n" + - " \"positive\": \"layer4\",\n" + - " \"negative\": \"NO_MATCH\",\n" + - " \"undefined\": \"NO_MATCH\",\n" + - " \"ignoreUndefined\": \"true\"\n" + - " },\n" + - " \"layer4\": {\n" + - " \"fields\": [\n" + - " {\n" + - " \"field\": \"legalname\",\n" + - " \"comparator\": \"keywordMatch\",\n" + - " \"weight\": 1.0,\n" + - " \"countIfUndefined\": \"true\",\n" + - " \"params\": {\n" + - " \"windowSize\": \"4\"\n" + - " }\n" + - " }\n" + - " ],\n" + - " \"threshold\": 0.7,\n" + - " \"aggregation\": \"AVG\",\n" + - " \"positive\": \"layer5\",\n" + - " \"negative\": \"NO_MATCH\",\n" + - " \"undefined\": \"layer5\",\n" + - " \"ignoreUndefined\": \"true\"\n" + - " },\n" + - " \"layer5\": {\n" + - " \"fields\": [\n" + - " {\n" + - " \"field\": \"legalname\",\n" + - " \"comparator\": \"jaroWinklerNormalizedName\",\n" + - " \"weight\": 0.9,\n" + - " \"countIfUndefined\": \"true\",\n" + - " \"params\": {\n" + - " \"windowSize\": \"4\"\n" + - " }\n" + - " },\n" + - " {\n" + - " \"field\": \"legalshortname\",\n" + - " \"comparator\": \"jaroWinklerNormalizedName\",\n" + - " \"weight\": 0.1,\n" + - " \"countIfUndefined\": \"false\",\n" + - " \"params\": {\n" + - " \"windowSize\": 4\n" + - " }\n" + - " }\n" + - " ],\n" + - " \"threshold\": 0.9,\n" + - " \"aggregation\": \"W_MEAN\",\n" + - " \"positive\": \"MATCH\",\n" + - " \"negative\": \"NO_MATCH\",\n" + - " \"undefined\": \"NO_MATCH\",\n" + - " \"ignoreUndefined\": \"true\"\n" + - " }\n" + - " },\n" + - " \"model\" : [\n" + - " { \"name\" : \"country\", \"type\" : \"String\", \"path\" : \"$.country.classid\"},\n" + - " { \"name\" : \"legalshortname\", \"type\" : \"String\", \"path\" : \"$.legalshortname.value\"},\n" + - " { \"name\" : \"legalname\", \"type\" : \"String\", \"path\" : \"$.legalname.value\" },\n" + - " { \"name\" : \"websiteurl\", \"type\" : \"URL\", \"path\" : \"$.websiteurl.value\" },\n" + - " { \"name\" : \"gridid\", \"type\" : \"String\", \"path\" : \"$.pid[?(@.qualifier.classid =='grid')].value\"},\n" + - " { \"name\" : \"originalId\", \"type\" : \"String\", \"path\" : \"$.id\" }\n" + - " ],\n" + - " \"blacklists\" : {\n" + - " \"legalname\" : []\n" + - " },\n" + - " \"synonyms\": {\n" + - " \"key::1\": [\"university\",\"università\", \"universitas\", \"università studi\",\"universitario\",\"universitaria\",\"université\", \"universite\", \"universitaire\",\"universitaires\",\"universidad\",\"universitade\",\"Universität\",\"universitaet\",\"Uniwersytet\",\"университет\",\"universiteit\",\"πανεπιστήμιο\",\"universitesi\",\"universiteti\", \"universiti\"],\n" + - " \"key::2\": [\"studies\",\"studi\",\"études\",\"estudios\",\"estudos\",\"Studien\",\"studia\",\"исследования\",\"studies\",\"σπουδές\"],\n" + - " \"key::3\": [\"advanced\",\"superiore\",\"supérieur\",\"supérieure\",\"supérieurs\",\"supérieures\",\"avancado\",\"avancados\",\"fortgeschrittene\",\"fortgeschritten\",\"zaawansowany\",\"передовой\",\"gevorderd\",\"gevorderde\",\"προχωρημένος\",\"προχωρημένη\",\"προχωρημένο\",\"προχωρημένες\",\"προχωρημένα\",\"wyzsza\"],\n" + - " \"key::4\": [\"institute\",\"istituto\",\"institut\",\"instituto\",\"instituto\",\"Institut\",\"instytut\",\"институт\",\"instituut\",\"ινστιτούτο\"],\n" + - " \"key::5\": [\"hospital\",\"ospedale\",\"hôpital\",\"hospital\",\"hospital\",\"Krankenhaus\",\"szpital\",\"больница\",\"ziekenhuis\",\"νοσοκομείο\"],\n" + - " \"key::6\": [\"research\",\"ricerca\",\"recherche\",\"investigacion\",\"pesquisa\",\"Forschung\",\"badania\",\"исследования\",\"onderzoek\",\"έρευνα\",\"erevna\",\"erevnas\"],\n" + - " \"key::7\": [\"college\",\"collegio\",\"colegio\",\"faculdade\",\"Hochschule\",\"Szkoła Wyższa\",\"Высшая школа\",\"κολλέγιο\"],\n" + - " \"key::8\": [\"foundation\",\"fondazione\",\"fondation\",\"fundación\",\"fundação\",\"Stiftung\",\"Fundacja\",\"фонд\",\"stichting\",\"ίδρυμα\",\"idryma\"],\n" + - " \"key::9\": [\"center\",\"centro\",\"centre\",\"centro\",\"centro\",\"zentrum\",\"centrum\",\"центр\",\"centrum\",\"κέντρο\"],\n" + - " \"key::10\": [\"national\",\"nazionale\",\"national\",\"nationale\",\"nationaux\",\"nationales\",\"nacional\",\"nacional\",\"national\",\"krajowy\",\"национальный\",\"nationaal\",\"nationale\",\"εθνικό\"],\n" + - " \"key::11\": [\"association\",\"associazione\",\"association\",\"asociación\",\"associação\",\"Verein\",\"verband\",\"stowarzyszenie\",\"ассоциация\",\"associatie\"],\n" + - " \"key::12\": [\"society\",\"societa\",\"société\",\"sociedad\",\"sociedade\",\"gesellschaft\",\"społeczeństwo\",\"общество\",\"maatschappij\",\"κοινωνία\"],\n" + - " \"key::13\": [\"international\",\"internazionale\",\"international\",\"internacional\",\"internacional\",\"international\",\"międzynarodowy\",\"Международный\",\"internationaal\",\"internationale\",\"διεθνής\",\"διεθνή\",\"διεθνές\"],\n" + - " \"key::14\": [\"community\",\"comunita\",\"communauté\",\"comunidad\",\"comunidade\",\"Gemeinschaft\",\"społeczność\",\"сообщество\",\"gemeenschap\",\"κοινότητα\"],\n" + - " \"key::15\": [\"school\",\"scuola\",\"école\",\"escuela\",\"escola\",\"schule\",\"Szkoła\",\"школа\",\"school\",\"σχολείο\"],\n" + - " \"key::16\": [\"education\",\"educazione\",\"éducation\",\"educacion\",\"Educação\",\"Bildung\",\"Edukacja\",\"образование\",\"opleiding\",\"εκπαίδευση\"],\n" + - " \"key::17\": [\"academy\",\"accademia\",\"académie\",\"academia\",\"academia\",\"Akademie\",\"akademie\",\"академия\",\"academie\",\"ακαδημία\"],\n" + - " \"key::18\": [\"public\",\"pubblico\",\"public\",\"publique\",\"publics\",\"publiques\",\"publico\",\"publico\",\"Öffentlichkeit\",\"publiczny\",\"публичный\",\"publiek\",\"publieke\",\"δημόσιος\",\"δημόσια\",\"δημόσιο\"],\n" + - " \"key::19\": [\"museum\",\"museo\",\"musée\",\"mueso\",\"museu\",\"museum\",\"muzeum\",\"музей\",\"museum\",\"μουσείο\"],\n" + - " \"key::20\": [\"group\",\"gruppo\",\"groupe\",\"grupo\",\"grupo\",\"gruppe\",\"grupa\",\"группа\",\"groep\",\"ομάδα\",\"όμιλος\"],\n" + - " \"key::21\": [\"department\",\"dipartimento\",\"département\",\"departamento\",\"departamento\",\"abteilung\",\"departament\",\"отдел\",\"afdeling\",\"τμήμα\"],\n" + - " \"key::22\": [\"council\",\"consiglio\",\"conseil\",\"Consejo\",\"conselho\",\"gesellschaft\",\"rada\",\"совет\",\"raad\",\"συμβούλιο\"],\n" + - " \"key::23\": [\"library\",\"biblioteca\",\"bibliothèque\",\"biblioteca\",\"biblioteca\",\"Bibliothek\",\"biblioteka\",\"библиотека\",\"bibliotheek\",\"βιβλιοθήκη\"],\n" + - " \"key::24\": [\"ministry\",\"ministero\",\"ministère\",\"ministerio\",\"ministério\",\"Ministerium\",\"ministerstwo\",\"министерство\",\"ministerie\",\"υπουργείο\"],\n" + - " \"key::25\": [\"services\",\"servizi\",\"services\",\"servicios\",\"Serviços\",\"Dienstleistungen\",\"usługi\",\"услуги\",\"diensten\",\"υπηρεσίες\"],\n" + - " \"key::26\": [\"central\",\"centrale\",\"central\",\"centrale\",\"centrales\",\"central\",\"central\",\"zentral\",\"centralny\",\"цетральный\",\"centraal\",\"κεντρικός\",\"κεντρική\",\"κεντρικό\",\"κεντρικά\"],\n" + - " \"key::27\": [\"general\",\"generale\",\"général\",\"générale\",\"généraux\",\"générales\",\"general\",\"geral\",\"general\",\"Allgemeines\",\"general\",\"общий\",\"algemeen\",\"algemene\",\"γενικός\",\"γενική\",\"γενικό\",\"γενικά\"],\n" + - " \"key::28\": [\"applied\",\"applicati\",\"appliqué\",\"appliquée\",\"appliqués\",\"appliquées\",\"aplicado\",\"aplicada\",\"angewendet\",\"stosowany\",\"прикладной\",\"toegepast\",\"toegepaste\",\"εφαρμοσμένος\",\"εφαρμοσμένη\",\"εφαρμοσμένο\",\"εφαρμοσμένα\"],\n" + - " \"key::29\": [\"european\",\"europee\",\"europea\",\"européen\",\"européenne\",\"européens\",\"européennes\",\"europeo\",\"europeu\",\"europäisch\",\"europejski\",\"европейский\",\"Europees\",\"Europese\",\"ευρωπαϊκός\",\"ευρωπαϊκή\",\"ευρωπαϊκό\",\"ευρωπαϊκά\"],\n" + - " \"key::30\": [\"agency\",\"agenzia\",\"agence\",\"agencia\",\"agencia\",\"agentur\",\"agencja\",\"агенция\",\"agentschap\",\"πρακτορείο\"],\n" + - " \"key::31\": [\"laboratory\",\"laboratorio\",\"laboratoire\",\"laboratorio\",\"laboratorio\",\"labor\",\"laboratorium\",\"лаборатория\",\"laboratorium\",\"εργαστήριο\"],\n" + - " \"key::32\": [\"industry\",\"industria\",\"industrie\",\"индустрия\",\"industrie\",\"βιομηχανία\"],\n" + - " \"key::33\": [\"industrial\",\"industriale\",\"industriel\",\"industrielle\",\"industriels\",\"industrielles\",\"индустриальный\",\"industrieel\",\"βιομηχανικός\",\"βιομηχανική\",\"βιομηχανικό\",\"βιομηχανικά\",\"βιομηχανικές\"],\n" + - " \"key::34\": [\"consortium\",\"consorzio\",\"consortium\",\"консорциум\",\"consortium\",\"κοινοπραξία\"],\n" + - " \"key::35\": [\"organization\",\"organizzazione\",\"organisation\",\"organización\",\"organização\",\"organizacja\",\"организация\",\"organisatie\",\"οργανισμός\"],\n" + - " \"key::36\": [\"authority\",\"autorità\",\"autorité\",\"авторитет\",\"autoriteit\"],\n" + - " \"key::37\": [\"federation\",\"federazione\",\"fédération\",\"федерация\",\"federatie\",\"ομοσπονδία\"],\n" + - " \"key::38\": [\"observatory\",\"osservatorio\",\"observatoire\",\"обсерватория\",\"observatorium\",\"αστεροσκοπείο\"],\n" + - " \"key::39\": [\"bureau\",\"ufficio\",\"bureau\",\"офис\",\"bureau\",\"γραφείο\"],\n" + - " \"key::40\": [\"company\",\"impresa\",\"compagnie\",\"société\",\"компания\",\"bedrijf\",\"εταιρία\"],\n" + - " \"key::41\": [\"polytechnic\",\"politecnico\",\"polytechnique\",\"политехника\",\"polytechnisch\",\"πολυτεχνείο\",\"universita politecnica\",\"polytechnic university\",\"universidad politecnica\",\"universitat politecnica\",\"politechnika\",\"politechniki\",\"university technology\",\"university science technology\"],\n" + - " \"key::42\": [\"coalition\",\"coalizione\",\"coalition\",\"коалиция\",\"coalitie\",\"συνασπισμός\"],\n" + - " \"key::43\": [\"initiative\",\"iniziativa\",\"initiative\",\"инициатива\",\"initiatief\",\"πρωτοβουλία\"],\n" + - " \"key::44\": [\"academic\",\"accademico\",\"académique\",\"universitaire\",\"акадеческий academisch\",\"ακαδημαϊκός\",\"ακαδημαϊκή\",\"ακαδημαϊκό\",\"ακαδημαϊκές\",\"ακαδημαϊκοί\"],\n" + - " \"key::45\": [\"institution\",\"istituzione\",\"institution\",\"институциональный\",\"instelling\",\"ινστιτούτο\"],\n" + - " \"key::46\": [\"division\",\"divisione\",\"division\",\"отделение\",\"divisie\",\"τμήμα\"],\n" + - " \"key::47\": [\"committee\",\"comitato\",\"comité\",\"комитет\",\"commissie\",\"επιτροπή\"],\n" + - " \"key::48\": [\"promotion\",\"promozione\",\"продвижение\",\"proothisis\",\"forderung\"],\n" + - " \"key::49\": [\"medical\",\"medicine\",\"clinical\",\"medicina\",\"clinici\",\"médico\",\"medicina\",\"clínica\",\"médico\",\"medicina\",\"clínica\",\"medizinisch\",\"Medizin\",\"klinisch\",\"medisch\",\"geneeskunde\",\"klinisch\",\"ιατρικός\",\"ιατρική\",\"ιατρικό\",\"ιατρικά\",\"κλινικός\",\"κλινική\",\"κλινικό\",\"κλινικά\",\"tıbbi\",\"tıp\",\"klinik\",\"orvosi\",\"orvostudomány\",\"klinikai\",\"zdravniški\",\"medicinski\",\"klinični\",\"meditsiini\",\"kliinik\",\"kliiniline\"],\n" + - " \"key::50\": [\"technology\",\"technological\",\"tecnologia\",\"tecnologie\",\"tecnología\",\"tecnológico\",\"tecnologia\",\"tecnológico\",\"Technologie\",\"technologisch\",\"technologie\",\"technologisch\",\"τεχνολογία\",\"τεχνολογικός\",\"τεχνολογική\",\"τεχνολογικό\",\"teknoloji\",\"teknolojik\",\"technológia\",\"technológiai\",\"tehnologija\",\"tehnološki\",\"tehnoloogia\",\"tehnoloogiline\",\"technologii\",\"technical\",\"texniki\",\"teknik\"],\n" + - " \"key::51\": [\"science\",\"scientific\",\"scienza\",\"scientifiche\",\"scienze\",\"ciencia\",\"científico\",\"ciência\",\"científico\",\"Wissenschaft\",\"wissenschaftlich\",\"wetenschap\",\"wetenschappelijk\",\"επιστήμη\",\"επιστημονικός\",\"επιστημονική\",\"επιστημονικό\",\"επιστημονικά\",\"bilim\",\"bilimsel\",\"tudomány\",\"tudományos\",\"znanost\",\"znanstveni\",\"teadus\",\"teaduslik\",\"\"],\n" + - " \"key::52\": [\"engineering\",\"ingegneria\",\"ingeniería\",\"engenharia\",\"Ingenieurwissenschaft\",\"ingenieurswetenschappen\",\"bouwkunde\",\"μηχανικός\",\"μηχανική\",\"μηχανικό\",\"mühendislik\",\"mérnöki\",\"Inženirstvo\",\"inseneeria\",\"inseneri\",\"\"],\n" + - " \"key::53\": [\"management\",\"gestione\",\"gestionale\",\"gestionali\",\"gestión\",\"administración\",\"gestão\",\"administração\",\"Verwaltung\",\"management\",\"διαχείριση\",\"yönetim\",\"menedzsment\",\"vodstvo\",\"upravljanje\",\"management\",\"juhtkond\",\"juhtimine\",\"haldus\",\"\"],\n" + - " \"key::54\": [\"energy\",\"energia\",\"energía\",\"energia\",\"Energie\",\"energie\",\"ενέργεια\",\"enerji\",\"energia\",\"energija\",\"energia\",\"\"],\n" + - " \"key::55\": [\"agricultural\",\"agriculture\",\"agricoltura\",\"agricole\",\"agrícola\",\"agricultura\",\"agrícola\",\"agricultura\",\"landwirtschaftlich\",\"Landwirtschaft\",\"landbouwkundig\",\"landbouw\",\"αγροτικός\",\"αγροτική\",\"αγροτικό\",\"γεωργικός\",\"γεωργική\",\"γεωργικό\",\"γεωργία\",\"tarımsal\",\"tarım\",\"mezőgazdasági\",\"mezőgazdaság\",\"poljedelski\",\"poljedelstvo\",\"põllumajandus\",\"põllumajanduslik\",\"\"],\n" + - " \"key::56\": [\"information\",\"informazione\",\"información\",\"informação\",\"Information\",\"informatie\",\"πληροφορία\",\"bilgi\",\"információ\",\"informacija\",\"informatsioon\",\"informatycznych\",\"\"],\n" + - " \"key::57\": [\"social\",\"sociali\",\"social\",\"social\",\"Sozial\",\"sociaal\",\"maatschappelijk\",\"κοινωνικός\",\"κοινωνική\",\"κοινωνικό\",\"κοινωνικά\",\"sosyal\",\"szociális\",\"družbeni\",\"sotsiaal\",\"sotsiaalne\",\"\"],\n" + - " \"key::58\": [\"environmental\",\"ambiente\",\"medioambiental\",\"ambiente\",\"medioambiente\",\"meioambiente\",\"Umwelt\",\"milieu\",\"milieuwetenschap\",\"milieukunde\",\"περιβαλλοντικός\",\"περιβαλλοντική\",\"περιβαλλοντικό\",\"περιβαλλοντικά\",\"çevre\",\"környezeti\",\"okoliški\",\"keskonna\",\"\"],\n" + - " \"key::59\": [\"business\",\"economia\",\"economiche\",\"economica\",\"negocio\",\"empresa\",\"negócio\",\"Unternehmen\",\"bedrijf\",\"bedrijfskunde\",\"επιχείρηση\",\"iş\",\"üzleti\",\"posel\",\"ettevõte/äri\",\"\"],\n" + - " \"key::60\": [\"pharmaceuticals\",\"pharmacy\",\"farmacia\",\"farmaceutica\",\"farmacéutica\",\"farmacia\",\"farmacêutica\",\"farmácia\",\"Pharmazeutika\",\"Arzneimittelkunde\",\"farmaceutica\",\"geneesmiddelen\",\"apotheek\",\"φαρμακευτικός\",\"φαρμακευτική\",\"φαρμακευτικό\",\"φαρμακευτικά\",\"φαρμακείο\",\"ilaç\",\"eczane\",\"gyógyszerészeti\",\"gyógyszertár\",\"farmacevtika\",\"lekarništvo\",\"farmaatsia\",\"farmatseutiline\",\"\"],\n" + - " \"key::61\": [\"healthcare\",\"health services\",\"salute\",\"atenciónmédica\",\"cuidadodelasalud\",\"cuidadoscomasaúde\",\"Gesundheitswesen\",\"gezondheidszorg\",\"ιατροφαρμακευτικήπερίθαλψη\",\"sağlıkhizmeti\",\"egészségügy\",\"zdravstvo\",\"tervishoid\",\"tervishoiu\",\"\"],\n" + - " \"key::62\": [\"history\",\"storia\",\"historia\",\"história\",\"Geschichte\",\"geschiedenis\",\"geschiedkunde\",\"ιστορία\",\"tarih\",\"történelem\",\"zgodovina\",\"ajalugu\",\"\"],\n" + - " \"key::63\": [\"materials\",\"materiali\",\"materia\",\"materiales\",\"materiais\",\"materialen\",\"υλικά\",\"τεκμήρια\",\"malzemeler\",\"anyagok\",\"materiali\",\"materjalid\",\"vahendid\",\"\"],\n" + - " \"key::64\": [\"economics\",\"economia\",\"economiche\",\"economica\",\"economía\",\"economia\",\"Wirtschaft\",\"economie\",\"οικονομικά\",\"οικονομικέςεπιστήμες\",\"ekonomi\",\"közgazdaságtan\",\"gospodarstvo\",\"ekonomija\",\"majanduslik\",\"majandus\",\"\"],\n" + - " \"key::65\": [\"therapeutics\",\"terapeutica\",\"terapéutica\",\"terapêutica\",\"therapie\",\"θεραπευτική\",\"tedavibilimi\",\"gyógykezelés\",\"terapevtika\",\"terapeutiline\",\"ravi\",\"\"],\n" + - " \"key::66\": [\"oncology\",\"oncologia\",\"oncologico\",\"oncología\",\"oncologia\",\"Onkologie\",\"oncologie\",\"ογκολογία\",\"onkoloji\",\"onkológia\",\"onkologija\",\"onkoloogia\",\"\"],\n" + - " \"key::67\": [\"natural\",\"naturali\",\"naturale\",\"natural\",\"natural\",\"natürlich\",\"natuurlijk\",\"φυσικός\",\"φυσική\",\"φυσικό\",\"φυσικά\",\"doğal\",\"természetes\",\"naraven\",\"loodus\",\"\"],\n" + - " \"key::68\": [\"educational\",\"educazione\",\"pedagogia\",\"educacional\",\"educativo\",\"educacional\",\"pädagogisch\",\"educatief\",\"εκπαιδευτικός\",\"εκπαιδευτική\",\"εκπαιδευτικό\",\"εκπαιδευτικά\",\"eğitimsel\",\"oktatási\",\"izobraževalen\",\"haridus\",\"hariduslik\",\"\"],\n" + - " \"key::69\": [\"biomedical\",\"biomedica\",\"biomédico\",\"biomédico\",\"biomedizinisch\",\"biomedisch\",\"βιοιατρικός\",\"βιοιατρική\",\"βιοιατρικό\",\"βιοιατρικά\",\"biyomedikal\",\"orvosbiológiai\",\"biomedicinski\",\"biomeditsiiniline\",\"\"],\n" + - " \"key::70\": [\"veterinary\",\"veterinaria\",\"veterinarie\",\"veterinaria\",\"veterinária\",\"tierärtzlich\",\"veterinair\",\"veeartsenijlkunde\",\"κτηνιατρικός\",\"κτηνιατρική\",\"κτηνιατρικό\",\"κτηνιατρικά\",\"veteriner\",\"állatorvosi\",\"veterinar\",\"veterinarski\",\"veterinaaria\",\"\"],\n" + - " \"key::71\": [\"chemistry\",\"chimica\",\"química\",\"química\",\"Chemie\",\"chemie\",\"scheikunde\",\"χημεία\",\"kimya\",\"kémia\",\"kemija\",\"keemia\",\"\"],\n" + - " \"key::72\": [\"security\",\"sicurezza\",\"seguridad\",\"segurança\",\"Sicherheit\",\"veiligheid\",\"ασφάλεια\",\"güvenlik\",\"biztonsági\",\"varnost\",\"turvalisus\",\"julgeolek\",\"\"],\n" + - " \"key::73\": [\"biotechnology\",\"biotecnologia\",\"biotecnologie\",\"biotecnología\",\"biotecnologia\",\"Biotechnologie\",\"biotechnologie\",\"βιοτεχνολογία\",\"biyoteknoloji\",\"biotechnológia\",\"biotehnologija\",\"biotehnoloogia\",\"\"],\n" + - " \"key::74\": [\"military\",\"militare\",\"militari\",\"militar\",\"militar\",\"Militär\",\"militair\",\"leger\",\"στρατιωτικός\",\"στρατιωτική\",\"στρατιωτικό\",\"στρατιωτικά\",\"askeri\",\"katonai\",\"vojaški\",\"vojni\",\"militaar\",\"wojskowa\",\"\"],\n" + - " \"key::75\": [\"theological\",\"teologia\",\"teologico\",\"teológico\",\"tecnológica\",\"theologisch\",\"theologisch\",\"θεολογικός\",\"θεολογική\",\"θεολογικό\",\"θεολογικά\",\"teolojik\",\"technológiai\",\"teološki\",\"teoloogia\",\"usuteadus\",\"teoloogiline\",\"\"],\n" + - " \"key::76\": [\"electronics\",\"elettronica\",\"electrónica\",\"eletrônicos\",\"Elektronik\",\"elektronica\",\"ηλεκτρονική\",\"elektronik\",\"elektronika\",\"elektronika\",\"elektroonika\",\"\"],\n" + - " \"key::77\": [\"forestry\",\"forestale\",\"forestali\",\"silvicultura\",\"forestal\",\"floresta\",\"Forstwirtschaft\",\"bosbouw\",\"δασοκομία\",\"δασολογία\",\"ormancılık\",\"erdészet\",\"gozdarstvo\",\"metsandus\",\"\"],\n" + - " \"key::78\": [\"maritime\",\"marittima\",\"marittime\",\"marittimo\",\"marítimo\",\"marítimo\",\"maritiem\",\"ναυτικός\",\"ναυτική\",\"ναυτικό\",\"ναυτικά\",\"ναυτιλιακός\",\"ναυτιλιακή\",\"ναυτιλιακό\",\"ναυτιλιακά\",\"θαλάσσιος\",\"θαλάσσια\",\"θαλάσσιο\",\"denizcilik\",\"tengeri\",\"morski\",\"mere\",\"merendus\",\"\"],\n" + - " \"key::79\": [\"sports\",\"sport\",\"deportes\",\"esportes\",\"Sport\",\"sport\",\"sportwetenschappen\",\"άθληση\",\"γυμναστικήδραστηριότητα\",\"spor\",\"sport\",\"šport\",\"sport\",\"spordi\",\"\"],\n" + - " \"key::80\": [\"surgery\",\"chirurgia\",\"chirurgiche\",\"cirugía\",\"cirurgia\",\"Chirurgie\",\"chirurgie\",\"heelkunde\",\"εγχείρηση\",\"επέμβαση\",\"χειρουργικήεπέμβαση\",\"cerrahi\",\"sebészet\",\"kirurgija\",\"kirurgia\",\"\"],\n" + - " \"key::81\": [\"cultural\",\"culturale\",\"culturali\",\"cultura\",\"cultural\",\"cultural\",\"kulturell\",\"cultureel\",\"πολιτιστικός\",\"πολιτιστική\",\"πολιτιστικό\",\"πολιτισμικός\",\"πολιτισμική\",\"πολιτισμικό\",\"kültürel\",\"kultúrális\",\"kulturni\",\"kultuuri\",\"kultuuriline\",\"\"],\n" + - " \"key::82\": [\"computerscience\",\"informatica\",\"ordenador\",\"computadora\",\"informática\",\"computación\",\"cienciasdelacomputación\",\"ciênciadacomputação\",\"Computer\",\"computer\",\"υπολογιστής\",\"ηλεκτρονικόςυπολογιστής\",\"bilgisayar\",\"számítógép\",\"računalnik\",\"arvuti\",\"\"],\n" + - " \"key::83\": [\"finance\",\"financial\",\"finanza\",\"finanziarie\",\"finanza\",\"financiero\",\"finanças\",\"financeiro\",\"Finanzen\",\"finanziell\",\"financiën\",\"financieel\",\"χρηματοοικονομικά\",\"χρηματοδότηση\",\"finanse\",\"finansal\",\"pénzügy\",\"pénzügyi\",\"finance\",\"finančni\",\"finants\",\"finantsiline\",\"\"],\n" + - " \"key::84\": [\"communication\",\"comunicazione\",\"comuniciación\",\"comunicação\",\"Kommunikation\",\"communication\",\"επικοινωνία\",\"iletişim\",\"kommunikáció\",\"komuniciranje\",\"kommunikatsioon\",\"\"],\n" + - " \"key::85\": [\"justice\",\"giustizia\",\"justicia\",\"justiça\",\"Recht\",\"Justiz\",\"justitie\",\"gerechtigheid\",\"δικαιοσύνη\",\"υπουργείοδικαιοσύνης\",\"δίκαιο\",\"adalet\",\"igazságügy\",\"pravo\",\"õigus\",\"\"],\n" + - " \"key::86\": [\"aerospace\",\"aerospaziale\",\"aerospaziali\",\"aeroespacio\",\"aeroespaço\",\"Luftfahrt\",\"luchtvaart\",\"ruimtevaart\",\"αεροπορικός\",\"αεροπορική\",\"αεροπορικό\",\"αεροναυπηγικός\",\"αεροναυπηγική\",\"αεροναυπηγικό\",\"αεροναυπηγικά\",\"havacılıkveuzay\",\"légtér\",\"zrakoplovstvo\",\"atmosfäär\",\"kosmos\",\"\"],\n" + - " \"key::87\": [\"dermatology\",\"dermatologia\",\"dermatología\",\"dermatologia\",\"Dermatologie\",\"dermatologie\",\"δρματολογία\",\"dermatoloji\",\"bőrgyógyászat\",\"dermatológia\",\"dermatologija\",\"dermatoloogia\",\"\"],\n" + - " \"key::88\": [\"architecture\",\"architettura\",\"arquitectura\",\"arquitetura\",\"Architektur\",\"architectuur\",\"αρχιτεκτονική\",\"mimarlık\",\"építészet\",\"arhitektura\",\"arhitektuur\",\"\"],\n" + - " \"key::89\": [\"mathematics\",\"matematica\",\"matematiche\",\"matemáticas\",\"matemáticas\",\"Mathematik\",\"wiskunde\",\"mathematica\",\"μαθηματικά\",\"matematik\",\"matematika\",\"matematika\",\"matemaatika\",\"\"],\n" + - " \"key::90\": [\"language\",\"lingue\",\"linguistica\",\"linguistiche\",\"lenguaje\",\"idioma\",\"língua\",\"idioma\",\"Sprache\",\"taal\",\"taalkunde\",\"γλώσσα\",\"dil\",\"nyelv\",\"jezik\",\"keel\",\"\"],\n" + - " \"key::91\": [\"neuroscience\",\"neuroscienza\",\"neurociencia\",\"neurociência\",\"Neurowissenschaft\",\"neurowetenschappen\",\"νευροεπιστήμη\",\"nörobilim\",\"idegtudomány\",\"nevroznanost\",\"neuroteadused\",\"\"],\n" + - " \"key::92\": [\"automation\",\"automazione\",\"automatización\",\"automação\",\"Automatisierung\",\"automatisering\",\"αυτοματοποίηση\",\"otomasyon\",\"automatizálás\",\"avtomatizacija\",\"automatiseeritud\",\"\"],\n" + - " \"key::93\": [\"pediatric\",\"pediatria\",\"pediatriche\",\"pediatrico\",\"pediátrico\",\"pediatría\",\"pediátrico\",\"pediatria\",\"pädiatrisch\",\"pediatrische\",\"παιδιατρική\",\"pediatrik\",\"gyermekgyógyászat\",\"pediatrija\",\"pediaatria\",\"\"],\n" + - " \"key::94\": [\"photonics\",\"fotonica\",\"fotoniche\",\"fotónica\",\"fotônica\",\"Photonik\",\"fotonica\",\"φωτονική\",\"fotonik\",\"fotonika\",\"fotonika\",\"fotoonika\",\"\"],\n" + - " \"key::95\": [\"mechanics\", \"mechanical\", \"meccanica\",\"meccaniche\",\"mecánica\",\"mecânica\",\"Mechanik\",\"Maschinenbau\",\"mechanica\",\"werktuigkunde\",\"μηχανικής\",\"mekanik\",\"gépészet\",\"mehanika\",\"mehaanika\",\"\"],\n" + - " \"key::96\": [\"psychiatrics\",\"psichiatria\",\"psichiatrica\",\"psichiatriche\",\"psiquiatría\",\"psiquiatria\",\"Psychiatrie\",\"psychiatrie\",\"ψυχιατρική\",\"psikiyatrik\",\"pszihiátria\",\"psihiatrija\",\"psühhaatria\",\"\"],\n" + - " \"key::97\": [\"psychology\",\"fisiologia\",\"psicología\",\"psicologia\",\"Psychologie\",\"psychologie\",\"ψυχολογία\",\"psikoloji\",\"pszihológia\",\"psihologija\",\"psühholoogia\",\"\"],\n" + - " \"key::98\": [\"automotive\",\"industriaautomobilistica\",\"industriadelautomóvil\",\"automotriz\",\"industriaautomotriz\",\"automotivo\",\"Automobilindustrie\",\"autoindustrie\",\"αυτοκίνητος\",\"αυτοκίνητη\",\"αυτοκίνητο\",\"αυτοκινούμενος\",\"αυτοκινούμενη\",\"αυτοκινούμενο\",\"αυτοκινητιστικός\",\"αυτοκινητιστική\",\"αυτοκινητιστικό\",\"otomotiv\",\"autóipari\",\"samogiben\",\"avtomobilskaindustrija\",\"auto-\",\"\"],\n" + - " \"key::99\": [\"neurology\",\"neurologia\",\"neurologiche\",\"neurología\",\"neurologia\",\"Neurologie\",\"neurologie\",\"zenuwleer\",\"νευρολογία\",\"nöroloji\",\"neurológia\",\"ideggyógyászat\",\"nevrologija\",\"neuroloogia\",\"\"],\n" + - " \"key::100\": [\"geology\",\"geologia\",\"geologiche\",\"geología\",\"geologia\",\"Geologie\",\"geologie\",\"aardkunde\",\"γεωλογία\",\"jeoloji\",\"geológia\",\"földtudomány\",\"geologija\",\"geoloogia\",\"\"],\n" + - " \"key::101\": [\"microbiology\",\"microbiologia\",\"micro-biologia\",\"microbiologiche\",\"microbiología\",\"microbiologia\",\"Mikrobiologie\",\"microbiologie\",\"μικροβιολογία\",\"mikrobiyoloji\",\"mikrobiológia\",\"mikrobiologija\",\"mikrobioloogia\",\"\"],\n" + - " \"key::102\": [\"informatics\",\"informatica\",\"informática\",\"informática\",\"informatica\",\"\"],\n" + - " \"key::103\": [\"forschungsgemeinschaft\",\"comunita ricerca\",\"research community\",\"research foundation\",\"research association\"],\n" + - " \"key::104\": [\"commerce\",\"ticaret\",\"ticarət\",\"commercio\",\"trade\",\"handel\",\"comercio\"],\n" + - " \"key::105\" : [\"state\", \"stato\", \"etade\", \"estado\", \"statale\", \"etat\", \"zustand\", \"estado\"],\n" + - " \"key::106\" : [\"seminary\", \"seminario\", \"seminaire\", \"seminar\"],\n" + - " \"key::107\" : [\"agricultural forestry\", \"af\", \"a f\"],\n" + - " \"key::108\" : [\"agricultural mechanical\", \"am\", \"a m\"],\n" + - " \"key::109\" : [\"catholic\", \"catholique\", \"katholische\", \"catolica\", \"cattolica\", \"catolico\"]\n" + - " }\n" + - " }\n" + - "}"); + String json = + "{\t\"dataInfo\":{\t\t\"invisible\":false,\t\t\"inferred\":false,\t\t\"deletedbyinference\":false,\t\t\"trust\":\"0.810000002384185791\",\t\t\"inferenceprovenance\":\"\",\t\t\"provenanceaction\":{\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t}\t},\t\"lastupdatetimestamp\":1584960968152,\t\"id\":\"20|corda__h2020::9faf23721249f26ac2c16eb857ea1fb9\",\t\"originalId\":[\t\t\"corda__h2020::927957582\"\t],\t\"collectedfrom\":[\t\t{\t\t\t\"key\":\"openaire____::corda_h2020\",\t\t\t\"value\":\"CORDA - COmmon Research DAta Warehouse - Horizon 2020\",\t\t\t\"dataInfo\":null\t\t}\t],\t\"pid\":[\t],\t\"dateofcollection\":\"2016-06-05\",\t\"dateoftransformation\":\"2019-11-19\",\t\"extraInfo\":[\t],\t\"oaiprovenance\":null,\t\"legalshortname\":{\t\t\"value\":\"Comentor AB\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"legalname\":{\t\t\"value\":\"Comentor AB\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"alternativeNames\":[\t],\t\"websiteurl\":{\t\t\"value\":\"http://www.comentor.se\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"logourl\":null,\t\"eclegalbody\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"eclegalperson\":{\t\t\"value\":\"true\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecnonprofit\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecresearchorganization\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"echighereducation\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecinternationalorganizationeurinterests\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecinternationalorganization\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecenterprise\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecsmevalidated\":{\t\t\"value\":\"true\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"ecnutscode\":{\t\t\"value\":\"false\",\t\t\"dataInfo\":{\t\t\t\"invisible\":false,\t\t\t\"inferred\":false,\t\t\t\"deletedbyinference\":false,\t\t\t\"trust\":\"0.810000002384185791\",\t\t\t\"inferenceprovenance\":\"\",\t\t\t\"provenanceaction\":{\t\t\t\t\"classid\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"classname\":\"sysimport:crosswalk:entityregistry\",\t\t\t\t\"schemeid\":\"dnet:provenance_actions\",\t\t\t\t\"schemename\":\"dnet:provenance_actions\"\t\t\t}\t\t}\t},\t\"country\":null}"; + DedupConfig conf = + DedupConfig.load( + "{\n" + + " \"wf\" : {\n" + + " \"threshold\" : \"0.99\",\n" + + " \"dedupRun\" : \"001\",\n" + + " \"entityType\" : \"organization\",\n" + + " \"subEntityValue\": \"organization\",\n" + + " \"orderField\" : \"legalname\",\n" + + " \"queueMaxSize\" : \"2000\",\n" + + " \"groupMaxSize\" : \"50\",\n" + + " \"slidingWindowSize\" : \"200\",\n" + + " \"idPath\":\"$.id\",\n" + + " \"rootBuilder\" : [ \"organization\", \"projectOrganization_participation_isParticipant\", \"datasourceOrganization_provision_isProvidedBy\" ],\n" + + " \"includeChildren\" : \"true\",\n" + + " \"maxIterations\": \"20\"\n" + + " },\n" + + " \"pace\" : {\n" + + " \"clustering\" : [\n" + + " { \"name\" : \"sortedngrampairs\", \"fields\" : [ \"legalname\" ], \"params\" : { \"max\" : 2, \"ngramLen\" : \"3\"} },\n" + + " { \"name\" : \"suffixprefix\", \"fields\" : [ \"legalname\" ], \"params\" : { \"max\" : 1, \"len\" : \"3\" } },\n" + + " { \"name\" : \"urlclustering\", \"fields\" : [ \"websiteurl\" ], \"params\" : { } },\n" + + " { \"name\" : \"keywordsclustering\", \"fields\" : [ \"legalname\" ], \"params\" : { \"max\": 2, \"windowSize\": 4} }\n" + + " ],\n" + + " \"decisionTree\" : {\n" + + " \"start\": {\n" + + " \"fields\": [\n" + + " {\n" + + " \"field\": \"gridid\",\n" + + " \"comparator\": \"exactMatch\",\n" + + " \"weight\": 1,\n" + + " \"countIfUndefined\": \"false\",\n" + + " \"params\": {}\n" + + " }\n" + + " ],\n" + + " \"threshold\": 1,\n" + + " \"aggregation\": \"AVG\",\n" + + " \"positive\": \"MATCH\",\n" + + " \"negative\": \"NO_MATCH\",\n" + + " \"undefined\": \"layer2\",\n" + + " \"ignoreUndefined\": \"false\"\n" + + " },\n" + + " \"layer2\": {\n" + + " \"fields\": [\n" + + " {\n" + + " \"field\": \"websiteurl\",\n" + + " \"comparator\": \"domainExactMatch\",\n" + + " \"weight\": 1,\n" + + " \"countIfUndefined\": \"false\",\n" + + " \"params\": {}\n" + + " },\n" + + " {\n" + + " \"field\": \"country\",\n" + + " \"comparator\": \"exactMatch\",\n" + + " \"weight\": 1,\n" + + " \"countIfUndefined\": \"true\",\n" + + " \"params\": {}\n" + + " },\n" + + " {\n" + + " \"field\": \"legalname\",\n" + + " \"comparator\": \"numbersMatch\",\n" + + " \"weight\": 1,\n" + + " \"countIfUndefined\": \"true\",\n" + + " \"params\": {}\n" + + " },\n" + + " {\n" + + " \"field\": \"legalname\",\n" + + " \"comparator\": \"romansMatch\",\n" + + " \"weight\": 1,\n" + + " \"countIfUndefined\": \"true\",\n" + + " \"params\": {}\n" + + " }\n" + + " ],\n" + + " \"threshold\": 1,\n" + + " \"aggregation\": \"AND\",\n" + + " \"positive\": \"layer3\",\n" + + " \"negative\": \"NO_MATCH\",\n" + + " \"undefined\": \"layer3\",\n" + + " \"ignoreUndefined\": \"true\"\n" + + " },\n" + + " \"layer3\": {\n" + + " \"fields\": [\n" + + " {\n" + + " \"field\": \"legalname\",\n" + + " \"comparator\": \"cityMatch\",\n" + + " \"weight\": 1.0,\n" + + " \"countIfUndefined\": \"true\",\n" + + " \"params\": {\n" + + " \"windowSize\": \"4\"\n" + + " }\n" + + " }\n" + + " ],\n" + + " \"threshold\": 0.1,\n" + + " \"aggregation\": \"AVG\",\n" + + " \"positive\": \"layer4\",\n" + + " \"negative\": \"NO_MATCH\",\n" + + " \"undefined\": \"NO_MATCH\",\n" + + " \"ignoreUndefined\": \"true\"\n" + + " },\n" + + " \"layer4\": {\n" + + " \"fields\": [\n" + + " {\n" + + " \"field\": \"legalname\",\n" + + " \"comparator\": \"keywordMatch\",\n" + + " \"weight\": 1.0,\n" + + " \"countIfUndefined\": \"true\",\n" + + " \"params\": {\n" + + " \"windowSize\": \"4\"\n" + + " }\n" + + " }\n" + + " ],\n" + + " \"threshold\": 0.7,\n" + + " \"aggregation\": \"AVG\",\n" + + " \"positive\": \"layer5\",\n" + + " \"negative\": \"NO_MATCH\",\n" + + " \"undefined\": \"layer5\",\n" + + " \"ignoreUndefined\": \"true\"\n" + + " },\n" + + " \"layer5\": {\n" + + " \"fields\": [\n" + + " {\n" + + " \"field\": \"legalname\",\n" + + " \"comparator\": \"jaroWinklerNormalizedName\",\n" + + " \"weight\": 0.9,\n" + + " \"countIfUndefined\": \"true\",\n" + + " \"params\": {\n" + + " \"windowSize\": \"4\"\n" + + " }\n" + + " },\n" + + " {\n" + + " \"field\": \"legalshortname\",\n" + + " \"comparator\": \"jaroWinklerNormalizedName\",\n" + + " \"weight\": 0.1,\n" + + " \"countIfUndefined\": \"false\",\n" + + " \"params\": {\n" + + " \"windowSize\": 4\n" + + " }\n" + + " }\n" + + " ],\n" + + " \"threshold\": 0.9,\n" + + " \"aggregation\": \"W_MEAN\",\n" + + " \"positive\": \"MATCH\",\n" + + " \"negative\": \"NO_MATCH\",\n" + + " \"undefined\": \"NO_MATCH\",\n" + + " \"ignoreUndefined\": \"true\"\n" + + " }\n" + + " },\n" + + " \"model\" : [\n" + + " { \"name\" : \"country\", \"type\" : \"String\", \"path\" : \"$.country.classid\"},\n" + + " { \"name\" : \"legalshortname\", \"type\" : \"String\", \"path\" : \"$.legalshortname.value\"},\n" + + " { \"name\" : \"legalname\", \"type\" : \"String\", \"path\" : \"$.legalname.value\" },\n" + + " { \"name\" : \"websiteurl\", \"type\" : \"URL\", \"path\" : \"$.websiteurl.value\" },\n" + + " { \"name\" : \"gridid\", \"type\" : \"String\", \"path\" : \"$.pid[?(@.qualifier.classid =='grid')].value\"},\n" + + " { \"name\" : \"originalId\", \"type\" : \"String\", \"path\" : \"$.id\" }\n" + + " ],\n" + + " \"blacklists\" : {\n" + + " \"legalname\" : []\n" + + " },\n" + + " \"synonyms\": {\n" + + " \"key::1\": [\"university\",\"università\", \"universitas\", \"università studi\",\"universitario\",\"universitaria\",\"université\", \"universite\", \"universitaire\",\"universitaires\",\"universidad\",\"universitade\",\"Universität\",\"universitaet\",\"Uniwersytet\",\"университет\",\"universiteit\",\"πανεπιστήμιο\",\"universitesi\",\"universiteti\", \"universiti\"],\n" + + " \"key::2\": [\"studies\",\"studi\",\"études\",\"estudios\",\"estudos\",\"Studien\",\"studia\",\"исследования\",\"studies\",\"σπουδές\"],\n" + + " \"key::3\": [\"advanced\",\"superiore\",\"supérieur\",\"supérieure\",\"supérieurs\",\"supérieures\",\"avancado\",\"avancados\",\"fortgeschrittene\",\"fortgeschritten\",\"zaawansowany\",\"передовой\",\"gevorderd\",\"gevorderde\",\"προχωρημένος\",\"προχωρημένη\",\"προχωρημένο\",\"προχωρημένες\",\"προχωρημένα\",\"wyzsza\"],\n" + + " \"key::4\": [\"institute\",\"istituto\",\"institut\",\"instituto\",\"instituto\",\"Institut\",\"instytut\",\"институт\",\"instituut\",\"ινστιτούτο\"],\n" + + " \"key::5\": [\"hospital\",\"ospedale\",\"hôpital\",\"hospital\",\"hospital\",\"Krankenhaus\",\"szpital\",\"больница\",\"ziekenhuis\",\"νοσοκομείο\"],\n" + + " \"key::6\": [\"research\",\"ricerca\",\"recherche\",\"investigacion\",\"pesquisa\",\"Forschung\",\"badania\",\"исследования\",\"onderzoek\",\"έρευνα\",\"erevna\",\"erevnas\"],\n" + + " \"key::7\": [\"college\",\"collegio\",\"colegio\",\"faculdade\",\"Hochschule\",\"Szkoła Wyższa\",\"Высшая школа\",\"κολλέγιο\"],\n" + + " \"key::8\": [\"foundation\",\"fondazione\",\"fondation\",\"fundación\",\"fundação\",\"Stiftung\",\"Fundacja\",\"фонд\",\"stichting\",\"ίδρυμα\",\"idryma\"],\n" + + " \"key::9\": [\"center\",\"centro\",\"centre\",\"centro\",\"centro\",\"zentrum\",\"centrum\",\"центр\",\"centrum\",\"κέντρο\"],\n" + + " \"key::10\": [\"national\",\"nazionale\",\"national\",\"nationale\",\"nationaux\",\"nationales\",\"nacional\",\"nacional\",\"national\",\"krajowy\",\"национальный\",\"nationaal\",\"nationale\",\"εθνικό\"],\n" + + " \"key::11\": [\"association\",\"associazione\",\"association\",\"asociación\",\"associação\",\"Verein\",\"verband\",\"stowarzyszenie\",\"ассоциация\",\"associatie\"],\n" + + " \"key::12\": [\"society\",\"societa\",\"société\",\"sociedad\",\"sociedade\",\"gesellschaft\",\"społeczeństwo\",\"общество\",\"maatschappij\",\"κοινωνία\"],\n" + + " \"key::13\": [\"international\",\"internazionale\",\"international\",\"internacional\",\"internacional\",\"international\",\"międzynarodowy\",\"Международный\",\"internationaal\",\"internationale\",\"διεθνής\",\"διεθνή\",\"διεθνές\"],\n" + + " \"key::14\": [\"community\",\"comunita\",\"communauté\",\"comunidad\",\"comunidade\",\"Gemeinschaft\",\"społeczność\",\"сообщество\",\"gemeenschap\",\"κοινότητα\"],\n" + + " \"key::15\": [\"school\",\"scuola\",\"école\",\"escuela\",\"escola\",\"schule\",\"Szkoła\",\"школа\",\"school\",\"σχολείο\"],\n" + + " \"key::16\": [\"education\",\"educazione\",\"éducation\",\"educacion\",\"Educação\",\"Bildung\",\"Edukacja\",\"образование\",\"opleiding\",\"εκπαίδευση\"],\n" + + " \"key::17\": [\"academy\",\"accademia\",\"académie\",\"academia\",\"academia\",\"Akademie\",\"akademie\",\"академия\",\"academie\",\"ακαδημία\"],\n" + + " \"key::18\": [\"public\",\"pubblico\",\"public\",\"publique\",\"publics\",\"publiques\",\"publico\",\"publico\",\"Öffentlichkeit\",\"publiczny\",\"публичный\",\"publiek\",\"publieke\",\"δημόσιος\",\"δημόσια\",\"δημόσιο\"],\n" + + " \"key::19\": [\"museum\",\"museo\",\"musée\",\"mueso\",\"museu\",\"museum\",\"muzeum\",\"музей\",\"museum\",\"μουσείο\"],\n" + + " \"key::20\": [\"group\",\"gruppo\",\"groupe\",\"grupo\",\"grupo\",\"gruppe\",\"grupa\",\"группа\",\"groep\",\"ομάδα\",\"όμιλος\"],\n" + + " \"key::21\": [\"department\",\"dipartimento\",\"département\",\"departamento\",\"departamento\",\"abteilung\",\"departament\",\"отдел\",\"afdeling\",\"τμήμα\"],\n" + + " \"key::22\": [\"council\",\"consiglio\",\"conseil\",\"Consejo\",\"conselho\",\"gesellschaft\",\"rada\",\"совет\",\"raad\",\"συμβούλιο\"],\n" + + " \"key::23\": [\"library\",\"biblioteca\",\"bibliothèque\",\"biblioteca\",\"biblioteca\",\"Bibliothek\",\"biblioteka\",\"библиотека\",\"bibliotheek\",\"βιβλιοθήκη\"],\n" + + " \"key::24\": [\"ministry\",\"ministero\",\"ministère\",\"ministerio\",\"ministério\",\"Ministerium\",\"ministerstwo\",\"министерство\",\"ministerie\",\"υπουργείο\"],\n" + + " \"key::25\": [\"services\",\"servizi\",\"services\",\"servicios\",\"Serviços\",\"Dienstleistungen\",\"usługi\",\"услуги\",\"diensten\",\"υπηρεσίες\"],\n" + + " \"key::26\": [\"central\",\"centrale\",\"central\",\"centrale\",\"centrales\",\"central\",\"central\",\"zentral\",\"centralny\",\"цетральный\",\"centraal\",\"κεντρικός\",\"κεντρική\",\"κεντρικό\",\"κεντρικά\"],\n" + + " \"key::27\": [\"general\",\"generale\",\"général\",\"générale\",\"généraux\",\"générales\",\"general\",\"geral\",\"general\",\"Allgemeines\",\"general\",\"общий\",\"algemeen\",\"algemene\",\"γενικός\",\"γενική\",\"γενικό\",\"γενικά\"],\n" + + " \"key::28\": [\"applied\",\"applicati\",\"appliqué\",\"appliquée\",\"appliqués\",\"appliquées\",\"aplicado\",\"aplicada\",\"angewendet\",\"stosowany\",\"прикладной\",\"toegepast\",\"toegepaste\",\"εφαρμοσμένος\",\"εφαρμοσμένη\",\"εφαρμοσμένο\",\"εφαρμοσμένα\"],\n" + + " \"key::29\": [\"european\",\"europee\",\"europea\",\"européen\",\"européenne\",\"européens\",\"européennes\",\"europeo\",\"europeu\",\"europäisch\",\"europejski\",\"европейский\",\"Europees\",\"Europese\",\"ευρωπαϊκός\",\"ευρωπαϊκή\",\"ευρωπαϊκό\",\"ευρωπαϊκά\"],\n" + + " \"key::30\": [\"agency\",\"agenzia\",\"agence\",\"agencia\",\"agencia\",\"agentur\",\"agencja\",\"агенция\",\"agentschap\",\"πρακτορείο\"],\n" + + " \"key::31\": [\"laboratory\",\"laboratorio\",\"laboratoire\",\"laboratorio\",\"laboratorio\",\"labor\",\"laboratorium\",\"лаборатория\",\"laboratorium\",\"εργαστήριο\"],\n" + + " \"key::32\": [\"industry\",\"industria\",\"industrie\",\"индустрия\",\"industrie\",\"βιομηχανία\"],\n" + + " \"key::33\": [\"industrial\",\"industriale\",\"industriel\",\"industrielle\",\"industriels\",\"industrielles\",\"индустриальный\",\"industrieel\",\"βιομηχανικός\",\"βιομηχανική\",\"βιομηχανικό\",\"βιομηχανικά\",\"βιομηχανικές\"],\n" + + " \"key::34\": [\"consortium\",\"consorzio\",\"consortium\",\"консорциум\",\"consortium\",\"κοινοπραξία\"],\n" + + " \"key::35\": [\"organization\",\"organizzazione\",\"organisation\",\"organización\",\"organização\",\"organizacja\",\"организация\",\"organisatie\",\"οργανισμός\"],\n" + + " \"key::36\": [\"authority\",\"autorità\",\"autorité\",\"авторитет\",\"autoriteit\"],\n" + + " \"key::37\": [\"federation\",\"federazione\",\"fédération\",\"федерация\",\"federatie\",\"ομοσπονδία\"],\n" + + " \"key::38\": [\"observatory\",\"osservatorio\",\"observatoire\",\"обсерватория\",\"observatorium\",\"αστεροσκοπείο\"],\n" + + " \"key::39\": [\"bureau\",\"ufficio\",\"bureau\",\"офис\",\"bureau\",\"γραφείο\"],\n" + + " \"key::40\": [\"company\",\"impresa\",\"compagnie\",\"société\",\"компания\",\"bedrijf\",\"εταιρία\"],\n" + + " \"key::41\": [\"polytechnic\",\"politecnico\",\"polytechnique\",\"политехника\",\"polytechnisch\",\"πολυτεχνείο\",\"universita politecnica\",\"polytechnic university\",\"universidad politecnica\",\"universitat politecnica\",\"politechnika\",\"politechniki\",\"university technology\",\"university science technology\"],\n" + + " \"key::42\": [\"coalition\",\"coalizione\",\"coalition\",\"коалиция\",\"coalitie\",\"συνασπισμός\"],\n" + + " \"key::43\": [\"initiative\",\"iniziativa\",\"initiative\",\"инициатива\",\"initiatief\",\"πρωτοβουλία\"],\n" + + " \"key::44\": [\"academic\",\"accademico\",\"académique\",\"universitaire\",\"акадеческий academisch\",\"ακαδημαϊκός\",\"ακαδημαϊκή\",\"ακαδημαϊκό\",\"ακαδημαϊκές\",\"ακαδημαϊκοί\"],\n" + + " \"key::45\": [\"institution\",\"istituzione\",\"institution\",\"институциональный\",\"instelling\",\"ινστιτούτο\"],\n" + + " \"key::46\": [\"division\",\"divisione\",\"division\",\"отделение\",\"divisie\",\"τμήμα\"],\n" + + " \"key::47\": [\"committee\",\"comitato\",\"comité\",\"комитет\",\"commissie\",\"επιτροπή\"],\n" + + " \"key::48\": [\"promotion\",\"promozione\",\"продвижение\",\"proothisis\",\"forderung\"],\n" + + " \"key::49\": [\"medical\",\"medicine\",\"clinical\",\"medicina\",\"clinici\",\"médico\",\"medicina\",\"clínica\",\"médico\",\"medicina\",\"clínica\",\"medizinisch\",\"Medizin\",\"klinisch\",\"medisch\",\"geneeskunde\",\"klinisch\",\"ιατρικός\",\"ιατρική\",\"ιατρικό\",\"ιατρικά\",\"κλινικός\",\"κλινική\",\"κλινικό\",\"κλινικά\",\"tıbbi\",\"tıp\",\"klinik\",\"orvosi\",\"orvostudomány\",\"klinikai\",\"zdravniški\",\"medicinski\",\"klinični\",\"meditsiini\",\"kliinik\",\"kliiniline\"],\n" + + " \"key::50\": [\"technology\",\"technological\",\"tecnologia\",\"tecnologie\",\"tecnología\",\"tecnológico\",\"tecnologia\",\"tecnológico\",\"Technologie\",\"technologisch\",\"technologie\",\"technologisch\",\"τεχνολογία\",\"τεχνολογικός\",\"τεχνολογική\",\"τεχνολογικό\",\"teknoloji\",\"teknolojik\",\"technológia\",\"technológiai\",\"tehnologija\",\"tehnološki\",\"tehnoloogia\",\"tehnoloogiline\",\"technologii\",\"technical\",\"texniki\",\"teknik\"],\n" + + " \"key::51\": [\"science\",\"scientific\",\"scienza\",\"scientifiche\",\"scienze\",\"ciencia\",\"científico\",\"ciência\",\"científico\",\"Wissenschaft\",\"wissenschaftlich\",\"wetenschap\",\"wetenschappelijk\",\"επιστήμη\",\"επιστημονικός\",\"επιστημονική\",\"επιστημονικό\",\"επιστημονικά\",\"bilim\",\"bilimsel\",\"tudomány\",\"tudományos\",\"znanost\",\"znanstveni\",\"teadus\",\"teaduslik\",\"\"],\n" + + " \"key::52\": [\"engineering\",\"ingegneria\",\"ingeniería\",\"engenharia\",\"Ingenieurwissenschaft\",\"ingenieurswetenschappen\",\"bouwkunde\",\"μηχανικός\",\"μηχανική\",\"μηχανικό\",\"mühendislik\",\"mérnöki\",\"Inženirstvo\",\"inseneeria\",\"inseneri\",\"\"],\n" + + " \"key::53\": [\"management\",\"gestione\",\"gestionale\",\"gestionali\",\"gestión\",\"administración\",\"gestão\",\"administração\",\"Verwaltung\",\"management\",\"διαχείριση\",\"yönetim\",\"menedzsment\",\"vodstvo\",\"upravljanje\",\"management\",\"juhtkond\",\"juhtimine\",\"haldus\",\"\"],\n" + + " \"key::54\": [\"energy\",\"energia\",\"energía\",\"energia\",\"Energie\",\"energie\",\"ενέργεια\",\"enerji\",\"energia\",\"energija\",\"energia\",\"\"],\n" + + " \"key::55\": [\"agricultural\",\"agriculture\",\"agricoltura\",\"agricole\",\"agrícola\",\"agricultura\",\"agrícola\",\"agricultura\",\"landwirtschaftlich\",\"Landwirtschaft\",\"landbouwkundig\",\"landbouw\",\"αγροτικός\",\"αγροτική\",\"αγροτικό\",\"γεωργικός\",\"γεωργική\",\"γεωργικό\",\"γεωργία\",\"tarımsal\",\"tarım\",\"mezőgazdasági\",\"mezőgazdaság\",\"poljedelski\",\"poljedelstvo\",\"põllumajandus\",\"põllumajanduslik\",\"\"],\n" + + " \"key::56\": [\"information\",\"informazione\",\"información\",\"informação\",\"Information\",\"informatie\",\"πληροφορία\",\"bilgi\",\"információ\",\"informacija\",\"informatsioon\",\"informatycznych\",\"\"],\n" + + " \"key::57\": [\"social\",\"sociali\",\"social\",\"social\",\"Sozial\",\"sociaal\",\"maatschappelijk\",\"κοινωνικός\",\"κοινωνική\",\"κοινωνικό\",\"κοινωνικά\",\"sosyal\",\"szociális\",\"družbeni\",\"sotsiaal\",\"sotsiaalne\",\"\"],\n" + + " \"key::58\": [\"environmental\",\"ambiente\",\"medioambiental\",\"ambiente\",\"medioambiente\",\"meioambiente\",\"Umwelt\",\"milieu\",\"milieuwetenschap\",\"milieukunde\",\"περιβαλλοντικός\",\"περιβαλλοντική\",\"περιβαλλοντικό\",\"περιβαλλοντικά\",\"çevre\",\"környezeti\",\"okoliški\",\"keskonna\",\"\"],\n" + + " \"key::59\": [\"business\",\"economia\",\"economiche\",\"economica\",\"negocio\",\"empresa\",\"negócio\",\"Unternehmen\",\"bedrijf\",\"bedrijfskunde\",\"επιχείρηση\",\"iş\",\"üzleti\",\"posel\",\"ettevõte/äri\",\"\"],\n" + + " \"key::60\": [\"pharmaceuticals\",\"pharmacy\",\"farmacia\",\"farmaceutica\",\"farmacéutica\",\"farmacia\",\"farmacêutica\",\"farmácia\",\"Pharmazeutika\",\"Arzneimittelkunde\",\"farmaceutica\",\"geneesmiddelen\",\"apotheek\",\"φαρμακευτικός\",\"φαρμακευτική\",\"φαρμακευτικό\",\"φαρμακευτικά\",\"φαρμακείο\",\"ilaç\",\"eczane\",\"gyógyszerészeti\",\"gyógyszertár\",\"farmacevtika\",\"lekarništvo\",\"farmaatsia\",\"farmatseutiline\",\"\"],\n" + + " \"key::61\": [\"healthcare\",\"health services\",\"salute\",\"atenciónmédica\",\"cuidadodelasalud\",\"cuidadoscomasaúde\",\"Gesundheitswesen\",\"gezondheidszorg\",\"ιατροφαρμακευτικήπερίθαλψη\",\"sağlıkhizmeti\",\"egészségügy\",\"zdravstvo\",\"tervishoid\",\"tervishoiu\",\"\"],\n" + + " \"key::62\": [\"history\",\"storia\",\"historia\",\"história\",\"Geschichte\",\"geschiedenis\",\"geschiedkunde\",\"ιστορία\",\"tarih\",\"történelem\",\"zgodovina\",\"ajalugu\",\"\"],\n" + + " \"key::63\": [\"materials\",\"materiali\",\"materia\",\"materiales\",\"materiais\",\"materialen\",\"υλικά\",\"τεκμήρια\",\"malzemeler\",\"anyagok\",\"materiali\",\"materjalid\",\"vahendid\",\"\"],\n" + + " \"key::64\": [\"economics\",\"economia\",\"economiche\",\"economica\",\"economía\",\"economia\",\"Wirtschaft\",\"economie\",\"οικονομικά\",\"οικονομικέςεπιστήμες\",\"ekonomi\",\"közgazdaságtan\",\"gospodarstvo\",\"ekonomija\",\"majanduslik\",\"majandus\",\"\"],\n" + + " \"key::65\": [\"therapeutics\",\"terapeutica\",\"terapéutica\",\"terapêutica\",\"therapie\",\"θεραπευτική\",\"tedavibilimi\",\"gyógykezelés\",\"terapevtika\",\"terapeutiline\",\"ravi\",\"\"],\n" + + " \"key::66\": [\"oncology\",\"oncologia\",\"oncologico\",\"oncología\",\"oncologia\",\"Onkologie\",\"oncologie\",\"ογκολογία\",\"onkoloji\",\"onkológia\",\"onkologija\",\"onkoloogia\",\"\"],\n" + + " \"key::67\": [\"natural\",\"naturali\",\"naturale\",\"natural\",\"natural\",\"natürlich\",\"natuurlijk\",\"φυσικός\",\"φυσική\",\"φυσικό\",\"φυσικά\",\"doğal\",\"természetes\",\"naraven\",\"loodus\",\"\"],\n" + + " \"key::68\": [\"educational\",\"educazione\",\"pedagogia\",\"educacional\",\"educativo\",\"educacional\",\"pädagogisch\",\"educatief\",\"εκπαιδευτικός\",\"εκπαιδευτική\",\"εκπαιδευτικό\",\"εκπαιδευτικά\",\"eğitimsel\",\"oktatási\",\"izobraževalen\",\"haridus\",\"hariduslik\",\"\"],\n" + + " \"key::69\": [\"biomedical\",\"biomedica\",\"biomédico\",\"biomédico\",\"biomedizinisch\",\"biomedisch\",\"βιοιατρικός\",\"βιοιατρική\",\"βιοιατρικό\",\"βιοιατρικά\",\"biyomedikal\",\"orvosbiológiai\",\"biomedicinski\",\"biomeditsiiniline\",\"\"],\n" + + " \"key::70\": [\"veterinary\",\"veterinaria\",\"veterinarie\",\"veterinaria\",\"veterinária\",\"tierärtzlich\",\"veterinair\",\"veeartsenijlkunde\",\"κτηνιατρικός\",\"κτηνιατρική\",\"κτηνιατρικό\",\"κτηνιατρικά\",\"veteriner\",\"állatorvosi\",\"veterinar\",\"veterinarski\",\"veterinaaria\",\"\"],\n" + + " \"key::71\": [\"chemistry\",\"chimica\",\"química\",\"química\",\"Chemie\",\"chemie\",\"scheikunde\",\"χημεία\",\"kimya\",\"kémia\",\"kemija\",\"keemia\",\"\"],\n" + + " \"key::72\": [\"security\",\"sicurezza\",\"seguridad\",\"segurança\",\"Sicherheit\",\"veiligheid\",\"ασφάλεια\",\"güvenlik\",\"biztonsági\",\"varnost\",\"turvalisus\",\"julgeolek\",\"\"],\n" + + " \"key::73\": [\"biotechnology\",\"biotecnologia\",\"biotecnologie\",\"biotecnología\",\"biotecnologia\",\"Biotechnologie\",\"biotechnologie\",\"βιοτεχνολογία\",\"biyoteknoloji\",\"biotechnológia\",\"biotehnologija\",\"biotehnoloogia\",\"\"],\n" + + " \"key::74\": [\"military\",\"militare\",\"militari\",\"militar\",\"militar\",\"Militär\",\"militair\",\"leger\",\"στρατιωτικός\",\"στρατιωτική\",\"στρατιωτικό\",\"στρατιωτικά\",\"askeri\",\"katonai\",\"vojaški\",\"vojni\",\"militaar\",\"wojskowa\",\"\"],\n" + + " \"key::75\": [\"theological\",\"teologia\",\"teologico\",\"teológico\",\"tecnológica\",\"theologisch\",\"theologisch\",\"θεολογικός\",\"θεολογική\",\"θεολογικό\",\"θεολογικά\",\"teolojik\",\"technológiai\",\"teološki\",\"teoloogia\",\"usuteadus\",\"teoloogiline\",\"\"],\n" + + " \"key::76\": [\"electronics\",\"elettronica\",\"electrónica\",\"eletrônicos\",\"Elektronik\",\"elektronica\",\"ηλεκτρονική\",\"elektronik\",\"elektronika\",\"elektronika\",\"elektroonika\",\"\"],\n" + + " \"key::77\": [\"forestry\",\"forestale\",\"forestali\",\"silvicultura\",\"forestal\",\"floresta\",\"Forstwirtschaft\",\"bosbouw\",\"δασοκομία\",\"δασολογία\",\"ormancılık\",\"erdészet\",\"gozdarstvo\",\"metsandus\",\"\"],\n" + + " \"key::78\": [\"maritime\",\"marittima\",\"marittime\",\"marittimo\",\"marítimo\",\"marítimo\",\"maritiem\",\"ναυτικός\",\"ναυτική\",\"ναυτικό\",\"ναυτικά\",\"ναυτιλιακός\",\"ναυτιλιακή\",\"ναυτιλιακό\",\"ναυτιλιακά\",\"θαλάσσιος\",\"θαλάσσια\",\"θαλάσσιο\",\"denizcilik\",\"tengeri\",\"morski\",\"mere\",\"merendus\",\"\"],\n" + + " \"key::79\": [\"sports\",\"sport\",\"deportes\",\"esportes\",\"Sport\",\"sport\",\"sportwetenschappen\",\"άθληση\",\"γυμναστικήδραστηριότητα\",\"spor\",\"sport\",\"šport\",\"sport\",\"spordi\",\"\"],\n" + + " \"key::80\": [\"surgery\",\"chirurgia\",\"chirurgiche\",\"cirugía\",\"cirurgia\",\"Chirurgie\",\"chirurgie\",\"heelkunde\",\"εγχείρηση\",\"επέμβαση\",\"χειρουργικήεπέμβαση\",\"cerrahi\",\"sebészet\",\"kirurgija\",\"kirurgia\",\"\"],\n" + + " \"key::81\": [\"cultural\",\"culturale\",\"culturali\",\"cultura\",\"cultural\",\"cultural\",\"kulturell\",\"cultureel\",\"πολιτιστικός\",\"πολιτιστική\",\"πολιτιστικό\",\"πολιτισμικός\",\"πολιτισμική\",\"πολιτισμικό\",\"kültürel\",\"kultúrális\",\"kulturni\",\"kultuuri\",\"kultuuriline\",\"\"],\n" + + " \"key::82\": [\"computerscience\",\"informatica\",\"ordenador\",\"computadora\",\"informática\",\"computación\",\"cienciasdelacomputación\",\"ciênciadacomputação\",\"Computer\",\"computer\",\"υπολογιστής\",\"ηλεκτρονικόςυπολογιστής\",\"bilgisayar\",\"számítógép\",\"računalnik\",\"arvuti\",\"\"],\n" + + " \"key::83\": [\"finance\",\"financial\",\"finanza\",\"finanziarie\",\"finanza\",\"financiero\",\"finanças\",\"financeiro\",\"Finanzen\",\"finanziell\",\"financiën\",\"financieel\",\"χρηματοοικονομικά\",\"χρηματοδότηση\",\"finanse\",\"finansal\",\"pénzügy\",\"pénzügyi\",\"finance\",\"finančni\",\"finants\",\"finantsiline\",\"\"],\n" + + " \"key::84\": [\"communication\",\"comunicazione\",\"comuniciación\",\"comunicação\",\"Kommunikation\",\"communication\",\"επικοινωνία\",\"iletişim\",\"kommunikáció\",\"komuniciranje\",\"kommunikatsioon\",\"\"],\n" + + " \"key::85\": [\"justice\",\"giustizia\",\"justicia\",\"justiça\",\"Recht\",\"Justiz\",\"justitie\",\"gerechtigheid\",\"δικαιοσύνη\",\"υπουργείοδικαιοσύνης\",\"δίκαιο\",\"adalet\",\"igazságügy\",\"pravo\",\"õigus\",\"\"],\n" + + " \"key::86\": [\"aerospace\",\"aerospaziale\",\"aerospaziali\",\"aeroespacio\",\"aeroespaço\",\"Luftfahrt\",\"luchtvaart\",\"ruimtevaart\",\"αεροπορικός\",\"αεροπορική\",\"αεροπορικό\",\"αεροναυπηγικός\",\"αεροναυπηγική\",\"αεροναυπηγικό\",\"αεροναυπηγικά\",\"havacılıkveuzay\",\"légtér\",\"zrakoplovstvo\",\"atmosfäär\",\"kosmos\",\"\"],\n" + + " \"key::87\": [\"dermatology\",\"dermatologia\",\"dermatología\",\"dermatologia\",\"Dermatologie\",\"dermatologie\",\"δρματολογία\",\"dermatoloji\",\"bőrgyógyászat\",\"dermatológia\",\"dermatologija\",\"dermatoloogia\",\"\"],\n" + + " \"key::88\": [\"architecture\",\"architettura\",\"arquitectura\",\"arquitetura\",\"Architektur\",\"architectuur\",\"αρχιτεκτονική\",\"mimarlık\",\"építészet\",\"arhitektura\",\"arhitektuur\",\"\"],\n" + + " \"key::89\": [\"mathematics\",\"matematica\",\"matematiche\",\"matemáticas\",\"matemáticas\",\"Mathematik\",\"wiskunde\",\"mathematica\",\"μαθηματικά\",\"matematik\",\"matematika\",\"matematika\",\"matemaatika\",\"\"],\n" + + " \"key::90\": [\"language\",\"lingue\",\"linguistica\",\"linguistiche\",\"lenguaje\",\"idioma\",\"língua\",\"idioma\",\"Sprache\",\"taal\",\"taalkunde\",\"γλώσσα\",\"dil\",\"nyelv\",\"jezik\",\"keel\",\"\"],\n" + + " \"key::91\": [\"neuroscience\",\"neuroscienza\",\"neurociencia\",\"neurociência\",\"Neurowissenschaft\",\"neurowetenschappen\",\"νευροεπιστήμη\",\"nörobilim\",\"idegtudomány\",\"nevroznanost\",\"neuroteadused\",\"\"],\n" + + " \"key::92\": [\"automation\",\"automazione\",\"automatización\",\"automação\",\"Automatisierung\",\"automatisering\",\"αυτοματοποίηση\",\"otomasyon\",\"automatizálás\",\"avtomatizacija\",\"automatiseeritud\",\"\"],\n" + + " \"key::93\": [\"pediatric\",\"pediatria\",\"pediatriche\",\"pediatrico\",\"pediátrico\",\"pediatría\",\"pediátrico\",\"pediatria\",\"pädiatrisch\",\"pediatrische\",\"παιδιατρική\",\"pediatrik\",\"gyermekgyógyászat\",\"pediatrija\",\"pediaatria\",\"\"],\n" + + " \"key::94\": [\"photonics\",\"fotonica\",\"fotoniche\",\"fotónica\",\"fotônica\",\"Photonik\",\"fotonica\",\"φωτονική\",\"fotonik\",\"fotonika\",\"fotonika\",\"fotoonika\",\"\"],\n" + + " \"key::95\": [\"mechanics\", \"mechanical\", \"meccanica\",\"meccaniche\",\"mecánica\",\"mecânica\",\"Mechanik\",\"Maschinenbau\",\"mechanica\",\"werktuigkunde\",\"μηχανικής\",\"mekanik\",\"gépészet\",\"mehanika\",\"mehaanika\",\"\"],\n" + + " \"key::96\": [\"psychiatrics\",\"psichiatria\",\"psichiatrica\",\"psichiatriche\",\"psiquiatría\",\"psiquiatria\",\"Psychiatrie\",\"psychiatrie\",\"ψυχιατρική\",\"psikiyatrik\",\"pszihiátria\",\"psihiatrija\",\"psühhaatria\",\"\"],\n" + + " \"key::97\": [\"psychology\",\"fisiologia\",\"psicología\",\"psicologia\",\"Psychologie\",\"psychologie\",\"ψυχολογία\",\"psikoloji\",\"pszihológia\",\"psihologija\",\"psühholoogia\",\"\"],\n" + + " \"key::98\": [\"automotive\",\"industriaautomobilistica\",\"industriadelautomóvil\",\"automotriz\",\"industriaautomotriz\",\"automotivo\",\"Automobilindustrie\",\"autoindustrie\",\"αυτοκίνητος\",\"αυτοκίνητη\",\"αυτοκίνητο\",\"αυτοκινούμενος\",\"αυτοκινούμενη\",\"αυτοκινούμενο\",\"αυτοκινητιστικός\",\"αυτοκινητιστική\",\"αυτοκινητιστικό\",\"otomotiv\",\"autóipari\",\"samogiben\",\"avtomobilskaindustrija\",\"auto-\",\"\"],\n" + + " \"key::99\": [\"neurology\",\"neurologia\",\"neurologiche\",\"neurología\",\"neurologia\",\"Neurologie\",\"neurologie\",\"zenuwleer\",\"νευρολογία\",\"nöroloji\",\"neurológia\",\"ideggyógyászat\",\"nevrologija\",\"neuroloogia\",\"\"],\n" + + " \"key::100\": [\"geology\",\"geologia\",\"geologiche\",\"geología\",\"geologia\",\"Geologie\",\"geologie\",\"aardkunde\",\"γεωλογία\",\"jeoloji\",\"geológia\",\"földtudomány\",\"geologija\",\"geoloogia\",\"\"],\n" + + " \"key::101\": [\"microbiology\",\"microbiologia\",\"micro-biologia\",\"microbiologiche\",\"microbiología\",\"microbiologia\",\"Mikrobiologie\",\"microbiologie\",\"μικροβιολογία\",\"mikrobiyoloji\",\"mikrobiológia\",\"mikrobiologija\",\"mikrobioloogia\",\"\"],\n" + + " \"key::102\": [\"informatics\",\"informatica\",\"informática\",\"informática\",\"informatica\",\"\"],\n" + + " \"key::103\": [\"forschungsgemeinschaft\",\"comunita ricerca\",\"research community\",\"research foundation\",\"research association\"],\n" + + " \"key::104\": [\"commerce\",\"ticaret\",\"ticarət\",\"commercio\",\"trade\",\"handel\",\"comercio\"],\n" + + " \"key::105\" : [\"state\", \"stato\", \"etade\", \"estado\", \"statale\", \"etat\", \"zustand\", \"estado\"],\n" + + " \"key::106\" : [\"seminary\", \"seminario\", \"seminaire\", \"seminar\"],\n" + + " \"key::107\" : [\"agricultural forestry\", \"af\", \"a f\"],\n" + + " \"key::108\" : [\"agricultural mechanical\", \"am\", \"a m\"],\n" + + " \"key::109\" : [\"catholic\", \"catholique\", \"katholische\", \"catolica\", \"cattolica\", \"catolico\"]\n" + + " }\n" + + " }\n" + + "}"); @Test - public void testJPath () throws Exception { + public void testJPath() throws Exception { MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(conf, json); System.out.println("d = " + d); - } } diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DatePicker.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DatePicker.java index 73f178edce..5c4111c204 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DatePicker.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DatePicker.java @@ -1,18 +1,17 @@ package eu.dnetlib.dedup; -import eu.dnetlib.dhp.schema.oaf.Field; -import org.apache.commons.lang.StringUtils; - -import java.time.Year; -import java.util.*; -import java.util.stream.Collectors; - import static java.util.Collections.reverseOrder; import static java.util.Map.Entry.comparingByValue; import static java.util.stream.Collectors.toMap; import static org.apache.commons.lang.StringUtils.endsWith; import static org.apache.commons.lang.StringUtils.substringBefore; +import eu.dnetlib.dhp.schema.oaf.Field; +import java.time.Year; +import java.util.*; +import java.util.stream.Collectors; +import org.apache.commons.lang.StringUtils; + public class DatePicker { private static final String DATE_PATTERN = "\\d{4}-\\d{2}-\\d{2}"; @@ -22,33 +21,32 @@ public class DatePicker { public static Field pick(final Collection dateofacceptance) { - final Map frequencies = dateofacceptance - .parallelStream() - .filter(StringUtils::isNotBlank) - .collect( - Collectors.toConcurrentMap( - w -> w, w -> 1, Integer::sum)); + final Map frequencies = + dateofacceptance + .parallelStream() + .filter(StringUtils::isNotBlank) + .collect(Collectors.toConcurrentMap(w -> w, w -> 1, Integer::sum)); if (frequencies.isEmpty()) { return new Field<>(); } final Field date = new Field<>(); - date.setValue(frequencies.keySet().iterator().next()); + date.setValue(frequencies.keySet().iterator().next()); // let's sort this map by values first, filtering out invalid dates - final Map sorted = frequencies - .entrySet() - .stream() - .filter(d -> StringUtils.isNotBlank(d.getKey())) - .filter(d -> d.getKey().matches(DATE_PATTERN)) - .filter(d -> inRange(d.getKey())) - .sorted(reverseOrder(comparingByValue())) - .collect( - toMap( - Map.Entry::getKey, - Map.Entry::getValue, (e1, e2) -> e2, - LinkedHashMap::new)); + final Map sorted = + frequencies.entrySet().stream() + .filter(d -> StringUtils.isNotBlank(d.getKey())) + .filter(d -> d.getKey().matches(DATE_PATTERN)) + .filter(d -> inRange(d.getKey())) + .sorted(reverseOrder(comparingByValue())) + .collect( + toMap( + Map.Entry::getKey, + Map.Entry::getValue, + (e1, e2) -> e2, + LinkedHashMap::new)); // shortcut if (sorted.size() == 0) { @@ -58,18 +56,24 @@ public class DatePicker { // voting method (1/3 + 1) wins if (sorted.size() >= 3) { final int acceptThreshold = (sorted.size() / 3) + 1; - final List accepted = sorted.entrySet().stream() - .filter(e -> e.getValue() >= acceptThreshold) - .map(e -> e.getKey()) - .collect(Collectors.toList()); + final List accepted = + sorted.entrySet().stream() + .filter(e -> e.getValue() >= acceptThreshold) + .map(e -> e.getKey()) + .collect(Collectors.toList()); // cannot find strong majority if (accepted.isEmpty()) { final int max = sorted.values().iterator().next(); - Optional first = sorted.entrySet().stream() - .filter(e -> e.getValue() == max && !endsWith(e.getKey(), DATE_DEFAULT_SUFFIX)) - .map(Map.Entry::getKey) - .findFirst(); + Optional first = + sorted.entrySet().stream() + .filter( + e -> + e.getValue() == max + && !endsWith( + e.getKey(), DATE_DEFAULT_SUFFIX)) + .map(Map.Entry::getKey) + .findFirst(); if (first.isPresent()) { date.setValue(first.get()); return date; @@ -83,9 +87,10 @@ public class DatePicker { date.setValue(accepted.get(0)); return date; } else { - final Optional first = accepted.stream() - .filter(d -> !endsWith(d, DATE_DEFAULT_SUFFIX)) - .findFirst(); + final Optional first = + accepted.stream() + .filter(d -> !endsWith(d, DATE_DEFAULT_SUFFIX)) + .findFirst(); if (first.isPresent()) { date.setValue(first.get()); return date; @@ -94,7 +99,7 @@ public class DatePicker { return date; } - //1st non YYYY-01-01 is returned + // 1st non YYYY-01-01 is returned } else { if (sorted.size() == 2) { for (Map.Entry e : sorted.entrySet()) { @@ -115,5 +120,4 @@ public class DatePicker { final int year = Integer.parseInt(substringBefore(date, "-")); return year >= YEAR_LB && year <= YEAR_UB; } - -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java index ebb5040781..f8b69cc14b 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java @@ -1,43 +1,64 @@ package eu.dnetlib.dedup; import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.util.MapDocumentUtil; +import java.util.Collection; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; -import com.fasterxml.jackson.databind.ObjectMapper; import scala.Tuple2; -import java.util.Collection; - public class DedupRecordFactory { - public static JavaRDD createDedupRecord(final JavaSparkContext sc, final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, final OafEntityType entityType, final DedupConfig dedupConf) { + public static JavaRDD createDedupRecord( + final JavaSparkContext sc, + final SparkSession spark, + final String mergeRelsInputPath, + final String entitiesInputPath, + final OafEntityType entityType, + final DedupConfig dedupConf) { long ts = System.currentTimeMillis(); - // - final JavaPairRDD inputJsonEntities = sc.textFile(entitiesInputPath) - .mapToPair((PairFunction) it -> - new Tuple2(MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), it), it) - ); + // + final JavaPairRDD inputJsonEntities = + sc.textFile(entitiesInputPath) + .mapToPair( + (PairFunction) + it -> + new Tuple2( + MapDocumentUtil.getJPathString( + dedupConf.getWf().getIdPath(), it), + it)); - //: source is the dedup_id, target is the id of the mergedIn - JavaPairRDD mergeRels = spark - .read().load(mergeRelsInputPath).as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .mapToPair( - (PairFunction) r -> - new Tuple2(r.getTarget(), r.getSource()) - ); + // : source is the dedup_id, target is the id of the mergedIn + JavaPairRDD mergeRels = + spark.read() + .load(mergeRelsInputPath) + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .mapToPair( + (PairFunction) + r -> + new Tuple2( + r.getTarget(), r.getSource())); - // - final JavaPairRDD joinResult = mergeRels.join(inputJsonEntities).mapToPair((PairFunction>, String, String>) Tuple2::_2); + // + final JavaPairRDD joinResult = + mergeRels + .join(inputJsonEntities) + .mapToPair( + (PairFunction< + Tuple2>, + String, + String>) + Tuple2::_2); JavaPairRDD> sortedJoinResult = joinResult.groupByKey(); @@ -55,42 +76,46 @@ public class DedupRecordFactory { case organization: return sortedJoinResult.map(o -> DedupRecordFactory.organizationMerger(o, ts)); case otherresearchproduct: - return sortedJoinResult.map(o -> DedupRecordFactory.otherresearchproductMerger(o, ts)); + return sortedJoinResult.map( + o -> DedupRecordFactory.otherresearchproductMerger(o, ts)); default: return null; } - } - private static Publication publicationMerger(Tuple2> e, final long ts) { + private static Publication publicationMerger( + Tuple2> e, final long ts) { - Publication p = new Publication(); //the result of the merge, to be returned at the end + Publication p = new Publication(); // the result of the merge, to be returned at the end p.setId(e._1()); final ObjectMapper mapper = new ObjectMapper(); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - final Collection dateofacceptance = Lists.newArrayList(); if (e._2() != null) - e._2().forEach(pub -> { - try { - Publication publication = mapper.readValue(pub, Publication.class); + e._2().forEach( + pub -> { + try { + Publication publication = + mapper.readValue(pub, Publication.class); - p.mergeFrom(publication); - p.setAuthor(DedupUtility.mergeAuthor(p.getAuthor(), publication.getAuthor())); - //add to the list if they are not null - if (publication.getDateofacceptance() != null) - dateofacceptance.add(publication.getDateofacceptance().getValue()); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); + p.mergeFrom(publication); + p.setAuthor( + DedupUtility.mergeAuthor( + p.getAuthor(), publication.getAuthor())); + // add to the list if they are not null + if (publication.getDateofacceptance() != null) + dateofacceptance.add( + publication.getDateofacceptance().getValue()); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); p.setDateofacceptance(DatePicker.pick(dateofacceptance)); - if (p.getDataInfo() == null) - p.setDataInfo(new DataInfo()); + if (p.getDataInfo() == null) p.setDataInfo(new DataInfo()); p.getDataInfo().setTrust("0.9"); p.setLastupdatetimestamp(ts); return p; @@ -98,7 +123,7 @@ public class DedupRecordFactory { private static Dataset datasetMerger(Tuple2> e, final long ts) { - Dataset d = new Dataset(); //the result of the merge, to be returned at the end + Dataset d = new Dataset(); // the result of the merge, to be returned at the end d.setId(e._1()); @@ -108,22 +133,25 @@ public class DedupRecordFactory { final Collection dateofacceptance = Lists.newArrayList(); if (e._2() != null) - e._2().forEach(dat -> { - try { - Dataset dataset = mapper.readValue(dat, Dataset.class); + e._2().forEach( + dat -> { + try { + Dataset dataset = mapper.readValue(dat, Dataset.class); - d.mergeFrom(dataset); - d.setAuthor(DedupUtility.mergeAuthor(d.getAuthor(), dataset.getAuthor())); - //add to the list if they are not null - if (dataset.getDateofacceptance() != null) - dateofacceptance.add(dataset.getDateofacceptance().getValue()); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); + d.mergeFrom(dataset); + d.setAuthor( + DedupUtility.mergeAuthor( + d.getAuthor(), dataset.getAuthor())); + // add to the list if they are not null + if (dataset.getDateofacceptance() != null) + dateofacceptance.add( + dataset.getDateofacceptance().getValue()); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); d.setDateofacceptance(DatePicker.pick(dateofacceptance)); - if (d.getDataInfo() == null) - d.setDataInfo(new DataInfo()); + if (d.getDataInfo() == null) d.setDataInfo(new DataInfo()); d.getDataInfo().setTrust("0.9"); d.setLastupdatetimestamp(ts); return d; @@ -131,24 +159,24 @@ public class DedupRecordFactory { private static Project projectMerger(Tuple2> e, final long ts) { - Project p = new Project(); //the result of the merge, to be returned at the end + Project p = new Project(); // the result of the merge, to be returned at the end p.setId(e._1()); final ObjectMapper mapper = new ObjectMapper(); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); if (e._2() != null) - e._2().forEach(proj -> { - try { - Project project = mapper.readValue(proj, Project.class); + e._2().forEach( + proj -> { + try { + Project project = mapper.readValue(proj, Project.class); - p.mergeFrom(project); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); - if (p.getDataInfo() == null) - p.setDataInfo(new DataInfo()); + p.mergeFrom(project); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); + if (p.getDataInfo() == null) p.setDataInfo(new DataInfo()); p.getDataInfo().setTrust("0.9"); p.setLastupdatetimestamp(ts); return p; @@ -156,100 +184,106 @@ public class DedupRecordFactory { private static Software softwareMerger(Tuple2> e, final long ts) { - Software s = new Software(); //the result of the merge, to be returned at the end + Software s = new Software(); // the result of the merge, to be returned at the end s.setId(e._1()); final ObjectMapper mapper = new ObjectMapper(); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); final Collection dateofacceptance = Lists.newArrayList(); if (e._2() != null) - e._2().forEach(soft -> { - try { - Software software = mapper.readValue(soft, Software.class); + e._2().forEach( + soft -> { + try { + Software software = mapper.readValue(soft, Software.class); - s.mergeFrom(software); - s.setAuthor(DedupUtility.mergeAuthor(s.getAuthor(), software.getAuthor())); - //add to the list if they are not null - if (software.getDateofacceptance() != null) - dateofacceptance.add(software.getDateofacceptance().getValue()); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); + s.mergeFrom(software); + s.setAuthor( + DedupUtility.mergeAuthor( + s.getAuthor(), software.getAuthor())); + // add to the list if they are not null + if (software.getDateofacceptance() != null) + dateofacceptance.add( + software.getDateofacceptance().getValue()); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); s.setDateofacceptance(DatePicker.pick(dateofacceptance)); - if (s.getDataInfo() == null) - s.setDataInfo(new DataInfo()); + if (s.getDataInfo() == null) s.setDataInfo(new DataInfo()); s.getDataInfo().setTrust("0.9"); s.setLastupdatetimestamp(ts); return s; } private static Datasource datasourceMerger(Tuple2> e, final long ts) { - Datasource d = new Datasource(); //the result of the merge, to be returned at the end + Datasource d = new Datasource(); // the result of the merge, to be returned at the end d.setId(e._1()); final ObjectMapper mapper = new ObjectMapper(); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); if (e._2() != null) - e._2().forEach(dat -> { - try { - Datasource datasource = mapper.readValue(dat, Datasource.class); + e._2().forEach( + dat -> { + try { + Datasource datasource = mapper.readValue(dat, Datasource.class); - d.mergeFrom(datasource); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); - if (d.getDataInfo() == null) - d.setDataInfo(new DataInfo()); + d.mergeFrom(datasource); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); + if (d.getDataInfo() == null) d.setDataInfo(new DataInfo()); d.getDataInfo().setTrust("0.9"); d.setLastupdatetimestamp(ts); return d; } - private static Organization organizationMerger(Tuple2> e, final long ts) { + private static Organization organizationMerger( + Tuple2> e, final long ts) { - Organization o = new Organization(); //the result of the merge, to be returned at the end + Organization o = new Organization(); // the result of the merge, to be returned at the end o.setId(e._1()); final ObjectMapper mapper = new ObjectMapper(); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - StringBuilder trust = new StringBuilder("0.0"); if (e._2() != null) - e._2().forEach(pub -> { - try { - Organization organization = mapper.readValue(pub, Organization.class); + e._2().forEach( + pub -> { + try { + Organization organization = + mapper.readValue(pub, Organization.class); - final String currentTrust = organization.getDataInfo().getTrust(); - if (!"1.0".equals(currentTrust)) { - trust.setLength(0); - trust.append(currentTrust); - } - o.mergeFrom(organization); + final String currentTrust = + organization.getDataInfo().getTrust(); + if (!"1.0".equals(currentTrust)) { + trust.setLength(0); + trust.append(currentTrust); + } + o.mergeFrom(organization); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); - if (o.getDataInfo() == null) - { + if (o.getDataInfo() == null) { o.setDataInfo(new DataInfo()); } - if (o.getDataInfo() == null) - o.setDataInfo(new DataInfo()); + if (o.getDataInfo() == null) o.setDataInfo(new DataInfo()); o.getDataInfo().setTrust("0.9"); o.setLastupdatetimestamp(ts); return o; } - private static OtherResearchProduct otherresearchproductMerger(Tuple2> e, final long ts) { + private static OtherResearchProduct otherresearchproductMerger( + Tuple2> e, final long ts) { - OtherResearchProduct o = new OtherResearchProduct(); //the result of the merge, to be returned at the end + OtherResearchProduct o = + new OtherResearchProduct(); // the result of the merge, to be returned at the end o.setId(e._1()); @@ -259,25 +293,31 @@ public class DedupRecordFactory { final Collection dateofacceptance = Lists.newArrayList(); if (e._2() != null) - e._2().forEach(orp -> { - try { - OtherResearchProduct otherResearchProduct = mapper.readValue(orp, OtherResearchProduct.class); + e._2().forEach( + orp -> { + try { + OtherResearchProduct otherResearchProduct = + mapper.readValue(orp, OtherResearchProduct.class); - o.mergeFrom(otherResearchProduct); - o.setAuthor(DedupUtility.mergeAuthor(o.getAuthor(), otherResearchProduct.getAuthor())); - //add to the list if they are not null - if (otherResearchProduct.getDateofacceptance() != null) - dateofacceptance.add(otherResearchProduct.getDateofacceptance().getValue()); - } catch (Exception exc) { - throw new RuntimeException(exc); - } - }); - if (o.getDataInfo() == null) - o.setDataInfo(new DataInfo()); + o.mergeFrom(otherResearchProduct); + o.setAuthor( + DedupUtility.mergeAuthor( + o.getAuthor(), + otherResearchProduct.getAuthor())); + // add to the list if they are not null + if (otherResearchProduct.getDateofacceptance() != null) + dateofacceptance.add( + otherResearchProduct + .getDateofacceptance() + .getValue()); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); + if (o.getDataInfo() == null) o.setDataInfo(new DataInfo()); o.setDateofacceptance(DatePicker.pick(dateofacceptance)); o.getDataInfo().setTrust("0.9"); o.setLastupdatetimestamp(ts); return o; } - } diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupUtility.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupUtility.java index 7ed102e031..977c14e138 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupUtility.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupUtility.java @@ -8,6 +8,13 @@ import eu.dnetlib.pace.clustering.BlacklistAwareClusteringCombiner; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.model.Person; +import java.io.IOException; +import java.io.StringWriter; +import java.nio.charset.StandardCharsets; +import java.security.MessageDigest; +import java.text.Normalizer; +import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.codec.binary.Hex; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; @@ -21,32 +28,43 @@ import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.util.LongAccumulator; import scala.Tuple2; -import java.io.IOException; -import java.io.StringWriter; -import java.nio.charset.StandardCharsets; -import java.security.MessageDigest; -import java.text.Normalizer; -import java.util.*; -import java.util.stream.Collectors; - public class DedupUtility { private static final Double THRESHOLD = 0.95; - public static Map constructAccumulator(final DedupConfig dedupConf, final SparkContext context) { + public static Map constructAccumulator( + final DedupConfig dedupConf, final SparkContext context) { Map accumulators = new HashMap<>(); - String acc1 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "records per hash key = 1"); + String acc1 = + String.format( + "%s::%s", dedupConf.getWf().getEntityType(), "records per hash key = 1"); accumulators.put(acc1, context.longAccumulator(acc1)); - String acc2 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "missing " + dedupConf.getWf().getOrderField()); + String acc2 = + String.format( + "%s::%s", + dedupConf.getWf().getEntityType(), + "missing " + dedupConf.getWf().getOrderField()); accumulators.put(acc2, context.longAccumulator(acc2)); - String acc3 = String.format("%s::%s", dedupConf.getWf().getEntityType(), String.format("Skipped records for count(%s) >= %s", dedupConf.getWf().getOrderField(), dedupConf.getWf().getGroupMaxSize())); + String acc3 = + String.format( + "%s::%s", + dedupConf.getWf().getEntityType(), + String.format( + "Skipped records for count(%s) >= %s", + dedupConf.getWf().getOrderField(), + dedupConf.getWf().getGroupMaxSize())); accumulators.put(acc3, context.longAccumulator(acc3)); String acc4 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "skip list"); accumulators.put(acc4, context.longAccumulator(acc4)); - String acc5 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "dedupSimilarity (x2)"); + String acc5 = + String.format("%s::%s", dedupConf.getWf().getEntityType(), "dedupSimilarity (x2)"); accumulators.put(acc5, context.longAccumulator(acc5)); - String acc6 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "d < " + dedupConf.getWf().getThreshold()); + String acc6 = + String.format( + "%s::%s", + dedupConf.getWf().getEntityType(), + "d < " + dedupConf.getWf().getThreshold()); accumulators.put(acc6, context.longAccumulator(acc6)); return accumulators; @@ -71,7 +89,6 @@ public class DedupUtility { FSDataInputStream inputStream = new FSDataInputStream(fileSystem.open(new Path(path))); return DedupConfig.load(IOUtils.toString(inputStream, StandardCharsets.UTF_8.name())); - } static String readFromClasspath(final String filename, final Class clazz) { @@ -99,7 +116,6 @@ public class DedupUtility { } } - public static List mergeAuthor(final List a, final List b) { int pa = countAuthorsPids(a); int pb = countAuthorsPids(b); @@ -119,29 +135,40 @@ public class DedupUtility { } private static void enrichPidFromList(List base, List enrich) { - if (base == null || enrich == null) - return; - final Map basePidAuthorMap = base.stream() - .filter(a -> a.getPid() != null && a.getPid().size() > 0) - .flatMap(a -> a.getPid() - .stream() - .map(p -> new Tuple2<>(p.toComparableString(), a)) - ).collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); + if (base == null || enrich == null) return; + final Map basePidAuthorMap = + base.stream() + .filter(a -> a.getPid() != null && a.getPid().size() > 0) + .flatMap( + a -> + a.getPid().stream() + .map(p -> new Tuple2<>(p.toComparableString(), a))) + .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); - final List> pidToEnrich = enrich - .stream() - .filter(a -> a.getPid() != null && a.getPid().size() > 0) - .flatMap(a -> a.getPid().stream().filter(p -> !basePidAuthorMap.containsKey(p.toComparableString())).map(p -> new Tuple2<>(p, a))) - .collect(Collectors.toList()); + final List> pidToEnrich = + enrich.stream() + .filter(a -> a.getPid() != null && a.getPid().size() > 0) + .flatMap( + a -> + a.getPid().stream() + .filter( + p -> + !basePidAuthorMap.containsKey( + p.toComparableString())) + .map(p -> new Tuple2<>(p, a))) + .collect(Collectors.toList()); - - pidToEnrich.forEach(a -> { - Optional> simAuhtor = base.stream().map(ba -> new Tuple2<>(sim(ba, a._2()), ba)).max(Comparator.comparing(Tuple2::_1)); - if (simAuhtor.isPresent() && simAuhtor.get()._1() > THRESHOLD) { - Author r = simAuhtor.get()._2(); - r.getPid().add(a._1()); - } - }); + pidToEnrich.forEach( + a -> { + Optional> simAuhtor = + base.stream() + .map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) + .max(Comparator.comparing(Tuple2::_1)); + if (simAuhtor.isPresent() && simAuhtor.get()._1() > THRESHOLD) { + Author r = simAuhtor.get()._2(); + r.getPid().add(a._1()); + } + }); } public static String createEntityPath(final String basePath, final String entityType) { @@ -162,19 +189,21 @@ public class DedupUtility { final Person pb = parse(b); if (pa.isAccurate() & pb.isAccurate()) { - return new JaroWinkler().score( - normalize(pa.getSurnameString()), - normalize(pb.getSurnameString())); + return new JaroWinkler() + .score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())); } else { - return new JaroWinkler().score( - normalize(pa.getNormalisedFullname()), - normalize(pb.getNormalisedFullname())); + return new JaroWinkler() + .score( + normalize(pa.getNormalisedFullname()), + normalize(pb.getNormalisedFullname())); } } private static String normalize(final String s) { return nfd(s).toLowerCase() - // do not compact the regexes in a single expression, would cause StackOverflowError in case of large input strings + // do not compact the regexes in a single expression, would cause StackOverflowError + // in case + // of large input strings .replaceAll("(\\W)+", " ") .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") .replaceAll("(\\p{Punct})+", " ") @@ -195,23 +224,19 @@ public class DedupUtility { } } - private static int countAuthorsPids(List authors) { - if (authors == null) - return 0; + if (authors == null) return 0; return (int) authors.stream().filter(DedupUtility::hasPid).count(); } private static int authorsSize(List authors) { - if (authors == null) - return 0; + if (authors == null) return 0; return authors.size(); } private static boolean hasPid(Author a) { - if (a == null || a.getPid() == null || a.getPid().size() == 0) - return false; + if (a == null || a.getPid() == null || a.getPid().size() == 0) return false; return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue())); } } diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/Deduper.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/Deduper.java index 7206f892f7..bec4229ee3 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/Deduper.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/Deduper.java @@ -1,10 +1,11 @@ package eu.dnetlib.dedup; import eu.dnetlib.pace.config.DedupConfig; -import eu.dnetlib.pace.model.Field; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.BlockProcessor; import eu.dnetlib.pace.util.MapDocumentUtil; +import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.spark.api.java.JavaPairRDD; @@ -17,9 +18,6 @@ import org.apache.spark.util.LongAccumulator; import scala.Serializable; import scala.Tuple2; -import java.util.*; -import java.util.stream.Collectors; - public class Deduper implements Serializable { private static final Log log = LogFactory.getLog(Deduper.class); @@ -30,26 +28,32 @@ public class Deduper implements Serializable { * @param: list of JSON entities to be deduped * @param: the dedup configuration */ - public static JavaPairRDD dedup(JavaSparkContext context, JavaRDD entities, DedupConfig config) { + public static JavaPairRDD dedup( + JavaSparkContext context, JavaRDD entities, DedupConfig config) { - Map accumulators = DedupUtility.constructAccumulator(config, context.sc()); + Map accumulators = + DedupUtility.constructAccumulator(config, context.sc()); - //create vertexes of the graph: + // create vertexes of the graph: JavaPairRDD mapDocs = mapToVertexes(context, entities, config); - - //create blocks for deduplication + // create blocks for deduplication JavaPairRDD> blocks = createBlocks(context, mapDocs, config); - //create relations by comparing only elements in the same group + // create relations by comparing only elements in the same group return computeRelations(context, blocks, config); -// final RDD> edgeRdd = relationRDD.map(it -> new Edge<>(it._1().hashCode(), it._2().hashCode(), "equalTo")).rdd(); -// -// RDD> vertexes = mapDocs.mapToPair((PairFunction, Object, MapDocument>) t -> new Tuple2((long) t._1().hashCode(), t._2())).rdd(); -// accumulators.forEach((name, acc) -> log.info(name + " -> " + acc.value())); -// -// return GraphProcessor.findCCs(vertexes, edgeRdd, 20).toJavaRDD(); + // final RDD> edgeRdd = relationRDD.map(it -> new + // Edge<>(it._1().hashCode(), + // it._2().hashCode(), "equalTo")).rdd(); + // + // RDD> vertexes = + // mapDocs.mapToPair((PairFunction, Object, MapDocument>) t -> + // new + // Tuple2((long) t._1().hashCode(), t._2())).rdd(); + // accumulators.forEach((name, acc) -> log.info(name + " -> " + acc.value())); + // + // return GraphProcessor.findCCs(vertexes, edgeRdd, 20).toJavaRDD(); } /** @@ -58,71 +62,92 @@ public class Deduper implements Serializable { * @param: list of blocks * @param: the dedup configuration */ - public static JavaPairRDD computeRelations(JavaSparkContext context, JavaPairRDD> blocks, DedupConfig config) { + public static JavaPairRDD computeRelations( + JavaSparkContext context, + JavaPairRDD> blocks, + DedupConfig config) { - Map accumulators = DedupUtility.constructAccumulator(config, context.sc()); + Map accumulators = + DedupUtility.constructAccumulator(config, context.sc()); - return blocks.flatMapToPair((PairFlatMapFunction>, String, String>) it -> { - final SparkReporter reporter = new SparkReporter(accumulators); - new BlockProcessor(config).process(it._1(), it._2(), reporter); - return reporter.getRelations().iterator(); - - }).mapToPair( - (PairFunction, String, Tuple2>) item -> - new Tuple2>(item._1() + item._2(), item)) + return blocks.flatMapToPair( + (PairFlatMapFunction>, String, String>) + it -> { + final SparkReporter reporter = new SparkReporter(accumulators); + new BlockProcessor(config).process(it._1(), it._2(), reporter); + return reporter.getRelations().iterator(); + }) + .mapToPair( + (PairFunction, String, Tuple2>) + item -> + new Tuple2>( + item._1() + item._2(), item)) .reduceByKey((a, b) -> a) - .mapToPair((PairFunction>, String, String>) Tuple2::_2); + .mapToPair( + (PairFunction>, String, String>) + Tuple2::_2); } - /** * @return the list of blocks based on clustering of dedup configuration * @param: the spark context * @param: list of entities: * @param: the dedup configuration */ - public static JavaPairRDD> createBlocks(JavaSparkContext context, JavaPairRDD mapDocs, DedupConfig config) { + public static JavaPairRDD> createBlocks( + JavaSparkContext context, + JavaPairRDD mapDocs, + DedupConfig config) { return mapDocs - //the reduce is just to be sure that we haven't document with same id + // the reduce is just to be sure that we haven't document with same id .reduceByKey((a, b) -> a) .map(Tuple2::_2) - //Clustering: from to List - .flatMapToPair((PairFlatMapFunction) a -> - DedupUtility.getGroupingKeys(config, a) - .stream() - .map(it -> new Tuple2<>(it, a)) - .collect(Collectors.toList()) - .iterator()) + // Clustering: from to List + .flatMapToPair( + (PairFlatMapFunction) + a -> + DedupUtility.getGroupingKeys(config, a).stream() + .map(it -> new Tuple2<>(it, a)) + .collect(Collectors.toList()) + .iterator()) .groupByKey(); } - - public static JavaPairRDD> createsortedBlocks(JavaSparkContext context, JavaPairRDD mapDocs, DedupConfig config) { + public static JavaPairRDD> createsortedBlocks( + JavaSparkContext context, + JavaPairRDD mapDocs, + DedupConfig config) { final String of = config.getWf().getOrderField(); final int maxQueueSize = config.getWf().getGroupMaxSize(); return mapDocs - //the reduce is just to be sure that we haven't document with same id + // the reduce is just to be sure that we haven't document with same id .reduceByKey((a, b) -> a) .map(Tuple2::_2) - //Clustering: from to List - .flatMapToPair((PairFlatMapFunction>) a -> - DedupUtility.getGroupingKeys(config, a) - .stream() - .map(it -> { - List tmp = new ArrayList<>(); - tmp.add(a); - return new Tuple2<>(it, tmp); - } - ) - .collect(Collectors.toList()) - .iterator()) - .reduceByKey((Function2, List, List>) (v1, v2) -> { - v1.addAll(v2); - v1.sort(Comparator.comparing(a -> a.getFieldMap().get(of).stringValue())); - if (v1.size() > maxQueueSize) - return new ArrayList<>(v1.subList(0, maxQueueSize)); - return v1; - }); + // Clustering: from to List + .flatMapToPair( + (PairFlatMapFunction>) + a -> + DedupUtility.getGroupingKeys(config, a).stream() + .map( + it -> { + List tmp = + new ArrayList<>(); + tmp.add(a); + return new Tuple2<>(it, tmp); + }) + .collect(Collectors.toList()) + .iterator()) + .reduceByKey( + (Function2, List, List>) + (v1, v2) -> { + v1.addAll(v2); + v1.sort( + Comparator.comparing( + a -> a.getFieldMap().get(of).stringValue())); + if (v1.size() > maxQueueSize) + return new ArrayList<>(v1.subList(0, maxQueueSize)); + return v1; + }); } /** @@ -131,32 +156,48 @@ public class Deduper implements Serializable { * @param: list of JSON entities * @param: the dedup configuration */ - public static JavaPairRDD mapToVertexes(JavaSparkContext context, JavaRDD entities, DedupConfig config) { + public static JavaPairRDD mapToVertexes( + JavaSparkContext context, JavaRDD entities, DedupConfig config) { - return entities.mapToPair((PairFunction) s -> { - - MapDocument mapDocument = MapDocumentUtil.asMapDocumentWithJPath(config, s); - return new Tuple2(mapDocument.getIdentifier(), mapDocument); - - - }); + return entities.mapToPair( + (PairFunction) + s -> { + MapDocument mapDocument = + MapDocumentUtil.asMapDocumentWithJPath(config, s); + return new Tuple2( + mapDocument.getIdentifier(), mapDocument); + }); } - public static JavaPairRDD computeRelations2(JavaSparkContext context, JavaPairRDD> blocks, DedupConfig config) { - Map accumulators = DedupUtility.constructAccumulator(config, context.sc()); + public static JavaPairRDD computeRelations2( + JavaSparkContext context, + JavaPairRDD> blocks, + DedupConfig config) { + Map accumulators = + DedupUtility.constructAccumulator(config, context.sc()); - return blocks.flatMapToPair((PairFlatMapFunction>, String, String>) it -> { - try { - final SparkReporter reporter = new SparkReporter(accumulators); - new BlockProcessor(config).processSortedBlock(it._1(), it._2(), reporter); - return reporter.getRelations().iterator(); - } catch (Exception e) { - throw new RuntimeException(it._2().get(0).getIdentifier(), e); - } - }).mapToPair( - (PairFunction, String, Tuple2>) item -> - new Tuple2>(item._1() + item._2(), item)) + return blocks.flatMapToPair( + (PairFlatMapFunction>, String, String>) + it -> { + try { + final SparkReporter reporter = + new SparkReporter(accumulators); + new BlockProcessor(config) + .processSortedBlock(it._1(), it._2(), reporter); + return reporter.getRelations().iterator(); + } catch (Exception e) { + throw new RuntimeException( + it._2().get(0).getIdentifier(), e); + } + }) + .mapToPair( + (PairFunction, String, Tuple2>) + item -> + new Tuple2>( + item._1() + item._2(), item)) .reduceByKey((a, b) -> a) - .mapToPair((PairFunction>, String, String>) Tuple2::_2); + .mapToPair( + (PairFunction>, String, String>) + Tuple2::_2); } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/OafEntityType.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/OafEntityType.java index fb347ed516..10632240a9 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/OafEntityType.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/OafEntityType.java @@ -1,7 +1,6 @@ package eu.dnetlib.dedup; public enum OafEntityType { - datasource, organization, project, @@ -9,7 +8,4 @@ public enum OafEntityType { otherresearchproduct, software, publication - - - } diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java index d3020b92c3..29068e1320 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java @@ -1,8 +1,5 @@ package eu.dnetlib.dedup; -import com.google.common.collect.Iterables; -import com.google.common.collect.Lists; -import com.google.common.hash.HashFunction; import com.google.common.hash.Hashing; import eu.dnetlib.dedup.graph.ConnectedComponent; import eu.dnetlib.dedup.graph.GraphProcessor; @@ -10,6 +7,8 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.util.MapDocumentUtil; +import java.util.ArrayList; +import java.util.List; import org.apache.commons.io.IOUtils; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; @@ -23,58 +22,91 @@ import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import scala.Tuple2; -import java.util.ArrayList; -import java.util.List; - public class SparkCreateConnectedComponent { public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/sx/dedup/dedup_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateConnectedComponent.class.getResourceAsStream( + "/eu/dnetlib/dhp/sx/dedup/dedup_parameters.json"))); parser.parseArgument(args); - final SparkSession spark = SparkSession - .builder() - .appName(SparkCreateConnectedComponent.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); + final SparkSession spark = + SparkSession.builder() + .appName(SparkCreateConnectedComponent.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final String inputPath = parser.get("sourcePath"); final String entity = parser.get("entity"); final String targetPath = parser.get("targetPath"); -// final DedupConfig dedupConf = DedupConfig.load(IOUtils.toString(SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf2.json"))); + // final DedupConfig dedupConf = + // DedupConfig.load(IOUtils.toString(SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf2.json"))); final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf")); - final JavaPairRDD vertexes = sc.textFile(inputPath + "/" + entity) - .map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s)) - .mapToPair((PairFunction) - s -> new Tuple2(getHashcode(s), s) - ); + final JavaPairRDD vertexes = + sc.textFile(inputPath + "/" + entity) + .map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s)) + .mapToPair( + (PairFunction) + s -> new Tuple2(getHashcode(s), s)); - final Dataset similarityRelations = spark.read().load(DedupUtility.createSimRelPath(targetPath,entity)).as(Encoders.bean(Relation.class)); - final RDD> edgeRdd = similarityRelations.javaRDD().map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())).rdd(); - final JavaRDD cc = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations()).toJavaRDD(); - final Dataset mergeRelation = spark.createDataset(cc.filter(k->k.getDocIds().size()>1).flatMap((FlatMapFunction) c -> - c.getDocIds() - .stream() - .flatMap(id -> { - List tmp = new ArrayList<>(); - Relation r = new Relation(); - r.setSource(c.getCcId()); - r.setTarget(id); - r.setRelClass("merges"); - tmp.add(r); - r = new Relation(); - r.setTarget(c.getCcId()); - r.setSource(id); - r.setRelClass("isMergedIn"); - tmp.add(r); - return tmp.stream(); - }).iterator()).rdd(), Encoders.bean(Relation.class)); - mergeRelation.write().mode("overwrite").save(DedupUtility.createMergeRelPath(targetPath,entity)); + final Dataset similarityRelations = + spark.read() + .load(DedupUtility.createSimRelPath(targetPath, entity)) + .as(Encoders.bean(Relation.class)); + final RDD> edgeRdd = + similarityRelations + .javaRDD() + .map( + it -> + new Edge<>( + getHashcode(it.getSource()), + getHashcode(it.getTarget()), + it.getRelClass())) + .rdd(); + final JavaRDD cc = + GraphProcessor.findCCs( + vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations()) + .toJavaRDD(); + final Dataset mergeRelation = + spark.createDataset( + cc.filter(k -> k.getDocIds().size() > 1) + .flatMap( + (FlatMapFunction) + c -> + c.getDocIds().stream() + .flatMap( + id -> { + List tmp = + new ArrayList<>(); + Relation r = + new Relation(); + r.setSource( + c.getCcId()); + r.setTarget(id); + r.setRelClass("merges"); + tmp.add(r); + r = new Relation(); + r.setTarget( + c.getCcId()); + r.setSource(id); + r.setRelClass( + "isMergedIn"); + tmp.add(r); + return tmp.stream(); + }) + .iterator()) + .rdd(), + Encoders.bean(Relation.class)); + mergeRelation + .write() + .mode("overwrite") + .save(DedupUtility.createMergeRelPath(targetPath, entity)); } - public static long getHashcode(final String id) { + public static long getHashcode(final String id) { return Hashing.murmur3_128().hashString(id).asLong(); } - } diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java index 09c0ba89be..780356fdf2 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java @@ -11,13 +11,17 @@ import org.apache.spark.sql.SparkSession; public class SparkCreateDedupRecord { public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/sx/dedup/dedupRecord_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateDedupRecord.class.getResourceAsStream( + "/eu/dnetlib/dhp/sx/dedup/dedupRecord_parameters.json"))); parser.parseArgument(args); - final SparkSession spark = SparkSession - .builder() - .appName(SparkCreateDedupRecord.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); + final SparkSession spark = + SparkSession.builder() + .appName(SparkCreateDedupRecord.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final String sourcePath = parser.get("sourcePath"); @@ -25,10 +29,20 @@ public class SparkCreateDedupRecord { final String dedupPath = parser.get("dedupPath"); final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf")); - final JavaRDD dedupRecord = DedupRecordFactory.createDedupRecord(sc, spark, DedupUtility.createMergeRelPath(dedupPath,entity), DedupUtility.createEntityPath(sourcePath,entity), OafEntityType.valueOf(entity), dedupConf); - dedupRecord.map(r-> { - ObjectMapper mapper = new ObjectMapper(); - return mapper.writeValueAsString(r); - }).saveAsTextFile(dedupPath+"/"+entity+"/dedup_records"); + final JavaRDD dedupRecord = + DedupRecordFactory.createDedupRecord( + sc, + spark, + DedupUtility.createMergeRelPath(dedupPath, entity), + DedupUtility.createEntityPath(sourcePath, entity), + OafEntityType.valueOf(entity), + dedupConf); + dedupRecord + .map( + r -> { + ObjectMapper mapper = new ObjectMapper(); + return mapper.writeValueAsString(r); + }) + .saveAsTextFile(dedupPath + "/" + entity + "/dedup_records"); } } diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java index b847c80dc4..1728433481 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java @@ -1,73 +1,81 @@ package eu.dnetlib.dedup; -import com.google.common.hash.Hashing; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.MapDocumentUtil; +import java.util.List; import org.apache.commons.io.IOUtils; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import scala.Tuple2; -import java.util.List; - - /** * This Spark class creates similarity relations between entities, saving result * - * param request: - * sourcePath - * entityType - * target Path + *

param request: sourcePath entityType target Path */ public class SparkCreateSimRels { public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/sx/dedup/dedup_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateSimRels.class.getResourceAsStream( + "/eu/dnetlib/dhp/sx/dedup/dedup_parameters.json"))); parser.parseArgument(args); - final SparkSession spark = SparkSession - .builder() - .appName(SparkCreateSimRels.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); + final SparkSession spark = + SparkSession.builder() + .appName(SparkCreateSimRels.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final String inputPath = parser.get("sourcePath"); final String entity = parser.get("entity"); final String targetPath = parser.get("targetPath"); -// final DedupConfig dedupConf = DedupConfig.load(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); + // final DedupConfig dedupConf = + // DedupConfig.load(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf")); + JavaPairRDD mapDocument = + sc.textFile(inputPath + "/" + entity) + .mapToPair( + s -> { + MapDocument d = + MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); + return new Tuple2<>(d.getIdentifier(), d); + }); + // create blocks for deduplication + JavaPairRDD> blocks = + Deduper.createsortedBlocks(sc, mapDocument, dedupConf); + // JavaPairRDD> blocks = Deduper.createBlocks(sc, + // mapDocument, dedupConf); - JavaPairRDD mapDocument = sc.textFile(inputPath + "/" + entity) - .mapToPair(s->{ - MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf,s); - return new Tuple2<>(d.getIdentifier(), d);}); + // create relations by comparing only elements in the same group + final JavaPairRDD dedupRels = + Deduper.computeRelations2(sc, blocks, dedupConf); + // final JavaPairRDD dedupRels = Deduper.computeRelations(sc, blocks, + // dedupConf); - //create blocks for deduplication - JavaPairRDD> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf); -// JavaPairRDD> blocks = Deduper.createBlocks(sc, mapDocument, dedupConf); - - //create relations by comparing only elements in the same group - final JavaPairRDD dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf); -// final JavaPairRDD dedupRels = Deduper.computeRelations(sc, blocks, dedupConf); - - final JavaRDD isSimilarToRDD = dedupRels.map(simRel -> { - final Relation r = new Relation(); - r.setSource(simRel._1()); - r.setTarget(simRel._2()); - r.setRelClass("isSimilarTo"); - return r; - }); - - spark.createDataset(isSimilarToRDD.rdd(), Encoders.bean(Relation.class)).write().mode("overwrite").save( DedupUtility.createSimRelPath(targetPath,entity)); + final JavaRDD isSimilarToRDD = + dedupRels.map( + simRel -> { + final Relation r = new Relation(); + r.setSource(simRel._1()); + r.setTarget(simRel._2()); + r.setRelClass("isSimilarTo"); + return r; + }); + spark.createDataset(isSimilarToRDD.rdd(), Encoders.bean(Relation.class)) + .write() + .mode("overwrite") + .save(DedupUtility.createSimRelPath(targetPath, entity)); } } diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkReporter.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkReporter.java index 165a10b25a..a77484892b 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkReporter.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkReporter.java @@ -1,33 +1,35 @@ package eu.dnetlib.dedup; import eu.dnetlib.pace.util.Reporter; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.spark.util.LongAccumulator; import scala.Serializable; import scala.Tuple2; -import java.util.ArrayList; -import java.util.List; -import java.util.Map; - public class SparkReporter implements Serializable, Reporter { final List> relations = new ArrayList<>(); private static final Log log = LogFactory.getLog(SparkReporter.class); Map accumulators; - public SparkReporter(Map accumulators){ + public SparkReporter(Map accumulators) { this.accumulators = accumulators; } - public void incrementCounter(String counterGroup, String counterName, long delta, Map accumulators) { + public void incrementCounter( + String counterGroup, + String counterName, + long delta, + Map accumulators) { final String accumulatorName = String.format("%s::%s", counterGroup, counterName); - if (accumulators.containsKey(accumulatorName)){ + if (accumulators.containsKey(accumulatorName)) { accumulators.get(accumulatorName).add(delta); } - } @Override diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/graph/ConnectedComponent.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/graph/ConnectedComponent.java index 27a61c02d7..41d53944f3 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/graph/ConnectedComponent.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/graph/ConnectedComponent.java @@ -3,21 +3,18 @@ package eu.dnetlib.dedup.graph; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dedup.DedupUtility; import eu.dnetlib.pace.util.PaceException; -import org.apache.commons.lang.StringUtils; -import org.codehaus.jackson.annotate.JsonIgnore; - import java.io.IOException; import java.io.Serializable; import java.util.Set; +import org.apache.commons.lang.StringUtils; +import org.codehaus.jackson.annotate.JsonIgnore; public class ConnectedComponent implements Serializable { private Set docIds; private String ccId; - - public ConnectedComponent() { - } + public ConnectedComponent() {} public ConnectedComponent(Set docIds) { this.docIds = docIds; @@ -28,7 +25,7 @@ public class ConnectedComponent implements Serializable { if (docIds.size() > 1) { final String s = getMin(); String prefix = s.split("\\|")[0]; - ccId =prefix + "|dedup_______::" + DedupUtility.md5(s); + ccId = prefix + "|dedup_______::" + DedupUtility.md5(s); return ccId; } else { return docIds.iterator().next(); @@ -36,24 +33,25 @@ public class ConnectedComponent implements Serializable { } @JsonIgnore - public String getMin(){ + public String getMin() { final StringBuilder min = new StringBuilder(); - docIds.forEach(i -> { - if (StringUtils.isBlank(min.toString())) { - min.append(i); - } else { - if (min.toString().compareTo(i) > 0) { - min.setLength(0); - min.append(i); - } - } - }); + docIds.forEach( + i -> { + if (StringUtils.isBlank(min.toString())) { + min.append(i); + } else { + if (min.toString().compareTo(i) > 0) { + min.setLength(0); + min.append(i); + } + } + }); return min.toString(); } @Override - public String toString(){ + public String toString() { ObjectMapper mapper = new ObjectMapper(); try { return mapper.writeValueAsString(this); diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkPropagateRelationsJob.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkPropagateRelationsJob.java index a725294430..968f71ef0f 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkPropagateRelationsJob.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkPropagateRelationsJob.java @@ -6,60 +6,79 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.DHPUtils; +import java.io.IOException; import org.apache.commons.io.IOUtils; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; import scala.Tuple2; -import java.io.IOException; - public class SparkPropagateRelationsJob { enum FieldType { SOURCE, TARGET } - final static String SOURCEJSONPATH = "$.source"; - final static String TARGETJSONPATH = "$.target"; + + static final String SOURCEJSONPATH = "$.source"; + static final String TARGETJSONPATH = "$.target"; public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkPropagateRelationsJob.class.getResourceAsStream("/eu/dnetlib/dhp/sx/dedup/dedup_propagate_relation_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkPropagateRelationsJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/sx/dedup/dedup_propagate_relation_parameters.json"))); parser.parseArgument(args); - final SparkSession spark = SparkSession - .builder() - .appName(SparkUpdateEntityJob.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); + final SparkSession spark = + SparkSession.builder() + .appName(SparkUpdateEntityJob.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final String relationPath = parser.get("relationPath"); final String mergeRelPath = parser.get("mergeRelPath"); final String targetRelPath = parser.get("targetRelPath"); + final Dataset merge = + spark.read() + .load(mergeRelPath) + .as(Encoders.bean(Relation.class)) + .where("relClass == 'merges'"); - final Dataset merge = spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class)).where("relClass == 'merges'"); + final Dataset rels = + spark.read().load(relationPath).as(Encoders.bean(Relation.class)); - final Dataset rels= spark.read().load(relationPath).as(Encoders.bean(Relation.class)); + final Dataset firstJoin = + rels.joinWith(merge, merge.col("target").equalTo(rels.col("source")), "left_outer") + .map( + (MapFunction, Relation>) + r -> { + final Relation mergeRelation = r._2(); + final Relation relation = r._1(); + if (mergeRelation != null) + relation.setSource(mergeRelation.getSource()); + return relation; + }, + Encoders.bean(Relation.class)); - final Dataset firstJoin = rels.joinWith(merge, merge.col("target").equalTo(rels.col("source")), "left_outer") - .map((MapFunction, Relation>) r -> { - final Relation mergeRelation = r._2(); - final Relation relation = r._1(); - - if(mergeRelation!= null) - relation.setSource(mergeRelation.getSource()); - return relation; - }, Encoders.bean(Relation.class)); - - final Dataset secondJoin = firstJoin.joinWith(merge, merge.col("target").equalTo(firstJoin.col("target")), "left_outer") - .map((MapFunction, Relation>) r -> { - final Relation mergeRelation = r._2(); - final Relation relation = r._1(); - if (mergeRelation != null ) - relation.setTarget(mergeRelation.getSource()); - return relation; - }, Encoders.bean(Relation.class)); + final Dataset secondJoin = + firstJoin + .joinWith( + merge, + merge.col("target").equalTo(firstJoin.col("target")), + "left_outer") + .map( + (MapFunction, Relation>) + r -> { + final Relation mergeRelation = r._2(); + final Relation relation = r._1(); + if (mergeRelation != null) + relation.setTarget(mergeRelation.getSource()); + return relation; + }, + Encoders.bean(Relation.class)); secondJoin.write().mode(SaveMode.Overwrite).save(targetRelPath); } @@ -71,14 +90,12 @@ public class SparkPropagateRelationsJob { return source.toLowerCase().contains("dedup") || target.toLowerCase().contains("dedup"); } - private static String replaceField(final String json, final String id, final FieldType type) { ObjectMapper mapper = new ObjectMapper(); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); try { Relation relation = mapper.readValue(json, Relation.class); - if (relation.getDataInfo() == null) - relation.setDataInfo(new DataInfo()); + if (relation.getDataInfo() == null) relation.setDataInfo(new DataInfo()); relation.getDataInfo().setDeletedbyinference(false); switch (type) { case SOURCE: diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkUpdateEntityJob.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkUpdateEntityJob.java index 44f7c551e5..c5a9581ecf 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkUpdateEntityJob.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkUpdateEntityJob.java @@ -10,6 +10,7 @@ import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset; import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication; import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown; import eu.dnetlib.dhp.utils.DHPUtils; +import java.io.IOException; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.api.java.JavaPairRDD; @@ -19,20 +20,22 @@ import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.*; import scala.Tuple2; -import java.io.IOException; - public class SparkUpdateEntityJob { - final static String IDJSONPATH = "$.id"; + static final String IDJSONPATH = "$.id"; public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkUpdateEntityJob.class.getResourceAsStream("/eu/dnetlib/dhp/sx/dedup/dedup_delete_by_inference_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkUpdateEntityJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/sx/dedup/dedup_delete_by_inference_parameters.json"))); parser.parseArgument(args); - final SparkSession spark = SparkSession - .builder() - .appName(SparkUpdateEntityJob.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); + final SparkSession spark = + SparkSession.builder() + .appName(SparkUpdateEntityJob.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final String entityPath = parser.get("entityPath"); @@ -41,52 +44,59 @@ public class SparkUpdateEntityJob { final String entity = parser.get("entity"); final String destination = parser.get("targetPath"); - final Dataset df = spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class)); - final JavaPairRDD mergedIds = df - .where("relClass == 'merges'") - .select(df.col("target")) - .distinct() - .toJavaRDD() - .mapToPair((PairFunction) r -> new Tuple2<>(r.getString(0), "d")); + final Dataset df = + spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class)); + final JavaPairRDD mergedIds = + df.where("relClass == 'merges'") + .select(df.col("target")) + .distinct() + .toJavaRDD() + .mapToPair( + (PairFunction) + r -> new Tuple2<>(r.getString(0), "d")); final JavaRDD sourceEntity = sc.textFile(entityPath); final JavaRDD dedupEntity = sc.textFile(dedupRecordPath); - JavaPairRDD entitiesWithId = sourceEntity.mapToPair((PairFunction) s -> new Tuple2<>(DHPUtils.getJPathString(IDJSONPATH, s), s)); - Class mainClass; - switch (entity) { - case "publication": - mainClass = DLIPublication.class; - break; - case "dataset": - mainClass = DLIDataset.class; - break; - case "unknown": - mainClass = DLIUnknown.class; - break; - default: - throw new IllegalArgumentException("Illegal type " + entity); - - } - JavaRDD map = entitiesWithId.leftOuterJoin(mergedIds).map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), mainClass) : k._2()._1()); - map.union(dedupEntity).saveAsTextFile(destination, GzipCodec.class); - + JavaPairRDD entitiesWithId = + sourceEntity.mapToPair( + (PairFunction) + s -> new Tuple2<>(DHPUtils.getJPathString(IDJSONPATH, s), s)); + Class mainClass; + switch (entity) { + case "publication": + mainClass = DLIPublication.class; + break; + case "dataset": + mainClass = DLIDataset.class; + break; + case "unknown": + mainClass = DLIUnknown.class; + break; + default: + throw new IllegalArgumentException("Illegal type " + entity); + } + JavaRDD map = + entitiesWithId + .leftOuterJoin(mergedIds) + .map( + k -> + k._2()._2().isPresent() + ? updateDeletedByInference(k._2()._1(), mainClass) + : k._2()._1()); + map.union(dedupEntity).saveAsTextFile(destination, GzipCodec.class); } - private static String updateDeletedByInference(final String json, final Class clazz) { + private static String updateDeletedByInference( + final String json, final Class clazz) { final ObjectMapper mapper = new ObjectMapper(); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); try { Oaf entity = mapper.readValue(json, clazz); - if (entity.getDataInfo()== null) - entity.setDataInfo(new DataInfo()); + if (entity.getDataInfo() == null) entity.setDataInfo(new DataInfo()); entity.getDataInfo().setDeletedbyinference(true); return mapper.writeValueAsString(entity); } catch (IOException e) { throw new RuntimeException("Unable to convert json", e); } - - } - - } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJob.java index 0270076dd4..d0fe95289d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJob.java @@ -1,8 +1,11 @@ package eu.dnetlib.dhp.oa.graph; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; + import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelSupport; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaSparkContext; @@ -12,26 +15,23 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - public class GraphHiveImporterJob { private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJob.class); public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(GraphHiveImporterJob.class.getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_graph_hive_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + GraphHiveImporterJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_graph_hive_parameters.json"))); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); String inputPath = parser.get("inputPath"); @@ -46,7 +46,9 @@ public class GraphHiveImporterJob { SparkConf conf = new SparkConf(); conf.set("hive.metastore.uris", hiveMetastoreUris); - runWithSparkHiveSession(conf, isSparkSessionManaged, + runWithSparkHiveSession( + conf, + isSparkSessionManaged, spark -> loadGraphAsHiveDB(spark, inputPath, hiveDbName)); } @@ -58,12 +60,15 @@ public class GraphHiveImporterJob { final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); // Read the input file and convert it into RDD of serializable object - ModelSupport.oafTypes.forEach((name, clazz) -> spark.createDataset(sc.textFile(inputPath + "/" + name) - .map(s -> new ObjectMapper().readValue(s, clazz)) - .rdd(), Encoders.bean(clazz)) - .write() - .mode(SaveMode.Overwrite) - .saveAsTable(hiveDbName + "." + name)); + ModelSupport.oafTypes.forEach( + (name, clazz) -> + spark.createDataset( + sc.textFile(inputPath + "/" + name) + .map(s -> new ObjectMapper().readValue(s, clazz)) + .rdd(), + Encoders.bean(clazz)) + .write() + .mode(SaveMode.Overwrite) + .saveAsTable(hiveDbName + "." + name)); } - } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 7d99a4774e..f1058db385 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -1,364 +1,443 @@ package eu.dnetlib.dhp.oa.graph.raw; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; + import eu.dnetlib.dhp.schema.oaf.*; +import java.util.*; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.DocumentFactory; import org.dom4j.DocumentHelper; import org.dom4j.Node; -import java.util.*; - -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; - public abstract class AbstractMdRecordToOafMapper { - protected final Map code2name; - - protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); - - protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER = - qualifier("publication", "publication", "dnet:result_typologies", "dnet:result_typologies"); - protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER = qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies"); - protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies"); - protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER = qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies"); - - protected AbstractMdRecordToOafMapper(final Map code2name) { - this.code2name = code2name; - } - - public List processMdRecord(final String xml) { - try { - final Map nsContext = new HashMap<>(); - nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); - nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); - nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); - nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); - nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); - nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); - nsContext.put("datacite", "http://datacite.org/schema/kernel-3"); - DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); - - final Document doc = DocumentHelper.parseText(xml.replaceAll("http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3")); - - final String type = doc.valueOf("//dr:CobjCategory/@type"); - final KeyValue collectedFrom = keyValue(doc.valueOf("//oaf:collectedFrom/@id"), doc.valueOf("//oaf:collectedFrom/@name")); - final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom - : keyValue(doc.valueOf("//oaf:hostedBy/@id"), doc.valueOf("//oaf:hostedBy/@name")); - - final DataInfo info = prepareDataInfo(doc); - final long lastUpdateTimestamp = new Date().getTime(); - - return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - protected List createOafs(final Document doc, - final String type, - final KeyValue collectedFrom, - final KeyValue hostedBy, - final DataInfo info, - final long lastUpdateTimestamp) { - - final List oafs = new ArrayList<>(); - - switch (type.toLowerCase()) { - case "": - case "publication": - final Publication p = new Publication(); - populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - p.setResulttype(PUBLICATION_RESULTTYPE_QUALIFIER); - p.setJournal(prepareJournal(doc, info)); - oafs.add(p); - break; - case "dataset": - final Dataset d = new Dataset(); - populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - d.setResulttype(DATASET_RESULTTYPE_QUALIFIER); - d.setStoragedate(prepareDatasetStorageDate(doc, info)); - d.setDevice(prepareDatasetDevice(doc, info)); - d.setSize(prepareDatasetSize(doc, info)); - d.setVersion(prepareDatasetVersion(doc, info)); - d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); - d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); - d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - oafs.add(d); - break; - case "software": - final Software s = new Software(); - populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - s.setResulttype(SOFTWARE_RESULTTYPE_QUALIFIER); - s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); - s.setLicense(prepareSoftwareLicenses(doc, info)); - s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); - s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - oafs.add(s); - break; - case "otherresearchproducts": - default: - final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - o.setResulttype(OTHER_RESULTTYPE_QUALIFIER); - o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); - o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); - o.setTool(prepareOtherResearchProductTools(doc, info)); - oafs.add(o); - break; - } - - if (!oafs.isEmpty()) { - oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp)); - oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp)); - } - - return oafs; - } - - private List addProjectRels(final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { - - final List res = new ArrayList<>(); - - final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); - - for (final Object o : doc.selectNodes("//oaf:projectid")) { - final String projectId = createOpenaireId(40, ((Node) o).getText(), true); - - final Relation r1 = new Relation(); - r1.setRelType("resultProject"); - r1.setSubRelType("outcome"); - r1.setRelClass("isProducedBy"); - r1.setSource(docId); - r1.setTarget(projectId); - r1.setCollectedFrom(Arrays.asList(collectedFrom)); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - res.add(r1); - - final Relation r2 = new Relation(); - r2.setRelType("resultProject"); - r2.setSubRelType("outcome"); - r2.setRelClass("produces"); - r2.setSource(projectId); - r2.setTarget(docId); - r2.setCollectedFrom(Arrays.asList(collectedFrom)); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - res.add(r2); - } - - return res; - } - - protected abstract List addOtherResultRels(final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp); - - private void populateResultFields(final Result r, - final Document doc, - final KeyValue collectedFrom, - final KeyValue hostedBy, - final DataInfo info, - final long lastUpdateTimestamp) { - r.setDataInfo(info); - r.setLastupdatetimestamp(lastUpdateTimestamp); - r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); - r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); - r.setCollectedfrom(Arrays.asList(collectedFrom)); - r.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); - r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); - r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); - r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setOaiprovenance(prepareOAIprovenance(doc)); - r.setAuthor(prepareAuthors(doc, info)); - r.setLanguage(prepareLanguages(doc)); - r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setSubject(prepareSubjects(doc, info)); - r.setTitle(prepareTitles(doc, info)); - r.setRelevantdate(prepareRelevantDates(doc, info)); - r.setDescription(prepareDescriptions(doc, info)); - r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info)); - r.setPublisher(preparePublisher(doc, info)); - r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); - r.setSource(prepareSources(doc, info)); - r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setFormat(prepareFormats(doc, info)); - r.setContributor(prepareContributors(doc, info)); - r.setResourcetype(prepareResourceType(doc, info)); - r.setCoverage(prepareCoverages(doc, info)); - r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy)); - } - - protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); - - protected abstract List prepareInstances(Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby); - - protected abstract List> prepareSources(Document doc, DataInfo info); - - protected abstract List prepareRelevantDates(Document doc, DataInfo info); - - protected abstract List> prepareCoverages(Document doc, DataInfo info); - - protected abstract List> prepareContributors(Document doc, DataInfo info); - - protected abstract List> prepareFormats(Document doc, DataInfo info); - - protected abstract Field preparePublisher(Document doc, DataInfo info); - - protected abstract List> prepareDescriptions(Document doc, DataInfo info); - - protected abstract List prepareTitles(Document doc, DataInfo info); - - protected abstract List prepareSubjects(Document doc, DataInfo info); - - protected abstract Qualifier prepareLanguages(Document doc); - - protected abstract List prepareAuthors(Document doc, DataInfo info); - - protected abstract List> prepareOtherResearchProductTools(Document doc, DataInfo info); - - protected abstract List> prepareOtherResearchProductContactGroups(Document doc, DataInfo info); - - protected abstract List> prepareOtherResearchProductContactPersons(Document doc, DataInfo info); - - protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); - - protected abstract Field prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); - - protected abstract List prepareSoftwareLicenses(Document doc, DataInfo info); - - protected abstract List> prepareSoftwareDocumentationUrls(Document doc, DataInfo info); - - protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); - - protected abstract Field prepareDatasetMetadataVersionNumber(Document doc, DataInfo info); - - protected abstract Field prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); - - protected abstract Field prepareDatasetVersion(Document doc, DataInfo info); - - protected abstract Field prepareDatasetSize(Document doc, DataInfo info); - - protected abstract Field prepareDatasetDevice(Document doc, DataInfo info); - - protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); - - private Journal prepareJournal(final Document doc, final DataInfo info) { - final Node n = doc.selectSingleNode("//oaf:journal"); - if (n != null) { - final String name = n.getText(); - final String issnPrinted = n.valueOf("@issn"); - final String issnOnline = n.valueOf("@eissn"); - final String issnLinking = n.valueOf("@lissn"); - final String ep = n.valueOf("@ep"); - final String iss = n.valueOf("@iss"); - final String sp = n.valueOf("@sp"); - final String vol = n.valueOf("@vol"); - final String edition = n.valueOf("@edition"); - if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } - } - return null; - } - - protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId, final String schemeName) { - final String classId = node.valueOf(xpath); - final String className = code2name.get(classId); - return qualifier(classId, className, schemeId, schemeName); - } - - protected List prepareListStructProps(final Node node, - final String xpath, - final String xpathClassId, - final String schemeId, - final String schemeName, - final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - final String classId = n.valueOf(xpathClassId); - final String className = code2name.get(classId); - res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info)); - } - return res; - } - - protected List prepareListStructProps(final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - res.add(structuredProperty(n.getText(), qualifier, info)); - } - return res; - } - - protected List prepareListStructProps(final Node node, final String xpath, final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - res.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n - .valueOf("@schemename"), info)); - } - return res; - } - - protected OAIProvenance prepareOAIprovenance(final Document doc) { - final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); - - if (n == null) { return null; } - - final String identifier = n.valueOf("./*[local-name()='identifier']"); - final String baseURL = n.valueOf("./*[local-name()='baseURL']");; - final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");; - final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); - final String datestamp = n.valueOf("./*[local-name()='datestamp']");; - final String harvestDate = n.valueOf("@harvestDate");; - - return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); - - } - - protected DataInfo prepareDataInfo(final Document doc) { - final Node n = doc.selectSingleNode("//oaf:datainfo"); - - if (n == null) { return null; } - - final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); - final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); - final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid"); - final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename"); - - final boolean deletedbyinference = Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference")); - final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance"); - final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); - final String trust = n.valueOf("./oaf:trust"); - - return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); - } - - protected Field prepareField(final Node node, final String xpath, final DataInfo info) { - return field(node.valueOf(xpath), info); - } - - protected List> prepareListFields(final Node node, final String xpath, final DataInfo info) { - return listFields(info, prepareListString(node, xpath)); - } - - protected List prepareListString(final Node node, final String xpath) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final String s = ((Node) o).getText().trim(); - if (StringUtils.isNotBlank(s)) { - res.add(s); - } - } - return res; - } - + protected final Map code2name; + + protected static final Qualifier MAIN_TITLE_QUALIFIER = + qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + + protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER = + qualifier( + "publication", + "publication", + "dnet:result_typologies", + "dnet:result_typologies"); + protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER = + qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies"); + protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = + qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies"); + protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER = + qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies"); + + protected AbstractMdRecordToOafMapper(final Map code2name) { + this.code2name = code2name; + } + + public List processMdRecord(final String xml) { + try { + final Map nsContext = new HashMap<>(); + nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); + nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); + nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); + nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); + nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); + nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); + nsContext.put("datacite", "http://datacite.org/schema/kernel-3"); + DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); + + final Document doc = + DocumentHelper.parseText( + xml.replaceAll( + "http://datacite.org/schema/kernel-4", + "http://datacite.org/schema/kernel-3")); + + final String type = doc.valueOf("//dr:CobjCategory/@type"); + final KeyValue collectedFrom = + keyValue( + doc.valueOf("//oaf:collectedFrom/@id"), + doc.valueOf("//oaf:collectedFrom/@name")); + final KeyValue hostedBy = + StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) + ? collectedFrom + : keyValue( + doc.valueOf("//oaf:hostedBy/@id"), + doc.valueOf("//oaf:hostedBy/@name")); + + final DataInfo info = prepareDataInfo(doc); + final long lastUpdateTimestamp = new Date().getTime(); + + return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + protected List createOafs( + final Document doc, + final String type, + final KeyValue collectedFrom, + final KeyValue hostedBy, + final DataInfo info, + final long lastUpdateTimestamp) { + + final List oafs = new ArrayList<>(); + + switch (type.toLowerCase()) { + case "": + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + p.setResulttype(PUBLICATION_RESULTTYPE_QUALIFIER); + p.setJournal(prepareJournal(doc, info)); + oafs.add(p); + break; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + d.setResulttype(DATASET_RESULTTYPE_QUALIFIER); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + oafs.add(d); + break; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + s.setResulttype(SOFTWARE_RESULTTYPE_QUALIFIER); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + oafs.add(s); + break; + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + o.setResulttype(OTHER_RESULTTYPE_QUALIFIER); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + oafs.add(o); + break; + } + + if (!oafs.isEmpty()) { + oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp)); + oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp)); + } + + return oafs; + } + + private List addProjectRels( + final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { + + final List res = new ArrayList<>(); + + final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); + + for (final Object o : doc.selectNodes("//oaf:projectid")) { + final String projectId = createOpenaireId(40, ((Node) o).getText(), true); + + final Relation r1 = new Relation(); + r1.setRelType("resultProject"); + r1.setSubRelType("outcome"); + r1.setRelClass("isProducedBy"); + r1.setSource(docId); + r1.setTarget(projectId); + r1.setCollectedFrom(Arrays.asList(collectedFrom)); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + res.add(r1); + + final Relation r2 = new Relation(); + r2.setRelType("resultProject"); + r2.setSubRelType("outcome"); + r2.setRelClass("produces"); + r2.setSource(projectId); + r2.setTarget(docId); + r2.setCollectedFrom(Arrays.asList(collectedFrom)); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + res.add(r2); + } + + return res; + } + + protected abstract List addOtherResultRels( + final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp); + + private void populateResultFields( + final Result r, + final Document doc, + final KeyValue collectedFrom, + final KeyValue hostedBy, + final DataInfo info, + final long lastUpdateTimestamp) { + r.setDataInfo(info); + r.setLastupdatetimestamp(lastUpdateTimestamp); + r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); + r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); + r.setCollectedfrom(Arrays.asList(collectedFrom)); + r.setPid( + prepareListStructProps( + doc, + "//oaf:identifier", + "@identifierType", + "dnet:pid_types", + "dnet:pid_types", + info)); + r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); + r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); + r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setOaiprovenance(prepareOAIprovenance(doc)); + r.setAuthor(prepareAuthors(doc, info)); + r.setLanguage(prepareLanguages(doc)); + r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setSubject(prepareSubjects(doc, info)); + r.setTitle(prepareTitles(doc, info)); + r.setRelevantdate(prepareRelevantDates(doc, info)); + r.setDescription(prepareDescriptions(doc, info)); + r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info)); + r.setPublisher(preparePublisher(doc, info)); + r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); + r.setSource(prepareSources(doc, info)); + r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setFormat(prepareFormats(doc, info)); + r.setContributor(prepareContributors(doc, info)); + r.setResourcetype(prepareResourceType(doc, info)); + r.setCoverage(prepareCoverages(doc, info)); + r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy)); + } + + protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); + + protected abstract List prepareInstances( + Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby); + + protected abstract List> prepareSources(Document doc, DataInfo info); + + protected abstract List prepareRelevantDates(Document doc, DataInfo info); + + protected abstract List> prepareCoverages(Document doc, DataInfo info); + + protected abstract List> prepareContributors(Document doc, DataInfo info); + + protected abstract List> prepareFormats(Document doc, DataInfo info); + + protected abstract Field preparePublisher(Document doc, DataInfo info); + + protected abstract List> prepareDescriptions(Document doc, DataInfo info); + + protected abstract List prepareTitles(Document doc, DataInfo info); + + protected abstract List prepareSubjects(Document doc, DataInfo info); + + protected abstract Qualifier prepareLanguages(Document doc); + + protected abstract List prepareAuthors(Document doc, DataInfo info); + + protected abstract List> prepareOtherResearchProductTools( + Document doc, DataInfo info); + + protected abstract List> prepareOtherResearchProductContactGroups( + Document doc, DataInfo info); + + protected abstract List> prepareOtherResearchProductContactPersons( + Document doc, DataInfo info); + + protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); + + protected abstract Field prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); + + protected abstract List prepareSoftwareLicenses( + Document doc, DataInfo info); + + protected abstract List> prepareSoftwareDocumentationUrls( + Document doc, DataInfo info); + + protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); + + protected abstract Field prepareDatasetMetadataVersionNumber( + Document doc, DataInfo info); + + protected abstract Field prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); + + protected abstract Field prepareDatasetVersion(Document doc, DataInfo info); + + protected abstract Field prepareDatasetSize(Document doc, DataInfo info); + + protected abstract Field prepareDatasetDevice(Document doc, DataInfo info); + + protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); + + private Journal prepareJournal(final Document doc, final DataInfo info) { + final Node n = doc.selectSingleNode("//oaf:journal"); + if (n != null) { + final String name = n.getText(); + final String issnPrinted = n.valueOf("@issn"); + final String issnOnline = n.valueOf("@eissn"); + final String issnLinking = n.valueOf("@lissn"); + final String ep = n.valueOf("@ep"); + final String iss = n.valueOf("@iss"); + final String sp = n.valueOf("@sp"); + final String vol = n.valueOf("@vol"); + final String edition = n.valueOf("@edition"); + if (StringUtils.isNotBlank(name)) { + return journal( + name, + issnPrinted, + issnOnline, + issnLinking, + ep, + iss, + sp, + vol, + edition, + null, + null, + info); + } + } + return null; + } + + protected Qualifier prepareQualifier( + final Node node, final String xpath, final String schemeId, final String schemeName) { + final String classId = node.valueOf(xpath); + final String className = code2name.get(classId); + return qualifier(classId, className, schemeId, schemeName); + } + + protected List prepareListStructProps( + final Node node, + final String xpath, + final String xpathClassId, + final String schemeId, + final String schemeName, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + final String classId = n.valueOf(xpathClassId); + final String className = code2name.get(classId); + res.add( + structuredProperty( + n.getText(), classId, className, schemeId, schemeName, info)); + } + return res; + } + + protected List prepareListStructProps( + final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res.add(structuredProperty(n.getText(), qualifier, info)); + } + return res; + } + + protected List prepareListStructProps( + final Node node, final String xpath, final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res.add( + structuredProperty( + n.getText(), + n.valueOf("@classid"), + n.valueOf("@classname"), + n.valueOf("@schemeid"), + n.valueOf("@schemename"), + info)); + } + return res; + } + + protected OAIProvenance prepareOAIprovenance(final Document doc) { + final Node n = + doc.selectSingleNode( + "//*[local-name()='provenance']/*[local-name()='originDescription']"); + + if (n == null) { + return null; + } + + final String identifier = n.valueOf("./*[local-name()='identifier']"); + final String baseURL = n.valueOf("./*[local-name()='baseURL']"); + ; + final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']"); + ; + final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); + final String datestamp = n.valueOf("./*[local-name()='datestamp']"); + ; + final String harvestDate = n.valueOf("@harvestDate"); + ; + + return oaiIProvenance( + identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); + } + + protected DataInfo prepareDataInfo(final Document doc) { + final Node n = doc.selectSingleNode("//oaf:datainfo"); + + if (n == null) { + return null; + } + + final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); + final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); + final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid"); + final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename"); + + final boolean deletedbyinference = + Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference")); + final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance"); + final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); + final String trust = n.valueOf("./oaf:trust"); + + return dataInfo( + deletedbyinference, + inferenceprovenance, + inferred, + false, + qualifier(paClassId, paClassName, paSchemeId, paSchemeName), + trust); + } + + protected Field prepareField(final Node node, final String xpath, final DataInfo info) { + return field(node.valueOf(xpath), info); + } + + protected List> prepareListFields( + final Node node, final String xpath, final DataInfo info) { + return listFields(info, prepareListString(node, xpath)); + } + + protected List prepareListString(final Node node, final String xpath) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final String s = ((Node) o).getText().trim(); + if (StringUtils.isNotBlank(s)) { + res.add(s); + } + } + return res; + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/DispatchEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/DispatchEntitiesApplication.java index 4812f1c304..4ee0ce3a45 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/DispatchEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/DispatchEntitiesApplication.java @@ -1,94 +1,96 @@ package eu.dnetlib.dhp.oa.graph.raw; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.oaf.*; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - public class DispatchEntitiesApplication { - private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesApplication.class); + private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesApplication.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(MigrateMongoMdstoresApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/dispatch_entities_parameters.json"))); - parser.parseArgument(args); + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + MigrateMongoMdstoresApplication.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dispatch_entities_parameters.json"))); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String sourcePath = parser.get("sourcePath"); - final String targetPath = parser.get("graphRawPath"); + final String sourcePath = parser.get("sourcePath"); + final String targetPath = parser.get("graphRawPath"); - SparkConf conf = new SparkConf(); - runWithSparkSession(conf, isSparkSessionManaged, spark -> { - removeOutputDir(spark, targetPath); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, targetPath); - processEntity(spark, Publication.class, sourcePath, targetPath); - processEntity(spark, Dataset.class, sourcePath, targetPath); - processEntity(spark, Software.class, sourcePath, targetPath); - processEntity(spark, OtherResearchProduct.class, sourcePath, targetPath); - processEntity(spark, Datasource.class, sourcePath, targetPath); - processEntity(spark, Organization.class, sourcePath, targetPath); - processEntity(spark, Project.class, sourcePath, targetPath); - processEntity(spark, Relation.class, sourcePath, targetPath); - }); - } + processEntity(spark, Publication.class, sourcePath, targetPath); + processEntity(spark, Dataset.class, sourcePath, targetPath); + processEntity(spark, Software.class, sourcePath, targetPath); + processEntity(spark, OtherResearchProduct.class, sourcePath, targetPath); + processEntity(spark, Datasource.class, sourcePath, targetPath); + processEntity(spark, Organization.class, sourcePath, targetPath); + processEntity(spark, Project.class, sourcePath, targetPath); + processEntity(spark, Relation.class, sourcePath, targetPath); + }); + } - private static void processEntity(final SparkSession spark, final Class clazz, final String sourcePath, final String targetPath) { - final String type = clazz.getSimpleName().toLowerCase(); + private static void processEntity( + final SparkSession spark, + final Class clazz, + final String sourcePath, + final String targetPath) { + final String type = clazz.getSimpleName().toLowerCase(); - log.info(String.format("Processing entities (%s) in file: %s", type, sourcePath)); + log.info(String.format("Processing entities (%s) in file: %s", type, sourcePath)); - /* - spark.read() - .textFile(sourcePath) - .filter((FilterFunction) value -> isEntityType(value, type)) - .map((MapFunction) value -> StringUtils.substringAfter(value, "|"), Encoders.STRING()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)) - .write() - .mode(SaveMode.Overwrite) - .parquet(targetPath + "/" + type); + /* + spark.read() + .textFile(sourcePath) + .filter((FilterFunction) value -> isEntityType(value, type)) + .map((MapFunction) value -> StringUtils.substringAfter(value, "|"), Encoders.STRING()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)) + .write() + .mode(SaveMode.Overwrite) + .parquet(targetPath + "/" + type); - */ + */ - JavaSparkContext.fromSparkContext(spark.sparkContext()) - .textFile(sourcePath) - .filter(l -> isEntityType(l, type)) - .map(l -> StringUtils.substringAfter(l, "|")) - .saveAsTextFile(targetPath + "/" + type, GzipCodec.class); // use repartition(XXX) ??? - } + JavaSparkContext.fromSparkContext(spark.sparkContext()) + .textFile(sourcePath) + .filter(l -> isEntityType(l, type)) + .map(l -> StringUtils.substringAfter(l, "|")) + .saveAsTextFile( + targetPath + "/" + type, GzipCodec.class); // use repartition(XXX) ??? + } - private static boolean isEntityType(final String line, final String type) { - return StringUtils.substringBefore(line, "|").equalsIgnoreCase(type); - } - - private static void removeOutputDir(SparkSession spark, String path) { - HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); - } + private static boolean isEntityType(final String line, final String type) { + return StringUtils.substringBefore(line, "|").equalsIgnoreCase(type); + } + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index a9f331f537..34ae2df9b5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -1,14 +1,18 @@ package eu.dnetlib.dhp.oa.graph.raw; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.oa.graph.raw.common.DbClient; import eu.dnetlib.dhp.schema.oaf.*; +import java.io.IOException; +import java.sql.SQLException; +import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.Text; @@ -21,152 +25,160 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import scala.Tuple2; -import java.io.IOException; -import java.sql.SQLException; -import java.util.*; -import java.util.stream.Collectors; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - public class GenerateEntitiesApplication { - private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.class); + private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.class); - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(MigrateMongoMdstoresApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json"))); + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + MigrateMongoMdstoresApplication.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json"))); - parser.parseArgument(args); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String sourcePaths = parser.get("sourcePaths"); - final String targetPath = parser.get("targetPath"); + final String sourcePaths = parser.get("sourcePaths"); + final String targetPath = parser.get("targetPath"); - final String dbUrl = parser.get("postgresUrl"); - final String dbUser = parser.get("postgresUser"); - final String dbPassword = parser.get("postgresPassword"); + final String dbUrl = parser.get("postgresUrl"); + final String dbUser = parser.get("postgresUser"); + final String dbPassword = parser.get("postgresPassword"); - final Map code2name = loadClassNames(dbUrl, dbUser, dbPassword); + final Map code2name = loadClassNames(dbUrl, dbUser, dbPassword); - SparkConf conf = new SparkConf(); - runWithSparkSession(conf, isSparkSessionManaged, spark -> { - removeOutputDir(spark, targetPath); - generateEntities(spark, code2name, sourcePaths, targetPath); - }); - } + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, targetPath); + generateEntities(spark, code2name, sourcePaths, targetPath); + }); + } - private static void generateEntities(final SparkSession spark, - final Map code2name, - final String sourcePaths, - final String targetPath) { + private static void generateEntities( + final SparkSession spark, + final Map code2name, + final String sourcePaths, + final String targetPath) { - JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - final List existingSourcePaths = Arrays.stream(sourcePaths.split(",")).filter(p -> exists(sc, p)).collect(Collectors.toList()); + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + final List existingSourcePaths = + Arrays.stream(sourcePaths.split(",")) + .filter(p -> exists(sc, p)) + .collect(Collectors.toList()); - log.info("Generate entities from files:"); - existingSourcePaths.forEach(log::info); + log.info("Generate entities from files:"); + existingSourcePaths.forEach(log::info); - JavaRDD inputRdd = sc.emptyRDD(); + JavaRDD inputRdd = sc.emptyRDD(); - for (final String sp : existingSourcePaths) { - inputRdd = inputRdd.union(sc.sequenceFile(sp, Text.class, Text.class) - .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) - .map(k -> convertToListOaf(k._1(), k._2(), code2name)) - .flatMap(list -> list.iterator()) - .map(oaf -> oaf.getClass().getSimpleName().toLowerCase() + "|" + convertToJson(oaf))); - } + for (final String sp : existingSourcePaths) { + inputRdd = + inputRdd.union( + sc.sequenceFile(sp, Text.class, Text.class) + .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) + .map(k -> convertToListOaf(k._1(), k._2(), code2name)) + .flatMap(list -> list.iterator()) + .map( + oaf -> + oaf.getClass().getSimpleName().toLowerCase() + + "|" + + convertToJson(oaf))); + } - inputRdd - .saveAsTextFile(targetPath, GzipCodec.class); + inputRdd.saveAsTextFile(targetPath, GzipCodec.class); + } - } + private static List convertToListOaf( + final String id, final String s, final Map code2name) { + final String type = StringUtils.substringAfter(id, ":"); - private static List convertToListOaf(final String id, final String s, final Map code2name) { - final String type = StringUtils.substringAfter(id, ":"); + switch (type.toLowerCase()) { + case "native_oaf": + return new OafToOafMapper(code2name).processMdRecord(s); + case "native_odf": + return new OdfToOafMapper(code2name).processMdRecord(s); + case "datasource": + return Arrays.asList(convertFromJson(s, Datasource.class)); + case "organization": + return Arrays.asList(convertFromJson(s, Organization.class)); + case "project": + return Arrays.asList(convertFromJson(s, Project.class)); + case "relation": + return Arrays.asList(convertFromJson(s, Relation.class)); + case "publication": + return Arrays.asList(convertFromJson(s, Publication.class)); + case "dataset": + return Arrays.asList(convertFromJson(s, Dataset.class)); + case "software": + return Arrays.asList(convertFromJson(s, Software.class)); + case "otherresearchproducts": + default: + return Arrays.asList(convertFromJson(s, OtherResearchProduct.class)); + } + } - switch (type.toLowerCase()) { - case "native_oaf": - return new OafToOafMapper(code2name).processMdRecord(s); - case "native_odf": - return new OdfToOafMapper(code2name).processMdRecord(s); - case "datasource": - return Arrays.asList(convertFromJson(s, Datasource.class)); - case "organization": - return Arrays.asList(convertFromJson(s, Organization.class)); - case "project": - return Arrays.asList(convertFromJson(s, Project.class)); - case "relation": - return Arrays.asList(convertFromJson(s, Relation.class)); - case "publication": - return Arrays.asList(convertFromJson(s, Publication.class)); - case "dataset": - return Arrays.asList(convertFromJson(s, Dataset.class)); - case "software": - return Arrays.asList(convertFromJson(s, Software.class)); - case "otherresearchproducts": - default: - return Arrays.asList(convertFromJson(s, OtherResearchProduct.class)); - } + private static Map loadClassNames( + final String dbUrl, final String dbUser, final String dbPassword) throws IOException { - } + log.info("Loading vocabulary terms from db..."); - private static Map loadClassNames(final String dbUrl, final String dbUser, final String dbPassword) throws IOException { + final Map map = new HashMap<>(); - log.info("Loading vocabulary terms from db..."); + try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) { + dbClient.processResults( + "select code, name from class", + rs -> { + try { + map.put(rs.getString("code"), rs.getString("name")); + } catch (final SQLException e) { + e.printStackTrace(); + } + }); + } - final Map map = new HashMap<>(); + log.info("Found " + map.size() + " terms."); - try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) { - dbClient.processResults("select code, name from class", rs -> { - try { - map.put(rs.getString("code"), rs.getString("name")); - } catch (final SQLException e) { - e.printStackTrace(); - } - }); - } + return map; + } - log.info("Found " + map.size() + " terms."); + private static String convertToJson(final Oaf oaf) { + try { + return new ObjectMapper().writeValueAsString(oaf); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } - return map; + private static Oaf convertFromJson(final String s, final Class clazz) { + try { + return new ObjectMapper().readValue(s, clazz); + } catch (final Exception e) { + log.error("Error parsing object of class: " + clazz); + log.error(s); + throw new RuntimeException(e); + } + } - } + private static boolean exists(final JavaSparkContext context, final String pathToFile) { + try { + final FileSystem hdfs = FileSystem.get(context.hadoopConfiguration()); + final Path path = new Path(pathToFile); + return hdfs.exists(path); + } catch (final IOException e) { + throw new RuntimeException(e); + } + } - private static String convertToJson(final Oaf oaf) { - try { - return new ObjectMapper().writeValueAsString(oaf); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - private static Oaf convertFromJson(final String s, final Class clazz) { - try { - return new ObjectMapper().readValue(s, clazz); - } catch (final Exception e) { - log.error("Error parsing object of class: " + clazz); - log.error(s); - throw new RuntimeException(e); - } - } - - private static boolean exists(final JavaSparkContext context, final String pathToFile) { - try { - final FileSystem hdfs = FileSystem.get(context.hadoopConfiguration()); - final Path path = new Path(pathToFile); - return hdfs.exists(path); - } catch (final IOException e) { - throw new RuntimeException(e); - } - } - - private static void removeOutputDir(SparkSession spark, String path) { - HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); - } + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java index 4b209c68ab..130b826e93 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java @@ -1,13 +1,17 @@ package eu.dnetlib.dhp.oa.graph.raw; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; + import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; +import java.util.Objects; +import java.util.Optional; +import java.util.function.Function; import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.FilterFunction; @@ -19,141 +23,186 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import scala.Tuple2; -import scala.reflect.ClassTag; -import scala.reflect.ClassTag$; - -import java.util.Objects; -import java.util.Optional; -import java.util.function.Function; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; public class MergeClaimsApplication { - private static final Logger log = LoggerFactory.getLogger(MergeClaimsApplication.class); + private static final Logger log = LoggerFactory.getLogger(MergeClaimsApplication.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(MigrateMongoMdstoresApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json"))); - parser.parseArgument(args); + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + MigrateMongoMdstoresApplication.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json"))); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String rawGraphPath = parser.get("rawGraphPath"); - log.info("rawGraphPath: {}", rawGraphPath); + final String rawGraphPath = parser.get("rawGraphPath"); + log.info("rawGraphPath: {}", rawGraphPath); - final String claimsGraphPath = parser.get("claimsGraphPath"); - log.info("claimsGraphPath: {}", claimsGraphPath); + final String claimsGraphPath = parser.get("claimsGraphPath"); + log.info("claimsGraphPath: {}", claimsGraphPath); - final String outputRawGaphPath = parser.get("outputRawGaphPath"); - log.info("outputRawGaphPath: {}", outputRawGaphPath); + final String outputRawGaphPath = parser.get("outputRawGaphPath"); + log.info("outputRawGaphPath: {}", outputRawGaphPath); - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); - Class clazz = (Class) Class.forName(graphTableClassName); + Class clazz = (Class) Class.forName(graphTableClassName); - SparkConf conf = new SparkConf(); - conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - runWithSparkSession(conf, isSparkSessionManaged, spark -> { - String type = clazz.getSimpleName().toLowerCase(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + String type = clazz.getSimpleName().toLowerCase(); - String rawPath = rawGraphPath + "/" + type; - String claimPath = claimsGraphPath + "/" + type; - String outPath = outputRawGaphPath + "/" + type; + String rawPath = rawGraphPath + "/" + type; + String claimPath = claimsGraphPath + "/" + type; + String outPath = outputRawGaphPath + "/" + type; - removeOutputDir(spark, outPath); - mergeByType(spark, rawPath, claimPath, outPath, clazz); - }); - } + removeOutputDir(spark, outPath); + mergeByType(spark, rawPath, claimPath, outPath, clazz); + }); + } - private static void mergeByType(SparkSession spark, String rawPath, String claimPath, String outPath, Class clazz) { - Dataset> raw = readFromPath(spark, rawPath, clazz) - .map((MapFunction>) value -> new Tuple2<>(idFn().apply(value), value), Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); + private static void mergeByType( + SparkSession spark, String rawPath, String claimPath, String outPath, Class clazz) { + Dataset> raw = + readFromPath(spark, rawPath, clazz) + .map( + (MapFunction>) + value -> new Tuple2<>(idFn().apply(value), value), + Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); - final JavaSparkContext jsc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - Dataset> claim = jsc.broadcast(readFromPath(spark, claimPath, clazz)) - .getValue() - .map((MapFunction>) value -> new Tuple2<>(idFn().apply(value), value), Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); + final JavaSparkContext jsc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + Dataset> claim = + jsc.broadcast(readFromPath(spark, claimPath, clazz)) + .getValue() + .map( + (MapFunction>) + value -> new Tuple2<>(idFn().apply(value), value), + Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); - /* - Dataset> claim = readFromPath(spark, claimPath, clazz) - .map((MapFunction>) value -> new Tuple2<>(idFn().apply(value), value), Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); - */ + /* + Dataset> claim = readFromPath(spark, claimPath, clazz) + .map((MapFunction>) value -> new Tuple2<>(idFn().apply(value), value), Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); + */ - raw.joinWith(claim, raw.col("_1").equalTo(claim.col("_1")), "full_outer") - .map((MapFunction, Tuple2>, T>) value -> { + raw.joinWith(claim, raw.col("_1").equalTo(claim.col("_1")), "full_outer") + .map( + (MapFunction, Tuple2>, T>) + value -> { + Optional> opRaw = + Optional.ofNullable(value._1()); + Optional> opClaim = + Optional.ofNullable(value._2()); - Optional> opRaw = Optional.ofNullable(value._1()); - Optional> opClaim = Optional.ofNullable(value._2()); + return opRaw.isPresent() + ? opRaw.get()._2() + : opClaim.isPresent() ? opClaim.get()._2() : null; + }, + Encoders.bean(clazz)) + .filter(Objects::nonNull) + .map( + (MapFunction) value -> OBJECT_MAPPER.writeValueAsString(value), + Encoders.STRING()) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .text(outPath); + } - return opRaw.isPresent() ? opRaw.get()._2() : opClaim.isPresent() ? opClaim.get()._2() : null; - }, Encoders.bean(clazz)) - .filter(Objects::nonNull) - .map((MapFunction) value -> OBJECT_MAPPER.writeValueAsString(value), Encoders.STRING()) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .text(outPath); - } + private static Dataset readFromPath( + SparkSession spark, String path, Class clazz) { + return spark.read() + .textFile(path) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), + Encoders.bean(clazz)) + .filter((FilterFunction) value -> Objects.nonNull(idFn().apply(value))); + /* + return spark.read() + .load(path) + .as(Encoders.bean(clazz)) + .filter((FilterFunction) value -> Objects.nonNull(idFn().apply(value))); + */ + } - private static Dataset readFromPath(SparkSession spark, String path, Class clazz) { - return spark.read() - .textFile(path) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)) - .filter((FilterFunction) value -> Objects.nonNull(idFn().apply(value))); - /* - return spark.read() - .load(path) - .as(Encoders.bean(clazz)) - .filter((FilterFunction) value -> Objects.nonNull(idFn().apply(value))); - */ - } + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } - private static void removeOutputDir(SparkSession spark, String path) { - HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); - } + private static Function idFn() { + return x -> { + if (isSubClass(x, Relation.class)) { + return idFnForRelation(x); + } + return idFnForOafEntity(x); + }; + } - private static Function idFn() { - return x -> { - if (isSubClass(x, Relation.class)) { - return idFnForRelation(x); - } - return idFnForOafEntity(x); - }; - } - - private static String idFnForRelation(T t) { - Relation r = (Relation) t; - return Optional.ofNullable(r.getSource()) - .map(source -> Optional.ofNullable(r.getTarget()) - .map(target -> Optional.ofNullable(r.getRelType()) - .map(relType -> Optional.ofNullable(r.getSubRelType()) - .map(subRelType -> Optional.ofNullable(r.getRelClass()) - .map(relClass -> String.join(source, target, relType, subRelType, relClass)) - .orElse(String.join(source, target, relType, subRelType)) - ) - .orElse(String.join(source, target, relType)) - ) - .orElse(String.join(source, target)) - ) - .orElse(source) - ) - .orElse(null); - } - - private static String idFnForOafEntity(T t) { - return ((OafEntity) t).getId(); - } + private static String idFnForRelation(T t) { + Relation r = (Relation) t; + return Optional.ofNullable(r.getSource()) + .map( + source -> + Optional.ofNullable(r.getTarget()) + .map( + target -> + Optional.ofNullable(r.getRelType()) + .map( + relType -> + Optional.ofNullable( + r + .getSubRelType()) + .map( + subRelType -> + Optional + .ofNullable( + r + .getRelClass()) + .map( + relClass -> + String + .join( + source, + target, + relType, + subRelType, + relClass)) + .orElse( + String + .join( + source, + target, + relType, + subRelType))) + .orElse( + String + .join( + source, + target, + relType))) + .orElse( + String.join( + source, target))) + .orElse(source)) + .orElse(null); + } + private static String idFnForOafEntity(T t) { + return ((OafEntity) t).getId(); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index f8f6b58cca..6de7303c35 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -1,14 +1,11 @@ package eu.dnetlib.dhp.oa.graph.raw; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; import eu.dnetlib.dhp.oa.graph.raw.common.DbClient; import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - import java.io.Closeable; import java.io.IOException; import java.sql.Array; @@ -20,437 +17,510 @@ import java.util.Date; import java.util.List; import java.util.function.Consumer; import java.util.function.Function; - -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; - -public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable { - - private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = - qualifier("sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", "dnet:provenance_actions", "dnet:provenance_actions"); - - private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class); - - private final DbClient dbClient; - - private final long lastUpdateTimestamp; - - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(MigrateDbEntitiesApplication.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json"))); - - parser.parseArgument(args); - - final String dbUrl = parser.get("postgresUrl"); - final String dbUser = parser.get("postgresUser"); - final String dbPassword = parser.get("postgresPassword"); - - final String hdfsPath = parser.get("hdfsPath"); - - final boolean processClaims = parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims"); - - try (final MigrateDbEntitiesApplication smdbe = new MigrateDbEntitiesApplication(hdfsPath, dbUrl, dbUser, dbPassword)) { - if (processClaims) { - log.info("Processing claims..."); - smdbe.execute("queryClaims.sql", smdbe::processClaims); - } else { - log.info("Processing datasources..."); - smdbe.execute("queryDatasources.sql", smdbe::processDatasource); - - log.info("Processing projects..."); - smdbe.execute("queryProjects.sql", smdbe::processProject); - - log.info("Processing orgs..."); - smdbe.execute("queryOrganizations.sql", smdbe::processOrganization); - - log.info("Processing relations ds <-> orgs ..."); - smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization); - - log.info("Processing projects <-> orgs ..."); - smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization); - } - log.info("All done."); - } - } - - protected MigrateDbEntitiesApplication() { // ONLY FOR UNIT TEST - super(); - this.dbClient = null; - this.lastUpdateTimestamp = new Date().getTime(); - } - - public MigrateDbEntitiesApplication(final String hdfsPath, final String dbUrl, final String dbUser, - final String dbPassword) throws Exception { - super(hdfsPath); - this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); - this.lastUpdateTimestamp = new Date().getTime(); - } - - public void execute(final String sqlFile, final Function> producer) throws Exception { - final String sql = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile)); - - final Consumer consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf)); - - dbClient.processResults(sql, consumer); - } - - public List processDatasource(final ResultSet rs) { - - try { - - final DataInfo info = prepareDataInfo(rs); - - final Datasource ds = new Datasource(); - - ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true)); - ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); - ds.setCollectedfrom(listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname"))); - ds.setPid(new ArrayList<>()); - ds.setDateofcollection(asString(rs.getDate("dateofcollection"))); - ds.setDateoftransformation(null); // Value not returned by the SQL query - ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB - ds.setOaiprovenance(null); // Values not present in the DB - ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype"))); - ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility"))); - ds.setOfficialname(field(rs.getString("officialname"), info)); - ds.setEnglishname(field(rs.getString("englishname"), info)); - ds.setWebsiteurl(field(rs.getString("websiteurl"), info)); - ds.setLogourl(field(rs.getString("logourl"), info)); - ds.setContactemail(field(rs.getString("contactemail"), info)); - ds.setNamespaceprefix(field(rs.getString("namespaceprefix"), info)); - ds.setLatitude(field(Double.toString(rs.getDouble("latitude")), info)); - ds.setLongitude(field(Double.toString(rs.getDouble("longitude")), info)); - ds.setDateofvalidation(field(asString(rs.getDate("dateofvalidation")), info)); - ds.setDescription(field(rs.getString("description"), info)); - ds.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); - ds.setOdnumberofitems(field(Double.toString(rs.getInt("odnumberofitems")), info)); - ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info)); - ds.setOdpolicies(field(rs.getString("odpolicies"), info)); - ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info)); - ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info)); - ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info)); - ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); - ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info)); - ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info)); - ds.setDataprovider(field(rs.getBoolean("dataprovider"), info)); - ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info)); - ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info)); - ds.setDatauploadtype(field(rs.getString("datauploadtype"), info)); - ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); - ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info)); - ds.setVersioning(field(rs.getBoolean("versioning"), info)); - ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info)); - ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info)); - ds.setPidsystems(field(rs.getString("pidsystems"), info)); - ds.setCertificates(field(rs.getString("certificates"), info)); - ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array - ds.setJournal(prepareJournal(rs.getString("officialname"), rs.getString("journal"), info)); // Journal - ds.setDataInfo(info); - ds.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(ds); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processProject(final ResultSet rs) { - try { - - final DataInfo info = prepareDataInfo(rs); - - final Project p = new Project(); - - p.setId(createOpenaireId(40, rs.getString("projectid"), true)); - p.setOriginalId(Arrays.asList(rs.getString("projectid"))); - p.setCollectedfrom(listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname"))); - p.setPid(new ArrayList<>()); - p.setDateofcollection(asString(rs.getDate("dateofcollection"))); - p.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); - p.setExtraInfo(new ArrayList<>()); // Values not present in the DB - p.setOaiprovenance(null); // Values not present in the DB - p.setWebsiteurl(field(rs.getString("websiteurl"), info)); - p.setCode(field(rs.getString("code"), info)); - p.setAcronym(field(rs.getString("acronym"), info)); - p.setTitle(field(rs.getString("title"), info)); - p.setStartdate(field(asString(rs.getDate("startdate")), info)); - p.setEnddate(field(asString(rs.getDate("enddate")), info)); - p.setCallidentifier(field(rs.getString("callidentifier"), info)); - p.setKeywords(field(rs.getString("keywords"), info)); - p.setDuration(field(Integer.toString(rs.getInt("duration")), info)); - p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info)); - p.setOamandatepublications(field(Boolean.toString(rs.getBoolean("oamandatepublications")), info)); - p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info)); - p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); - p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info)); - p.setContracttype(prepareQualifierSplitting(rs.getString("contracttype"))); - p.setOptional1(field(rs.getString("optional1"), info)); - p.setOptional2(field(rs.getString("optional2"), info)); - p.setJsonextrainfo(field(rs.getString("jsonextrainfo"), info)); - p.setContactfullname(field(rs.getString("contactfullname"), info)); - p.setContactfax(field(rs.getString("contactfax"), info)); - p.setContactphone(field(rs.getString("contactphone"), info)); - p.setContactemail(field(rs.getString("contactemail"), info)); - p.setSummary(field(rs.getString("summary"), info)); - p.setCurrency(field(rs.getString("currency"), info)); - p.setTotalcost(new Float(rs.getDouble("totalcost"))); - p.setFundedamount(new Float(rs.getDouble("fundedamount"))); - p.setDataInfo(info); - p.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(p); - - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processOrganization(final ResultSet rs) { - - try { - - final DataInfo info = prepareDataInfo(rs); - - final Organization o = new Organization(); - - o.setId(createOpenaireId(20, rs.getString("organizationid"), true)); - o.setOriginalId(Arrays.asList(rs.getString("organizationid"))); - o.setCollectedfrom(listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname"))); - o.setPid(new ArrayList<>()); - o.setDateofcollection(asString(rs.getDate("dateofcollection"))); - o.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); - o.setExtraInfo(new ArrayList<>()); // Values not present in the DB - o.setOaiprovenance(null); // Values not present in the DB - o.setLegalshortname(field(rs.getString("legalshortname"), info)); - o.setLegalname(field(rs.getString("legalname"), info)); - o.setAlternativeNames(new ArrayList<>()); // Values not returned by the SQL query - o.setWebsiteurl(field(rs.getString("websiteurl"), info)); - o.setLogourl(field(rs.getString("logourl"), info)); - o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info)); - o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info)); - o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info)); - o.setEcresearchorganization(field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info)); - o.setEchighereducation(field(Boolean.toString(rs.getBoolean("echighereducation")), info)); - o.setEcinternationalorganizationeurinterests(field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info)); - o.setEcinternationalorganization(field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info)); - o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info)); - o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info)); - o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info)); - o.setCountry(prepareQualifierSplitting(rs.getString("country"))); - o.setDataInfo(info); - o.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(o); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processDatasourceOrganization(final ResultSet rs) { - try { - final DataInfo info = prepareDataInfo(rs); - final String orgId = createOpenaireId(20, rs.getString("organization"), true); - final String dsId = createOpenaireId(10, rs.getString("datasource"), true); - final List collectedFrom = listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")); - - final Relation r1 = new Relation(); - r1.setRelType("datasourceOrganization"); - r1.setSubRelType("provision"); - r1.setRelClass("isProvidedBy"); - r1.setSource(dsId); - r1.setTarget(orgId); - r1.setCollectedFrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - - final Relation r2 = new Relation(); - r2.setRelType("datasourceOrganization"); - r2.setSubRelType("provision"); - r2.setRelClass("provides"); - r2.setSource(orgId); - r2.setTarget(dsId); - r2.setCollectedFrom(collectedFrom); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(r1, r2); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processProjectOrganization(final ResultSet rs) { - try { - final DataInfo info = prepareDataInfo(rs); - final String orgId = createOpenaireId(20, rs.getString("resporganization"), true); - final String projectId = createOpenaireId(40, rs.getString("project"), true); - final List collectedFrom = listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")); - - final Relation r1 = new Relation(); - r1.setRelType("projectOrganization"); - r1.setSubRelType("participation"); - r1.setRelClass("isParticipant"); - r1.setSource(projectId); - r1.setTarget(orgId); - r1.setCollectedFrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - - final Relation r2 = new Relation(); - r2.setRelType("projectOrganization"); - r2.setSubRelType("participation"); - r2.setRelClass("hasParticipant"); - r2.setSource(orgId); - r2.setTarget(projectId); - r2.setCollectedFrom(collectedFrom); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(r1, r2); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processClaims(final ResultSet rs) { - - final DataInfo info = - dataInfo(false, null, false, false, qualifier("user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"), "0.9"); - - try { - - if (rs.getString("source_type").equals("context")) { - final Result r; - - if (rs.getString("target_type").equals("dataset")) { - r = new Dataset(); - } else if (rs.getString("target_type").equals("software")) { - r = new Software(); - } else if (rs.getString("target_type").equals("other")) { - r = new OtherResearchProduct(); - } else { - r = new Publication(); - } - r.setId(createOpenaireId(50, rs.getString("target_id"), false)); - r.setLastupdatetimestamp(lastUpdateTimestamp); - r.setContext(prepareContext(rs.getString("source_id"), info)); - r.setDataInfo(info); - - return Arrays.asList(r); - } else { - final String sourceId = createOpenaireId(rs.getString("source_type"), rs.getString("source_id"), false); - final String targetId = createOpenaireId(rs.getString("target_type"), rs.getString("target_id"), false); - - final Relation r1 = new Relation(); - final Relation r2 = new Relation(); - - if (rs.getString("source_type").equals("project")) { - r1.setRelType("resultProject"); - r1.setSubRelType("outcome"); - r1.setRelClass("produces"); - - r2.setRelType("resultProject"); - r2.setSubRelType("outcome"); - r2.setRelClass("isProducedBy"); - } else { - r1.setRelType("resultResult"); - r1.setSubRelType("relationship"); - r1.setRelClass("isRelatedTo"); - - r2.setRelType("resultResult"); - r2.setSubRelType("relationship"); - r2.setRelClass("isRelatedTo"); - } - - r1.setSource(sourceId); - r1.setTarget(targetId); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - - r2.setSource(targetId); - r2.setTarget(sourceId); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(r1, r2); - } - - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - private List prepareContext(final String id, final DataInfo dataInfo) { - final Context context = new Context(); - context.setId(id); - context.setDataInfo(Arrays.asList(dataInfo)); - return Arrays.asList(context); - } - - private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException { - final Boolean deletedbyinference = rs.getBoolean("deletedbyinference"); - final String inferenceprovenance = rs.getString("inferenceprovenance"); - final Boolean inferred = rs.getBoolean("inferred"); - final String trust = rs.getString("trust"); - return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, ENTITYREGISTRY_PROVENANCE_ACTION, trust); - } - - private Qualifier prepareQualifierSplitting(final String s) { - if (StringUtils.isBlank(s)) { return null; } - final String[] arr = s.split("@@@"); - return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null; - } - - private List> prepareListFields(final Array array, final DataInfo info) { - try { - return array != null ? listFields(info, (String[]) array.getArray()) : new ArrayList<>(); - } catch (final SQLException e) { - throw new RuntimeException("Invalid SQL array", e); - } - } - - private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) { - if (StringUtils.isBlank(s)) { return null; } - final String[] parts = s.split("###"); - if (parts.length == 2) { - final String value = parts[0]; - final String[] arr = parts[1].split("@@@"); - if (arr.length == 4) { return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); } - } - return null; - } - - private List prepareListOfStructProps(final Array array, final DataInfo dataInfo) throws SQLException { - final List res = new ArrayList<>(); - if (array != null) { - for (final String s : (String[]) array.getArray()) { - final StructuredProperty sp = prepareStructProp(s, dataInfo); - if (sp != null) { - res.add(sp); - } - } - } - - return res; - } - - private Journal prepareJournal(final String name, final String sj, final DataInfo info) { - if (StringUtils.isNotBlank(sj)) { - final String[] arr = sj.split("@@@"); - if (arr.length == 3) { - final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null; - final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;; - final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;; - if (issn != null || eissn != null - || lissn != null) { return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info); } - } - } - return null; - } - - @Override - public void close() throws IOException { - super.close(); - dbClient.close(); - } - +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +public class MigrateDbEntitiesApplication extends AbstractMigrationApplication + implements Closeable { + + private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = + qualifier( + "sysimport:crosswalk:entityregistry", + "sysimport:crosswalk:entityregistry", + "dnet:provenance_actions", + "dnet:provenance_actions"); + + private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class); + + private final DbClient dbClient; + + private final long lastUpdateTimestamp; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + MigrateDbEntitiesApplication.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json"))); + + parser.parseArgument(args); + + final String dbUrl = parser.get("postgresUrl"); + final String dbUser = parser.get("postgresUser"); + final String dbPassword = parser.get("postgresPassword"); + + final String hdfsPath = parser.get("hdfsPath"); + + final boolean processClaims = + parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims"); + + try (final MigrateDbEntitiesApplication smdbe = + new MigrateDbEntitiesApplication(hdfsPath, dbUrl, dbUser, dbPassword)) { + if (processClaims) { + log.info("Processing claims..."); + smdbe.execute("queryClaims.sql", smdbe::processClaims); + } else { + log.info("Processing datasources..."); + smdbe.execute("queryDatasources.sql", smdbe::processDatasource); + + log.info("Processing projects..."); + smdbe.execute("queryProjects.sql", smdbe::processProject); + + log.info("Processing orgs..."); + smdbe.execute("queryOrganizations.sql", smdbe::processOrganization); + + log.info("Processing relations ds <-> orgs ..."); + smdbe.execute( + "queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization); + + log.info("Processing projects <-> orgs ..."); + smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization); + } + log.info("All done."); + } + } + + protected MigrateDbEntitiesApplication() { // ONLY FOR UNIT TEST + super(); + this.dbClient = null; + this.lastUpdateTimestamp = new Date().getTime(); + } + + public MigrateDbEntitiesApplication( + final String hdfsPath, final String dbUrl, final String dbUser, final String dbPassword) + throws Exception { + super(hdfsPath); + this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); + this.lastUpdateTimestamp = new Date().getTime(); + } + + public void execute(final String sqlFile, final Function> producer) + throws Exception { + final String sql = + IOUtils.toString( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile)); + + final Consumer consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf)); + + dbClient.processResults(sql, consumer); + } + + public List processDatasource(final ResultSet rs) { + + try { + + final DataInfo info = prepareDataInfo(rs); + + final Datasource ds = new Datasource(); + + ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true)); + ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); + ds.setCollectedfrom( + listKeyValues( + rs.getString("collectedfromid"), rs.getString("collectedfromname"))); + ds.setPid(new ArrayList<>()); + ds.setDateofcollection(asString(rs.getDate("dateofcollection"))); + ds.setDateoftransformation(null); // Value not returned by the SQL query + ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB + ds.setOaiprovenance(null); // Values not present in the DB + ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype"))); + ds.setOpenairecompatibility( + prepareQualifierSplitting(rs.getString("openairecompatibility"))); + ds.setOfficialname(field(rs.getString("officialname"), info)); + ds.setEnglishname(field(rs.getString("englishname"), info)); + ds.setWebsiteurl(field(rs.getString("websiteurl"), info)); + ds.setLogourl(field(rs.getString("logourl"), info)); + ds.setContactemail(field(rs.getString("contactemail"), info)); + ds.setNamespaceprefix(field(rs.getString("namespaceprefix"), info)); + ds.setLatitude(field(Double.toString(rs.getDouble("latitude")), info)); + ds.setLongitude(field(Double.toString(rs.getDouble("longitude")), info)); + ds.setDateofvalidation(field(asString(rs.getDate("dateofvalidation")), info)); + ds.setDescription(field(rs.getString("description"), info)); + ds.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); + ds.setOdnumberofitems(field(Double.toString(rs.getInt("odnumberofitems")), info)); + ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info)); + ds.setOdpolicies(field(rs.getString("odpolicies"), info)); + ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info)); + ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info)); + ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info)); + ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); + ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info)); + ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info)); + ds.setDataprovider(field(rs.getBoolean("dataprovider"), info)); + ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info)); + ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info)); + ds.setDatauploadtype(field(rs.getString("datauploadtype"), info)); + ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); + ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info)); + ds.setVersioning(field(rs.getBoolean("versioning"), info)); + ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info)); + ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info)); + ds.setPidsystems(field(rs.getString("pidsystems"), info)); + ds.setCertificates(field(rs.getString("certificates"), info)); + ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array + ds.setJournal( + prepareJournal( + rs.getString("officialname"), + rs.getString("journal"), + info)); // Journal + ds.setDataInfo(info); + ds.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(ds); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processProject(final ResultSet rs) { + try { + + final DataInfo info = prepareDataInfo(rs); + + final Project p = new Project(); + + p.setId(createOpenaireId(40, rs.getString("projectid"), true)); + p.setOriginalId(Arrays.asList(rs.getString("projectid"))); + p.setCollectedfrom( + listKeyValues( + rs.getString("collectedfromid"), rs.getString("collectedfromname"))); + p.setPid(new ArrayList<>()); + p.setDateofcollection(asString(rs.getDate("dateofcollection"))); + p.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); + p.setExtraInfo(new ArrayList<>()); // Values not present in the DB + p.setOaiprovenance(null); // Values not present in the DB + p.setWebsiteurl(field(rs.getString("websiteurl"), info)); + p.setCode(field(rs.getString("code"), info)); + p.setAcronym(field(rs.getString("acronym"), info)); + p.setTitle(field(rs.getString("title"), info)); + p.setStartdate(field(asString(rs.getDate("startdate")), info)); + p.setEnddate(field(asString(rs.getDate("enddate")), info)); + p.setCallidentifier(field(rs.getString("callidentifier"), info)); + p.setKeywords(field(rs.getString("keywords"), info)); + p.setDuration(field(Integer.toString(rs.getInt("duration")), info)); + p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info)); + p.setOamandatepublications( + field(Boolean.toString(rs.getBoolean("oamandatepublications")), info)); + p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info)); + p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); + p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info)); + p.setContracttype(prepareQualifierSplitting(rs.getString("contracttype"))); + p.setOptional1(field(rs.getString("optional1"), info)); + p.setOptional2(field(rs.getString("optional2"), info)); + p.setJsonextrainfo(field(rs.getString("jsonextrainfo"), info)); + p.setContactfullname(field(rs.getString("contactfullname"), info)); + p.setContactfax(field(rs.getString("contactfax"), info)); + p.setContactphone(field(rs.getString("contactphone"), info)); + p.setContactemail(field(rs.getString("contactemail"), info)); + p.setSummary(field(rs.getString("summary"), info)); + p.setCurrency(field(rs.getString("currency"), info)); + p.setTotalcost(new Float(rs.getDouble("totalcost"))); + p.setFundedamount(new Float(rs.getDouble("fundedamount"))); + p.setDataInfo(info); + p.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(p); + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processOrganization(final ResultSet rs) { + + try { + + final DataInfo info = prepareDataInfo(rs); + + final Organization o = new Organization(); + + o.setId(createOpenaireId(20, rs.getString("organizationid"), true)); + o.setOriginalId(Arrays.asList(rs.getString("organizationid"))); + o.setCollectedfrom( + listKeyValues( + rs.getString("collectedfromid"), rs.getString("collectedfromname"))); + o.setPid(new ArrayList<>()); + o.setDateofcollection(asString(rs.getDate("dateofcollection"))); + o.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); + o.setExtraInfo(new ArrayList<>()); // Values not present in the DB + o.setOaiprovenance(null); // Values not present in the DB + o.setLegalshortname(field(rs.getString("legalshortname"), info)); + o.setLegalname(field(rs.getString("legalname"), info)); + o.setAlternativeNames(new ArrayList<>()); // Values not returned by the SQL query + o.setWebsiteurl(field(rs.getString("websiteurl"), info)); + o.setLogourl(field(rs.getString("logourl"), info)); + o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info)); + o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info)); + o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info)); + o.setEcresearchorganization( + field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info)); + o.setEchighereducation( + field(Boolean.toString(rs.getBoolean("echighereducation")), info)); + o.setEcinternationalorganizationeurinterests( + field( + Boolean.toString( + rs.getBoolean("ecinternationalorganizationeurinterests")), + info)); + o.setEcinternationalorganization( + field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info)); + o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info)); + o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info)); + o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info)); + o.setCountry(prepareQualifierSplitting(rs.getString("country"))); + o.setDataInfo(info); + o.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(o); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processDatasourceOrganization(final ResultSet rs) { + try { + final DataInfo info = prepareDataInfo(rs); + final String orgId = createOpenaireId(20, rs.getString("organization"), true); + final String dsId = createOpenaireId(10, rs.getString("datasource"), true); + final List collectedFrom = + listKeyValues( + rs.getString("collectedfromid"), rs.getString("collectedfromname")); + + final Relation r1 = new Relation(); + r1.setRelType("datasourceOrganization"); + r1.setSubRelType("provision"); + r1.setRelClass("isProvidedBy"); + r1.setSource(dsId); + r1.setTarget(orgId); + r1.setCollectedFrom(collectedFrom); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + + final Relation r2 = new Relation(); + r2.setRelType("datasourceOrganization"); + r2.setSubRelType("provision"); + r2.setRelClass("provides"); + r2.setSource(orgId); + r2.setTarget(dsId); + r2.setCollectedFrom(collectedFrom); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(r1, r2); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processProjectOrganization(final ResultSet rs) { + try { + final DataInfo info = prepareDataInfo(rs); + final String orgId = createOpenaireId(20, rs.getString("resporganization"), true); + final String projectId = createOpenaireId(40, rs.getString("project"), true); + final List collectedFrom = + listKeyValues( + rs.getString("collectedfromid"), rs.getString("collectedfromname")); + + final Relation r1 = new Relation(); + r1.setRelType("projectOrganization"); + r1.setSubRelType("participation"); + r1.setRelClass("isParticipant"); + r1.setSource(projectId); + r1.setTarget(orgId); + r1.setCollectedFrom(collectedFrom); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + + final Relation r2 = new Relation(); + r2.setRelType("projectOrganization"); + r2.setSubRelType("participation"); + r2.setRelClass("hasParticipant"); + r2.setSource(orgId); + r2.setTarget(projectId); + r2.setCollectedFrom(collectedFrom); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(r1, r2); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processClaims(final ResultSet rs) { + + final DataInfo info = + dataInfo( + false, + null, + false, + false, + qualifier( + "user:claim", + "user:claim", + "dnet:provenanceActions", + "dnet:provenanceActions"), + "0.9"); + + try { + + if (rs.getString("source_type").equals("context")) { + final Result r; + + if (rs.getString("target_type").equals("dataset")) { + r = new Dataset(); + } else if (rs.getString("target_type").equals("software")) { + r = new Software(); + } else if (rs.getString("target_type").equals("other")) { + r = new OtherResearchProduct(); + } else { + r = new Publication(); + } + r.setId(createOpenaireId(50, rs.getString("target_id"), false)); + r.setLastupdatetimestamp(lastUpdateTimestamp); + r.setContext(prepareContext(rs.getString("source_id"), info)); + r.setDataInfo(info); + + return Arrays.asList(r); + } else { + final String sourceId = + createOpenaireId( + rs.getString("source_type"), rs.getString("source_id"), false); + final String targetId = + createOpenaireId( + rs.getString("target_type"), rs.getString("target_id"), false); + + final Relation r1 = new Relation(); + final Relation r2 = new Relation(); + + if (rs.getString("source_type").equals("project")) { + r1.setRelType("resultProject"); + r1.setSubRelType("outcome"); + r1.setRelClass("produces"); + + r2.setRelType("resultProject"); + r2.setSubRelType("outcome"); + r2.setRelClass("isProducedBy"); + } else { + r1.setRelType("resultResult"); + r1.setSubRelType("relationship"); + r1.setRelClass("isRelatedTo"); + + r2.setRelType("resultResult"); + r2.setSubRelType("relationship"); + r2.setRelClass("isRelatedTo"); + } + + r1.setSource(sourceId); + r1.setTarget(targetId); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + + r2.setSource(targetId); + r2.setTarget(sourceId); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(r1, r2); + } + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + private List prepareContext(final String id, final DataInfo dataInfo) { + final Context context = new Context(); + context.setId(id); + context.setDataInfo(Arrays.asList(dataInfo)); + return Arrays.asList(context); + } + + private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException { + final Boolean deletedbyinference = rs.getBoolean("deletedbyinference"); + final String inferenceprovenance = rs.getString("inferenceprovenance"); + final Boolean inferred = rs.getBoolean("inferred"); + final String trust = rs.getString("trust"); + return dataInfo( + deletedbyinference, + inferenceprovenance, + inferred, + false, + ENTITYREGISTRY_PROVENANCE_ACTION, + trust); + } + + private Qualifier prepareQualifierSplitting(final String s) { + if (StringUtils.isBlank(s)) { + return null; + } + final String[] arr = s.split("@@@"); + return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null; + } + + private List> prepareListFields(final Array array, final DataInfo info) { + try { + return array != null + ? listFields(info, (String[]) array.getArray()) + : new ArrayList<>(); + } catch (final SQLException e) { + throw new RuntimeException("Invalid SQL array", e); + } + } + + private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) { + if (StringUtils.isBlank(s)) { + return null; + } + final String[] parts = s.split("###"); + if (parts.length == 2) { + final String value = parts[0]; + final String[] arr = parts[1].split("@@@"); + if (arr.length == 4) { + return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); + } + } + return null; + } + + private List prepareListOfStructProps( + final Array array, final DataInfo dataInfo) throws SQLException { + final List res = new ArrayList<>(); + if (array != null) { + for (final String s : (String[]) array.getArray()) { + final StructuredProperty sp = prepareStructProp(s, dataInfo); + if (sp != null) { + res.add(sp); + } + } + } + + return res; + } + + private Journal prepareJournal(final String name, final String sj, final DataInfo info) { + if (StringUtils.isNotBlank(sj)) { + final String[] arr = sj.split("@@@"); + if (arr.length == 3) { + final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null; + final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null; + ; + final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null; + ; + if (issn != null || eissn != null || lissn != null) { + return journal( + name, issn, eissn, eissn, null, null, null, null, null, null, null, + info); + } + } + } + return null; + } + + @Override + public void close() throws IOException { + super.close(); + dbClient.close(); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateMongoMdstoresApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateMongoMdstoresApplication.java index 585209ac9c..90966429a4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateMongoMdstoresApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateMongoMdstoresApplication.java @@ -3,64 +3,74 @@ package eu.dnetlib.dhp.oa.graph.raw; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; import eu.dnetlib.dhp.oa.graph.raw.common.MdstoreClient; -import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - import java.io.Closeable; import java.io.IOException; import java.util.Map; import java.util.Map.Entry; +import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; -public class MigrateMongoMdstoresApplication extends AbstractMigrationApplication implements Closeable { +public class MigrateMongoMdstoresApplication extends AbstractMigrationApplication + implements Closeable { - private static final Log log = LogFactory.getLog(MigrateMongoMdstoresApplication.class); + private static final Log log = LogFactory.getLog(MigrateMongoMdstoresApplication.class); - private final MdstoreClient mdstoreClient; + private final MdstoreClient mdstoreClient; - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(MigrateMongoMdstoresApplication.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_mongo_mstores_parameters.json"))); - parser.parseArgument(args); + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + MigrateMongoMdstoresApplication.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/migrate_mongo_mstores_parameters.json"))); + parser.parseArgument(args); - final String mongoBaseUrl = parser.get("mongoBaseUrl"); - final String mongoDb = parser.get("mongoDb"); + final String mongoBaseUrl = parser.get("mongoBaseUrl"); + final String mongoDb = parser.get("mongoDb"); - final String mdFormat = parser.get("mdFormat"); - final String mdLayout = parser.get("mdLayout"); - final String mdInterpretation = parser.get("mdInterpretation"); + final String mdFormat = parser.get("mdFormat"); + final String mdLayout = parser.get("mdLayout"); + final String mdInterpretation = parser.get("mdInterpretation"); - final String hdfsPath = parser.get("hdfsPath"); + final String hdfsPath = parser.get("hdfsPath"); - try (MigrateMongoMdstoresApplication app = new MigrateMongoMdstoresApplication(hdfsPath, mongoBaseUrl, mongoDb)) { - app.execute(mdFormat, mdLayout, mdInterpretation); - } + try (MigrateMongoMdstoresApplication app = + new MigrateMongoMdstoresApplication(hdfsPath, mongoBaseUrl, mongoDb)) { + app.execute(mdFormat, mdLayout, mdInterpretation); + } + } - } + public MigrateMongoMdstoresApplication( + final String hdfsPath, final String mongoBaseUrl, final String mongoDb) + throws Exception { + super(hdfsPath); + this.mdstoreClient = new MdstoreClient(mongoBaseUrl, mongoDb); + } - public MigrateMongoMdstoresApplication(final String hdfsPath, final String mongoBaseUrl, final String mongoDb) throws Exception { - super(hdfsPath); - this.mdstoreClient = new MdstoreClient(mongoBaseUrl, mongoDb); - } + public void execute(final String format, final String layout, final String interpretation) { + final Map colls = + mdstoreClient.validCollections(format, layout, interpretation); + log.info("Found " + colls.size() + " mdstores"); - public void execute(final String format, final String layout, final String interpretation) { - final Map colls = mdstoreClient.validCollections(format, layout, interpretation); - log.info("Found " + colls.size() + " mdstores"); + for (final Entry entry : colls.entrySet()) { + log.info( + "Processing mdstore " + + entry.getKey() + + " (collection: " + + entry.getValue() + + ")"); + final String currentColl = entry.getValue(); - for (final Entry entry : colls.entrySet()) { - log.info("Processing mdstore " + entry.getKey() + " (collection: " + entry.getValue() + ")"); - final String currentColl = entry.getValue(); - - for (final String xml : mdstoreClient.listRecords(currentColl)) { - emit(xml, "native_" + format); - } - } - } - - @Override - public void close() throws IOException { - super.close(); - mdstoreClient.close(); - } + for (final String xml : mdstoreClient.listRecords(currentColl)) { + emit(xml, "native_" + format); + } + } + } + @Override + public void close() throws IOException { + super.close(); + mdstoreClient.close(); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index aed582d8f4..e77b1f87fe 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -1,232 +1,258 @@ package eu.dnetlib.dhp.oa.graph.raw; -import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson; -import eu.dnetlib.dhp.schema.oaf.*; -import org.dom4j.Document; -import org.dom4j.Node; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Map; - import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; +import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson; +import eu.dnetlib.dhp.schema.oaf.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Map; +import org.dom4j.Document; +import org.dom4j.Node; + public class OafToOafMapper extends AbstractMdRecordToOafMapper { - public OafToOafMapper(final Map code2name) { - super(code2name); - } + public OafToOafMapper(final Map code2name) { + super(code2name); + } - @Override - protected List prepareAuthors(final Document doc, final DataInfo info) { - final List res = new ArrayList<>(); - int pos = 1; - for (final Object o : doc.selectNodes("//dc:creator")) { - final Node n = (Node) o; - final Author author = new Author(); - author.setFullname(n.getText()); - author.setRank(pos++); - final PacePerson p = new PacePerson(n.getText(), false); - if (p.isAccurate()) { - author.setName(p.getNormalisedFirstName()); - author.setSurname(p.getNormalisedSurname()); - } - res.add(author); - } - return res; - } + @Override + protected List prepareAuthors(final Document doc, final DataInfo info) { + final List res = new ArrayList<>(); + int pos = 1; + for (final Object o : doc.selectNodes("//dc:creator")) { + final Node n = (Node) o; + final Author author = new Author(); + author.setFullname(n.getText()); + author.setRank(pos++); + final PacePerson p = new PacePerson(n.getText(), false); + if (p.isAccurate()) { + author.setName(p.getNormalisedFirstName()); + author.setSurname(p.getNormalisedSurname()); + } + res.add(author); + } + return res; + } - @Override - protected Qualifier prepareLanguages(final Document doc) { - return prepareQualifier(doc, "//dc:language", "dnet:languages", "dnet:languages"); - } + @Override + protected Qualifier prepareLanguages(final Document doc) { + return prepareQualifier(doc, "//dc:language", "dnet:languages", "dnet:languages"); + } - @Override - protected List prepareSubjects(final Document doc, final DataInfo info) { - return prepareListStructProps(doc, "//dc:subject", info); - } + @Override + protected List prepareSubjects(final Document doc, final DataInfo info) { + return prepareListStructProps(doc, "//dc:subject", info); + } - @Override - protected List prepareTitles(final Document doc, final DataInfo info) { - return prepareListStructProps(doc, "//dc:title", MAIN_TITLE_QUALIFIER, info); - } + @Override + protected List prepareTitles(final Document doc, final DataInfo info) { + return prepareListStructProps(doc, "//dc:title", MAIN_TITLE_QUALIFIER, info); + } - @Override - protected List> prepareDescriptions(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//dc:description", info); - } + @Override + protected List> prepareDescriptions(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:description", info); + } - @Override - protected Field preparePublisher(final Document doc, final DataInfo info) { - return prepareField(doc, "//dc:publisher", info); - } + @Override + protected Field preparePublisher(final Document doc, final DataInfo info) { + return prepareField(doc, "//dc:publisher", info); + } - @Override - protected List> prepareFormats(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//dc:format", info); - } + @Override + protected List> prepareFormats(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:format", info); + } - @Override - protected List> prepareContributors(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//dc:contributor", info); - } + @Override + protected List> prepareContributors(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:contributor", info); + } - @Override - protected List> prepareCoverages(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//dc:coverage", info); - } + @Override + protected List> prepareCoverages(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:coverage", info); + } - @Override - protected List prepareInstances(final Document doc, final DataInfo info, final KeyValue collectedfrom, final KeyValue hostedby) { - final List res = new ArrayList<>(); - for (final Object o : doc.selectNodes("//dc:identifier")) { - final String url = ((Node) o).getText().trim(); - if (url.startsWith("http")) { - final Instance instance = new Instance(); - instance.setUrl(Arrays.asList(url)); - instance.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", "dnet:publication_resource", "dnet:publication_resource")); - instance.setCollectedfrom(collectedfrom); - instance.setHostedby(hostedby); - instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); - instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); - instance.setAccessright(prepareQualifier(doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes")); - instance.setLicense(field(doc.valueOf("//oaf:license"), info)); - instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); - instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); - instance.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); - res.add(instance); - } - } - return res; - } + @Override + protected List prepareInstances( + final Document doc, + final DataInfo info, + final KeyValue collectedfrom, + final KeyValue hostedby) { + final List res = new ArrayList<>(); + for (final Object o : doc.selectNodes("//dc:identifier")) { + final String url = ((Node) o).getText().trim(); + if (url.startsWith("http")) { + final Instance instance = new Instance(); + instance.setUrl(Arrays.asList(url)); + instance.setInstancetype( + prepareQualifier( + doc, + "//dr:CobjCategory", + "dnet:publication_resource", + "dnet:publication_resource")); + instance.setCollectedfrom(collectedfrom); + instance.setHostedby(hostedby); + instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); + instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); + instance.setAccessright( + prepareQualifier( + doc, + "//oaf:accessrights", + "dnet:access_modes", + "dnet:access_modes")); + instance.setLicense(field(doc.valueOf("//oaf:license"), info)); + instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); + instance.setProcessingchargeamount( + field(doc.valueOf("//oaf:processingchargeamount"), info)); + instance.setProcessingchargecurrency( + field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); + res.add(instance); + } + } + return res; + } - @Override - protected List> prepareSources(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//dc:source", info); - } + @Override + protected List> prepareSources(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:source", info); + } - @Override - protected List prepareRelevantDates(final Document doc, final DataInfo info) { - return new ArrayList<>(); // NOT PRESENT IN OAF - } + @Override + protected List prepareRelevantDates( + final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } - // SOFTWARES + // SOFTWARES - @Override - protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) { - return null; // NOT PRESENT IN OAF - } + @Override + protected Qualifier prepareSoftwareProgrammingLanguage( + final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } - @Override - protected Field prepareSoftwareCodeRepositoryUrl(final Document doc, final DataInfo info) { - return null; // NOT PRESENT IN OAF - } + @Override + protected Field prepareSoftwareCodeRepositoryUrl( + final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } - @Override - protected List prepareSoftwareLicenses(final Document doc, final DataInfo info) { - return new ArrayList<>(); // NOT PRESENT IN OAF - } + @Override + protected List prepareSoftwareLicenses( + final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } - @Override - protected List> prepareSoftwareDocumentationUrls(final Document doc, final DataInfo info) { - return new ArrayList<>(); // NOT PRESENT IN OAF - } + @Override + protected List> prepareSoftwareDocumentationUrls( + final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } - // DATASETS - @Override - protected List prepareDatasetGeoLocations(final Document doc, final DataInfo info) { - return new ArrayList<>(); // NOT PRESENT IN OAF - } + // DATASETS + @Override + protected List prepareDatasetGeoLocations( + final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } - @Override - protected Field prepareDatasetMetadataVersionNumber(final Document doc, final DataInfo info) { - return null; // NOT PRESENT IN OAF - } + @Override + protected Field prepareDatasetMetadataVersionNumber( + final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } - @Override - protected Field prepareDatasetLastMetadataUpdate(final Document doc, final DataInfo info) { - return null; // NOT PRESENT IN OAF - } + @Override + protected Field prepareDatasetLastMetadataUpdate( + final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } - @Override - protected Field prepareDatasetVersion(final Document doc, final DataInfo info) { - return null; // NOT PRESENT IN OAF - } + @Override + protected Field prepareDatasetVersion(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } - @Override - protected Field prepareDatasetSize(final Document doc, final DataInfo info) { - return null; // NOT PRESENT IN OAF - } + @Override + protected Field prepareDatasetSize(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } - @Override - protected Field prepareDatasetDevice(final Document doc, final DataInfo info) { - return null; // NOT PRESENT IN OAF - } + @Override + protected Field prepareDatasetDevice(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } - @Override - protected Field prepareDatasetStorageDate(final Document doc, final DataInfo info) { - return null; // NOT PRESENT IN OAF - } + @Override + protected Field prepareDatasetStorageDate(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } - // OTHER PRODUCTS + // OTHER PRODUCTS - @Override - protected List> prepareOtherResearchProductTools(final Document doc, final DataInfo info) { - return new ArrayList<>(); // NOT PRESENT IN OAF - } + @Override + protected List> prepareOtherResearchProductTools( + final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } - @Override - protected List> prepareOtherResearchProductContactGroups(final Document doc, final DataInfo info) { - return new ArrayList<>(); // NOT PRESENT IN OAF - } + @Override + protected List> prepareOtherResearchProductContactGroups( + final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } - @Override - protected List> prepareOtherResearchProductContactPersons(final Document doc, final DataInfo info) { - return new ArrayList<>(); // NOT PRESENT IN OAF - } + @Override + protected List> prepareOtherResearchProductContactPersons( + final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } - @Override - protected List addOtherResultRels(final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { - final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); + @Override + protected List addOtherResultRels( + final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { + final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); - final List res = new ArrayList<>(); + final List res = new ArrayList<>(); - for (final Object o : doc.selectNodes("//*[local-name()='relatedDataset']")) { - final String otherId = createOpenaireId(50, ((Node) o).getText(), false); + for (final Object o : doc.selectNodes("//*[local-name()='relatedDataset']")) { + final String otherId = createOpenaireId(50, ((Node) o).getText(), false); - final Relation r1 = new Relation(); - r1.setRelType("resultResult"); - r1.setSubRelType("publicationDataset"); - r1.setRelClass("isRelatedTo"); - r1.setSource(docId); - r1.setTarget(otherId); - r1.setCollectedFrom(Arrays.asList(collectedFrom)); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - res.add(r1); + final Relation r1 = new Relation(); + r1.setRelType("resultResult"); + r1.setSubRelType("publicationDataset"); + r1.setRelClass("isRelatedTo"); + r1.setSource(docId); + r1.setTarget(otherId); + r1.setCollectedFrom(Arrays.asList(collectedFrom)); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + res.add(r1); - final Relation r2 = new Relation(); - r2.setRelType("resultResult"); - r2.setSubRelType("publicationDataset"); - r2.setRelClass("isRelatedTo"); - r2.setSource(otherId); - r2.setTarget(docId); - r2.setCollectedFrom(Arrays.asList(collectedFrom)); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - res.add(r2); - } - return res; - } - - @Override - protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { - return null; // NOT PRESENT IN OAF - } + final Relation r2 = new Relation(); + r2.setRelType("resultResult"); + r2.setSubRelType("publicationDataset"); + r2.setRelClass("isRelatedTo"); + r2.setSource(otherId); + r2.setTarget(docId); + r2.setCollectedFrom(Arrays.asList(collectedFrom)); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + res.add(r2); + } + return res; + } + @Override + protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 6a6def9777..5e64624170 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -1,253 +1,351 @@ package eu.dnetlib.dhp.oa.graph.raw; -import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.commons.lang3.StringUtils; -import org.dom4j.Document; -import org.dom4j.Node; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; +import eu.dnetlib.dhp.schema.oaf.*; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Map; - -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; +import org.apache.commons.lang3.StringUtils; +import org.dom4j.Document; +import org.dom4j.Node; public class OdfToOafMapper extends AbstractMdRecordToOafMapper { - public OdfToOafMapper(final Map code2name) { - super(code2name); - } + public OdfToOafMapper(final Map code2name) { + super(code2name); + } - @Override - protected List prepareTitles(final Document doc, final DataInfo info) { - return prepareListStructProps(doc, "//datacite:title", MAIN_TITLE_QUALIFIER, info); - } + @Override + protected List prepareTitles(final Document doc, final DataInfo info) { + return prepareListStructProps(doc, "//datacite:title", MAIN_TITLE_QUALIFIER, info); + } - @Override - protected List prepareAuthors(final Document doc, final DataInfo info) { - final List res = new ArrayList<>(); - int pos = 1; - for (final Object o : doc.selectNodes("//datacite:creator")) { - final Node n = (Node) o; - final Author author = new Author(); - author.setFullname(n.valueOf("./datacite:creatorName")); - author.setName(n.valueOf("./datacite:givenName")); - author.setSurname(n.valueOf("./datacite:familyName")); - author.setAffiliation(prepareListFields(doc, "./datacite:affiliation", info)); - author.setPid(preparePids(doc, info)); - author.setRank(pos++); - res.add(author); - } - return res; - } + @Override + protected List prepareAuthors(final Document doc, final DataInfo info) { + final List res = new ArrayList<>(); + int pos = 1; + for (final Object o : doc.selectNodes("//datacite:creator")) { + final Node n = (Node) o; + final Author author = new Author(); + author.setFullname(n.valueOf("./datacite:creatorName")); + author.setName(n.valueOf("./datacite:givenName")); + author.setSurname(n.valueOf("./datacite:familyName")); + author.setAffiliation(prepareListFields(doc, "./datacite:affiliation", info)); + author.setPid(preparePids(doc, info)); + author.setRank(pos++); + res.add(author); + } + return res; + } - private List preparePids(final Document doc, final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : doc.selectNodes("./datacite:nameIdentifier")) { - res.add(structuredProperty(((Node) o).getText(), prepareQualifier((Node) o, "./@nameIdentifierScheme", "dnet:pid_types", "dnet:pid_types"), info)); - } - return res; - } + private List preparePids(final Document doc, final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : doc.selectNodes("./datacite:nameIdentifier")) { + res.add( + structuredProperty( + ((Node) o).getText(), + prepareQualifier( + (Node) o, + "./@nameIdentifierScheme", + "dnet:pid_types", + "dnet:pid_types"), + info)); + } + return res; + } - @Override - protected List prepareInstances(final Document doc, final DataInfo info, final KeyValue collectedfrom, final KeyValue hostedby) { - final List res = new ArrayList<>(); - for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) { - final Instance instance = new Instance(); - instance.setUrl(Arrays.asList(((Node) o).getText().trim())); - instance.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", "dnet:publication_resource", "dnet:publication_resource")); - instance.setCollectedfrom(collectedfrom); - instance.setHostedby(hostedby); - instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); - instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); - instance.setAccessright(prepareQualifier(doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes")); - instance.setLicense(field(doc.valueOf("//oaf:license"), info)); - instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); - instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); - instance.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); - res.add(instance); - } - return res; - } + @Override + protected List prepareInstances( + final Document doc, + final DataInfo info, + final KeyValue collectedfrom, + final KeyValue hostedby) { + final List res = new ArrayList<>(); + for (final Object o : + doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) { + final Instance instance = new Instance(); + instance.setUrl(Arrays.asList(((Node) o).getText().trim())); + instance.setInstancetype( + prepareQualifier( + doc, + "//dr:CobjCategory", + "dnet:publication_resource", + "dnet:publication_resource")); + instance.setCollectedfrom(collectedfrom); + instance.setHostedby(hostedby); + instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); + instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); + instance.setAccessright( + prepareQualifier( + doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes")); + instance.setLicense(field(doc.valueOf("//oaf:license"), info)); + instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); + instance.setProcessingchargeamount( + field(doc.valueOf("//oaf:processingchargeamount"), info)); + instance.setProcessingchargecurrency( + field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); + res.add(instance); + } + return res; + } - @Override - protected List> prepareSources(final Document doc, final DataInfo info) { - return new ArrayList<>(); // Not present in ODF ??? - } + @Override + protected List> prepareSources(final Document doc, final DataInfo info) { + return new ArrayList<>(); // Not present in ODF ??? + } - @Override - protected List prepareRelevantDates(final Document doc, final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : doc.selectNodes("//datacite:date")) { - final String dateType = ((Node) o).valueOf("@dateType"); - if (StringUtils.isBlank(dateType) && !dateType.equalsIgnoreCase("Accepted") && !dateType.equalsIgnoreCase("Issued") - && !dateType.equalsIgnoreCase("Updated") && !dateType.equalsIgnoreCase("Available")) { - res.add(structuredProperty(((Node) o).getText(), "UNKNOWN", "UNKNOWN", "dnet:dataCite_date", "dnet:dataCite_date", info)); - } - } - return res; - } + @Override + protected List prepareRelevantDates( + final Document doc, final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : doc.selectNodes("//datacite:date")) { + final String dateType = ((Node) o).valueOf("@dateType"); + if (StringUtils.isBlank(dateType) + && !dateType.equalsIgnoreCase("Accepted") + && !dateType.equalsIgnoreCase("Issued") + && !dateType.equalsIgnoreCase("Updated") + && !dateType.equalsIgnoreCase("Available")) { + res.add( + structuredProperty( + ((Node) o).getText(), + "UNKNOWN", + "UNKNOWN", + "dnet:dataCite_date", + "dnet:dataCite_date", + info)); + } + } + return res; + } - @Override - protected List> prepareCoverages(final Document doc, final DataInfo info) { - return new ArrayList<>(); // Not present in ODF ??? - } + @Override + protected List> prepareCoverages(final Document doc, final DataInfo info) { + return new ArrayList<>(); // Not present in ODF ??? + } - @Override - protected List> prepareContributors(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//datacite:contributorName", info); - } + @Override + protected List> prepareContributors(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//datacite:contributorName", info); + } - @Override - protected List> prepareFormats(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//datacite:format", info); - } + @Override + protected List> prepareFormats(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//datacite:format", info); + } - @Override - protected Field preparePublisher(final Document doc, final DataInfo info) { - return prepareField(doc, "//datacite:publisher", info); - } + @Override + protected Field preparePublisher(final Document doc, final DataInfo info) { + return prepareField(doc, "//datacite:publisher", info); + } - @Override - protected List> prepareDescriptions(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//datacite:description[@descriptionType='Abstract']", info); - } + @Override + protected List> prepareDescriptions(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//datacite:description[@descriptionType='Abstract']", info); + } - @Override - protected List prepareSubjects(final Document doc, final DataInfo info) { - return prepareListStructProps(doc, "//datacite:subject", info); - } + @Override + protected List prepareSubjects(final Document doc, final DataInfo info) { + return prepareListStructProps(doc, "//datacite:subject", info); + } - @Override - protected Qualifier prepareLanguages(final Document doc) { - return prepareQualifier(doc, "//datacite:language", "dnet:languages", "dnet:languages"); - } + @Override + protected Qualifier prepareLanguages(final Document doc) { + return prepareQualifier(doc, "//datacite:language", "dnet:languages", "dnet:languages"); + } - @Override - protected List> prepareOtherResearchProductTools(final Document doc, final DataInfo info) { - return new ArrayList<>(); // Not present in ODF ??? - } + @Override + protected List> prepareOtherResearchProductTools( + final Document doc, final DataInfo info) { + return new ArrayList<>(); // Not present in ODF ??? + } - @Override - protected List> prepareOtherResearchProductContactGroups(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info); - } + @Override + protected List> prepareOtherResearchProductContactGroups( + final Document doc, final DataInfo info) { + return prepareListFields( + doc, + "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", + info); + } - @Override - protected List> prepareOtherResearchProductContactPersons(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info); - } + @Override + protected List> prepareOtherResearchProductContactPersons( + final Document doc, final DataInfo info) { + return prepareListFields( + doc, + "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", + info); + } - @Override - protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) { - return prepareQualifier(doc, "//datacite:format", "dnet:programming_languages", "dnet:programming_languages"); - } + @Override + protected Qualifier prepareSoftwareProgrammingLanguage( + final Document doc, final DataInfo info) { + return prepareQualifier( + doc, + "//datacite:format", + "dnet:programming_languages", + "dnet:programming_languages"); + } - @Override - protected Field prepareSoftwareCodeRepositoryUrl(final Document doc, final DataInfo info) { - return null; // Not present in ODF ??? - } + @Override + protected Field prepareSoftwareCodeRepositoryUrl( + final Document doc, final DataInfo info) { + return null; // Not present in ODF ??? + } - @Override - protected List prepareSoftwareLicenses(final Document doc, final DataInfo info) { - return new ArrayList<>(); // Not present in ODF ??? - } + @Override + protected List prepareSoftwareLicenses( + final Document doc, final DataInfo info) { + return new ArrayList<>(); // Not present in ODF ??? + } - @Override - protected List> prepareSoftwareDocumentationUrls(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info); - } + @Override + protected List> prepareSoftwareDocumentationUrls( + final Document doc, final DataInfo info) { + return prepareListFields( + doc, + "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", + info); + } - // DATASETS + // DATASETS - @Override - protected List prepareDatasetGeoLocations(final Document doc, final DataInfo info) { - final List res = new ArrayList<>(); + @Override + protected List prepareDatasetGeoLocations( + final Document doc, final DataInfo info) { + final List res = new ArrayList<>(); - for (final Object o : doc.selectNodes("//datacite:geoLocation")) { - final GeoLocation loc = new GeoLocation(); - loc.setBox(((Node) o).valueOf("./datacite:geoLocationBox")); - loc.setPlace(((Node) o).valueOf("./datacite:geoLocationPlace")); - loc.setPoint(((Node) o).valueOf("./datacite:geoLocationPoint")); - res.add(loc); - } - return res; - } + for (final Object o : doc.selectNodes("//datacite:geoLocation")) { + final GeoLocation loc = new GeoLocation(); + loc.setBox(((Node) o).valueOf("./datacite:geoLocationBox")); + loc.setPlace(((Node) o).valueOf("./datacite:geoLocationPlace")); + loc.setPoint(((Node) o).valueOf("./datacite:geoLocationPoint")); + res.add(loc); + } + return res; + } - @Override - protected Field prepareDatasetMetadataVersionNumber(final Document doc, final DataInfo info) { - return null; // Not present in ODF ??? - } + @Override + protected Field prepareDatasetMetadataVersionNumber( + final Document doc, final DataInfo info) { + return null; // Not present in ODF ??? + } - @Override - protected Field prepareDatasetLastMetadataUpdate(final Document doc, final DataInfo info) { - return prepareField(doc, "//datacite:date[@dateType='Updated']", info); - } + @Override + protected Field prepareDatasetLastMetadataUpdate( + final Document doc, final DataInfo info) { + return prepareField(doc, "//datacite:date[@dateType='Updated']", info); + } - @Override - protected Field prepareDatasetVersion(final Document doc, final DataInfo info) { - return prepareField(doc, "//datacite:version", info); - } + @Override + protected Field prepareDatasetVersion(final Document doc, final DataInfo info) { + return prepareField(doc, "//datacite:version", info); + } - @Override - protected Field prepareDatasetSize(final Document doc, final DataInfo info) { - return prepareField(doc, "//datacite:size", info); - } + @Override + protected Field prepareDatasetSize(final Document doc, final DataInfo info) { + return prepareField(doc, "//datacite:size", info); + } - @Override - protected Field prepareDatasetDevice(final Document doc, final DataInfo info) { - return null; // Not present in ODF ??? - } + @Override + protected Field prepareDatasetDevice(final Document doc, final DataInfo info) { + return null; // Not present in ODF ??? + } - @Override - protected Field prepareDatasetStorageDate(final Document doc, final DataInfo info) { - return prepareField(doc, "//datacite:date[@dateType='Issued']", info); - } + @Override + protected Field prepareDatasetStorageDate(final Document doc, final DataInfo info) { + return prepareField(doc, "//datacite:date[@dateType='Issued']", info); + } - @Override - protected List addOtherResultRels(final Document doc, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { + @Override + protected List addOtherResultRels( + final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { - final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); + final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); - final List res = new ArrayList<>(); + final List res = new ArrayList<>(); - for (final Object o : doc.selectNodes("//datacite:relatedIdentifier[@relatedIdentifierType='OPENAIRE']")) { - final String otherId = createOpenaireId(50, ((Node) o).getText(), false); - final String type = ((Node) o).valueOf("@relationType"); + for (final Object o : + doc.selectNodes( + "//datacite:relatedIdentifier[@relatedIdentifierType='OPENAIRE']")) { + final String otherId = createOpenaireId(50, ((Node) o).getText(), false); + final String type = ((Node) o).valueOf("@relationType"); - if (type.equals("IsSupplementTo")) { - res.add(prepareOtherResultRel(collectedFrom, info, lastUpdateTimestamp, docId, otherId, "supplement", "isSupplementTo")); - res.add(prepareOtherResultRel(collectedFrom, info, lastUpdateTimestamp, otherId, docId, "supplement", "isSupplementedBy")); - } else if (type.equals("IsPartOf")) { - res.add(prepareOtherResultRel(collectedFrom, info, lastUpdateTimestamp, docId, otherId, "part", "IsPartOf")); - res.add(prepareOtherResultRel(collectedFrom, info, lastUpdateTimestamp, otherId, docId, "part", "HasParts")); - } else {} - } - return res; - } + if (type.equals("IsSupplementTo")) { + res.add( + prepareOtherResultRel( + collectedFrom, + info, + lastUpdateTimestamp, + docId, + otherId, + "supplement", + "isSupplementTo")); + res.add( + prepareOtherResultRel( + collectedFrom, + info, + lastUpdateTimestamp, + otherId, + docId, + "supplement", + "isSupplementedBy")); + } else if (type.equals("IsPartOf")) { + res.add( + prepareOtherResultRel( + collectedFrom, + info, + lastUpdateTimestamp, + docId, + otherId, + "part", + "IsPartOf")); + res.add( + prepareOtherResultRel( + collectedFrom, + info, + lastUpdateTimestamp, + otherId, + docId, + "part", + "HasParts")); + } else { + } + } + return res; + } - private Relation prepareOtherResultRel(final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp, - final String source, - final String target, - final String subRelType, - final String relClass) { - final Relation r = new Relation(); - r.setRelType("resultResult"); - r.setSubRelType(subRelType); - r.setRelClass(relClass); - r.setSource(source); - r.setTarget(target); - r.setCollectedFrom(Arrays.asList(collectedFrom)); - r.setDataInfo(info); - r.setLastupdatetimestamp(lastUpdateTimestamp); - return r; - } - - @Override - protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { - return prepareQualifier(doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", "dnet:dataCite_resource", "dnet:dataCite_resource"); - } + private Relation prepareOtherResultRel( + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp, + final String source, + final String target, + final String subRelType, + final String relClass) { + final Relation r = new Relation(); + r.setRelType("resultResult"); + r.setSubRelType(subRelType); + r.setRelClass(relClass); + r.setSource(source); + r.setTarget(target); + r.setCollectedFrom(Arrays.asList(collectedFrom)); + r.setDataInfo(info); + r.setLastupdatetimestamp(lastUpdateTimestamp); + return r; + } + @Override + protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { + return prepareQualifier( + doc, + "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", + "dnet:dataCite_resource", + "dnet:dataCite_resource"); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java index aec1ea50dd..c22f7afd05 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java @@ -1,6 +1,9 @@ package eu.dnetlib.dhp.oa.graph.raw.common; import eu.dnetlib.dhp.schema.oaf.Oaf; +import java.io.Closeable; +import java.io.IOException; +import java.util.concurrent.atomic.AtomicInteger; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; @@ -9,72 +12,73 @@ import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; import org.codehaus.jackson.map.ObjectMapper; -import java.io.Closeable; -import java.io.IOException; -import java.util.concurrent.atomic.AtomicInteger; - public class AbstractMigrationApplication implements Closeable { - private final AtomicInteger counter = new AtomicInteger(0); + private final AtomicInteger counter = new AtomicInteger(0); - private final Text key = new Text(); + private final Text key = new Text(); - private final Text value = new Text(); + private final Text value = new Text(); - private final SequenceFile.Writer writer; + private final SequenceFile.Writer writer; - private final ObjectMapper objectMapper = new ObjectMapper(); + private final ObjectMapper objectMapper = new ObjectMapper(); - private static final Log log = LogFactory.getLog(AbstractMigrationApplication.class); + private static final Log log = LogFactory.getLog(AbstractMigrationApplication.class); - protected AbstractMigrationApplication() { // ONLY FOR UNIT TEST - this.writer = null; - } + protected AbstractMigrationApplication() { // ONLY FOR UNIT TEST + this.writer = null; + } - public AbstractMigrationApplication(final String hdfsPath) throws Exception { + public AbstractMigrationApplication(final String hdfsPath) throws Exception { - log.info(String.format("Creating SequenceFile Writer, hdfsPath=%s", hdfsPath)); + log.info(String.format("Creating SequenceFile Writer, hdfsPath=%s", hdfsPath)); - this.writer = SequenceFile.createWriter(getConf(), SequenceFile.Writer.file(new Path(hdfsPath)), SequenceFile.Writer - .keyClass(Text.class), SequenceFile.Writer.valueClass(Text.class)); - } + this.writer = + SequenceFile.createWriter( + getConf(), + SequenceFile.Writer.file(new Path(hdfsPath)), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class)); + } - private Configuration getConf() throws IOException { - final Configuration conf = new Configuration(); - /* - * conf.set("fs.defaultFS", hdfsNameNode); conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); - * conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); System.setProperty("HADOOP_USER_NAME", hdfsUser); - * System.setProperty("hadoop.home.dir", "/"); FileSystem.get(URI.create(hdfsNameNode), conf); - */ - return conf; - } + private Configuration getConf() throws IOException { + final Configuration conf = new Configuration(); + /* + * conf.set("fs.defaultFS", hdfsNameNode); conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); + * conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); System.setProperty("HADOOP_USER_NAME", hdfsUser); + * System.setProperty("hadoop.home.dir", "/"); FileSystem.get(URI.create(hdfsNameNode), conf); + */ + return conf; + } - protected void emit(final String s, final String type) { - try { - key.set(counter.getAndIncrement() + ":" + type); - value.set(s); - writer.append(key, value); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } + protected void emit(final String s, final String type) { + try { + key.set(counter.getAndIncrement() + ":" + type); + value.set(s); + writer.append(key, value); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } - protected void emitOaf(final Oaf oaf) { - try { - emit(objectMapper.writeValueAsString(oaf), oaf.getClass().getSimpleName().toLowerCase()); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } + protected void emitOaf(final Oaf oaf) { + try { + emit( + objectMapper.writeValueAsString(oaf), + oaf.getClass().getSimpleName().toLowerCase()); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } - public ObjectMapper getObjectMapper() { - return objectMapper; - } - - @Override - public void close() throws IOException { - writer.hflush(); - writer.close(); - } + public ObjectMapper getObjectMapper() { + return objectMapper; + } + @Override + public void close() throws IOException { + writer.hflush(); + writer.close(); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/DbClient.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/DbClient.java index 9c0562946e..436015d2dd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/DbClient.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/DbClient.java @@ -1,61 +1,61 @@ package eu.dnetlib.dhp.oa.graph.raw.common; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - import java.io.Closeable; import java.io.IOException; import java.sql.*; import java.util.function.Consumer; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; public class DbClient implements Closeable { - private static final Log log = LogFactory.getLog(DbClient.class); + private static final Log log = LogFactory.getLog(DbClient.class); - private Connection connection; + private Connection connection; - public DbClient(final String address, final String login, final String password) { + public DbClient(final String address, final String login, final String password) { - try { - Class.forName("org.postgresql.Driver"); + try { + Class.forName("org.postgresql.Driver"); - this.connection = - StringUtils.isNoneBlank(login, password) ? DriverManager.getConnection(address, login, password) : DriverManager.getConnection(address); - this.connection.setAutoCommit(false); - } catch (final Exception e) { - log.error("Connection to postgresDB failed"); - throw new RuntimeException("Connection to postgresDB failed", e); - } - log.info("Opened database successfully"); - } + this.connection = + StringUtils.isNoneBlank(login, password) + ? DriverManager.getConnection(address, login, password) + : DriverManager.getConnection(address); + this.connection.setAutoCommit(false); + } catch (final Exception e) { + log.error("Connection to postgresDB failed"); + throw new RuntimeException("Connection to postgresDB failed", e); + } + log.info("Opened database successfully"); + } - public void processResults(final String sql, final Consumer consumer) { + public void processResults(final String sql, final Consumer consumer) { - try (final Statement stmt = connection.createStatement()) { - stmt.setFetchSize(100); + try (final Statement stmt = connection.createStatement()) { + stmt.setFetchSize(100); - try (final ResultSet rs = stmt.executeQuery(sql)) { - while (rs.next()) { - consumer.accept(rs); - } - } catch (final SQLException e) { - log.error("Error executing sql query: " + sql, e); - throw new RuntimeException("Error executing sql query", e); - } - } catch (final SQLException e1) { - log.error("Error preparing sql statement", e1); - throw new RuntimeException("Error preparing sql statement", e1); - } - } - - @Override - public void close() throws IOException { - try { - connection.close(); - } catch (final SQLException e) { - throw new RuntimeException(e); - } - } + try (final ResultSet rs = stmt.executeQuery(sql)) { + while (rs.next()) { + consumer.accept(rs); + } + } catch (final SQLException e) { + log.error("Error executing sql query: " + sql, e); + throw new RuntimeException("Error executing sql query", e); + } + } catch (final SQLException e1) { + log.error("Error preparing sql statement", e1); + throw new RuntimeException("Error preparing sql statement", e1); + } + } + @Override + public void close() throws IOException { + try { + connection.close(); + } catch (final SQLException e) { + throw new RuntimeException(e); + } + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/MdstoreClient.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/MdstoreClient.java index ac700ef63e..321daf1e70 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/MdstoreClient.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/MdstoreClient.java @@ -5,89 +5,98 @@ import com.mongodb.MongoClient; import com.mongodb.MongoClientURI; import com.mongodb.client.MongoCollection; import com.mongodb.client.MongoDatabase; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.bson.Document; - import java.io.Closeable; import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; import java.util.Map; import java.util.stream.StreamSupport; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.bson.Document; public class MdstoreClient implements Closeable { - private final MongoClient client; - private final MongoDatabase db; + private final MongoClient client; + private final MongoDatabase db; - private static final String COLL_METADATA = "metadata"; - private static final String COLL_METADATA_MANAGER = "metadataManager"; + private static final String COLL_METADATA = "metadata"; + private static final String COLL_METADATA_MANAGER = "metadataManager"; - private static final Log log = LogFactory.getLog(MdstoreClient.class); + private static final Log log = LogFactory.getLog(MdstoreClient.class); - public MdstoreClient(final String baseUrl, final String dbName) { - this.client = new MongoClient(new MongoClientURI(baseUrl)); - this.db = getDb(client, dbName); - } + public MdstoreClient(final String baseUrl, final String dbName) { + this.client = new MongoClient(new MongoClientURI(baseUrl)); + this.db = getDb(client, dbName); + } - public Map validCollections(final String mdFormat, final String mdLayout, final String mdInterpretation) { + public Map validCollections( + final String mdFormat, final String mdLayout, final String mdInterpretation) { - final Map transactions = new HashMap<>(); - for (final Document entry : getColl(db, COLL_METADATA_MANAGER, true).find()) { - final String mdId = entry.getString("mdId"); - final String currentId = entry.getString("currentId"); - if (StringUtils.isNoneBlank(mdId, currentId)) { - transactions.put(mdId, currentId); - } - } + final Map transactions = new HashMap<>(); + for (final Document entry : getColl(db, COLL_METADATA_MANAGER, true).find()) { + final String mdId = entry.getString("mdId"); + final String currentId = entry.getString("currentId"); + if (StringUtils.isNoneBlank(mdId, currentId)) { + transactions.put(mdId, currentId); + } + } - final Map res = new HashMap<>(); - for (final Document entry : getColl(db, COLL_METADATA, true).find()) { - if (entry.getString("format").equals(mdFormat) && entry.getString("layout").equals(mdLayout) - && entry.getString("interpretation").equals(mdInterpretation) && transactions.containsKey(entry.getString("mdId"))) { - res.put(entry.getString("mdId"), transactions.get(entry.getString("mdId"))); - } - } + final Map res = new HashMap<>(); + for (final Document entry : getColl(db, COLL_METADATA, true).find()) { + if (entry.getString("format").equals(mdFormat) + && entry.getString("layout").equals(mdLayout) + && entry.getString("interpretation").equals(mdInterpretation) + && transactions.containsKey(entry.getString("mdId"))) { + res.put(entry.getString("mdId"), transactions.get(entry.getString("mdId"))); + } + } - return res; - } + return res; + } - private MongoDatabase getDb(final MongoClient client, final String dbName) { - if (!Iterables.contains(client.listDatabaseNames(), dbName)) { - final String err = String.format("Database '%s' not found in %s", dbName, client.getAddress()); - log.warn(err); - throw new RuntimeException(err); - } - return client.getDatabase(dbName); - } + private MongoDatabase getDb(final MongoClient client, final String dbName) { + if (!Iterables.contains(client.listDatabaseNames(), dbName)) { + final String err = + String.format("Database '%s' not found in %s", dbName, client.getAddress()); + log.warn(err); + throw new RuntimeException(err); + } + return client.getDatabase(dbName); + } - private MongoCollection getColl(final MongoDatabase db, final String collName, final boolean abortIfMissing) { - if (!Iterables.contains(db.listCollectionNames(), collName)) { - final String err = String.format(String.format("Missing collection '%s' in database '%s'", collName, db.getName())); - log.warn(err); - if (abortIfMissing) { - throw new RuntimeException(err); - } else { - return null; - } - } - return db.getCollection(collName); - } + private MongoCollection getColl( + final MongoDatabase db, final String collName, final boolean abortIfMissing) { + if (!Iterables.contains(db.listCollectionNames(), collName)) { + final String err = + String.format( + String.format( + "Missing collection '%s' in database '%s'", + collName, db.getName())); + log.warn(err); + if (abortIfMissing) { + throw new RuntimeException(err); + } else { + return null; + } + } + return db.getCollection(collName); + } - public Iterable listRecords(final String collName) { - final MongoCollection coll = getColl(db, collName, false); - return coll == null ? new ArrayList<>() - : () -> StreamSupport.stream(coll.find().spliterator(), false) - .filter(e -> e.containsKey("body")) - .map(e -> e.getString("body")) - .iterator(); - } - - @Override - public void close() throws IOException { - client.close(); - } + public Iterable listRecords(final String collName) { + final MongoCollection coll = getColl(db, collName, false); + return coll == null + ? new ArrayList<>() + : () -> + StreamSupport.stream(coll.find().spliterator(), false) + .filter(e -> e.containsKey("body")) + .map(e -> e.getString("body")) + .iterator(); + } + @Override + public void close() throws IOException { + client.close(); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java index d02070a8b6..0f844cda08 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java @@ -2,185 +2,215 @@ package eu.dnetlib.dhp.oa.graph.raw.common; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.utils.DHPUtils; -import org.apache.commons.lang3.StringUtils; - import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Objects; import java.util.stream.Collectors; +import org.apache.commons.lang3.StringUtils; public class OafMapperUtils { - public static KeyValue keyValue(final String k, final String v) { - final KeyValue kv = new KeyValue(); - kv.setKey(k); - kv.setValue(v); - return kv; - } + public static KeyValue keyValue(final String k, final String v) { + final KeyValue kv = new KeyValue(); + kv.setKey(k); + kv.setValue(v); + return kv; + } - public static List listKeyValues(final String... s) { - if (s.length % 2 > 0) { throw new RuntimeException("Invalid number of parameters (k,v,k,v,....)"); } + public static List listKeyValues(final String... s) { + if (s.length % 2 > 0) { + throw new RuntimeException("Invalid number of parameters (k,v,k,v,....)"); + } - final List list = new ArrayList<>(); - for (int i = 0; i < s.length; i += 2) { - list.add(keyValue(s[i], s[i + 1])); - } - return list; - } + final List list = new ArrayList<>(); + for (int i = 0; i < s.length; i += 2) { + list.add(keyValue(s[i], s[i + 1])); + } + return list; + } - public static Field field(final T value, final DataInfo info) { - if (value == null || StringUtils.isBlank(value.toString())) { return null; } + public static Field field(final T value, final DataInfo info) { + if (value == null || StringUtils.isBlank(value.toString())) { + return null; + } - final Field field = new Field<>(); - field.setValue(value); - field.setDataInfo(info); - return field; - } + final Field field = new Field<>(); + field.setValue(value); + field.setDataInfo(info); + return field; + } - public static List> listFields(final DataInfo info, final String... values) { - return Arrays.stream(values).map(v -> field(v, info)).filter(Objects::nonNull).collect(Collectors.toList()); - } + public static List> listFields(final DataInfo info, final String... values) { + return Arrays.stream(values) + .map(v -> field(v, info)) + .filter(Objects::nonNull) + .collect(Collectors.toList()); + } - public static List> listFields(final DataInfo info, final List values) { - return values.stream().map(v -> field(v, info)).filter(Objects::nonNull).collect(Collectors.toList()); - } + public static List> listFields(final DataInfo info, final List values) { + return values.stream() + .map(v -> field(v, info)) + .filter(Objects::nonNull) + .collect(Collectors.toList()); + } - public static Qualifier qualifier(final String classid, final String classname, final String schemeid, final String schemename) { - final Qualifier q = new Qualifier(); - q.setClassid(classid); - q.setClassname(classname); - q.setSchemeid(schemeid); - q.setSchemename(schemename); - return q; - } + public static Qualifier qualifier( + final String classid, + final String classname, + final String schemeid, + final String schemename) { + final Qualifier q = new Qualifier(); + q.setClassid(classid); + q.setClassname(classname); + q.setSchemeid(schemeid); + q.setSchemename(schemename); + return q; + } - public static StructuredProperty structuredProperty(final String value, - final String classid, - final String classname, - final String schemeid, - final String schemename, - final DataInfo dataInfo) { + public static StructuredProperty structuredProperty( + final String value, + final String classid, + final String classname, + final String schemeid, + final String schemename, + final DataInfo dataInfo) { - return structuredProperty(value, qualifier(classid, classname, schemeid, schemename), dataInfo); - } + return structuredProperty( + value, qualifier(classid, classname, schemeid, schemename), dataInfo); + } - public static StructuredProperty structuredProperty(final String value, final Qualifier qualifier, final DataInfo dataInfo) { - if (value == null) { return null; } - final StructuredProperty sp = new StructuredProperty(); - sp.setValue(value); - sp.setQualifier(qualifier); - sp.setDataInfo(dataInfo); - return sp; - } + public static StructuredProperty structuredProperty( + final String value, final Qualifier qualifier, final DataInfo dataInfo) { + if (value == null) { + return null; + } + final StructuredProperty sp = new StructuredProperty(); + sp.setValue(value); + sp.setQualifier(qualifier); + sp.setDataInfo(dataInfo); + return sp; + } - public static ExtraInfo extraInfo(final String name, final String value, final String typology, final String provenance, final String trust) { - final ExtraInfo info = new ExtraInfo(); - info.setName(name); - info.setValue(value); - info.setTypology(typology); - info.setProvenance(provenance); - info.setTrust(trust); - return info; - } + public static ExtraInfo extraInfo( + final String name, + final String value, + final String typology, + final String provenance, + final String trust) { + final ExtraInfo info = new ExtraInfo(); + info.setName(name); + info.setValue(value); + info.setTypology(typology); + info.setProvenance(provenance); + info.setTrust(trust); + return info; + } - public static OAIProvenance oaiIProvenance(final String identifier, - final String baseURL, - final String metadataNamespace, - final Boolean altered, - final String datestamp, - final String harvestDate) { + public static OAIProvenance oaiIProvenance( + final String identifier, + final String baseURL, + final String metadataNamespace, + final Boolean altered, + final String datestamp, + final String harvestDate) { - final OriginDescription desc = new OriginDescription(); - desc.setIdentifier(identifier); - desc.setBaseURL(baseURL); - desc.setMetadataNamespace(metadataNamespace); - desc.setAltered(altered); - desc.setDatestamp(datestamp); - desc.setHarvestDate(harvestDate); + final OriginDescription desc = new OriginDescription(); + desc.setIdentifier(identifier); + desc.setBaseURL(baseURL); + desc.setMetadataNamespace(metadataNamespace); + desc.setAltered(altered); + desc.setDatestamp(datestamp); + desc.setHarvestDate(harvestDate); - final OAIProvenance p = new OAIProvenance(); - p.setOriginDescription(desc); + final OAIProvenance p = new OAIProvenance(); + p.setOriginDescription(desc); - return p; - } + return p; + } - public static Journal journal(final String name, - final String issnPrinted, - final String issnOnline, - final String issnLinking, - final String ep, - final String iss, - final String sp, - final String vol, - final String edition, - final String conferenceplace, - final String conferencedate, - final DataInfo dataInfo) { + public static Journal journal( + final String name, + final String issnPrinted, + final String issnOnline, + final String issnLinking, + final String ep, + final String iss, + final String sp, + final String vol, + final String edition, + final String conferenceplace, + final String conferencedate, + final DataInfo dataInfo) { - if (StringUtils.isNotBlank(name) || StringUtils.isNotBlank(issnPrinted) || StringUtils.isNotBlank(issnOnline) || StringUtils.isNotBlank(issnLinking)) { - final Journal j = new Journal(); - j.setName(name); - j.setIssnPrinted(issnPrinted); - j.setIssnOnline(issnOnline); - j.setIssnLinking(issnLinking); - j.setEp(ep); - j.setIss(iss); - j.setSp(sp); - j.setVol(vol); - j.setEdition(edition); - j.setConferenceplace(conferenceplace); - j.setConferencedate(conferencedate); - j.setDataInfo(dataInfo); - return j; - } else { - return null; - } - } + if (StringUtils.isNotBlank(name) + || StringUtils.isNotBlank(issnPrinted) + || StringUtils.isNotBlank(issnOnline) + || StringUtils.isNotBlank(issnLinking)) { + final Journal j = new Journal(); + j.setName(name); + j.setIssnPrinted(issnPrinted); + j.setIssnOnline(issnOnline); + j.setIssnLinking(issnLinking); + j.setEp(ep); + j.setIss(iss); + j.setSp(sp); + j.setVol(vol); + j.setEdition(edition); + j.setConferenceplace(conferenceplace); + j.setConferencedate(conferencedate); + j.setDataInfo(dataInfo); + return j; + } else { + return null; + } + } - public static DataInfo dataInfo(final Boolean deletedbyinference, - final String inferenceprovenance, - final Boolean inferred, - final Boolean invisible, - final Qualifier provenanceaction, - final String trust) { - final DataInfo d = new DataInfo(); - d.setDeletedbyinference(deletedbyinference); - d.setInferenceprovenance(inferenceprovenance); - d.setInferred(inferred); - d.setInvisible(invisible); - d.setProvenanceaction(provenanceaction); - d.setTrust(trust); - return d; - } + public static DataInfo dataInfo( + final Boolean deletedbyinference, + final String inferenceprovenance, + final Boolean inferred, + final Boolean invisible, + final Qualifier provenanceaction, + final String trust) { + final DataInfo d = new DataInfo(); + d.setDeletedbyinference(deletedbyinference); + d.setInferenceprovenance(inferenceprovenance); + d.setInferred(inferred); + d.setInvisible(invisible); + d.setProvenanceaction(provenanceaction); + d.setTrust(trust); + return d; + } - public static String createOpenaireId(final int prefix, final String originalId, final boolean to_md5) { - if (to_md5) { - final String nsPrefix = StringUtils.substringBefore(originalId, "::"); - final String rest = StringUtils.substringAfter(originalId, "::"); - return String.format("%s|%s::%s", prefix, nsPrefix, DHPUtils.md5(rest)); - } else { - return String.format("%s|%s", prefix, originalId); - } - } + public static String createOpenaireId( + final int prefix, final String originalId, final boolean to_md5) { + if (to_md5) { + final String nsPrefix = StringUtils.substringBefore(originalId, "::"); + final String rest = StringUtils.substringAfter(originalId, "::"); + return String.format("%s|%s::%s", prefix, nsPrefix, DHPUtils.md5(rest)); + } else { + return String.format("%s|%s", prefix, originalId); + } + } - public static String createOpenaireId(final String type, final String originalId, final boolean to_md5) { - switch (type) { - case "datasource": - return createOpenaireId(10, originalId, to_md5); - case "organization": - return createOpenaireId(20, originalId, to_md5); - case "person": - return createOpenaireId(30, originalId, to_md5); - case "project": - return createOpenaireId(40, originalId, to_md5); - default: - return createOpenaireId(50, originalId, to_md5); - } - } - - public static String asString(final Object o) { - return o == null ? "" : o.toString(); - } + public static String createOpenaireId( + final String type, final String originalId, final boolean to_md5) { + switch (type) { + case "datasource": + return createOpenaireId(10, originalId, to_md5); + case "organization": + return createOpenaireId(20, originalId, to_md5); + case "person": + return createOpenaireId(30, originalId, to_md5); + case "project": + return createOpenaireId(40, originalId, to_md5); + default: + return createOpenaireId(50, originalId, to_md5); + } + } + public static String asString(final Object o) { + return o == null ? "" : o.toString(); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java index a72788728c..8d29835d16 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java @@ -5,171 +5,175 @@ import com.google.common.base.Splitter; import com.google.common.collect.Iterables; import com.google.common.collect.Lists; import com.google.common.hash.Hashing; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.text.WordUtils; - import java.nio.charset.Charset; import java.text.Normalizer; import java.util.HashSet; import java.util.List; import java.util.Set; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.text.WordUtils; public class PacePerson { - private static final String UTF8 = "UTF-8"; - private List name = Lists.newArrayList(); - private List surname = Lists.newArrayList(); - private List fullname = Lists.newArrayList(); - private final String original; + private static final String UTF8 = "UTF-8"; + private List name = Lists.newArrayList(); + private List surname = Lists.newArrayList(); + private List fullname = Lists.newArrayList(); + private final String original; - private static Set particles = null; + private static Set particles = null; - public static final String capitalize(final String s) { - return WordUtils.capitalize(s.toLowerCase(), ' ', '-'); - } + public static final String capitalize(final String s) { + return WordUtils.capitalize(s.toLowerCase(), ' ', '-'); + } - public static final String dotAbbreviations(final String s) { - return s.length() == 1 ? s + "." : s; - } + public static final String dotAbbreviations(final String s) { + return s.length() == 1 ? s + "." : s; + } - public static Set loadFromClasspath(final String classpath) { - final Set h = new HashSet<>(); - try { - for (final String s : IOUtils.readLines(PacePerson.class.getResourceAsStream(classpath))) { - h.add(s); - } - } catch (final Throwable e) { - return new HashSet<>(); - } - return h; - } + public static Set loadFromClasspath(final String classpath) { + final Set h = new HashSet<>(); + try { + for (final String s : + IOUtils.readLines(PacePerson.class.getResourceAsStream(classpath))) { + h.add(s); + } + } catch (final Throwable e) { + return new HashSet<>(); + } + return h; + } - public PacePerson(String s, final boolean aggressive) { - original = s; - s = Normalizer.normalize(s, Normalizer.Form.NFD); - s = s.replaceAll("\\(.+\\)", ""); - s = s.replaceAll("\\[.+\\]", ""); - s = s.replaceAll("\\{.+\\}", ""); - s = s.replaceAll("\\s+-\\s+", "-"); - s = s.replaceAll("[\\p{Punct}&&[^,-]]", " "); - s = s.replaceAll("\\d", " "); - s = s.replaceAll("\\n", " "); - s = s.replaceAll("\\.", " "); - s = s.replaceAll("\\s+", " "); + public PacePerson(String s, final boolean aggressive) { + original = s; + s = Normalizer.normalize(s, Normalizer.Form.NFD); + s = s.replaceAll("\\(.+\\)", ""); + s = s.replaceAll("\\[.+\\]", ""); + s = s.replaceAll("\\{.+\\}", ""); + s = s.replaceAll("\\s+-\\s+", "-"); + s = s.replaceAll("[\\p{Punct}&&[^,-]]", " "); + s = s.replaceAll("\\d", " "); + s = s.replaceAll("\\n", " "); + s = s.replaceAll("\\.", " "); + s = s.replaceAll("\\s+", " "); - if (aggressive) { - s = s.replaceAll("[\\p{InCombiningDiacriticalMarks}&&[^,-]]", ""); - // s = s.replaceAll("[\\W&&[^,-]]", ""); - } + if (aggressive) { + s = s.replaceAll("[\\p{InCombiningDiacriticalMarks}&&[^,-]]", ""); + // s = s.replaceAll("[\\W&&[^,-]]", ""); + } - if (s.contains(",")) { - final String[] arr = s.split(","); - if (arr.length == 1) { - fullname = splitTerms(arr[0]); - } else if (arr.length > 1) { - surname = splitTerms(arr[0]); - name = splitTerms(arr[1]); - fullname.addAll(surname); - fullname.addAll(name); - } - } else { - fullname = splitTerms(s); + if (s.contains(",")) { + final String[] arr = s.split(","); + if (arr.length == 1) { + fullname = splitTerms(arr[0]); + } else if (arr.length > 1) { + surname = splitTerms(arr[0]); + name = splitTerms(arr[1]); + fullname.addAll(surname); + fullname.addAll(name); + } + } else { + fullname = splitTerms(s); - int lastInitialPosition = fullname.size(); - boolean hasSurnameInUpperCase = false; + int lastInitialPosition = fullname.size(); + boolean hasSurnameInUpperCase = false; - for (int i = 0; i < fullname.size(); i++) { - final String term = fullname.get(i); - if (term.length() == 1) { - lastInitialPosition = i; - } else if (term.equals(term.toUpperCase())) { - hasSurnameInUpperCase = true; - } - } + for (int i = 0; i < fullname.size(); i++) { + final String term = fullname.get(i); + if (term.length() == 1) { + lastInitialPosition = i; + } else if (term.equals(term.toUpperCase())) { + hasSurnameInUpperCase = true; + } + } - if (lastInitialPosition < fullname.size() - 1) { // Case: Michele G. Artini - name = fullname.subList(0, lastInitialPosition + 1); - surname = fullname.subList(lastInitialPosition + 1, fullname.size()); - } else if (hasSurnameInUpperCase) { // Case: Michele ARTINI - for (final String term : fullname) { - if (term.length() > 1 && term.equals(term.toUpperCase())) { - surname.add(term); - } else { - name.add(term); - } - } - } - } - } + if (lastInitialPosition < fullname.size() - 1) { // Case: Michele G. Artini + name = fullname.subList(0, lastInitialPosition + 1); + surname = fullname.subList(lastInitialPosition + 1, fullname.size()); + } else if (hasSurnameInUpperCase) { // Case: Michele ARTINI + for (final String term : fullname) { + if (term.length() > 1 && term.equals(term.toUpperCase())) { + surname.add(term); + } else { + name.add(term); + } + } + } + } + } - private List splitTerms(final String s) { - if (particles == null) { - particles = loadFromClasspath("/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt"); - } + private List splitTerms(final String s) { + if (particles == null) { + particles = loadFromClasspath("/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt"); + } - final List list = Lists.newArrayList(); - for (final String part : Splitter.on(" ").omitEmptyStrings().split(s)) { - if (!particles.contains(part.toLowerCase())) { - list.add(part); - } - } - return list; - } + final List list = Lists.newArrayList(); + for (final String part : Splitter.on(" ").omitEmptyStrings().split(s)) { + if (!particles.contains(part.toLowerCase())) { + list.add(part); + } + } + return list; + } - public List getName() { - return name; - } + public List getName() { + return name; + } - public String getNameString() { - return Joiner.on(" ").join(getName()); - } + public String getNameString() { + return Joiner.on(" ").join(getName()); + } - public List getSurname() { - return surname; - } + public List getSurname() { + return surname; + } - public List getFullname() { - return fullname; - } + public List getFullname() { + return fullname; + } - public String getOriginal() { - return original; - } + public String getOriginal() { + return original; + } - public String hash() { - return Hashing.murmur3_128().hashString(getNormalisedFullname(), Charset.forName(UTF8)).toString(); - } + public String hash() { + return Hashing.murmur3_128() + .hashString(getNormalisedFullname(), Charset.forName(UTF8)) + .toString(); + } - public String getNormalisedFirstName() { - return Joiner.on(" ").join(getCapitalFirstnames()); - } + public String getNormalisedFirstName() { + return Joiner.on(" ").join(getCapitalFirstnames()); + } - public String getNormalisedSurname() { - return Joiner.on(" ").join(getCapitalSurname()); - } + public String getNormalisedSurname() { + return Joiner.on(" ").join(getCapitalSurname()); + } - public String getSurnameString() { - return Joiner.on(" ").join(getSurname()); - } + public String getSurnameString() { + return Joiner.on(" ").join(getSurname()); + } - public String getNormalisedFullname() { - return isAccurate() ? getNormalisedSurname() + ", " + getNormalisedFirstName() : Joiner.on(" ").join(fullname); - } + public String getNormalisedFullname() { + return isAccurate() + ? getNormalisedSurname() + ", " + getNormalisedFirstName() + : Joiner.on(" ").join(fullname); + } - public List getCapitalFirstnames() { - return Lists.newArrayList(Iterables.transform(getNameWithAbbreviations(), PacePerson::capitalize)); - } + public List getCapitalFirstnames() { + return Lists.newArrayList( + Iterables.transform(getNameWithAbbreviations(), PacePerson::capitalize)); + } - public List getCapitalSurname() { - return Lists.newArrayList(Iterables.transform(surname, PacePerson::capitalize)); - } + public List getCapitalSurname() { + return Lists.newArrayList(Iterables.transform(surname, PacePerson::capitalize)); + } - public List getNameWithAbbreviations() { - return Lists.newArrayList(Iterables.transform(name, PacePerson::dotAbbreviations)); - } - - public boolean isAccurate() { - return name != null && surname != null && !name.isEmpty() && !surname.isEmpty(); - } + public List getNameWithAbbreviations() { + return Lists.newArrayList(Iterables.transform(name, PacePerson::dotAbbreviations)); + } + public boolean isAccurate() { + return name != null && surname != null && !name.isEmpty() && !surname.isEmpty(); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ImportDataFromMongo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ImportDataFromMongo.java index c313c139ec..a5803134e5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ImportDataFromMongo.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ImportDataFromMongo.java @@ -7,6 +7,14 @@ import com.mongodb.client.FindIterable; import com.mongodb.client.MongoCollection; import com.mongodb.client.MongoDatabase; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import java.io.IOException; +import java.net.URI; +import java.util.ArrayList; +import java.util.List; +import java.util.Objects; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.function.Consumer; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; @@ -16,61 +24,38 @@ import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; import org.bson.Document; import org.bson.conversions.Bson; -import java.io.IOException; -import java.net.URI; -import java.util.ArrayList; -import java.util.List; -import java.util.Objects; -import java.util.concurrent.atomic.AtomicInteger; -import java.util.function.Consumer; -import java.util.stream.Collectors; /** - * This job is responsible to collect - * data from mongoDatabase and store in a sequence File on HDFS - * Mongo database contains information of each MDSTore in two collections: - * -metadata - * That contains info like: - * ID, format, layout, interpretation - * -metadataManager: - * that contains info : - * ID, mongoCollectionName - * from the metadata collection we filter the ids with Format, layout, and Interpretation - * from the metadataManager we get the current MONGO collection name which contains metadata XML - * see function getCurrentId - * - * This Job will be called different times in base at the triple we want import, - * and generates for each triple a sequence file of XML + * This job is responsible to collect data from mongoDatabase and store in a sequence File on HDFS + * Mongo database contains information of each MDSTore in two collections: -metadata That contains + * info like: ID, format, layout, interpretation -metadataManager: that contains info : ID, + * mongoCollectionName from the metadata collection we filter the ids with Format, layout, and + * Interpretation from the metadataManager we get the current MONGO collection name which contains + * metadata XML see function getCurrentId * + *

This Job will be called different times in base at the triple we want import, and generates + * for each triple a sequence file of XML */ - public class ImportDataFromMongo { /** - * It requires in input some parameters described on a file eu/dnetlib/dhp/graph/sx/import_from_mongo_parameters.json + * It requires in input some parameters described on a file + * eu/dnetlib/dhp/graph/sx/import_from_mongo_parameters.json * - * - the name node - * - the paht where store HDFS File - * - the mongo host - * - the mongo port - * - the metadata format to import - * - the metadata layout to import - * - the metadata interpretation to import - * - the mongo database Name - * - * This params are encoded into args - * - * - + *

- the name node - the paht where store HDFS File - the mongo host - the mongo port - the + * metadata format to import - the metadata layout to import - the metadata interpretation to + * import - the mongo database Name * + *

This params are encoded into args * * @param args * @throws Exception */ public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - ImportDataFromMongo.class.getResourceAsStream( - "/eu/dnetlib/dhp/sx/graph/argumentparser/import_from_mongo_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + ImportDataFromMongo.class.getResourceAsStream( + "/eu/dnetlib/dhp/sx/graph/argumentparser/import_from_mongo_parameters.json"))); parser.parseArgument(args); final int port = Integer.parseInt(parser.get("dbport")); final String host = parser.get("dbhost"); @@ -85,11 +70,22 @@ public class ImportDataFromMongo { MongoCollection metadata = database.getCollection("metadata"); MongoCollection metadataManager = database.getCollection("metadataManager"); - final DBObject query = QueryBuilder.start("format").is(format).and("layout").is(layout).and("interpretation").is(interpretation).get(); + final DBObject query = + QueryBuilder.start("format") + .is(format) + .and("layout") + .is(layout) + .and("interpretation") + .is(interpretation) + .get(); final List ids = new ArrayList<>(); - metadata.find((Bson) query).forEach((Consumer) document -> ids.add(document.getString("mdId"))); - List databaseId = ids.stream().map(it -> getCurrentId(it, metadataManager)).filter(Objects::nonNull).collect(Collectors.toList()); - + metadata.find((Bson) query) + .forEach((Consumer) document -> ids.add(document.getString("mdId"))); + List databaseId = + ids.stream() + .map(it -> getCurrentId(it, metadataManager)) + .filter(Objects::nonNull) + .collect(Collectors.toList()); final String hdfsuri = parser.get("namenode"); // ====== Init HDFS File System Object @@ -104,43 +100,53 @@ public class ImportDataFromMongo { Path hdfswritepath = new Path(parser.get("targetPath")); final AtomicInteger counter = new AtomicInteger(0); - try (SequenceFile.Writer writer = SequenceFile.createWriter(conf, - SequenceFile.Writer.file(hdfswritepath), SequenceFile.Writer.keyClass(IntWritable.class), - SequenceFile.Writer.valueClass(Text.class))) { + try (SequenceFile.Writer writer = + SequenceFile.createWriter( + conf, + SequenceFile.Writer.file(hdfswritepath), + SequenceFile.Writer.keyClass(IntWritable.class), + SequenceFile.Writer.valueClass(Text.class))) { final IntWritable key = new IntWritable(counter.get()); final Text value = new Text(); - databaseId.forEach(id -> { - System.out.println("Reading :"+id); - MongoCollection collection = database.getCollection(id); - collection.find().forEach((Consumer) document -> - { - key.set(counter.getAndIncrement()); - value.set(document.getString("body")); + databaseId.forEach( + id -> { + System.out.println("Reading :" + id); + MongoCollection collection = database.getCollection(id); + collection + .find() + .forEach( + (Consumer) + document -> { + key.set(counter.getAndIncrement()); + value.set(document.getString("body")); - if (counter.get() % 10000 == 0) { - System.out.println("Added "+counter.get()); - } - try { - writer.append(key, value); - } catch (IOException e) { - throw new RuntimeException(e); - } - } - ); - }); + if (counter.get() % 10000 == 0) { + System.out.println( + "Added " + counter.get()); + } + try { + writer.append(key, value); + } catch (IOException e) { + throw new RuntimeException(e); + } + }); + }); } } /** * Return the name of mongo collection giving an MdStore ID + * * @param mdId The id of the MDStore - * @param metadataManager The collection metadataManager on mongo which contains this information + * @param metadataManager The collection metadataManager on mongo which contains this + * information * @return */ - private static String getCurrentId(final String mdId, final MongoCollection metadataManager) { - FindIterable result = metadataManager.find((Bson) QueryBuilder.start("mdId").is(mdId).get()); + private static String getCurrentId( + final String mdId, final MongoCollection metadataManager) { + FindIterable result = + metadataManager.find((Bson) QueryBuilder.start("mdId").is(mdId).get()); final Document item = result.first(); return item == null ? null : item.getString("currentId"); } - } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkExtractEntitiesJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkExtractEntitiesJob.java index f2a1aa4d71..41bc86c529 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkExtractEntitiesJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkExtractEntitiesJob.java @@ -2,92 +2,87 @@ package eu.dnetlib.dhp.sx.graph; import com.jayway.jsonpath.JsonPath; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; +import net.minidev.json.JSONArray; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.sql.SparkSession; -import net.minidev.json.JSONArray; - -import java.util.Arrays; -import java.util.List; -import java.util.stream.Collectors; - /** - * This Job extracts a typology of entity and stores it in a new RDD - * This job is called different times, for each file generated by the Job {@link ImportDataFromMongo} - * and store the new RDD in a path that should be under a folder: - * extractedEntities/entity/version1 + * This Job extracts a typology of entity and stores it in a new RDD This job is called different + * times, for each file generated by the Job {@link ImportDataFromMongo} and store the new RDD in a + * path that should be under a folder: extractedEntities/entity/version1 * - * at the end of this process we will have : - * extractedEntities/dataset/version1 - * extractedEntities/dataset/version2 - * extractedEntities/dataset/... - * extractedEntities/publication/version1 - * extractedEntities/publication/version2 - * extractedEntities/publication/... - * extractedEntities/unknown/version1 - * extractedEntities/unknown/version2 - * extractedEntities/unknown/... - * extractedEntities/relation/version1 - * extractedEntities/relation/version2 - * extractedEntities/relation/... + *

at the end of this process we will have : extractedEntities/dataset/version1 + * extractedEntities/dataset/version2 extractedEntities/dataset/... + * extractedEntities/publication/version1 extractedEntities/publication/version2 + * extractedEntities/publication/... extractedEntities/unknown/version1 + * extractedEntities/unknown/version2 extractedEntities/unknown/... + * extractedEntities/relation/version1 extractedEntities/relation/version2 + * extractedEntities/relation/... */ - public class SparkExtractEntitiesJob { - final static String IDJSONPATH = "$.id"; - final static String SOURCEJSONPATH = "$.source"; - final static String TARGETJSONPATH = "$.target"; - + static final String IDJSONPATH = "$.id"; + static final String SOURCEJSONPATH = "$.source"; + static final String TARGETJSONPATH = "$.target"; public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkExtractEntitiesJob.class.getResourceAsStream( - "/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkExtractEntitiesJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json"))); parser.parseArgument(args); - final SparkSession spark = SparkSession - .builder() - .appName(SparkExtractEntitiesJob.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); + final SparkSession spark = + SparkSession.builder() + .appName(SparkExtractEntitiesJob.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final String inputPath = parser.get("sourcePath"); final String targetPath = parser.get("targetPath"); - final String tdir =parser.get("targetDir"); + final String tdir = parser.get("targetDir"); final JavaRDD inputRDD = sc.textFile(inputPath); - List entities = Arrays.stream(parser.get("entities").split(",")).map(String::trim).collect(Collectors.toList()); + List entities = + Arrays.stream(parser.get("entities").split(",")) + .map(String::trim) + .collect(Collectors.toList()); if (entities.stream().anyMatch("dataset"::equalsIgnoreCase)) { - //Extract Dataset - inputRDD.filter(SparkExtractEntitiesJob::isDataset).saveAsTextFile(targetPath + "/dataset/"+tdir, GzipCodec.class); + // Extract Dataset + inputRDD.filter(SparkExtractEntitiesJob::isDataset) + .saveAsTextFile(targetPath + "/dataset/" + tdir, GzipCodec.class); } if (entities.stream().anyMatch("unknown"::equalsIgnoreCase)) { - //Extract Unknown - inputRDD.filter(SparkExtractEntitiesJob::isUnknown).saveAsTextFile(targetPath + "/unknown/"+tdir, GzipCodec.class); + // Extract Unknown + inputRDD.filter(SparkExtractEntitiesJob::isUnknown) + .saveAsTextFile(targetPath + "/unknown/" + tdir, GzipCodec.class); } if (entities.stream().anyMatch("relation"::equalsIgnoreCase)) { - //Extract Relation - inputRDD.filter(SparkExtractEntitiesJob::isRelation).saveAsTextFile(targetPath + "/relation/"+tdir, GzipCodec.class); + // Extract Relation + inputRDD.filter(SparkExtractEntitiesJob::isRelation) + .saveAsTextFile(targetPath + "/relation/" + tdir, GzipCodec.class); } if (entities.stream().anyMatch("publication"::equalsIgnoreCase)) { - //Extract Relation - inputRDD.filter(SparkExtractEntitiesJob::isPublication).saveAsTextFile(targetPath + "/publication/"+tdir, GzipCodec.class); + // Extract Relation + inputRDD.filter(SparkExtractEntitiesJob::isPublication) + .saveAsTextFile(targetPath + "/publication/" + tdir, GzipCodec.class); } } - public static boolean isDataset(final String json) { final String id = getJPathString(IDJSONPATH, json); if (StringUtils.isBlank(id)) return false; return id.startsWith("60|"); } - public static boolean isPublication(final String json) { final String id = getJPathString(IDJSONPATH, json); if (StringUtils.isBlank(id)) return false; @@ -106,12 +101,10 @@ public class SparkExtractEntitiesJob { return StringUtils.isNotBlank(source) && StringUtils.isNotBlank(target); } - public static String getJPathString(final String jsonPath, final String json) { try { Object o = JsonPath.read(json, jsonPath); - if (o instanceof String) - return (String) o; + if (o instanceof String) return (String) o; if (o instanceof JSONArray && ((JSONArray) o).size() > 0) return (String) ((JSONArray) o).get(0); return ""; @@ -119,6 +112,4 @@ public class SparkExtractEntitiesJob { return ""; } } - - } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSXGeneratePidSimlarity.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSXGeneratePidSimlarity.java index aa2f2cc584..fa446b3d10 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSXGeneratePidSimlarity.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSXGeneratePidSimlarity.java @@ -1,6 +1,5 @@ package eu.dnetlib.dhp.sx.graph; -import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.scholexplorer.DLIRelation; import eu.dnetlib.dhp.utils.DHPUtils; import org.apache.commons.lang3.StringUtils; @@ -13,52 +12,69 @@ import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import scala.Tuple2; - /** - * In some case the identifier generated for the Entity in @{@link SparkExtractEntitiesJob} is different from the identifier - * * associated by the aggregator, this means that some relation points to missing identifier - * To avoid this problem we store in the model the Id and the OriginalObJIdentifier - * This jobs extract this pair and creates a Similar relation that will be used in SparkMergeEntities - * + * In some case the identifier generated for the Entity in @{@link SparkExtractEntitiesJob} is + * different from the identifier * associated by the aggregator, this means that some relation + * points to missing identifier To avoid this problem we store in the model the Id and the + * OriginalObJIdentifier This jobs extract this pair and creates a Similar relation that will be + * used in SparkMergeEntities */ - public class SparkSXGeneratePidSimlarity { - final static String IDJSONPATH = "$.id"; - final static String OBJIDPATH = "$.originalObjIdentifier"; + static final String IDJSONPATH = "$.id"; + static final String OBJIDPATH = "$.originalObjIdentifier"; + public static void generateDataFrame( + final SparkSession spark, + final JavaSparkContext sc, + final String inputPath, + final String targetPath) { + final JavaPairRDD datasetSimRel = + sc.textFile(inputPath + "/dataset/*") + .mapToPair( + (PairFunction) + k -> + new Tuple2<>( + DHPUtils.getJPathString(IDJSONPATH, k), + DHPUtils.getJPathString(OBJIDPATH, k))) + .filter( + t -> + !StringUtils.substringAfter(t._1(), "|") + .equalsIgnoreCase( + StringUtils.substringAfter(t._2(), "::"))) + .distinct(); + final JavaPairRDD publicationSimRel = + sc.textFile(inputPath + "/publication/*") + .mapToPair( + (PairFunction) + k -> + new Tuple2<>( + DHPUtils.getJPathString(IDJSONPATH, k), + DHPUtils.getJPathString(OBJIDPATH, k))) + .filter( + t -> + !StringUtils.substringAfter(t._1(), "|") + .equalsIgnoreCase( + StringUtils.substringAfter(t._2(), "::"))) + .distinct(); - - public static void generateDataFrame(final SparkSession spark, final JavaSparkContext sc, final String inputPath, final String targetPath) { - - - final JavaPairRDD datasetSimRel = sc.textFile(inputPath+"/dataset/*") - .mapToPair((PairFunction) k -> - new Tuple2<>(DHPUtils.getJPathString(IDJSONPATH, k),DHPUtils.getJPathString(OBJIDPATH, k))) - .filter(t -> - !StringUtils.substringAfter(t._1(), "|") - .equalsIgnoreCase(StringUtils.substringAfter(t._2(), "::"))) - .distinct(); - - final JavaPairRDD publicationSimRel = sc.textFile(inputPath+"/publication/*") - .mapToPair((PairFunction) k -> - new Tuple2<>(DHPUtils.getJPathString(IDJSONPATH, k),DHPUtils.getJPathString(OBJIDPATH, k))) - .filter(t -> - !StringUtils.substringAfter(t._1(), "|") - .equalsIgnoreCase(StringUtils.substringAfter(t._2(), "::"))) - .distinct(); - - JavaRDD simRel = datasetSimRel.union(publicationSimRel).map(s -> { - final DLIRelation r = new DLIRelation(); - r.setSource(s._1()); - r.setTarget(s._2()); - r.setRelType("similar"); - return r; - } - ); - spark.createDataset(simRel.rdd(), Encoders.bean(DLIRelation.class)).distinct().write() - .mode(SaveMode.Overwrite).save(targetPath+"/pid_simRel"); + JavaRDD simRel = + datasetSimRel + .union(publicationSimRel) + .map( + s -> { + final DLIRelation r = new DLIRelation(); + r.setSource(s._1()); + r.setTarget(s._2()); + r.setRelType("similar"); + return r; + }); + spark.createDataset(simRel.rdd(), Encoders.bean(DLIRelation.class)) + .distinct() + .write() + .mode(SaveMode.Overwrite) + .save(targetPath + "/pid_simRel"); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerCreateRawGraphJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerCreateRawGraphJob.java index 36c94f595e..b528f473b7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerCreateRawGraphJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerCreateRawGraphJob.java @@ -10,6 +10,10 @@ import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication; import eu.dnetlib.dhp.schema.scholexplorer.DLIRelation; import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown; import eu.dnetlib.dhp.utils.DHPUtils; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; import net.minidev.json.JSONArray; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; @@ -29,59 +33,54 @@ import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import scala.Tuple2; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.stream.Collectors; - - /** - * This job is responsible of the creation of RAW Graph - * It is applied to the different entities generated from {@link SparkExtractEntitiesJob} - * In case of dataset, publication and Unknown Entities - * we group all the entities of the same type by their identifier, - * and then in the reduce phase we merge all the entities. - * Merge means: - * -merge all the metadata - * -merge the collected From values + * This job is responsible of the creation of RAW Graph It is applied to the different entities + * generated from {@link SparkExtractEntitiesJob} In case of dataset, publication and Unknown + * Entities we group all the entities of the same type by their identifier, and then in the reduce + * phase we merge all the entities. Merge means: -merge all the metadata -merge the collected From + * values * - * In case of relation we need to make a different work: - * -Phase 1: Map reduce jobs - * Map: Get all Relation and emit a key constructed by (source, relType, Target) and the relation itself - * Reduce: Merge all relations - * Looking at the javadoc of {@link SparkSXGeneratePidSimlarity} we take the dataset of pid relation - * and joining by source and target we replace the wrong identifier in the relation with the correct ones. - * At the end we replace the new Dataset of Relation + *

In case of relation we need to make a different work: -Phase 1: Map reduce jobs Map: Get all + * Relation and emit a key constructed by (source, relType, Target) and the relation itself Reduce: + * Merge all relations Looking at the javadoc of {@link SparkSXGeneratePidSimlarity} we take the + * dataset of pid relation and joining by source and target we replace the wrong identifier in the + * relation with the correct ones. At the end we replace the new Dataset of Relation */ - public class SparkScholexplorerCreateRawGraphJob { - final static String IDJSONPATH = "$.id"; - final static String SOURCEJSONPATH = "$.source"; - final static String TARGETJSONPATH = "$.target"; - final static String RELJSONPATH = "$.relType"; + static final String IDJSONPATH = "$.id"; + static final String SOURCEJSONPATH = "$.source"; + static final String TARGETJSONPATH = "$.target"; + static final String RELJSONPATH = "$.relType"; public static void main(String[] args) throws Exception { - - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkScholexplorerCreateRawGraphJob.class.getResourceAsStream( - "/eu/dnetlib/dhp/sx/graph/argumentparser/merge_entities_scholix_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkScholexplorerCreateRawGraphJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/sx/graph/argumentparser/merge_entities_scholix_parameters.json"))); parser.parseArgument(args); - final SparkSession spark = SparkSession - .builder() - .config(new SparkConf() - .set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")) - .appName(SparkScholexplorerCreateRawGraphJob.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); + final SparkSession spark = + SparkSession.builder() + .config( + new SparkConf() + .set( + "spark.serializer", + "org.apache.spark.serializer.KryoSerializer")) + .appName(SparkScholexplorerCreateRawGraphJob.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final String inputPath = parser.get("sourcePath"); final String targetPath = parser.get("targetPath"); final String entity = parser.get("entity"); FileSystem fs = FileSystem.get(sc.sc().hadoopConfiguration()); - List subFolder = Arrays.stream(fs.listStatus(new Path(inputPath))).filter(FileStatus::isDirectory).map(FileStatus::getPath).collect(Collectors.toList()); + List subFolder = + Arrays.stream(fs.listStatus(new Path(inputPath))) + .filter(FileStatus::isDirectory) + .map(FileStatus::getPath) + .collect(Collectors.toList()); List> inputRdd = new ArrayList<>(); subFolder.forEach(p -> inputRdd.add(sc.textFile(p.toUri().getRawPath()))); JavaRDD union = sc.emptyRDD(); @@ -90,118 +89,192 @@ public class SparkScholexplorerCreateRawGraphJob { } switch (entity) { case "dataset": - union.mapToPair((PairFunction) f -> { - final String id = getJPathString(IDJSONPATH, f); - ObjectMapper mapper = new ObjectMapper(); - mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - return new Tuple2<>(id, mapper.readValue(f, DLIDataset.class)); - }).reduceByKey((a, b) -> { - a.mergeFrom(b); - return a; - }).map(item -> { - ObjectMapper mapper = new ObjectMapper(); - return mapper.writeValueAsString(item._2()); - }).saveAsTextFile(targetPath, GzipCodec.class); + union.mapToPair( + (PairFunction) + f -> { + final String id = getJPathString(IDJSONPATH, f); + ObjectMapper mapper = new ObjectMapper(); + mapper.configure( + DeserializationFeature + .FAIL_ON_UNKNOWN_PROPERTIES, + false); + return new Tuple2<>( + id, mapper.readValue(f, DLIDataset.class)); + }) + .reduceByKey( + (a, b) -> { + a.mergeFrom(b); + return a; + }) + .map( + item -> { + ObjectMapper mapper = new ObjectMapper(); + return mapper.writeValueAsString(item._2()); + }) + .saveAsTextFile(targetPath, GzipCodec.class); break; case "publication": - union.mapToPair((PairFunction) f -> { - final String id = getJPathString(IDJSONPATH, f); - ObjectMapper mapper = new ObjectMapper(); - mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - return new Tuple2<>(id, mapper.readValue(f, DLIPublication.class)); - }).reduceByKey((a, b) -> { - a.mergeFrom(b); - return a; - }).map(item -> { - ObjectMapper mapper = new ObjectMapper(); - return mapper.writeValueAsString(item._2()); - }).saveAsTextFile(targetPath, GzipCodec.class); + union.mapToPair( + (PairFunction) + f -> { + final String id = getJPathString(IDJSONPATH, f); + ObjectMapper mapper = new ObjectMapper(); + mapper.configure( + DeserializationFeature + .FAIL_ON_UNKNOWN_PROPERTIES, + false); + return new Tuple2<>( + id, mapper.readValue(f, DLIPublication.class)); + }) + .reduceByKey( + (a, b) -> { + a.mergeFrom(b); + return a; + }) + .map( + item -> { + ObjectMapper mapper = new ObjectMapper(); + return mapper.writeValueAsString(item._2()); + }) + .saveAsTextFile(targetPath, GzipCodec.class); break; case "unknown": - union.mapToPair((PairFunction) f -> { - final String id = getJPathString(IDJSONPATH, f); - ObjectMapper mapper = new ObjectMapper(); - mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - return new Tuple2<>(id, mapper.readValue(f, DLIUnknown.class)); - }).reduceByKey((a, b) -> { - a.mergeFrom(b); - return a; - }).map(item -> { - ObjectMapper mapper = new ObjectMapper(); - return mapper.writeValueAsString(item._2()); - }).saveAsTextFile(targetPath, GzipCodec.class); + union.mapToPair( + (PairFunction) + f -> { + final String id = getJPathString(IDJSONPATH, f); + ObjectMapper mapper = new ObjectMapper(); + mapper.configure( + DeserializationFeature + .FAIL_ON_UNKNOWN_PROPERTIES, + false); + return new Tuple2<>( + id, mapper.readValue(f, DLIUnknown.class)); + }) + .reduceByKey( + (a, b) -> { + a.mergeFrom(b); + return a; + }) + .map( + item -> { + ObjectMapper mapper = new ObjectMapper(); + return mapper.writeValueAsString(item._2()); + }) + .saveAsTextFile(targetPath, GzipCodec.class); break; case "relation": + SparkSXGeneratePidSimlarity.generateDataFrame( + spark, + sc, + inputPath.replace("/relation", ""), + targetPath.replace("/relation", "")); + RDD rdd = + union.mapToPair( + (PairFunction) + f -> { + final String source = + getJPathString(SOURCEJSONPATH, f); + final String target = + getJPathString(TARGETJSONPATH, f); + final String reltype = + getJPathString(RELJSONPATH, f); + ObjectMapper mapper = new ObjectMapper(); + mapper.configure( + DeserializationFeature + .FAIL_ON_UNKNOWN_PROPERTIES, + false); + return new Tuple2<>( + DHPUtils.md5( + String.format( + "%s::%s::%s", + source.toLowerCase(), + reltype.toLowerCase(), + target.toLowerCase())), + mapper.readValue(f, DLIRelation.class)); + }) + .reduceByKey( + (a, b) -> { + a.mergeFrom(b); + return a; + }) + .map(Tuple2::_2) + .rdd(); + spark.createDataset(rdd, Encoders.bean(DLIRelation.class)) + .write() + .mode(SaveMode.Overwrite) + .save(targetPath); + Dataset rel_ds = + spark.read().load(targetPath).as(Encoders.bean(Relation.class)); + System.out.println( + "LOADING PATH :" + targetPath.replace("/relation", "") + "/pid_simRel"); + Dataset sim_ds = + spark.read() + .load(targetPath.replace("/relation", "") + "/pid_simRel") + .as(Encoders.bean(Relation.class)); - SparkSXGeneratePidSimlarity.generateDataFrame(spark, sc, inputPath.replace("/relation",""),targetPath.replace("/relation","") ); - RDD rdd = union.mapToPair((PairFunction) f -> { - final String source = getJPathString(SOURCEJSONPATH, f); - final String target = getJPathString(TARGETJSONPATH, f); - final String reltype = getJPathString(RELJSONPATH, f); - ObjectMapper mapper = new ObjectMapper(); - mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - return new Tuple2<>(DHPUtils.md5(String.format("%s::%s::%s", source.toLowerCase(), reltype.toLowerCase(), target.toLowerCase())), mapper.readValue(f, DLIRelation.class)); - }).reduceByKey((a, b) -> { - a.mergeFrom(b); - return a; - }).map(Tuple2::_2).rdd(); + Dataset ids = + sim_ds.map( + (MapFunction) + relation -> { + final String type = + StringUtils.substringBefore( + relation.getSource(), "|"); + relation.setTarget( + String.format( + "%s|%s", + type, + StringUtils.substringAfter( + relation.getTarget(), "::"))); + return relation; + }, + Encoders.bean(Relation.class)); - spark.createDataset(rdd, Encoders.bean(DLIRelation.class)).write().mode(SaveMode.Overwrite).save(targetPath); - Dataset rel_ds =spark.read().load(targetPath).as(Encoders.bean(Relation.class)); - - System.out.println("LOADING PATH :"+targetPath.replace("/relation","")+"/pid_simRel"); - Datasetsim_ds =spark.read().load(targetPath.replace("/relation","")+"/pid_simRel").as(Encoders.bean(Relation.class)); - - Dataset ids = sim_ds.map((MapFunction) relation-> - { - final String type = StringUtils.substringBefore(relation.getSource(), "|"); - relation.setTarget(String.format("%s|%s", type, StringUtils.substringAfter(relation.getTarget(),"::"))); - return relation; - } - , Encoders.bean(Relation.class)); - - - final Dataset firstJoin = rel_ds - .joinWith(ids, ids.col("target") - .equalTo(rel_ds.col("source")), "left_outer") - .map((MapFunction, Relation>) s -> - { - if (s._2() != null) { - s._1().setSource(s._2().getSource()); - } - return s._1(); - } - , Encoders.bean(Relation.class)); - - - Dataset secondJoin = firstJoin.joinWith(ids, ids.col("target").equalTo(firstJoin.col("target")),"left_outer") - .map((MapFunction, Relation>) s -> - { - if (s._2() != null) { - s._1().setTarget(s._2().getSource()); - } - return s._1(); - } - , Encoders.bean(Relation.class)); - secondJoin.write().mode(SaveMode.Overwrite).save(targetPath+"_fixed"); + final Dataset firstJoin = + rel_ds.joinWith( + ids, + ids.col("target").equalTo(rel_ds.col("source")), + "left_outer") + .map( + (MapFunction, Relation>) + s -> { + if (s._2() != null) { + s._1().setSource(s._2().getSource()); + } + return s._1(); + }, + Encoders.bean(Relation.class)); + Dataset secondJoin = + firstJoin + .joinWith( + ids, + ids.col("target").equalTo(firstJoin.col("target")), + "left_outer") + .map( + (MapFunction, Relation>) + s -> { + if (s._2() != null) { + s._1().setTarget(s._2().getSource()); + } + return s._1(); + }, + Encoders.bean(Relation.class)); + secondJoin.write().mode(SaveMode.Overwrite).save(targetPath + "_fixed"); FileSystem fileSystem = FileSystem.get(sc.hadoopConfiguration()); - fileSystem.delete(new Path(targetPath), true); - fileSystem.rename(new Path(targetPath+"_fixed"),new Path(targetPath)); - + fileSystem.rename(new Path(targetPath + "_fixed"), new Path(targetPath)); } } public static String getJPathString(final String jsonPath, final String json) { try { Object o = JsonPath.read(json, jsonPath); - if (o instanceof String) - return (String) o; + if (o instanceof String) return (String) o; if (o instanceof JSONArray && ((JSONArray) o).size() > 0) return (String) ((JSONArray) o).get(0); return ""; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerGraphImporter.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerGraphImporter.java index 90606f1b81..b998c1b045 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerGraphImporter.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerGraphImporter.java @@ -2,9 +2,9 @@ package eu.dnetlib.dhp.sx.graph; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.sx.graph.parser.DatasetScholexplorerParser; import eu.dnetlib.dhp.sx.graph.parser.PublicationScholexplorerParser; -import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.scholexplorer.relation.RelationMapper; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.IntWritable; @@ -15,47 +15,57 @@ import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.sql.SparkSession; import scala.Tuple2; - /** - * This Job read a sequential File containing XML stored in the aggregator - * and generates an RDD of heterogeneous entities like Dataset, Relation, Publication and Unknown + * This Job read a sequential File containing XML stored in the aggregator and generates an RDD of + * heterogeneous entities like Dataset, Relation, Publication and Unknown */ - public class SparkScholexplorerGraphImporter { public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkScholexplorerGraphImporter.class.getResourceAsStream( - "/eu/dnetlib/dhp/sx/graph/argumentparser/input_graph_scholix_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkScholexplorerGraphImporter.class.getResourceAsStream( + "/eu/dnetlib/dhp/sx/graph/argumentparser/input_graph_scholix_parameters.json"))); parser.parseArgument(args); - final SparkSession spark = SparkSession - .builder() - .appName(SparkScholexplorerGraphImporter.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); + final SparkSession spark = + SparkSession.builder() + .appName(SparkScholexplorerGraphImporter.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final String inputPath = parser.get("sourcePath"); RelationMapper relationMapper = RelationMapper.load(); - sc.sequenceFile(inputPath, IntWritable.class, Text.class).map(Tuple2::_2).map(Text::toString).repartition(500) - .flatMap((FlatMapFunction) record -> { - switch (parser.get("entity")) { - case "dataset": - final DatasetScholexplorerParser d = new DatasetScholexplorerParser(); - return d.parseObject(record,relationMapper).iterator(); - case "publication": - final PublicationScholexplorerParser p = new PublicationScholexplorerParser(); - return p.parseObject(record,relationMapper).iterator(); - default: - throw new IllegalArgumentException("wrong values of entities"); - } - }).map(k -> { - ObjectMapper mapper = new ObjectMapper(); - return mapper.writeValueAsString(k); - }).saveAsTextFile(parser.get("targetPath"), GzipCodec.class); + sc.sequenceFile(inputPath, IntWritable.class, Text.class) + .map(Tuple2::_2) + .map(Text::toString) + .repartition(500) + .flatMap( + (FlatMapFunction) + record -> { + switch (parser.get("entity")) { + case "dataset": + final DatasetScholexplorerParser d = + new DatasetScholexplorerParser(); + return d.parseObject(record, relationMapper).iterator(); + case "publication": + final PublicationScholexplorerParser p = + new PublicationScholexplorerParser(); + return p.parseObject(record, relationMapper).iterator(); + default: + throw new IllegalArgumentException( + "wrong values of entities"); + } + }) + .map( + k -> { + ObjectMapper mapper = new ObjectMapper(); + return mapper.writeValueAsString(k); + }) + .saveAsTextFile(parser.get("targetPath"), GzipCodec.class); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java index 9eeff9613f..bfd5d5c7f4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java @@ -1,30 +1,39 @@ package eu.dnetlib.dhp.sx.graph.parser; - import eu.dnetlib.dhp.parser.utility.VtdUtilityParser; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset; import eu.dnetlib.dhp.schema.scholexplorer.DLIRelation; import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown; import eu.dnetlib.dhp.schema.scholexplorer.ProvenaceInfo; import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.scholexplorer.relation.RelInfo; import eu.dnetlib.scholexplorer.relation.RelationMapper; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -import javax.xml.stream.XMLStreamReader; import java.util.*; import java.util.regex.Matcher; import java.util.regex.Pattern; import java.util.stream.Collectors; +import javax.xml.stream.XMLStreamReader; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; public abstract class AbstractScholexplorerParser { protected static final Log log = LogFactory.getLog(AbstractScholexplorerParser.class); - final static Pattern pattern = Pattern.compile("10\\.\\d{4,9}/[-._;()/:A-Z0-9]+$", Pattern.CASE_INSENSITIVE); - private List datasetSubTypes = Arrays.asList("dataset", "software", "film", "sound", "physicalobject", "audiovisual", "collection", "other", "study", "metadata"); + static final Pattern pattern = + Pattern.compile("10\\.\\d{4,9}/[-._;()/:A-Z0-9]+$", Pattern.CASE_INSENSITIVE); + private List datasetSubTypes = + Arrays.asList( + "dataset", + "software", + "film", + "sound", + "physicalobject", + "audiovisual", + "collection", + "other", + "study", + "metadata"); public abstract List parseObject(final String record, final RelationMapper relMapper); @@ -36,27 +45,27 @@ public abstract class AbstractScholexplorerParser { return attributesMap; } - protected List extractSubject(List subjects) { final List subjectResult = new ArrayList<>(); if (subjects != null && subjects.size() > 0) { - subjects.forEach(subjectMap -> { - final StructuredProperty subject = new StructuredProperty(); - subject.setValue(subjectMap.getTextValue()); - final Qualifier schema = new Qualifier(); - schema.setClassid("dnet:subject"); - schema.setClassname("dnet:subject"); - schema.setSchemeid(subjectMap.getAttributes().get("subjectScheme")); - schema.setSchemename(subjectMap.getAttributes().get("subjectScheme")); - subject.setQualifier(schema); - subjectResult.add(subject); - }); + subjects.forEach( + subjectMap -> { + final StructuredProperty subject = new StructuredProperty(); + subject.setValue(subjectMap.getTextValue()); + final Qualifier schema = new Qualifier(); + schema.setClassid("dnet:subject"); + schema.setClassname("dnet:subject"); + schema.setSchemeid(subjectMap.getAttributes().get("subjectScheme")); + schema.setSchemename(subjectMap.getAttributes().get("subjectScheme")); + subject.setQualifier(schema); + subjectResult.add(subject); + }); } return subjectResult; } - - protected StructuredProperty extractIdentifier(List identifierType, final String fieldName) { + protected StructuredProperty extractIdentifier( + List identifierType, final String fieldName) { final StructuredProperty pid = new StructuredProperty(); if (identifierType != null && identifierType.size() > 0) { final VtdUtilityParser.Node result = identifierType.get(0); @@ -88,7 +97,7 @@ public abstract class AbstractScholexplorerParser { protected String generateId(final String pid, final String pidType, final String entityType) { String type; - switch (entityType){ + switch (entityType) { case "publication": type = "50|"; break; @@ -99,16 +108,22 @@ public abstract class AbstractScholexplorerParser { type = "70|"; break; default: - throw new IllegalArgumentException("unexpected value "+entityType); - + throw new IllegalArgumentException("unexpected value " + entityType); } - if ("dnet".equalsIgnoreCase(pidType)) - return type+StringUtils.substringAfter(pid, "::"); + if ("dnet".equalsIgnoreCase(pidType)) return type + StringUtils.substringAfter(pid, "::"); - return type+ DHPUtils.md5(String.format("%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim())); + return type + + DHPUtils.md5( + String.format( + "%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim())); } - protected DLIUnknown createUnknownObject(final String pid, final String pidType, final KeyValue cf, final DataInfo di, final String dateOfCollection) { + protected DLIUnknown createUnknownObject( + final String pid, + final String pidType, + final KeyValue cf, + final DataInfo di, + final String dateOfCollection) { final DLIUnknown uk = new DLIUnknown(); uk.setId(generateId(pid, pidType, "unknown")); ProvenaceInfo pi = new ProvenaceInfo(); @@ -130,56 +145,70 @@ public abstract class AbstractScholexplorerParser { return uk; } - protected void generateRelations(RelationMapper relationMapper, Result parsedObject, List result, DataInfo di, String dateOfCollection, List relatedIdentifiers) { - if(relatedIdentifiers!= null) { - result.addAll(relatedIdentifiers.stream() - .flatMap(n -> { - final List rels = new ArrayList<>(); - DLIRelation r = new DLIRelation(); - r.setSource(parsedObject.getId()); - final String relatedPid = n.getTextValue(); - final String relatedPidType = n.getAttributes().get("relatedIdentifierType"); - final String relatedType = n.getAttributes().getOrDefault("entityType", "unknown"); - String relationSemantic = n.getAttributes().get("relationType"); - String inverseRelation; - final String targetId = generateId(relatedPid, relatedPidType, relatedType); - r.setDateOfCollection(dateOfCollection); - if (relationMapper.containsKey(relationSemantic.toLowerCase())) - { - RelInfo relInfo = relationMapper.get(relationSemantic.toLowerCase()); - relationSemantic = relInfo.getOriginal(); - inverseRelation = relInfo.getInverse(); - } - else { - relationSemantic = "Unknown"; - inverseRelation = "Unknown"; - } - r.setTarget(targetId); - r.setRelType(relationSemantic); - r.setRelClass("datacite"); - r.setCollectedFrom(parsedObject.getCollectedfrom()); - r.setDataInfo(di); - rels.add(r); - r = new DLIRelation(); - r.setDataInfo(di); - r.setSource(targetId); - r.setTarget(parsedObject.getId()); - r.setRelType(inverseRelation); - r.setRelClass("datacite"); - r.setCollectedFrom(parsedObject.getCollectedfrom()); - r.setDateOfCollection(dateOfCollection); - rels.add(r); - if("unknown".equalsIgnoreCase(relatedType)) - result.add(createUnknownObject(relatedPid, relatedPidType, parsedObject.getCollectedfrom().get(0), di, dateOfCollection)); - return rels.stream(); - }).collect(Collectors.toList())); + protected void generateRelations( + RelationMapper relationMapper, + Result parsedObject, + List result, + DataInfo di, + String dateOfCollection, + List relatedIdentifiers) { + if (relatedIdentifiers != null) { + result.addAll( + relatedIdentifiers.stream() + .flatMap( + n -> { + final List rels = new ArrayList<>(); + DLIRelation r = new DLIRelation(); + r.setSource(parsedObject.getId()); + final String relatedPid = n.getTextValue(); + final String relatedPidType = + n.getAttributes().get("relatedIdentifierType"); + final String relatedType = + n.getAttributes() + .getOrDefault("entityType", "unknown"); + String relationSemantic = + n.getAttributes().get("relationType"); + String inverseRelation; + final String targetId = + generateId(relatedPid, relatedPidType, relatedType); + r.setDateOfCollection(dateOfCollection); + if (relationMapper.containsKey( + relationSemantic.toLowerCase())) { + RelInfo relInfo = + relationMapper.get( + relationSemantic.toLowerCase()); + relationSemantic = relInfo.getOriginal(); + inverseRelation = relInfo.getInverse(); + } else { + relationSemantic = "Unknown"; + inverseRelation = "Unknown"; + } + r.setTarget(targetId); + r.setRelType(relationSemantic); + r.setRelClass("datacite"); + r.setCollectedFrom(parsedObject.getCollectedfrom()); + r.setDataInfo(di); + rels.add(r); + r = new DLIRelation(); + r.setDataInfo(di); + r.setSource(targetId); + r.setTarget(parsedObject.getId()); + r.setRelType(inverseRelation); + r.setRelClass("datacite"); + r.setCollectedFrom(parsedObject.getCollectedfrom()); + r.setDateOfCollection(dateOfCollection); + rels.add(r); + if ("unknown".equalsIgnoreCase(relatedType)) + result.add( + createUnknownObject( + relatedPid, + relatedPidType, + parsedObject.getCollectedfrom().get(0), + di, + dateOfCollection)); + return rels.stream(); + }) + .collect(Collectors.toList())); } } - - - - } - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java index f1915c5cf3..1fb77c147a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java @@ -4,21 +4,17 @@ import com.ximpleware.AutoPilot; import com.ximpleware.VTDGen; import com.ximpleware.VTDNav; import eu.dnetlib.dhp.parser.utility.VtdUtilityParser; +import eu.dnetlib.dhp.parser.utility.VtdUtilityParser.Node; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset; -import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown; import eu.dnetlib.dhp.schema.scholexplorer.ProvenaceInfo; - -import eu.dnetlib.dhp.parser.utility.VtdUtilityParser.Node; -import eu.dnetlib.scholexplorer.relation.RelInfo; import eu.dnetlib.scholexplorer.relation.RelationMapper; -import org.apache.commons.lang3.StringUtils; - import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.stream.Collectors; +import org.apache.commons.lang3.StringUtils; public class DatasetScholexplorerParser extends AbstractScholexplorerParser { @Override @@ -39,13 +35,19 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser { di.setInvisible(false); parsedObject.setDataInfo(di); - parsedObject.setOriginalId(Collections.singletonList(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='recordIdentifier']"))); + parsedObject.setOriginalId( + Collections.singletonList( + VtdUtilityParser.getSingleValue( + ap, vn, "//*[local-name()='recordIdentifier']"))); - parsedObject.setOriginalObjIdentifier(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='objIdentifier']")); - String dateOfCollection = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='dateOfCollection']"); + parsedObject.setOriginalObjIdentifier( + VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='objIdentifier']")); + String dateOfCollection = + VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='dateOfCollection']"); parsedObject.setDateofcollection(dateOfCollection); - final String resolvedDate = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='resolvedDate']"); + final String resolvedDate = + VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='resolvedDate']"); if (StringUtils.isNotBlank(resolvedDate)) { StructuredProperty currentDate = new StructuredProperty(); @@ -59,16 +61,28 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser { parsedObject.setRelevantdate(Collections.singletonList(currentDate)); } - final String completionStatus = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='completionStatus']"); - final String provisionMode = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='provisionMode']"); + final String completionStatus = + VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='completionStatus']"); + final String provisionMode = + VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='provisionMode']"); - final String publisher = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='resource']/*[local-name()='publisher']"); + final String publisher = + VtdUtilityParser.getSingleValue( + ap, vn, "//*[local-name()='resource']/*[local-name()='publisher']"); List collectedFromNodes = - VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='collectedFrom']", Arrays.asList("name", "id", "mode", "completionStatus")); + VtdUtilityParser.getTextValuesWithAttributes( + ap, + vn, + "//*[local-name()='collectedFrom']", + Arrays.asList("name", "id", "mode", "completionStatus")); List resolvededFromNodes = - VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='resolvedFrom']", Arrays.asList("name", "id", "mode", "completionStatus")); + VtdUtilityParser.getTextValuesWithAttributes( + ap, + vn, + "//*[local-name()='resolvedFrom']", + Arrays.asList("name", "id", "mode", "completionStatus")); Field pf = new Field<>(); pf.setValue(publisher); @@ -76,90 +90,122 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser { parsedObject.setPublisher(pf); final List provenances = new ArrayList<>(); if (collectedFromNodes != null && collectedFromNodes.size() > 0) { - collectedFromNodes.forEach(it -> { - final ProvenaceInfo provenance = new ProvenaceInfo(); - provenance.setId(it.getAttributes().get("id")); - provenance.setName(it.getAttributes().get("name")); - provenance.setCollectionMode(provisionMode); - provenance.setCompletionStatus(it.getAttributes().get("completionStatus")); - provenances.add(provenance); - }); + collectedFromNodes.forEach( + it -> { + final ProvenaceInfo provenance = new ProvenaceInfo(); + provenance.setId(it.getAttributes().get("id")); + provenance.setName(it.getAttributes().get("name")); + provenance.setCollectionMode(provisionMode); + provenance.setCompletionStatus( + it.getAttributes().get("completionStatus")); + provenances.add(provenance); + }); } if (resolvededFromNodes != null && resolvededFromNodes.size() > 0) { - resolvededFromNodes.forEach(it -> { - final ProvenaceInfo provenance = new ProvenaceInfo(); - provenance.setId(it.getAttributes().get("id")); - provenance.setName(it.getAttributes().get("name")); - provenance.setCollectionMode("resolved"); - provenance.setCompletionStatus(it.getAttributes().get("completionStatus")); - provenances.add(provenance); - }); + resolvededFromNodes.forEach( + it -> { + final ProvenaceInfo provenance = new ProvenaceInfo(); + provenance.setId(it.getAttributes().get("id")); + provenance.setName(it.getAttributes().get("name")); + provenance.setCollectionMode("resolved"); + provenance.setCompletionStatus( + it.getAttributes().get("completionStatus")); + provenances.add(provenance); + }); } parsedObject.setDlicollectedfrom(provenances); - parsedObject.setCollectedfrom(parsedObject.getDlicollectedfrom().stream().map( - p-> { - final KeyValue cf = new KeyValue(); - cf.setKey(p.getId()); - cf.setValue(p.getName()); - return cf; - } - ).collect(Collectors.toList())); - parsedObject.setCompletionStatus(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='completionStatus']")); + parsedObject.setCollectedfrom( + parsedObject.getDlicollectedfrom().stream() + .map( + p -> { + final KeyValue cf = new KeyValue(); + cf.setKey(p.getId()); + cf.setValue(p.getName()); + return cf; + }) + .collect(Collectors.toList())); + parsedObject.setCompletionStatus( + VtdUtilityParser.getSingleValue( + ap, vn, "//*[local-name()='completionStatus']")); final List identifierType = - VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='resource']/*[local-name()='identifier']", Collections.singletonList("identifierType")); + VtdUtilityParser.getTextValuesWithAttributes( + ap, + vn, + "//*[local-name()='resource']/*[local-name()='identifier']", + Collections.singletonList("identifierType")); StructuredProperty currentPid = extractIdentifier(identifierType, "identifierType"); if (currentPid == null) return null; inferPid(currentPid); parsedObject.setPid(Collections.singletonList(currentPid)); - - final String sourceId = generateId(currentPid.getValue(), currentPid.getQualifier().getClassid(), "dataset"); + final String sourceId = + generateId( + currentPid.getValue(), + currentPid.getQualifier().getClassid(), + "dataset"); parsedObject.setId(sourceId); - - List descs = VtdUtilityParser.getTextValue(ap, vn, "//*[local-name()='description']"); + List descs = + VtdUtilityParser.getTextValue(ap, vn, "//*[local-name()='description']"); if (descs != null && descs.size() > 0) - parsedObject.setDescription(descs.stream() - .map(it -> it.length() < 10000 ? it : it.substring(0, 10000)) - .map(it -> { - final Field d = new Field<>(); - d.setValue(it); - return d; - }) - .collect(Collectors.toList())); - + parsedObject.setDescription( + descs.stream() + .map(it -> it.length() < 10000 ? it : it.substring(0, 10000)) + .map( + it -> { + final Field d = new Field<>(); + d.setValue(it); + return d; + }) + .collect(Collectors.toList())); final List relatedIdentifiers = - VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='relatedIdentifier']", - Arrays.asList("relatedIdentifierType", "relationType", "entityType", "inverseRelationType")); - - - generateRelations(relationMapper, parsedObject, result, di, dateOfCollection, relatedIdentifiers); + VtdUtilityParser.getTextValuesWithAttributes( + ap, + vn, + "//*[local-name()='relatedIdentifier']", + Arrays.asList( + "relatedIdentifierType", + "relationType", + "entityType", + "inverseRelationType")); + generateRelations( + relationMapper, parsedObject, result, di, dateOfCollection, relatedIdentifiers); final List hostedBy = - VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='hostedBy']", Arrays.asList("id", "name")); - + VtdUtilityParser.getTextValuesWithAttributes( + ap, vn, "//*[local-name()='hostedBy']", Arrays.asList("id", "name")); if (hostedBy != null) { - parsedObject.setInstance(hostedBy.stream().map(it -> - { - final Instance i = new Instance(); - i.setUrl(Collections.singletonList(currentPid.getValue())); - KeyValue h = new KeyValue(); - i.setHostedby(h); - h.setKey(it.getAttributes().get("id")); - h.setValue(it.getAttributes().get("name")); - return i; - }).collect(Collectors.toList())); + parsedObject.setInstance( + hostedBy.stream() + .map( + it -> { + final Instance i = new Instance(); + i.setUrl( + Collections.singletonList( + currentPid.getValue())); + KeyValue h = new KeyValue(); + i.setHostedby(h); + h.setKey(it.getAttributes().get("id")); + h.setValue(it.getAttributes().get("name")); + return i; + }) + .collect(Collectors.toList())); } - - List subjects = extractSubject(VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='resource']//*[local-name()='subject']", Collections.singletonList("subjectScheme"))); + List subjects = + extractSubject( + VtdUtilityParser.getTextValuesWithAttributes( + ap, + vn, + "//*[local-name()='resource']//*[local-name()='subject']", + Collections.singletonList("subjectScheme"))); parsedObject.setSubject(subjects); @@ -172,50 +218,61 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser { parsedObject.setCompletionStatus(completionStatus); - final List creators = VtdUtilityParser.getTextValue(ap, vn, "//*[local-name()='resource']//*[local-name()='creator']/*[local-name()='creatorName']"); + final List creators = + VtdUtilityParser.getTextValue( + ap, + vn, + "//*[local-name()='resource']//*[local-name()='creator']/*[local-name()='creatorName']"); if (creators != null && creators.size() > 0) { - parsedObject.setAuthor(creators - .stream() - .map(a -> { - final Author author = new Author(); - author.setFullname(a); - return author; - }).collect(Collectors.toList()) - ); + parsedObject.setAuthor( + creators.stream() + .map( + a -> { + final Author author = new Author(); + author.setFullname(a); + return author; + }) + .collect(Collectors.toList())); } - final List titles = VtdUtilityParser.getTextValue(ap, vn, "//*[local-name()='resource']//*[local-name()='title']"); + final List titles = + VtdUtilityParser.getTextValue( + ap, vn, "//*[local-name()='resource']//*[local-name()='title']"); if (titles != null && titles.size() > 0) { - parsedObject.setTitle(titles.stream() - .map(t -> { - final StructuredProperty st = new StructuredProperty(); - st.setValue(t); - return st; - } - ).collect(Collectors.toList()) - ); + parsedObject.setTitle( + titles.stream() + .map( + t -> { + final StructuredProperty st = new StructuredProperty(); + st.setValue(t); + return st; + }) + .collect(Collectors.toList())); } - final List dates = VtdUtilityParser.getTextValue(ap, vn, "//*[local-name()='resource']/*[local-name()='dates']/*[local-name()='date']"); - + final List dates = + VtdUtilityParser.getTextValue( + ap, + vn, + "//*[local-name()='resource']/*[local-name()='dates']/*[local-name()='date']"); if (dates != null && dates.size() > 0) { - parsedObject.setRelevantdate(dates.stream().map( - cd -> { - StructuredProperty date = new StructuredProperty(); - date.setValue(cd); - final Qualifier dq = new Qualifier(); - dq.setClassname("date"); - dq.setClassid("date"); - dq.setSchemename("dnet::date"); - dq.setSchemeid("dnet::date"); - date.setQualifier(dq); - return date; - } - ).collect(Collectors.toList())); + parsedObject.setRelevantdate( + dates.stream() + .map( + cd -> { + StructuredProperty date = new StructuredProperty(); + date.setValue(cd); + final Qualifier dq = new Qualifier(); + dq.setClassname("date"); + dq.setClassid("date"); + dq.setSchemename("dnet::date"); + dq.setSchemeid("dnet::date"); + date.setQualifier(dq); + return date; + }) + .collect(Collectors.toList())); } - - result.add(parsedObject); return result; } catch (Throwable e) { @@ -223,8 +280,4 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser { return null; } } - - - - } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java index aa2f860769..ad560805a1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java @@ -8,15 +8,13 @@ import eu.dnetlib.dhp.parser.utility.VtdUtilityParser.Node; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication; import eu.dnetlib.dhp.schema.scholexplorer.ProvenaceInfo; -import eu.dnetlib.scholexplorer.relation.RelInfo; import eu.dnetlib.scholexplorer.relation.RelationMapper; -import org.apache.commons.lang3.StringUtils; - import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.stream.Collectors; +import org.apache.commons.lang3.StringUtils; public class PublicationScholexplorerParser extends AbstractScholexplorerParser { @@ -29,7 +27,6 @@ public class PublicationScholexplorerParser extends AbstractScholexplorerParser vg.setDoc(record.getBytes()); vg.parse(true); - final VTDNav vn = vg.getNav(); final AutoPilot ap = new AutoPilot(vn); @@ -38,11 +35,16 @@ public class PublicationScholexplorerParser extends AbstractScholexplorerParser di.setDeletedbyinference(false); di.setInvisible(false); - String dateOfCollection = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='dateOfCollection']"); + String dateOfCollection = + VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='dateOfCollection']"); parsedObject.setDateofcollection(dateOfCollection); - final String resolvedDate = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='resolvedDate']"); - parsedObject.setOriginalId(Collections.singletonList(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='recordIdentifier']"))); + final String resolvedDate = + VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='resolvedDate']"); + parsedObject.setOriginalId( + Collections.singletonList( + VtdUtilityParser.getSingleValue( + ap, vn, "//*[local-name()='recordIdentifier']"))); if (StringUtils.isNotBlank(resolvedDate)) { StructuredProperty currentDate = new StructuredProperty(); @@ -56,123 +58,164 @@ public class PublicationScholexplorerParser extends AbstractScholexplorerParser parsedObject.setRelevantdate(Collections.singletonList(currentDate)); } - - final List pid = VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='pid']", Arrays.asList("type")); + final List pid = + VtdUtilityParser.getTextValuesWithAttributes( + ap, vn, "//*[local-name()='pid']", Arrays.asList("type")); StructuredProperty currentPid = extractIdentifier(pid, "type"); if (currentPid == null) return null; inferPid(currentPid); parsedObject.setPid(Collections.singletonList(currentPid)); - final String sourceId = generateId(currentPid.getValue(), currentPid.getQualifier().getClassid(), "publication"); + final String sourceId = + generateId( + currentPid.getValue(), + currentPid.getQualifier().getClassid(), + "publication"); parsedObject.setId(sourceId); - parsedObject.setOriginalObjIdentifier(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='objIdentifier']")); + parsedObject.setOriginalObjIdentifier( + VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='objIdentifier']")); - String provisionMode = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='provisionMode']"); + String provisionMode = + VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='provisionMode']"); List collectedFromNodes = - VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='collectedFrom']", Arrays.asList("name", "id", "mode", "completionStatus")); + VtdUtilityParser.getTextValuesWithAttributes( + ap, + vn, + "//*[local-name()='collectedFrom']", + Arrays.asList("name", "id", "mode", "completionStatus")); List resolvededFromNodes = - VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='resolvedFrom']", Arrays.asList("name", "id", "mode", "completionStatus")); + VtdUtilityParser.getTextValuesWithAttributes( + ap, + vn, + "//*[local-name()='resolvedFrom']", + Arrays.asList("name", "id", "mode", "completionStatus")); - final String publisher = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='publisher']"); + final String publisher = + VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='publisher']"); Field pf = new Field<>(); pf.setValue(publisher); parsedObject.setPublisher(pf); final List provenances = new ArrayList<>(); if (collectedFromNodes != null && collectedFromNodes.size() > 0) { - collectedFromNodes.forEach(it -> { - final ProvenaceInfo provenance = new ProvenaceInfo(); - provenance.setId(it.getAttributes().get("id")); - provenance.setName(it.getAttributes().get("name")); - provenance.setCollectionMode(provisionMode); - provenance.setCompletionStatus(it.getAttributes().get("completionStatus")); - provenances.add(provenance); - }); + collectedFromNodes.forEach( + it -> { + final ProvenaceInfo provenance = new ProvenaceInfo(); + provenance.setId(it.getAttributes().get("id")); + provenance.setName(it.getAttributes().get("name")); + provenance.setCollectionMode(provisionMode); + provenance.setCompletionStatus( + it.getAttributes().get("completionStatus")); + provenances.add(provenance); + }); } if (resolvededFromNodes != null && resolvededFromNodes.size() > 0) { - resolvededFromNodes.forEach(it -> { - final ProvenaceInfo provenance = new ProvenaceInfo(); - provenance.setId(it.getAttributes().get("id")); - provenance.setName(it.getAttributes().get("name")); - provenance.setCollectionMode("resolved"); - provenance.setCompletionStatus(it.getAttributes().get("completionStatus")); - provenances.add(provenance); - }); + resolvededFromNodes.forEach( + it -> { + final ProvenaceInfo provenance = new ProvenaceInfo(); + provenance.setId(it.getAttributes().get("id")); + provenance.setName(it.getAttributes().get("name")); + provenance.setCollectionMode("resolved"); + provenance.setCompletionStatus( + it.getAttributes().get("completionStatus")); + provenances.add(provenance); + }); } parsedObject.setDlicollectedfrom(provenances); - parsedObject.setCompletionStatus(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='completionStatus']")); + parsedObject.setCompletionStatus( + VtdUtilityParser.getSingleValue( + ap, vn, "//*[local-name()='completionStatus']")); - parsedObject.setCollectedfrom(parsedObject.getDlicollectedfrom().stream().map( - p -> { - final KeyValue cf = new KeyValue(); - cf.setKey(p.getId()); - cf.setValue(p.getName()); - return cf; - } - ).collect(Collectors.toList())); + parsedObject.setCollectedfrom( + parsedObject.getDlicollectedfrom().stream() + .map( + p -> { + final KeyValue cf = new KeyValue(); + cf.setKey(p.getId()); + cf.setValue(p.getName()); + return cf; + }) + .collect(Collectors.toList())); final List relatedIdentifiers = - VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='relatedIdentifier']", - Arrays.asList("relatedIdentifierType", "relationType", "entityType", "inverseRelationType")); - generateRelations(relationMapper, parsedObject, result, di, dateOfCollection, relatedIdentifiers); + VtdUtilityParser.getTextValuesWithAttributes( + ap, + vn, + "//*[local-name()='relatedIdentifier']", + Arrays.asList( + "relatedIdentifierType", + "relationType", + "entityType", + "inverseRelationType")); + generateRelations( + relationMapper, parsedObject, result, di, dateOfCollection, relatedIdentifiers); final List hostedBy = - VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='hostedBy']", Arrays.asList("id", "name")); - + VtdUtilityParser.getTextValuesWithAttributes( + ap, vn, "//*[local-name()='hostedBy']", Arrays.asList("id", "name")); if (hostedBy != null) { - parsedObject.setInstance(hostedBy.stream().map(it -> - { - final Instance i = new Instance(); - i.setUrl(Collections.singletonList(currentPid.getValue())); - KeyValue h = new KeyValue(); - i.setHostedby(h); - h.setKey(it.getAttributes().get("id")); - h.setValue(it.getAttributes().get("name")); - return i; - }).collect(Collectors.toList())); + parsedObject.setInstance( + hostedBy.stream() + .map( + it -> { + final Instance i = new Instance(); + i.setUrl( + Collections.singletonList( + currentPid.getValue())); + KeyValue h = new KeyValue(); + i.setHostedby(h); + h.setKey(it.getAttributes().get("id")); + h.setValue(it.getAttributes().get("name")); + return i; + }) + .collect(Collectors.toList())); } - final List authorsNode = VtdUtilityParser.getTextValue(ap, vn, "//*[local-name()='creator']"); + final List authorsNode = + VtdUtilityParser.getTextValue(ap, vn, "//*[local-name()='creator']"); if (authorsNode != null) - parsedObject.setAuthor(authorsNode - .stream() - .map(a -> { - final Author author = new Author(); - author.setFullname(a); - return author; - }).collect(Collectors.toList()) - ); + parsedObject.setAuthor( + authorsNode.stream() + .map( + a -> { + final Author author = new Author(); + author.setFullname(a); + return author; + }) + .collect(Collectors.toList())); - final List titles = VtdUtilityParser.getTextValue(ap, vn, "//*[local-name()='title']"); + final List titles = + VtdUtilityParser.getTextValue(ap, vn, "//*[local-name()='title']"); if (titles != null) { - parsedObject.setTitle(titles.stream() - .map(t -> { - final StructuredProperty st = new StructuredProperty(); - st.setValue(t); - return st; - } - ).collect(Collectors.toList()) - ); + parsedObject.setTitle( + titles.stream() + .map( + t -> { + final StructuredProperty st = new StructuredProperty(); + st.setValue(t); + return st; + }) + .collect(Collectors.toList())); } - Field description = new Field<>(); - description.setValue(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='description']")); + description.setValue( + VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='description']")); - if (StringUtils.isNotBlank(description.getValue()) && description.getValue().length() > 10000) { + if (StringUtils.isNotBlank(description.getValue()) + && description.getValue().length() > 10000) { description.setValue(description.getValue().substring(0, 10000)); } parsedObject.setDescription(Collections.singletonList(description)); - final String cd = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='date']"); StructuredProperty date = new StructuredProperty(); @@ -185,7 +228,13 @@ public class PublicationScholexplorerParser extends AbstractScholexplorerParser date.setQualifier(dq); parsedObject.setRelevantdate(Collections.singletonList(date)); - List subjects = extractSubject(VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='subject']", Collections.singletonList("scheme"))); + List subjects = + extractSubject( + VtdUtilityParser.getTextValuesWithAttributes( + ap, + vn, + "//*[local-name()='subject']", + Collections.singletonList("scheme"))); parsedObject.setSubject(subjects); parsedObject.setDataInfo(di); @@ -205,8 +254,5 @@ public class PublicationScholexplorerParser extends AbstractScholexplorerParser log.error("Error on parsing record ", e); return null; } - } - - } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java index ecadbe9813..e35339bfab 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java @@ -1,6 +1,9 @@ package eu.dnetlib.dhp.oa.graph; import eu.dnetlib.dhp.schema.common.ModelSupport; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.RandomStringUtils; import org.apache.spark.SparkConf; @@ -12,15 +15,12 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - public class GraphHiveImporterJobTest { private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJobTest.class); - public static final String JDBC_DERBY_TEMPLATE = "jdbc:derby:;databaseName=%s/junit_metastore_db;create=true"; + public static final String JDBC_DERBY_TEMPLATE = + "jdbc:derby:;databaseName=%s/junit_metastore_db;create=true"; private static SparkSession spark; @@ -45,14 +45,16 @@ public class GraphHiveImporterJobTest { conf.set("spark.ui.enabled", "false"); conf.set("spark.sql.warehouse.dir", workingDir.toString()); conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - conf.set("javax.jdo.option.ConnectionURL", String.format(JDBC_DERBY_TEMPLATE, workingDir.resolve("warehouse").toString())); + conf.set( + "javax.jdo.option.ConnectionURL", + String.format(JDBC_DERBY_TEMPLATE, workingDir.resolve("warehouse").toString())); - spark = SparkSession - .builder() - .appName(GraphHiveImporterJobTest.class.getSimpleName()) - .config(conf) - .enableHiveSupport() - .getOrCreate(); + spark = + SparkSession.builder() + .appName(GraphHiveImporterJobTest.class.getSimpleName()) + .config(conf) + .enableHiveSupport() + .getOrCreate(); } @AfterAll @@ -64,20 +66,25 @@ public class GraphHiveImporterJobTest { @Test public void testImportGraphAsHiveDB() throws Exception { - GraphHiveImporterJob.main(new String[]{ - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-inputPath", getClass().getResource("/eu/dnetlib/dhp/oa/graph/sample").getPath(), - "-hiveMetastoreUris", "", - "-hiveDbName", dbName - }); + GraphHiveImporterJob.main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + getClass().getResource("/eu/dnetlib/dhp/oa/graph/sample").getPath(), + "-hiveMetastoreUris", + "", + "-hiveDbName", + dbName + }); - ModelSupport.oafTypes.forEach((name, clazz) -> { - long count = spark.read().table(dbName + "." + name).count(); - int expected = name.equals("relation") ? 100 : 10; - - Assertions.assertEquals(expected, count, String.format("%s should be %s", name, expected)); - }); + ModelSupport.oafTypes.forEach( + (name, clazz) -> { + long count = spark.read().table(dbName + "." + name).count(); + int expected = name.equals("relation") ? 100 : 10; + Assertions.assertEquals( + expected, count, String.format("%s should be %s", name, expected)); + }); } - } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 63d7d50db3..6af314d76e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -1,106 +1,102 @@ package eu.dnetlib.dhp.oa.graph.raw; -import com.google.common.collect.Maps; -import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; - -import java.io.IOException; -import java.util.List; -import java.util.Map; - import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertTrue; import static org.mockito.ArgumentMatchers.anyString; import static org.mockito.Mockito.when; +import eu.dnetlib.dhp.schema.oaf.*; +import java.io.IOException; +import java.util.List; +import java.util.Map; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + @ExtendWith(MockitoExtension.class) public class MappersTest { - @Mock - private Map code2name; + @Mock private Map code2name; - @BeforeEach - public void setUp() throws Exception { - when(code2name.get(anyString())).thenAnswer(invocation -> invocation.getArgument(0)); - } + @BeforeEach + public void setUp() throws Exception { + when(code2name.get(anyString())).thenAnswer(invocation -> invocation.getArgument(0)); + } - @Test - void testPublication() throws IOException { - final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml")); + @Test + void testPublication() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml")); - final List list = new OafToOafMapper(code2name).processMdRecord(xml); + final List list = new OafToOafMapper(code2name).processMdRecord(xml); - assertEquals(3, list.size()); - assertTrue(list.get(0) instanceof Publication); - assertTrue(list.get(1) instanceof Relation); - assertTrue(list.get(2) instanceof Relation); + assertEquals(3, list.size()); + assertTrue(list.get(0) instanceof Publication); + assertTrue(list.get(1) instanceof Relation); + assertTrue(list.get(2) instanceof Relation); - final Publication p = (Publication) list.get(0); - final Relation r1 = (Relation) list.get(1); - final Relation r2 = (Relation) list.get(2); + final Publication p = (Publication) list.get(0); + final Relation r1 = (Relation) list.get(1); + final Relation r2 = (Relation) list.get(2); - assertValidId(p.getId()); - assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); - assertTrue(p.getAuthor().size() > 0); - assertTrue(p.getSubject().size() > 0); - assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); - assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); + assertValidId(p.getId()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + assertTrue(p.getAuthor().size() > 0); + assertTrue(p.getSubject().size() > 0); + assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); + assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); - assertValidId(r1.getSource()); - assertValidId(r2.getSource()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - assertTrue(StringUtils.isNotBlank(r1.getRelClass())); - assertTrue(StringUtils.isNotBlank(r2.getRelClass())); - assertTrue(StringUtils.isNotBlank(r1.getRelType())); - assertTrue(StringUtils.isNotBlank(r2.getRelType())); - } + assertValidId(r1.getSource()); + assertValidId(r2.getSource()); + assertEquals(r1.getSource(), r2.getTarget()); + assertEquals(r2.getSource(), r1.getTarget()); + assertTrue(StringUtils.isNotBlank(r1.getRelClass())); + assertTrue(StringUtils.isNotBlank(r2.getRelClass())); + assertTrue(StringUtils.isNotBlank(r1.getRelType())); + assertTrue(StringUtils.isNotBlank(r2.getRelType())); + } - @Test - void testDataset() throws IOException { - final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml")); + @Test + void testDataset() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml")); - final List list = new OdfToOafMapper(code2name).processMdRecord(xml); + final List list = new OdfToOafMapper(code2name).processMdRecord(xml); - assertEquals(1, list.size()); - assertTrue(list.get(0) instanceof Dataset); + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Dataset); - final Dataset d = (Dataset) list.get(0); + final Dataset d = (Dataset) list.get(0); - assertValidId(d.getId()); - assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); - assertTrue(d.getAuthor().size() > 0); - assertTrue(d.getSubject().size() > 0); - } + assertValidId(d.getId()); + assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); + assertTrue(d.getAuthor().size() > 0); + assertTrue(d.getSubject().size() > 0); + } - @Test - void testSoftware() throws IOException { - final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml")); + @Test + void testSoftware() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml")); - final List list = new OdfToOafMapper(code2name).processMdRecord(xml); + final List list = new OdfToOafMapper(code2name).processMdRecord(xml); - assertEquals(1, list.size()); - assertTrue(list.get(0) instanceof Software); + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Software); - final Software s = (Software) list.get(0); + final Software s = (Software) list.get(0); - assertValidId(s.getId()); - assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue())); - assertTrue(s.getAuthor().size() > 0); - assertTrue(s.getSubject().size() > 0); - } + assertValidId(s.getId()); + assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue())); + assertTrue(s.getAuthor().size() > 0); + assertTrue(s.getSubject().size() > 0); + } - private void assertValidId(final String id) { - assertEquals(49, id.length()); - assertEquals('|', id.charAt(2)); - assertEquals(':', id.charAt(15)); - assertEquals(':', id.charAt(16)); - } + private void assertValidId(final String id) { + assertEquals(49, id.length()); + assertEquals('|', id.charAt(2)); + assertEquals(':', id.charAt(15)); + assertEquals(':', id.charAt(16)); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index b1fc9131fb..3c7bc684d3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -1,8 +1,17 @@ package eu.dnetlib.dhp.oa.graph.raw; +import static org.junit.jupiter.api.Assertions.assertEquals; + import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.oaf.*; +import java.io.IOException; +import java.sql.Array; +import java.sql.Date; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.List; +import java.util.Objects; import org.apache.commons.io.IOUtils; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; @@ -11,283 +20,294 @@ import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; -import java.io.IOException; -import java.sql.Array; -import java.sql.Date; -import java.sql.ResultSet; -import java.sql.SQLException; -import java.util.List; -import java.util.Objects; - -import static org.junit.jupiter.api.Assertions.assertEquals; - @ExtendWith(MockitoExtension.class) public class MigrateDbEntitiesApplicationTest { - private MigrateDbEntitiesApplication app; + private MigrateDbEntitiesApplication app; - @Mock - private ResultSet rs; + @Mock private ResultSet rs; - @BeforeEach - public void setUp() { - this.app = new MigrateDbEntitiesApplication(); - } + @BeforeEach + public void setUp() { + this.app = new MigrateDbEntitiesApplication(); + } - @Test - public void testProcessDatasource() throws Exception { - final List fields = prepareMocks("datasources_resultset_entry.json"); + @Test + public void testProcessDatasource() throws Exception { + final List fields = prepareMocks("datasources_resultset_entry.json"); - final List list = app.processDatasource(rs); - assertEquals(1, list.size()); - verifyMocks(fields); + final List list = app.processDatasource(rs); + assertEquals(1, list.size()); + verifyMocks(fields); - final Datasource ds = (Datasource) list.get(0); - assertValidId(ds.getId()); - assertEquals(ds.getOfficialname().getValue(), getValueAsString("officialname", fields)); - assertEquals(ds.getEnglishname().getValue(), getValueAsString("englishname", fields)); - assertEquals(ds.getContactemail().getValue(), getValueAsString("contactemail", fields)); - assertEquals(ds.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); - assertEquals(ds.getNamespaceprefix().getValue(), getValueAsString("namespaceprefix", fields)); - assertEquals(ds.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); - assertEquals(ds.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); - } + final Datasource ds = (Datasource) list.get(0); + assertValidId(ds.getId()); + assertEquals(ds.getOfficialname().getValue(), getValueAsString("officialname", fields)); + assertEquals(ds.getEnglishname().getValue(), getValueAsString("englishname", fields)); + assertEquals(ds.getContactemail().getValue(), getValueAsString("contactemail", fields)); + assertEquals(ds.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); + assertEquals( + ds.getNamespaceprefix().getValue(), getValueAsString("namespaceprefix", fields)); + assertEquals( + ds.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); + assertEquals( + ds.getCollectedfrom().get(0).getValue(), + getValueAsString("collectedfromname", fields)); + } - @Test - public void testProcessProject() throws Exception { - final List fields = prepareMocks("projects_resultset_entry.json"); + @Test + public void testProcessProject() throws Exception { + final List fields = prepareMocks("projects_resultset_entry.json"); - final List list = app.processProject(rs); - assertEquals(1, list.size()); - verifyMocks(fields); + final List list = app.processProject(rs); + assertEquals(1, list.size()); + verifyMocks(fields); - final Project p = (Project) list.get(0); - assertValidId(p.getId()); - assertEquals(p.getAcronym().getValue(), getValueAsString("acronym", fields)); - assertEquals(p.getTitle().getValue(), getValueAsString("title", fields)); - assertEquals(p.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); - assertEquals(p.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); - } + final Project p = (Project) list.get(0); + assertValidId(p.getId()); + assertEquals(p.getAcronym().getValue(), getValueAsString("acronym", fields)); + assertEquals(p.getTitle().getValue(), getValueAsString("title", fields)); + assertEquals( + p.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); + assertEquals( + p.getCollectedfrom().get(0).getValue(), + getValueAsString("collectedfromname", fields)); + } - @Test - public void testProcessOrganization() throws Exception { - final List fields = prepareMocks("organizations_resultset_entry.json"); + @Test + public void testProcessOrganization() throws Exception { + final List fields = prepareMocks("organizations_resultset_entry.json"); - final List list = app.processOrganization(rs); + final List list = app.processOrganization(rs); - assertEquals(1, list.size()); + assertEquals(1, list.size()); - verifyMocks(fields); + verifyMocks(fields); - final Organization o = (Organization) list.get(0); - assertValidId(o.getId()); - assertEquals(o.getLegalshortname().getValue(), getValueAsString("legalshortname", fields)); - assertEquals(o.getLegalname().getValue(), getValueAsString("legalname", fields)); - assertEquals(o.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); - assertEquals(o.getCountry().getClassid(), getValueAsString("country", fields).split("@@@")[0]); - assertEquals(o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[1]); - assertEquals(o.getCountry().getSchemeid(), getValueAsString("country", fields).split("@@@")[2]); - assertEquals(o.getCountry().getSchemename(), getValueAsString("country", fields).split("@@@")[3]); - assertEquals(o.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); - assertEquals(o.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); - } + final Organization o = (Organization) list.get(0); + assertValidId(o.getId()); + assertEquals(o.getLegalshortname().getValue(), getValueAsString("legalshortname", fields)); + assertEquals(o.getLegalname().getValue(), getValueAsString("legalname", fields)); + assertEquals(o.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); + assertEquals( + o.getCountry().getClassid(), getValueAsString("country", fields).split("@@@")[0]); + assertEquals( + o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[1]); + assertEquals( + o.getCountry().getSchemeid(), getValueAsString("country", fields).split("@@@")[2]); + assertEquals( + o.getCountry().getSchemename(), + getValueAsString("country", fields).split("@@@")[3]); + assertEquals( + o.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); + assertEquals( + o.getCollectedfrom().get(0).getValue(), + getValueAsString("collectedfromname", fields)); + } - @Test - public void testProcessDatasourceOrganization() throws Exception { - final List fields = prepareMocks("datasourceorganization_resultset_entry.json"); + @Test + public void testProcessDatasourceOrganization() throws Exception { + final List fields = prepareMocks("datasourceorganization_resultset_entry.json"); - final List list = app.processDatasourceOrganization(rs); + final List list = app.processDatasourceOrganization(rs); - assertEquals(2, list.size()); - verifyMocks(fields); + assertEquals(2, list.size()); + verifyMocks(fields); - final Relation r1 = (Relation) list.get(0); - final Relation r2 = (Relation) list.get(1); - assertValidId(r1.getSource()); - assertValidId(r2.getSource()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - } + final Relation r1 = (Relation) list.get(0); + final Relation r2 = (Relation) list.get(1); + assertValidId(r1.getSource()); + assertValidId(r2.getSource()); + assertEquals(r1.getSource(), r2.getTarget()); + assertEquals(r2.getSource(), r1.getTarget()); + } - @Test - public void testProcessProjectOrganization() throws Exception { - final List fields = prepareMocks("projectorganization_resultset_entry.json"); + @Test + public void testProcessProjectOrganization() throws Exception { + final List fields = prepareMocks("projectorganization_resultset_entry.json"); - final List list = app.processProjectOrganization(rs); + final List list = app.processProjectOrganization(rs); - assertEquals(2, list.size()); - verifyMocks(fields); + assertEquals(2, list.size()); + verifyMocks(fields); - final Relation r1 = (Relation) list.get(0); - final Relation r2 = (Relation) list.get(1); - assertValidId(r1.getSource()); - assertValidId(r2.getSource()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - } + final Relation r1 = (Relation) list.get(0); + final Relation r2 = (Relation) list.get(1); + assertValidId(r1.getSource()); + assertValidId(r2.getSource()); + assertEquals(r1.getSource(), r2.getTarget()); + assertEquals(r2.getSource(), r1.getTarget()); + } - @Test - public void testProcessClaims_context() throws Exception { - final List fields = prepareMocks("claimscontext_resultset_entry.json"); + @Test + public void testProcessClaims_context() throws Exception { + final List fields = prepareMocks("claimscontext_resultset_entry.json"); - final List list = app.processClaims(rs); + final List list = app.processClaims(rs); - assertEquals(1, list.size()); - verifyMocks(fields); - } + assertEquals(1, list.size()); + verifyMocks(fields); + } - @Test - public void testProcessClaims_rels() throws Exception { - final List fields = prepareMocks("claimsrel_resultset_entry.json"); + @Test + public void testProcessClaims_rels() throws Exception { + final List fields = prepareMocks("claimsrel_resultset_entry.json"); - final List list = app.processClaims(rs); + final List list = app.processClaims(rs); - assertEquals(2, list.size()); - verifyMocks(fields); - } + assertEquals(2, list.size()); + verifyMocks(fields); + } - private List prepareMocks(final String jsonFile) throws IOException, SQLException { - final String json = IOUtils.toString(getClass().getResourceAsStream(jsonFile)); - final ObjectMapper mapper = new ObjectMapper(); - final List list = mapper.readValue(json, new TypeReference>() {}); + private List prepareMocks(final String jsonFile) throws IOException, SQLException { + final String json = IOUtils.toString(getClass().getResourceAsStream(jsonFile)); + final ObjectMapper mapper = new ObjectMapper(); + final List list = + mapper.readValue(json, new TypeReference>() {}); - for (final TypedField tf : list) { - if (tf.getValue() == null) { - switch (tf.getType()) { - case "not_used": - break; - case "boolean": - Mockito.when(rs.getBoolean(tf.getField())).thenReturn(false); - break; - case "date": - Mockito.when(rs.getDate(tf.getField())).thenReturn(null); - break; - case "int": - Mockito.when(rs.getInt(tf.getField())).thenReturn(0); - break; - case "double": - Mockito.when(rs.getDouble(tf.getField())).thenReturn(0.0); - break; - case "array": - Mockito.when(rs.getArray(tf.getField())).thenReturn(null); - break; - case "string": - default: - Mockito.when(rs.getString(tf.getField())).thenReturn(null); - break; - } - } else { - switch (tf.getType()) { - case "not_used": - break; - case "boolean": - Mockito.when(rs.getBoolean(tf.getField())).thenReturn(Boolean.parseBoolean(tf.getValue().toString())); - break; - case "date": - Mockito.when(rs.getDate(tf.getField())).thenReturn(Date.valueOf(tf.getValue().toString())); - break; - case "int": - Mockito.when(rs.getInt(tf.getField())).thenReturn(new Integer(tf.getValue().toString())); - break; - case "double": - Mockito.when(rs.getDouble(tf.getField())).thenReturn(new Double(tf.getValue().toString())); - break; - case "array": - final Array arr = Mockito.mock(Array.class); - final String[] values = ((List) tf.getValue()).stream() - .filter(Objects::nonNull) - .map(o -> o.toString()) - .toArray(String[]::new); + for (final TypedField tf : list) { + if (tf.getValue() == null) { + switch (tf.getType()) { + case "not_used": + break; + case "boolean": + Mockito.when(rs.getBoolean(tf.getField())).thenReturn(false); + break; + case "date": + Mockito.when(rs.getDate(tf.getField())).thenReturn(null); + break; + case "int": + Mockito.when(rs.getInt(tf.getField())).thenReturn(0); + break; + case "double": + Mockito.when(rs.getDouble(tf.getField())).thenReturn(0.0); + break; + case "array": + Mockito.when(rs.getArray(tf.getField())).thenReturn(null); + break; + case "string": + default: + Mockito.when(rs.getString(tf.getField())).thenReturn(null); + break; + } + } else { + switch (tf.getType()) { + case "not_used": + break; + case "boolean": + Mockito.when(rs.getBoolean(tf.getField())) + .thenReturn(Boolean.parseBoolean(tf.getValue().toString())); + break; + case "date": + Mockito.when(rs.getDate(tf.getField())) + .thenReturn(Date.valueOf(tf.getValue().toString())); + break; + case "int": + Mockito.when(rs.getInt(tf.getField())) + .thenReturn(new Integer(tf.getValue().toString())); + break; + case "double": + Mockito.when(rs.getDouble(tf.getField())) + .thenReturn(new Double(tf.getValue().toString())); + break; + case "array": + final Array arr = Mockito.mock(Array.class); + final String[] values = + ((List) tf.getValue()) + .stream() + .filter(Objects::nonNull) + .map(o -> o.toString()) + .toArray(String[]::new); - Mockito.when(arr.getArray()).thenReturn(values); - Mockito.when(rs.getArray(tf.getField())).thenReturn(arr); - break; - case "string": - default: - Mockito.when(rs.getString(tf.getField())).thenReturn(tf.getValue().toString()); - break; - } - } - } + Mockito.when(arr.getArray()).thenReturn(values); + Mockito.when(rs.getArray(tf.getField())).thenReturn(arr); + break; + case "string": + default: + Mockito.when(rs.getString(tf.getField())) + .thenReturn(tf.getValue().toString()); + break; + } + } + } - return list; - } + return list; + } - private void verifyMocks(final List list) throws SQLException { - for (final TypedField tf : list) { + private void verifyMocks(final List list) throws SQLException { + for (final TypedField tf : list) { - switch (tf.getType()) { - case "not_used": - break; - case "boolean": - Mockito.verify(rs, Mockito.atLeastOnce()).getBoolean(tf.getField()); - break; - case "date": - Mockito.verify(rs, Mockito.atLeastOnce()).getDate(tf.getField()); - break; - case "int": - Mockito.verify(rs, Mockito.atLeastOnce()).getInt(tf.getField()); - break; - case "double": - Mockito.verify(rs, Mockito.atLeastOnce()).getDouble(tf.getField()); - break; - case "array": - Mockito.verify(rs, Mockito.atLeastOnce()).getArray(tf.getField()); - break; - case "string": - default: - Mockito.verify(rs, Mockito.atLeastOnce()).getString(tf.getField()); - break; - } - } - } + switch (tf.getType()) { + case "not_used": + break; + case "boolean": + Mockito.verify(rs, Mockito.atLeastOnce()).getBoolean(tf.getField()); + break; + case "date": + Mockito.verify(rs, Mockito.atLeastOnce()).getDate(tf.getField()); + break; + case "int": + Mockito.verify(rs, Mockito.atLeastOnce()).getInt(tf.getField()); + break; + case "double": + Mockito.verify(rs, Mockito.atLeastOnce()).getDouble(tf.getField()); + break; + case "array": + Mockito.verify(rs, Mockito.atLeastOnce()).getArray(tf.getField()); + break; + case "string": + default: + Mockito.verify(rs, Mockito.atLeastOnce()).getString(tf.getField()); + break; + } + } + } - private void assertValidId(final String id) { - assertEquals(49, id.length()); - assertEquals('|', id.charAt(2)); - assertEquals(':', id.charAt(15)); - assertEquals(':', id.charAt(16)); - } + private void assertValidId(final String id) { + assertEquals(49, id.length()); + assertEquals('|', id.charAt(2)); + assertEquals(':', id.charAt(15)); + assertEquals(':', id.charAt(16)); + } - private String getValueAsString(final String name, final List fields) { - return fields.stream() - .filter(f -> f.getField().equals(name)) - .map(TypedField::getValue) - .filter(Objects::nonNull) - .map(o -> o.toString()) - .findFirst() - .get(); - } + private String getValueAsString(final String name, final List fields) { + return fields.stream() + .filter(f -> f.getField().equals(name)) + .map(TypedField::getValue) + .filter(Objects::nonNull) + .map(o -> o.toString()) + .findFirst() + .get(); + } } class TypedField { - private String field; - private String type; - private Object value; + private String field; + private String type; + private Object value; - public String getField() { - return field; - } + public String getField() { + return field; + } - public void setField(final String field) { - this.field = field; - } + public void setField(final String field) { + this.field = field; + } - public String getType() { - return type; - } + public String getType() { + return type; + } - public void setType(final String type) { - this.type = type; - } + public void setType(final String type) { + this.type = type; + } - public Object getValue() { - return value; - } - - public void setValue(final Object value) { - this.value = value; - } + public Object getValue() { + return value; + } + public void setValue(final Object value) { + this.value = value; + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/ScholexplorerParserTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/ScholexplorerParserTest.java index 5741dd628e..eb7a25a75e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/ScholexplorerParserTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/ScholexplorerParserTest.java @@ -3,17 +3,15 @@ package eu.dnetlib.dhp.sx.graph; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.SerializationFeature; -import eu.dnetlib.dhp.sx.graph.parser.DatasetScholexplorerParser; import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.sx.graph.parser.DatasetScholexplorerParser; import eu.dnetlib.scholexplorer.relation.RelationMapper; +import java.util.List; import org.apache.commons.io.IOUtils; import org.junit.jupiter.api.Test; -import java.util.List; - public class ScholexplorerParserTest { - @Test public void testDataciteParser() throws Exception { String xml = IOUtils.toString(this.getClass().getResourceAsStream("dmf.xml")); @@ -24,15 +22,14 @@ public class ScholexplorerParserTest { ObjectMapper m = new ObjectMapper(); m.enable(SerializationFeature.INDENT_OUTPUT); + oaves.forEach( + oaf -> { + try { + System.out.println(m.writeValueAsString(oaf)); + System.out.println("----------------------------"); + } catch (JsonProcessingException e) { - oaves.forEach(oaf -> { - try { - System.out.println(m.writeValueAsString(oaf)); - System.out.println("----------------------------"); - } catch (JsonProcessingException e) { - - } - }); - + } + }); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerGraphImporterTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerGraphImporterTest.java index 4c4d5372cc..7f32de3188 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerGraphImporterTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerGraphImporterTest.java @@ -1,11 +1,3 @@ package eu.dnetlib.dhp.sx.graph; - - - -public class SparkScholexplorerGraphImporterTest { - - - - -} +public class SparkScholexplorerGraphImporterTest {} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerMergeEntitiesJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerMergeEntitiesJobTest.java index f080b36cbd..af63858031 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerMergeEntitiesJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerMergeEntitiesJobTest.java @@ -1,8 +1,3 @@ package eu.dnetlib.dhp.sx.graph; - - -public class SparkScholexplorerMergeEntitiesJobTest { - - -} +public class SparkScholexplorerMergeEntitiesJobTest {} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/ProvisionUtil.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/ProvisionUtil.java index aed4446604..6d1609e253 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/ProvisionUtil.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/ProvisionUtil.java @@ -6,25 +6,25 @@ import org.apache.commons.lang3.StringUtils; public class ProvisionUtil { - public final static String deletedByInferenceJPATH = "$.dataInfo.deletedbyinference"; - public final static String TARGETJSONPATH = "$.target"; - public final static String SOURCEJSONPATH = "$.source"; + public static final String deletedByInferenceJPATH = "$.dataInfo.deletedbyinference"; + public static final String TARGETJSONPATH = "$.target"; + public static final String SOURCEJSONPATH = "$.source"; -// public static RelatedItemInfo getItemType(final String item, final String idPath) { -// String targetId = DHPUtils.getJPathString(idPath, item); -// switch (StringUtils.substringBefore(targetId, "|")) { -// case "50": -// return new RelatedItemInfo(null,0,1,0); -// case "60": -// return new RelatedItemInfo(null,1,0,0); -// case "70": -// return new RelatedItemInfo(null,0,0,1); -// default: -// throw new RuntimeException("Unknonw target ID"); -// -// } -// -// } + // public static RelatedItemInfo getItemType(final String item, final String idPath) { + // String targetId = DHPUtils.getJPathString(idPath, item); + // switch (StringUtils.substringBefore(targetId, "|")) { + // case "50": + // return new RelatedItemInfo(null,0,1,0); + // case "60": + // return new RelatedItemInfo(null,1,0,0); + // case "70": + // return new RelatedItemInfo(null,0,0,1); + // default: + // throw new RuntimeException("Unknonw target ID"); + // + // } + // + // } public static Boolean isNotDeleted(final String item) { return !"true".equalsIgnoreCase(DHPUtils.getJPathString(deletedByInferenceJPATH, item)); @@ -41,7 +41,6 @@ public class ProvisionUtil { return Typology.unknown; default: throw new RuntimeException("Unknonw ID type"); - } } } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/RelatedItemInfo.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/RelatedItemInfo.java index 3b07aab8d0..145ee5b394 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/RelatedItemInfo.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/RelatedItemInfo.java @@ -2,10 +2,7 @@ package eu.dnetlib.dhp.provision; import java.io.Serializable; -/** - * This class models the information of related items - */ - +/** This class models the information of related items */ public class RelatedItemInfo implements Serializable { private String source; @@ -16,10 +13,10 @@ public class RelatedItemInfo implements Serializable { private long relatedUnknown = 0; - public RelatedItemInfo() { - } + public RelatedItemInfo() {} - public RelatedItemInfo(String source, long relatedDataset, long relatedPublication, long relatedUnknown) { + public RelatedItemInfo( + String source, long relatedDataset, long relatedPublication, long relatedUnknown) { this.source = source; this.relatedDataset = relatedDataset; this.relatedPublication = relatedPublication; diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkExtractRelationCount.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkExtractRelationCount.java index 2c96427940..90bde451b0 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkExtractRelationCount.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkExtractRelationCount.java @@ -1,57 +1,32 @@ package eu.dnetlib.dhp.provision; -import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.utils.DHPUtils; import org.apache.commons.io.IOUtils; -import org.apache.hadoop.io.compress.GzipCodec; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.Function2; -import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.*; -import org.apache.spark.sql.catalyst.expressions.Expression; -import scala.Tuple2; - -import java.util.Arrays; -import java.util.HashMap; -import java.util.Map; - /** - * SparkExtractRelationCount is a spark job that takes in input relation RDD - * and retrieve for each item in relation which are the number of - * - Related Dataset - * - Related Publication - * - Related Unknown + * SparkExtractRelationCount is a spark job that takes in input relation RDD and retrieve for each + * item in relation which are the number of - Related Dataset - Related Publication - Related + * Unknown */ public class SparkExtractRelationCount { - - - - public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkExtractRelationCount.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_related_entities_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkExtractRelationCount.class.getResourceAsStream( + "/eu/dnetlib/dhp/provision/input_related_entities_parameters.json"))); parser.parseArgument(args); - final SparkSession spark = SparkSession - .builder() - .appName(SparkExtractRelationCount.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); - + final SparkSession spark = + SparkSession.builder() + .appName(SparkExtractRelationCount.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); final String workingDirPath = parser.get("workingDirPath"); final String relationPath = parser.get("relationPath"); - DatasetJoiner.startJoin(spark, relationPath,workingDirPath + "/relatedItemCount"); - + DatasetJoiner.startJoin(spark, relationPath, workingDirPath + "/relatedItemCount"); } - - - - - - - } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholix.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholix.java index 58a98e4903..989e1877a8 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholix.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholix.java @@ -18,67 +18,94 @@ import scala.Tuple2; public class SparkGenerateScholix { - public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkGenerateScholix.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkGenerateScholix.class.getResourceAsStream( + "/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json"))); parser.parseArgument(args); SparkConf conf = new SparkConf(); - conf.set("spark.sql.shuffle.partitions","4000"); + conf.set("spark.sql.shuffle.partitions", "4000"); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - final SparkSession spark = SparkSession - .builder() - .config(conf) - .appName(SparkExtractRelationCount.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); - - conf.registerKryoClasses(new Class[]{ - Scholix.class, - ScholixCollectedFrom.class, - ScholixEntityId.class, - ScholixIdentifier.class, - ScholixRelationship.class, - ScholixResource.class - }); - + final SparkSession spark = + SparkSession.builder() + .config(conf) + .appName(SparkExtractRelationCount.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); + conf.registerKryoClasses( + new Class[] { + Scholix.class, + ScholixCollectedFrom.class, + ScholixEntityId.class, + ScholixIdentifier.class, + ScholixRelationship.class, + ScholixResource.class + }); final String graphPath = parser.get("graphPath"); final String workingDirPath = parser.get("workingDirPath"); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - final Dataset scholixSummary = spark.read().load(workingDirPath + "/summary").as(Encoders.bean(ScholixSummary.class)); - final Dataset rels = spark.read().load(graphPath + "/relation").as(Encoders.bean(Relation.class)); + final Dataset scholixSummary = + spark.read() + .load(workingDirPath + "/summary") + .as(Encoders.bean(ScholixSummary.class)); + final Dataset rels = + spark.read().load(graphPath + "/relation").as(Encoders.bean(Relation.class)); + Dataset firstJoin = + scholixSummary + .joinWith(rels, scholixSummary.col("id").equalTo(rels.col("source"))) + .map( + (MapFunction, Scholix>) + f -> Scholix.generateScholixWithSource(f._1(), f._2()), + Encoders.bean(Scholix.class)); - Dataset firstJoin = scholixSummary.joinWith(rels, scholixSummary.col("id").equalTo(rels.col("source"))) - .map((MapFunction, Scholix>) f -> Scholix.generateScholixWithSource(f._1(), f._2()), Encoders.bean(Scholix.class)); + firstJoin.write().mode(SaveMode.Overwrite).save(workingDirPath + "/scholix_1"); - firstJoin.write().mode(SaveMode.Overwrite).save(workingDirPath+"/scholix_1"); - - Dataset scholix_final = spark.read().load(workingDirPath+"/scholix_1").as(Encoders.bean(Scholix.class)); + Dataset scholix_final = + spark.read().load(workingDirPath + "/scholix_1").as(Encoders.bean(Scholix.class)); scholixSummary - .map((MapFunction) ScholixResource::fromSummary, Encoders.bean(ScholixResource.class)) + .map( + (MapFunction) ScholixResource::fromSummary, + Encoders.bean(ScholixResource.class)) .repartition(1000) .write() .mode(SaveMode.Overwrite) - .save(workingDirPath+"/scholix_target"); + .save(workingDirPath + "/scholix_target"); - Dataset target = spark.read().load(workingDirPath+"/scholix_target").as(Encoders.bean(ScholixResource.class)); + Dataset target = + spark.read() + .load(workingDirPath + "/scholix_target") + .as(Encoders.bean(ScholixResource.class)); - scholix_final.joinWith(target, scholix_final.col("identifier").equalTo(target.col("dnetIdentifier")), "inner") - .map((MapFunction, Scholix>) f -> { - final Scholix scholix = f._1(); - final ScholixResource scholixTarget = f._2(); - scholix.setTarget(scholixTarget); - scholix.generateIdentifier(); - scholix.generatelinkPublisher(); - return scholix; - }, Encoders.kryo(Scholix.class)).javaRDD().map(s-> { - ObjectMapper mapper = new ObjectMapper(); - return mapper.writeValueAsString(s); - }).saveAsTextFile(workingDirPath+"/scholix_json", GzipCodec.class); + scholix_final + .joinWith( + target, + scholix_final.col("identifier").equalTo(target.col("dnetIdentifier")), + "inner") + .map( + (MapFunction, Scholix>) + f -> { + final Scholix scholix = f._1(); + final ScholixResource scholixTarget = f._2(); + scholix.setTarget(scholixTarget); + scholix.generateIdentifier(); + scholix.generatelinkPublisher(); + return scholix; + }, + Encoders.kryo(Scholix.class)) + .javaRDD() + .map( + s -> { + ObjectMapper mapper = new ObjectMapper(); + return mapper.writeValueAsString(s); + }) + .saveAsTextFile(workingDirPath + "/scholix_json", GzipCodec.class); } } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateSummary.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateSummary.java index 39b7a9468e..ea7599788b 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateSummary.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateSummary.java @@ -1,17 +1,11 @@ package eu.dnetlib.dhp.provision; -import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary; import eu.dnetlib.dhp.utils.DHPUtils; import org.apache.commons.io.IOUtils; -import org.apache.hadoop.io.compress.GzipCodec; -import org.apache.spark.api.java.JavaPairRDD; -import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.Function; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; @@ -21,68 +15,99 @@ public class SparkGenerateSummary { private static final String jsonIDPath = "$.id"; - public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkGenerateSummary.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkGenerateSummary.class.getResourceAsStream( + "/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json"))); parser.parseArgument(args); - final SparkSession spark = SparkSession - .builder() - .appName(SparkExtractRelationCount.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); - + final SparkSession spark = + SparkSession.builder() + .appName(SparkExtractRelationCount.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); final String graphPath = parser.get("graphPath"); final String workingDirPath = parser.get("workingDirPath"); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - Dataset rInfo = spark.read().load(workingDirPath + "/relatedItemCount").as(Encoders.bean(RelatedItemInfo.class)); + Dataset rInfo = + spark.read() + .load(workingDirPath + "/relatedItemCount") + .as(Encoders.bean(RelatedItemInfo.class)); + Dataset entity = + spark.createDataset( + sc.textFile( + graphPath + + "/publication," + + graphPath + + "/dataset," + + graphPath + + "/unknown") + .map( + s -> + ScholixSummary.fromJsonOAF( + ProvisionUtil.getItemTypeFromId( + DHPUtils.getJPathString( + jsonIDPath, s)), + s)) + .rdd(), + Encoders.bean(ScholixSummary.class)); - Dataset entity = spark.createDataset(sc.textFile(graphPath + "/publication," + graphPath + "/dataset," + graphPath + "/unknown") - .map(s -> - ScholixSummary.fromJsonOAF(ProvisionUtil.getItemTypeFromId(DHPUtils.getJPathString(jsonIDPath, s)), s) + Dataset summaryComplete = + rInfo.joinWith(entity, rInfo.col("source").equalTo(entity.col("id"))) + .map( + (MapFunction< + Tuple2, + ScholixSummary>) + t -> { + ScholixSummary scholixSummary = t._2(); + RelatedItemInfo relatedItemInfo = t._1(); + scholixSummary.setRelatedDatasets( + relatedItemInfo.getRelatedDataset()); + scholixSummary.setRelatedPublications( + relatedItemInfo.getRelatedPublication()); + scholixSummary.setRelatedUnknown( + relatedItemInfo.getRelatedUnknown()); + return scholixSummary; + }, + Encoders.bean(ScholixSummary.class)); + summaryComplete.write().save(workingDirPath + "/summary"); - ).rdd(), Encoders.bean(ScholixSummary.class)); - - - Dataset summaryComplete = rInfo.joinWith(entity, rInfo.col("source").equalTo(entity.col("id"))).map((MapFunction, ScholixSummary>) t -> - { - ScholixSummary scholixSummary = t._2(); - RelatedItemInfo relatedItemInfo = t._1(); - scholixSummary.setRelatedDatasets(relatedItemInfo.getRelatedDataset()); - scholixSummary.setRelatedPublications(relatedItemInfo.getRelatedPublication()); - scholixSummary.setRelatedUnknown(relatedItemInfo.getRelatedUnknown()); - return scholixSummary; - }, Encoders.bean(ScholixSummary.class) - ); - - summaryComplete.write().save(workingDirPath+"/summary"); - - -// JavaPairRDD relationCount = sc.textFile(workingDirPath+"/relatedItemCount").mapToPair((PairFunction) i -> new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i)); -// -// JavaPairRDD entities = -// sc.textFile(graphPath + "/publication") -// .filter(ProvisionUtil::isNotDeleted) -// .mapToPair((PairFunction) i -> new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i)) -// .union( -// sc.textFile(graphPath + "/dataset") -// .filter(ProvisionUtil::isNotDeleted) -// .mapToPair((PairFunction) i -> new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i)) -// ) -// .union( -// sc.textFile(graphPath + "/unknown") -// .filter(ProvisionUtil::isNotDeleted) -// .mapToPair((PairFunction) i -> new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i)) -// ); -// entities.join(relationCount).map((Function>, String>) k -> -// ScholixSummary.fromJsonOAF(ProvisionUtil.getItemTypeFromId(k._1()), k._2()._1(), k._2()._2())).saveAsTextFile(workingDirPath+"/summary", GzipCodec.class); -// -// -// ; + // JavaPairRDD relationCount = + // sc.textFile(workingDirPath+"/relatedItemCount").mapToPair((PairFunction) i -> new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i)); + // + // JavaPairRDD entities = + // sc.textFile(graphPath + "/publication") + // .filter(ProvisionUtil::isNotDeleted) + // .mapToPair((PairFunction) i -> new + // Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i)) + // .union( + // sc.textFile(graphPath + "/dataset") + // .filter(ProvisionUtil::isNotDeleted) + // .mapToPair((PairFunction) + // i -> + // new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i)) + // ) + // .union( + // sc.textFile(graphPath + "/unknown") + // .filter(ProvisionUtil::isNotDeleted) + // .mapToPair((PairFunction) + // i -> + // new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i)) + // ); + // entities.join(relationCount).map((Function>, + // String>) k -> + // ScholixSummary.fromJsonOAF(ProvisionUtil.getItemTypeFromId(k._1()), + // k._2()._1(), k._2()._2())).saveAsTextFile(workingDirPath+"/summary", GzipCodec.class); + // + // + // ; } } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java index ce3c6315c1..d597f42a4b 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java @@ -2,34 +2,35 @@ package eu.dnetlib.dhp.provision; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.provision.scholix.Scholix; import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary; +import java.util.HashMap; +import java.util.Map; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.elasticsearch.spark.rdd.api.java.JavaEsSpark; -import java.nio.file.attribute.AclFileAttributeView; -import java.util.HashMap; -import java.util.Map; - public class SparkIndexCollectionOnES { - public static void main(String[] args) throws Exception{ + public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkIndexCollectionOnES.class.getResourceAsStream("/eu/dnetlib/dhp/provision/index_on_es.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkIndexCollectionOnES.class.getResourceAsStream( + "/eu/dnetlib/dhp/provision/index_on_es.json"))); parser.parseArgument(args); - SparkConf conf = new SparkConf().setAppName(SparkIndexCollectionOnES.class.getSimpleName()) - .setMaster(parser.get("master")); - - conf.set("spark.sql.shuffle.partitions","4000"); + SparkConf conf = + new SparkConf() + .setAppName(SparkIndexCollectionOnES.class.getSimpleName()) + .setMaster(parser.get("master")); + conf.set("spark.sql.shuffle.partitions", "4000"); final String sourcePath = parser.get("sourcePath"); final String index = parser.get("index"); @@ -38,20 +39,24 @@ public class SparkIndexCollectionOnES { final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); JavaRDD inputRdd; - - if("summary".equalsIgnoreCase(type)) - inputRdd = spark.read().load(sourcePath).as(Encoders.bean(ScholixSummary.class)).map((MapFunction) f -> { - final ObjectMapper mapper = new ObjectMapper(); - return mapper.writeValueAsString(f); - }, Encoders.STRING()).javaRDD(); - - else - inputRdd = sc.textFile(sourcePath); + if ("summary".equalsIgnoreCase(type)) + inputRdd = + spark.read() + .load(sourcePath) + .as(Encoders.bean(ScholixSummary.class)) + .map( + (MapFunction) + f -> { + final ObjectMapper mapper = new ObjectMapper(); + return mapper.writeValueAsString(f); + }, + Encoders.STRING()) + .javaRDD(); + else inputRdd = sc.textFile(sourcePath); Map esCfg = new HashMap<>(); esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54"); @@ -60,7 +65,6 @@ public class SparkIndexCollectionOnES { esCfg.put("es.batch.write.retry.wait", "60s"); esCfg.put("es.batch.size.entries", "200"); esCfg.put("es.nodes.wan.only", "true"); - JavaEsSpark.saveJsonToEs(inputRdd,index, esCfg); - + JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); } } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/Scholix.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/Scholix.java index c3ccf6899e..d10cfcabdc 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/Scholix.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/Scholix.java @@ -23,7 +23,6 @@ public class Scholix implements Serializable { private String identifier; - public Scholix clone(final ScholixResource t) { final Scholix clone = new Scholix(); clone.setPublicationDate(publicationDate); @@ -34,70 +33,100 @@ public class Scholix implements Serializable { clone.setTarget(t); clone.generatelinkPublisher(); clone.generateIdentifier(); - return clone; + return clone; } - - public static Scholix generateScholixWithSource(final String sourceSummaryJson, final String relation) { + public static Scholix generateScholixWithSource( + final String sourceSummaryJson, final String relation) { final ObjectMapper mapper = new ObjectMapper(); try { - ScholixSummary scholixSummary = mapper.readValue(sourceSummaryJson, ScholixSummary.class); + ScholixSummary scholixSummary = + mapper.readValue(sourceSummaryJson, ScholixSummary.class); Relation rel = mapper.readValue(relation, Relation.class); final Scholix s = new Scholix(); - if (scholixSummary.getDate() != null && scholixSummary.getDate().size()>0) + if (scholixSummary.getDate() != null && scholixSummary.getDate().size() > 0) s.setPublicationDate(scholixSummary.getDate().get(0)); - s.setLinkprovider(rel.getCollectedFrom().stream().map(cf -> - new ScholixEntityId(cf.getValue(), Collections.singletonList( - new ScholixIdentifier(cf.getKey(), "dnet_identifier") - ))).collect(Collectors.toList())); - s.setRelationship(new ScholixRelationship(rel.getRelType(),rel.getRelClass(),null )); + s.setLinkprovider( + rel.getCollectedFrom().stream() + .map( + cf -> + new ScholixEntityId( + cf.getValue(), + Collections.singletonList( + new ScholixIdentifier( + cf.getKey(), + "dnet_identifier")))) + .collect(Collectors.toList())); + s.setRelationship(new ScholixRelationship(rel.getRelType(), rel.getRelClass(), null)); s.setSource(ScholixResource.fromSummary(scholixSummary)); return s; } catch (Throwable e) { - throw new RuntimeException(String.format("Summary: %s \n relation:%s",sourceSummaryJson, relation), e); + throw new RuntimeException( + String.format("Summary: %s \n relation:%s", sourceSummaryJson, relation), e); } } - public static Scholix generateScholixWithSource(final ScholixSummary scholixSummary, final Relation rel) { + public static Scholix generateScholixWithSource( + final ScholixSummary scholixSummary, final Relation rel) { final Scholix s = new Scholix(); - if (scholixSummary.getDate() != null && scholixSummary.getDate().size()>0) + if (scholixSummary.getDate() != null && scholixSummary.getDate().size() > 0) s.setPublicationDate(scholixSummary.getDate().get(0)); - s.setLinkprovider(rel.getCollectedFrom().stream().map(cf -> - new ScholixEntityId(cf.getValue(), Collections.singletonList( - new ScholixIdentifier(cf.getKey(), "dnet_identifier") - ))).collect(Collectors.toList())); - s.setRelationship(new ScholixRelationship(rel.getRelType(),rel.getRelClass(),null )); + s.setLinkprovider( + rel.getCollectedFrom().stream() + .map( + cf -> + new ScholixEntityId( + cf.getValue(), + Collections.singletonList( + new ScholixIdentifier( + cf.getKey(), "dnet_identifier")))) + .collect(Collectors.toList())); + s.setRelationship(new ScholixRelationship(rel.getRelType(), rel.getRelClass(), null)); s.setSource(ScholixResource.fromSummary(scholixSummary)); s.setIdentifier(rel.getTarget()); -// ScholixResource mockTarget = new ScholixResource(); -// mockTarget.setDnetIdentifier(rel.getTarget()); -// s.setTarget(mockTarget); -// s.generateIdentifier(); + // ScholixResource mockTarget = new ScholixResource(); + // mockTarget.setDnetIdentifier(rel.getTarget()); + // s.setTarget(mockTarget); + // s.generateIdentifier(); return s; } - public void generatelinkPublisher() { Set publisher = new HashSet<>(); if (source.getPublisher() != null) - publisher.addAll(source.getPublisher().stream().map(ScholixEntityId::getName).collect(Collectors.toList())); + publisher.addAll( + source.getPublisher().stream() + .map(ScholixEntityId::getName) + .collect(Collectors.toList())); if (target.getPublisher() != null) - publisher.addAll(target.getPublisher().stream().map(ScholixEntityId::getName).collect(Collectors.toList())); - this.publisher = publisher.stream().map(k -> new ScholixEntityId(k ,null)).collect(Collectors.toList()); + publisher.addAll( + target.getPublisher().stream() + .map(ScholixEntityId::getName) + .collect(Collectors.toList())); + this.publisher = + publisher.stream() + .map(k -> new ScholixEntityId(k, null)) + .collect(Collectors.toList()); } - public void generateIdentifier( ) { - setIdentifier(DHPUtils.md5(String.format("%s::%s::%s",source.getDnetIdentifier(),relationship.getName(), target.getDnetIdentifier()))); - + public void generateIdentifier() { + setIdentifier( + DHPUtils.md5( + String.format( + "%s::%s::%s", + source.getDnetIdentifier(), + relationship.getName(), + target.getDnetIdentifier()))); } public Scholix addTarget(final String targetSummaryJson) { final ObjectMapper mapper = new ObjectMapper(); try { - ScholixSummary targetSummary = mapper.readValue(targetSummaryJson, ScholixSummary.class); + ScholixSummary targetSummary = + mapper.readValue(targetSummaryJson, ScholixSummary.class); setTarget(ScholixResource.fromSummary(targetSummary)); generateIdentifier(); return this; @@ -157,6 +186,7 @@ public class Scholix implements Serializable { public String getIdentifier() { return identifier; } + public void setIdentifier(String identifier) { this.identifier = identifier; } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixCollectedFrom.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixCollectedFrom.java index 2ba84188da..d3278268ab 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixCollectedFrom.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixCollectedFrom.java @@ -8,10 +8,10 @@ public class ScholixCollectedFrom implements Serializable { private String provisionMode; private String completionStatus; - public ScholixCollectedFrom() { - } + public ScholixCollectedFrom() {} - public ScholixCollectedFrom(ScholixEntityId provider, String provisionMode, String completionStatus) { + public ScholixCollectedFrom( + ScholixEntityId provider, String provisionMode, String completionStatus) { this.provider = provider; this.provisionMode = provisionMode; this.completionStatus = completionStatus; diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixEntityId.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixEntityId.java index 0f43a8d44a..3b0f0f29ec 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixEntityId.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixEntityId.java @@ -7,8 +7,7 @@ public class ScholixEntityId implements Serializable { private String name; private List identifiers; - public ScholixEntityId() { - } + public ScholixEntityId() {} public ScholixEntityId(String name, List identifiers) { this.name = name; diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixIdentifier.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixIdentifier.java index f354ef10a2..9ad4fd7520 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixIdentifier.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixIdentifier.java @@ -6,8 +6,7 @@ public class ScholixIdentifier implements Serializable { private String identifier; private String schema; - public ScholixIdentifier() { - } + public ScholixIdentifier() {} public ScholixIdentifier(String identifier, String schema) { this.identifier = identifier; diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixRelationship.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixRelationship.java index 1a35038b9a..77cdbc7644 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixRelationship.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixRelationship.java @@ -7,8 +7,7 @@ public class ScholixRelationship implements Serializable { private String schema; private String inverse; - public ScholixRelationship() { - } + public ScholixRelationship() {} public ScholixRelationship(String name, String schema, String inverse) { this.name = name; diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixResource.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixResource.java index f29722eb8b..d3ed3a4a44 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixResource.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixResource.java @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.provision.scholix; import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary; - import java.io.Serializable; import java.util.Collections; import java.util.List; @@ -25,42 +24,47 @@ public class ScholixResource implements Serializable { resource.setDnetIdentifier(summary.getId()); - resource.setIdentifier(summary.getLocalIdentifier().stream() - .map(i -> - new ScholixIdentifier(i.getId(), i.getType())) - .collect(Collectors.toList())); + resource.setIdentifier( + summary.getLocalIdentifier().stream() + .map(i -> new ScholixIdentifier(i.getId(), i.getType())) + .collect(Collectors.toList())); resource.setObjectType(summary.getTypology().toString()); - if (summary.getTitle() != null && summary.getTitle().size() > 0) resource.setTitle(summary.getTitle().get(0)); if (summary.getAuthor() != null) - resource.setCreator(summary.getAuthor().stream() - .map(c -> new ScholixEntityId(c, null)) - .collect(Collectors.toList()) - ); + resource.setCreator( + summary.getAuthor().stream() + .map(c -> new ScholixEntityId(c, null)) + .collect(Collectors.toList())); if (summary.getDate() != null && summary.getDate().size() > 0) resource.setPublicationDate(summary.getDate().get(0)); if (summary.getPublisher() != null) - resource.setPublisher(summary.getPublisher().stream() - .map(p -> new ScholixEntityId(p, null)) - .collect(Collectors.toList()) - ); + resource.setPublisher( + summary.getPublisher().stream() + .map(p -> new ScholixEntityId(p, null)) + .collect(Collectors.toList())); if (summary.getDatasources() != null) - resource.setCollectedFrom(summary.getDatasources().stream() - .map(d -> - new ScholixCollectedFrom(new ScholixEntityId(d.getDatasourceName(), - Collections.singletonList(new ScholixIdentifier(d.getDatasourceId(), "dnet_identifier")) - ), "collected", d.getCompletionStatus())) - .collect(Collectors.toList())); + resource.setCollectedFrom( + summary.getDatasources().stream() + .map( + d -> + new ScholixCollectedFrom( + new ScholixEntityId( + d.getDatasourceName(), + Collections.singletonList( + new ScholixIdentifier( + d.getDatasourceId(), + "dnet_identifier"))), + "collected", + d.getCompletionStatus())) + .collect(Collectors.toList())); return resource; - } - public List getIdentifier() { return identifier; } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/CollectedFromType.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/CollectedFromType.java index 6fc0c7b293..045b85a028 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/CollectedFromType.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/CollectedFromType.java @@ -8,9 +8,7 @@ public class CollectedFromType implements Serializable { private String datasourceId; private String completionStatus; - - public CollectedFromType() { - } + public CollectedFromType() {} public CollectedFromType(String datasourceName, String datasourceId, String completionStatus) { this.datasourceName = datasourceName; diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/SchemeValue.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/SchemeValue.java index 95a292b9df..807a1d38f4 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/SchemeValue.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/SchemeValue.java @@ -6,9 +6,7 @@ public class SchemeValue implements Serializable { private String scheme; private String value; - public SchemeValue() { - - } + public SchemeValue() {} public SchemeValue(String scheme, String value) { this.scheme = scheme; diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/ScholixSummary.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/ScholixSummary.java index 26538d1569..676ae8cae4 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/ScholixSummary.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/ScholixSummary.java @@ -9,7 +9,6 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset; import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication; import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown; - import java.io.Serializable; import java.util.Collections; import java.util.List; @@ -30,7 +29,6 @@ public class ScholixSummary implements Serializable { private long relatedUnknown; private List datasources; - public String getId() { return id; } @@ -137,7 +135,6 @@ public class ScholixSummary implements Serializable { this.datasources = datasources; } - public static ScholixSummary fromJsonOAF(final Typology oafType, final String oafJson) { try { final ObjectMapper mapper = new ObjectMapper(); @@ -145,11 +142,14 @@ public class ScholixSummary implements Serializable { mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); switch (oafType) { case dataset: - return summaryFromDataset(mapper.readValue(oafJson, DLIDataset.class), relatedItemInfo); + return summaryFromDataset( + mapper.readValue(oafJson, DLIDataset.class), relatedItemInfo); case publication: - return summaryFromPublication(mapper.readValue(oafJson, DLIPublication.class), relatedItemInfo); + return summaryFromPublication( + mapper.readValue(oafJson, DLIPublication.class), relatedItemInfo); case unknown: - return summaryFromUnknown(mapper.readValue(oafJson, DLIUnknown.class), relatedItemInfo); + return summaryFromUnknown( + mapper.readValue(oafJson, DLIUnknown.class), relatedItemInfo); } } catch (Throwable e) { throw new RuntimeException(e); @@ -157,23 +157,31 @@ public class ScholixSummary implements Serializable { return null; } - public static String fromJsonOAF(final Typology oafType, final String oafJson, final String relEntityJson) { + public static String fromJsonOAF( + final Typology oafType, final String oafJson, final String relEntityJson) { try { final ObjectMapper mapper = new ObjectMapper(); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - RelatedItemInfo relatedItemInfo = mapper.readValue(relEntityJson, RelatedItemInfo.class); + RelatedItemInfo relatedItemInfo = + mapper.readValue(relEntityJson, RelatedItemInfo.class); switch (oafType) { case dataset: - return mapper.writeValueAsString(summaryFromDataset(mapper.readValue(oafJson, DLIDataset.class), relatedItemInfo)); + return mapper.writeValueAsString( + summaryFromDataset( + mapper.readValue(oafJson, DLIDataset.class), relatedItemInfo)); case publication: - return mapper.writeValueAsString(summaryFromPublication(mapper.readValue(oafJson, DLIPublication.class), relatedItemInfo)); + return mapper.writeValueAsString( + summaryFromPublication( + mapper.readValue(oafJson, DLIPublication.class), + relatedItemInfo)); case unknown: - return mapper.writeValueAsString(summaryFromUnknown(mapper.readValue(oafJson, DLIUnknown.class), relatedItemInfo)); + return mapper.writeValueAsString( + summaryFromUnknown( + mapper.readValue(oafJson, DLIUnknown.class), relatedItemInfo)); } - } catch (Throwable e) { throw new RuntimeException(e); } @@ -181,23 +189,32 @@ public class ScholixSummary implements Serializable { return null; } - - private static ScholixSummary summaryFromDataset(final DLIDataset item, final RelatedItemInfo relatedItemInfo) { + private static ScholixSummary summaryFromDataset( + final DLIDataset item, final RelatedItemInfo relatedItemInfo) { ScholixSummary summary = new ScholixSummary(); summary.setId(item.getId()); if (item.getPid() != null) - summary.setLocalIdentifier(item.getPid().stream() - .map(p -> new TypedIdentifier(p.getValue(), p.getQualifier().getClassid())) - .collect(Collectors.toList()) - ); + summary.setLocalIdentifier( + item.getPid().stream() + .map( + p -> + new TypedIdentifier( + p.getValue(), p.getQualifier().getClassid())) + .collect(Collectors.toList())); summary.setTypology(Typology.dataset); if (item.getTitle() != null) - summary.setTitle(item.getTitle().stream().map(StructuredProperty::getValue).collect(Collectors.toList())); + summary.setTitle( + item.getTitle().stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toList())); if (item.getAuthor() != null) { - summary.setAuthor(item.getAuthor().stream().map(Author::getFullname).collect(Collectors.toList())); + summary.setAuthor( + item.getAuthor().stream() + .map(Author::getFullname) + .collect(Collectors.toList())); } if (item.getRelevantdate() != null) @@ -205,19 +222,18 @@ public class ScholixSummary implements Serializable { item.getRelevantdate().stream() .filter(d -> "date".equalsIgnoreCase(d.getQualifier().getClassname())) .map(StructuredProperty::getValue) - .collect(Collectors.toList()) - ); + .collect(Collectors.toList())); if (item.getDescription() != null && item.getDescription().size() > 0) summary.setDescription(item.getDescription().get(0).getValue()); if (item.getSubject() != null) { - summary.setSubject(item.getSubject().stream() - .map(s -> new SchemeValue(s.getQualifier().getClassid(), s.getValue())) - .collect(Collectors.toList()) - ); + summary.setSubject( + item.getSubject().stream() + .map(s -> new SchemeValue(s.getQualifier().getClassid(), s.getValue())) + .collect(Collectors.toList())); } - if (item.getPublisher()!= null) + if (item.getPublisher() != null) summary.setPublisher(Collections.singletonList(item.getPublisher().getValue())); summary.setRelatedDatasets(relatedItemInfo.getRelatedDataset()); @@ -225,29 +241,44 @@ public class ScholixSummary implements Serializable { summary.setRelatedUnknown(relatedItemInfo.getRelatedUnknown()); if (item.getDlicollectedfrom() != null) - summary.setDatasources(item.getDlicollectedfrom().stream() - .map( - c -> new CollectedFromType(c.getName(), c.getId(), c.getCompletionStatus()) - ).collect(Collectors.toList())); + summary.setDatasources( + item.getDlicollectedfrom().stream() + .map( + c -> + new CollectedFromType( + c.getName(), + c.getId(), + c.getCompletionStatus())) + .collect(Collectors.toList())); return summary; } - private static ScholixSummary summaryFromPublication(final DLIPublication item, final RelatedItemInfo relatedItemInfo) { + private static ScholixSummary summaryFromPublication( + final DLIPublication item, final RelatedItemInfo relatedItemInfo) { ScholixSummary summary = new ScholixSummary(); summary.setId(item.getId()); if (item.getPid() != null) - summary.setLocalIdentifier(item.getPid().stream() - .map(p -> new TypedIdentifier(p.getValue(), p.getQualifier().getClassid())) - .collect(Collectors.toList()) - ); + summary.setLocalIdentifier( + item.getPid().stream() + .map( + p -> + new TypedIdentifier( + p.getValue(), p.getQualifier().getClassid())) + .collect(Collectors.toList())); summary.setTypology(Typology.publication); if (item.getTitle() != null) - summary.setTitle(item.getTitle().stream().map(StructuredProperty::getValue).collect(Collectors.toList())); + summary.setTitle( + item.getTitle().stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toList())); if (item.getAuthor() != null) { - summary.setAuthor(item.getAuthor().stream().map(Author::getFullname).collect(Collectors.toList())); + summary.setAuthor( + item.getAuthor().stream() + .map(Author::getFullname) + .collect(Collectors.toList())); } if (item.getRelevantdate() != null) @@ -255,55 +286,66 @@ public class ScholixSummary implements Serializable { item.getRelevantdate().stream() .filter(d -> "date".equalsIgnoreCase(d.getQualifier().getClassname())) .map(StructuredProperty::getValue) - .collect(Collectors.toList()) - ); + .collect(Collectors.toList())); if (item.getDescription() != null && item.getDescription().size() > 0) summary.setDescription(item.getDescription().get(0).getValue()); if (item.getSubject() != null) { - summary.setSubject(item.getSubject().stream() - .map(s -> new SchemeValue(s.getQualifier().getClassid(), s.getValue())) - .collect(Collectors.toList()) - ); + summary.setSubject( + item.getSubject().stream() + .map(s -> new SchemeValue(s.getQualifier().getClassid(), s.getValue())) + .collect(Collectors.toList())); } - if (item.getPublisher()!= null) + if (item.getPublisher() != null) summary.setPublisher(Collections.singletonList(item.getPublisher().getValue())); - summary.setRelatedDatasets(relatedItemInfo.getRelatedDataset()); summary.setRelatedPublications(relatedItemInfo.getRelatedPublication()); summary.setRelatedUnknown(relatedItemInfo.getRelatedUnknown()); if (item.getDlicollectedfrom() != null) - summary.setDatasources(item.getDlicollectedfrom().stream() - .map( - c -> new CollectedFromType(c.getName(), c.getId(), c.getCompletionStatus()) - ).collect(Collectors.toList())); - + summary.setDatasources( + item.getDlicollectedfrom().stream() + .map( + c -> + new CollectedFromType( + c.getName(), + c.getId(), + c.getCompletionStatus())) + .collect(Collectors.toList())); return summary; } - private static ScholixSummary summaryFromUnknown(final DLIUnknown item, final RelatedItemInfo relatedItemInfo) { + private static ScholixSummary summaryFromUnknown( + final DLIUnknown item, final RelatedItemInfo relatedItemInfo) { ScholixSummary summary = new ScholixSummary(); summary.setId(item.getId()); if (item.getPid() != null) - summary.setLocalIdentifier(item.getPid().stream() - .map(p -> new TypedIdentifier(p.getValue(), p.getQualifier().getClassid())) - .collect(Collectors.toList()) - ); + summary.setLocalIdentifier( + item.getPid().stream() + .map( + p -> + new TypedIdentifier( + p.getValue(), p.getQualifier().getClassid())) + .collect(Collectors.toList())); summary.setRelatedDatasets(relatedItemInfo.getRelatedDataset()); summary.setRelatedPublications(relatedItemInfo.getRelatedPublication()); summary.setRelatedUnknown(relatedItemInfo.getRelatedUnknown()); summary.setTypology(Typology.unknown); if (item.getDlicollectedfrom() != null) - summary.setDatasources(item.getDlicollectedfrom().stream() - .map( - c -> new CollectedFromType(c.getName(), c.getId(), c.getCompletionStatus()) - ).collect(Collectors.toList())); + summary.setDatasources( + item.getDlicollectedfrom().stream() + .map( + c -> + new CollectedFromType( + c.getName(), + c.getId(), + c.getCompletionStatus())) + .collect(Collectors.toList())); return summary; } } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/TypedIdentifier.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/TypedIdentifier.java index fd6c05ce30..a452de4445 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/TypedIdentifier.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/TypedIdentifier.java @@ -6,8 +6,7 @@ public class TypedIdentifier implements Serializable { private String id; private String type; - public TypedIdentifier() { - } + public TypedIdentifier() {} public TypedIdentifier(String id, String type) { this.id = id; @@ -29,4 +28,4 @@ public class TypedIdentifier implements Serializable { public void setType(String type) { this.type = type; } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossRefParserJSON.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossRefParserJSON.java index 828d8f9b52..79e91799d7 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossRefParserJSON.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossRefParserJSON.java @@ -9,14 +9,14 @@ import eu.dnetlib.dhp.provision.scholix.ScholixEntityId; import eu.dnetlib.dhp.provision.scholix.ScholixIdentifier; import eu.dnetlib.dhp.provision.scholix.ScholixResource; import eu.dnetlib.dhp.utils.DHPUtils; - import java.util.ArrayList; import java.util.Collections; import java.util.List; public class CrossRefParserJSON { - private static List collectedFrom =generateCrossrefCollectedFrom("complete"); + private static List collectedFrom = + generateCrossrefCollectedFrom("complete"); public static ScholixResource parseRecord(final String record) { if (record == null) return null; @@ -24,10 +24,8 @@ public class CrossRefParserJSON { JsonElement source = null; if (jElement.getAsJsonObject().has("_source")) { source = jElement.getAsJsonObject().get("_source"); - if (source == null || !source.isJsonObject()) - return null; - } - else if(jElement.getAsJsonObject().has("DOI")){ + if (source == null || !source.isJsonObject()) return null; + } else if (jElement.getAsJsonObject().has("DOI")) { source = jElement; } else { return null; @@ -38,14 +36,19 @@ public class CrossRefParserJSON { if (message.get("DOI") != null) { final String doi = message.get("DOI").getAsString(); - currentObject.setIdentifier(Collections.singletonList(new ScholixIdentifier(doi, "doi"))); + currentObject.setIdentifier( + Collections.singletonList(new ScholixIdentifier(doi, "doi"))); } - if ((!message.get("created").isJsonNull()) && (message.getAsJsonObject("created").get("date-time") != null)) { - currentObject.setPublicationDate(message.getAsJsonObject("created").get("date-time").getAsString()); + if ((!message.get("created").isJsonNull()) + && (message.getAsJsonObject("created").get("date-time") != null)) { + currentObject.setPublicationDate( + message.getAsJsonObject("created").get("date-time").getAsString()); } - if (message.get("title")!= null && !message.get("title").isJsonNull() && message.get("title").isJsonArray() ) { + if (message.get("title") != null + && !message.get("title").isJsonNull() + && message.get("title").isJsonArray()) { JsonArray array = message.get("title").getAsJsonArray(); currentObject.setTitle(array.get(0).getAsString()); @@ -58,10 +61,14 @@ public class CrossRefParserJSON { String family = ""; String given = ""; - if (currentAuth != null && currentAuth.get("family") != null && !currentAuth.get("family").isJsonNull()) { + if (currentAuth != null + && currentAuth.get("family") != null + && !currentAuth.get("family").isJsonNull()) { family = currentAuth.get("family").getAsString(); } - if (currentAuth != null && currentAuth.get("given") != null && !currentAuth.get("given").isJsonNull()) { + if (currentAuth != null + && currentAuth.get("given") != null + && !currentAuth.get("given").isJsonNull()) { given = currentAuth.get("given").getAsString(); } authorList.add(new ScholixEntityId(String.format("%s %s", family, given), null)); @@ -69,26 +76,34 @@ public class CrossRefParserJSON { currentObject.setCreator(authorList); } if (message.get("publisher") != null && !message.get("publisher").isJsonNull()) { - currentObject.setPublisher(Collections.singletonList(new ScholixEntityId(message.get("publisher").getAsString(), null))); + currentObject.setPublisher( + Collections.singletonList( + new ScholixEntityId(message.get("publisher").getAsString(), null))); } currentObject.setCollectedFrom(collectedFrom); currentObject.setObjectType("publication"); - currentObject.setDnetIdentifier(generateId(message.get("DOI").getAsString(), "doi", "publication")); + currentObject.setDnetIdentifier( + generateId(message.get("DOI").getAsString(), "doi", "publication")); return currentObject; } - private static List generateCrossrefCollectedFrom(final String completionStatus) { - final ScholixEntityId scholixEntityId = new ScholixEntityId("Crossref", - Collections.singletonList(new ScholixIdentifier("dli_________::crossref", "dnet_identifier"))); + private static List generateCrossrefCollectedFrom( + final String completionStatus) { + final ScholixEntityId scholixEntityId = + new ScholixEntityId( + "Crossref", + Collections.singletonList( + new ScholixIdentifier( + "dli_________::crossref", "dnet_identifier"))); return Collections.singletonList( - new ScholixCollectedFrom( - scholixEntityId,"resolved", completionStatus)); + new ScholixCollectedFrom(scholixEntityId, "resolved", completionStatus)); } - private static String generateId(final String pid, final String pidType, final String entityType) { + private static String generateId( + final String pid, final String pidType, final String entityType) { String type; - switch (entityType){ + switch (entityType) { case "publication": type = "50|"; break; @@ -99,10 +114,11 @@ public class CrossRefParserJSON { type = "70|"; break; default: - throw new IllegalArgumentException("unexpected value "+entityType); + throw new IllegalArgumentException("unexpected value " + entityType); } - return type+ DHPUtils.md5(String.format("%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim())); + return type + + DHPUtils.md5( + String.format( + "%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim())); } - - } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossrefClient.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossrefClient.java index 3190ee5168..e000dcbce0 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossrefClient.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossrefClient.java @@ -3,6 +3,8 @@ package eu.dnetlib.dhp.provision.update; import com.google.gson.JsonElement; import com.google.gson.JsonParser; import eu.dnetlib.dhp.provision.scholix.ScholixResource; +import java.io.ByteArrayOutputStream; +import java.util.zip.Inflater; import org.apache.commons.codec.binary.Base64; import org.apache.commons.io.IOUtils; import org.apache.http.client.methods.CloseableHttpResponse; @@ -10,16 +12,12 @@ import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; -import java.io.ByteArrayOutputStream; -import java.util.zip.Inflater; - public class CrossrefClient { private String host; - private String index ="crossref"; + private String index = "crossref"; private String indexType = "item"; - public CrossrefClient(String host) { this.host = host; } @@ -63,26 +61,33 @@ public class CrossrefClient { decompresser.end(); return new String(unzippeddata); } catch (Throwable e) { - throw new RuntimeException("Wrong record:" + blob,e); + throw new RuntimeException("Wrong record:" + blob, e); } } - - public ScholixResource getResourceByDOI(final String doi) { try (CloseableHttpClient client = HttpClients.createDefault()) { - HttpGet httpGet = new HttpGet(String.format("http://%s:9200/%s/%s/%s", host, index,indexType, doi.replaceAll("/","%2F"))); + HttpGet httpGet = + new HttpGet( + String.format( + "http://%s:9200/%s/%s/%s", + host, index, indexType, doi.replaceAll("/", "%2F"))); CloseableHttpResponse response = client.execute(httpGet); String json = IOUtils.toString(response.getEntity().getContent()); if (json.contains("blob")) { JsonParser p = new JsonParser(); final JsonElement root = p.parse(json); - json =decompressBlob(root.getAsJsonObject().get("_source").getAsJsonObject().get("blob").getAsString()); + json = + decompressBlob( + root.getAsJsonObject() + .get("_source") + .getAsJsonObject() + .get("blob") + .getAsString()); } return CrossRefParserJSON.parseRecord(json); } catch (Throwable e) { return null; } - } } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/Datacite2Scholix.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/Datacite2Scholix.java index fd2e37837a..39f2dbaa68 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/Datacite2Scholix.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/Datacite2Scholix.java @@ -5,13 +5,12 @@ import eu.dnetlib.dhp.provision.scholix.*; import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.scholexplorer.relation.RelInfo; import eu.dnetlib.scholexplorer.relation.RelationMapper; -import org.apache.commons.lang3.StringUtils; - import java.util.ArrayList; import java.util.Collections; import java.util.List; import java.util.Map; import java.util.stream.Collectors; +import org.apache.commons.lang3.StringUtils; public class Datacite2Scholix { @@ -24,24 +23,38 @@ public class Datacite2Scholix { public List generateScholixFromJson(final String dJson) { List> relIds = getRelatedIendtifiers(dJson); - relIds = relIds!= null ? relIds.stream().filter(m-> - m.containsKey("relatedIdentifierType") && m.containsKey("relationType" ) && m.containsKey( "relatedIdentifier") - ).collect(Collectors.toList()) : null; - if(relIds== null || relIds.size() ==0 ) - return null; + relIds = + relIds != null + ? relIds.stream() + .filter( + m -> + m.containsKey("relatedIdentifierType") + && m.containsKey("relationType") + && m.containsKey("relatedIdentifier")) + .collect(Collectors.toList()) + : null; + if (relIds == null || relIds.size() == 0) return null; final String updated = JsonPath.read(dJson, rootPath + ".updated"); ScholixResource resource = generateDataciteScholixResource(dJson); - return relIds.stream().flatMap(s-> { - try { - final List result = generateScholix(resource, ""+s.get("relatedIdentifier"), s.get("relatedIdentifierType"), s.get("relationType"), updated); - return result.stream(); - } catch (Throwable e) - { - return new ArrayList().stream(); - } - }).collect(Collectors.toList()); + return relIds.stream() + .flatMap( + s -> { + try { + final List result = + generateScholix( + resource, + "" + s.get("relatedIdentifier"), + s.get("relatedIdentifierType"), + s.get("relationType"), + updated); + return result.stream(); + } catch (Throwable e) { + return new ArrayList().stream(); + } + }) + .collect(Collectors.toList()); } public String getRootPath() { @@ -52,13 +65,20 @@ public class Datacite2Scholix { this.rootPath = rootPath; } - private List generateScholix(ScholixResource source, final String pid, final String pidtype, final String relType, final String updated) { + private List generateScholix( + ScholixResource source, + final String pid, + final String pidtype, + final String relType, + final String updated) { if ("doi".equalsIgnoreCase(pidtype)) { ScholixResource target = new ScholixResource(); target.setIdentifier(Collections.singletonList(new ScholixIdentifier(pid, pidtype))); final RelInfo relInfo = relationMapper.get(relType.toLowerCase()); - final ScholixRelationship rel = new ScholixRelationship(relInfo.getOriginal(), "datacite", relInfo.getInverse()); + final ScholixRelationship rel = + new ScholixRelationship( + relInfo.getOriginal(), "datacite", relInfo.getInverse()); final ScholixEntityId provider = source.getCollectedFrom().get(0).getProvider(); final Scholix s = new Scholix(); s.setSource(source); @@ -76,7 +96,9 @@ public class Datacite2Scholix { target.setObjectType("unknown"); target.setCollectedFrom(generateDataciteCollectedFrom("incomplete")); final RelInfo relInfo = relationMapper.get(relType.toLowerCase()); - final ScholixRelationship rel = new ScholixRelationship(relInfo.getOriginal(), "datacite", relInfo.getInverse()); + final ScholixRelationship rel = + new ScholixRelationship( + relInfo.getOriginal(), "datacite", relInfo.getInverse()); final ScholixEntityId provider = source.getCollectedFrom().get(0).getProvider(); final Scholix s = new Scholix(); s.setSource(source); @@ -92,7 +114,9 @@ public class Datacite2Scholix { s2.setTarget(source); s2.setLinkprovider(Collections.singletonList(provider)); s2.setPublisher(source.getPublisher()); - s2.setRelationship(new ScholixRelationship(relInfo.getInverse(), "datacite", relInfo.getOriginal())); + s2.setRelationship( + new ScholixRelationship( + relInfo.getInverse(), "datacite", relInfo.getOriginal())); s2.setPublicationDate(updated); s2.generateIdentifier(); result.add(s2); @@ -112,45 +136,51 @@ public class Datacite2Scholix { if (StringUtils.isNotBlank(publisher)) resource.setPublisher(Collections.singletonList(new ScholixEntityId(publisher, null))); final String date = getDate(dJson); - if (StringUtils.isNotBlank(date)) - resource.setPublicationDate(date); + if (StringUtils.isNotBlank(date)) resource.setPublicationDate(date); final String title = getTitle(dJson); - if(StringUtils.isNotBlank(title)) - resource.setTitle(title); + if (StringUtils.isNotBlank(title)) resource.setTitle(title); resource.setCreator(getCreators(dJson)); return resource; } private List getCreators(final String json) { final List creatorName = JsonPath.read(json, rootPath + ".creators[*].name"); - if (creatorName!= null && creatorName.size() >0) { - return creatorName.stream().map(s-> new ScholixEntityId(s, null)).collect(Collectors.toList()); + if (creatorName != null && creatorName.size() > 0) { + return creatorName.stream() + .map(s -> new ScholixEntityId(s, null)) + .collect(Collectors.toList()); } return null; } - private String getTitle(final String json){ + private String getTitle(final String json) { final List titles = JsonPath.read(json, rootPath + ".titles[*].title"); - return titles!= null && titles.size()>0?titles.get(0): null; + return titles != null && titles.size() > 0 ? titles.get(0) : null; } private String getDate(final String json) { - final List> dates = JsonPath.read(json, rootPath + ".dates"); - if(dates!= null && dates.size()>0){ + final List> dates = JsonPath.read(json, rootPath + ".dates"); + if (dates != null && dates.size() > 0) { - List> issued = dates.stream().filter(s -> "issued".equalsIgnoreCase(s.get("dateType"))).collect(Collectors.toList()); - if (issued.size()>0) - return issued.get(0).get("date"); + List> issued = + dates.stream() + .filter(s -> "issued".equalsIgnoreCase(s.get("dateType"))) + .collect(Collectors.toList()); + if (issued.size() > 0) return issued.get(0).get("date"); } return null; } - private List generateDataciteCollectedFrom(final String completionStatus) { - final ScholixEntityId scholixEntityId = new ScholixEntityId("Datasets in Datacite", - Collections.singletonList(new ScholixIdentifier("dli_________::datacite", "dnet_identifier"))); + private List generateDataciteCollectedFrom( + final String completionStatus) { + final ScholixEntityId scholixEntityId = + new ScholixEntityId( + "Datasets in Datacite", + Collections.singletonList( + new ScholixIdentifier( + "dli_________::datacite", "dnet_identifier"))); return Collections.singletonList( - new ScholixCollectedFrom( - scholixEntityId,"collected", completionStatus)); + new ScholixCollectedFrom(scholixEntityId, "collected", completionStatus)); } private String getType(final String json) { @@ -171,9 +201,10 @@ public class Datacite2Scholix { return res; } - public static String generateId(final String pid, final String pidType, final String entityType) { + public static String generateId( + final String pid, final String pidType, final String entityType) { String type; - switch (entityType){ + switch (entityType) { case "publication": type = "50|"; break; @@ -184,8 +215,11 @@ public class Datacite2Scholix { type = "70|"; break; default: - throw new IllegalArgumentException("unexpected value "+entityType); + throw new IllegalArgumentException("unexpected value " + entityType); } - return type+ DHPUtils.md5(String.format("%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim())); + return type + + DHPUtils.md5( + String.format( + "%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim())); } } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClient.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClient.java index e1d25bf2e2..635dc0c54a 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClient.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClient.java @@ -1,19 +1,17 @@ package eu.dnetlib.dhp.provision.update; import eu.dnetlib.dhp.provision.scholix.ScholixResource; +import java.io.IOException; import org.apache.commons.io.IOUtils; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; -import java.io.IOException; - public class DataciteClient { - private String host; - private String index ="datacite"; + private String index = "datacite"; private String indexType = "dump"; private Datacite2Scholix d2s; @@ -25,15 +23,13 @@ public class DataciteClient { } public Iterable getDatasetsFromTs(final Long timestamp) { - return ()-> { + return () -> { try { return new DataciteClientIterator(host, index, timestamp); } catch (IOException e) { throw new RuntimeException(e); } }; - - } public String getHost() { @@ -62,14 +58,16 @@ public class DataciteClient { public ScholixResource getDatasetByDOI(final String doi) { try (CloseableHttpClient client = HttpClients.createDefault()) { - HttpGet httpGet = new HttpGet(String.format("http://%s:9200/%s/%s/%s", host, index,indexType, doi.replaceAll("/","%2F"))); + HttpGet httpGet = + new HttpGet( + String.format( + "http://%s:9200/%s/%s/%s", + host, index, indexType, doi.replaceAll("/", "%2F"))); CloseableHttpResponse response = client.execute(httpGet); - final String json =IOUtils.toString(response.getEntity().getContent()); + final String json = IOUtils.toString(response.getEntity().getContent()); return d2s.generateDataciteScholixResource(json); } catch (Throwable e) { return null; } } - - } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClientIterator.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClientIterator.java index 61c1aa39f5..94937d7d3b 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClientIterator.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClientIterator.java @@ -1,6 +1,11 @@ package eu.dnetlib.dhp.provision.update; + import com.fasterxml.jackson.databind.ObjectMapper; import com.jayway.jsonpath.JsonPath; +import java.io.IOException; +import java.util.Iterator; +import java.util.List; +import java.util.stream.Collectors; import net.minidev.json.JSONArray; import org.apache.commons.io.IOUtils; import org.apache.http.client.methods.CloseableHttpResponse; @@ -9,15 +14,10 @@ import org.apache.http.entity.StringEntity; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; -import java.io.IOException; -import java.util.Iterator; -import java.util.List; -import java.util.stream.Collectors; - public class DataciteClientIterator implements Iterator { - final static String blobPath = "$.hits.hits[*]._source"; - final static String scrollIdPath = "$._scroll_id"; + static final String blobPath = "$.hits.hits[*]._source"; + static final String scrollIdPath = "$._scroll_id"; String scrollId; @@ -27,25 +27,29 @@ public class DataciteClientIterator implements Iterator { final String esIndex; final ObjectMapper mapper = new ObjectMapper(); - public DataciteClientIterator(final String esHost, final String esIndex, long timestamp) throws IOException { + public DataciteClientIterator(final String esHost, final String esIndex, long timestamp) + throws IOException { this.esHost = esHost; this.esIndex = esIndex; // THIS FIX IS NECESSARY to avoid different timezone - timestamp -= (60 *60 *2); - final String body =getResponse(String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), String.format("{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}", timestamp)); - scrollId= getJPathString(scrollIdPath, body); + timestamp -= (60 * 60 * 2); + final String body = + getResponse( + String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), + String.format( + "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}", + timestamp)); + scrollId = getJPathString(scrollIdPath, body); buffer = getBlobs(body); - } - - public String getResponse(final String url,final String json ) { + public String getResponse(final String url, final String json) { CloseableHttpClient client = HttpClients.createDefault(); try { HttpPost httpPost = new HttpPost(url); - if (json!= null) { + if (json != null) { StringEntity entity = new StringEntity(json); httpPost.setEntity(entity); httpPost.setHeader("Accept", "application/json"); @@ -55,22 +59,20 @@ public class DataciteClientIterator implements Iterator { return IOUtils.toString(response.getEntity().getContent()); } catch (Throwable e) { - throw new RuntimeException("Error on executing request ",e); + throw new RuntimeException("Error on executing request ", e); } finally { try { client.close(); } catch (IOException e) { - throw new RuntimeException("Unable to close client ",e); + throw new RuntimeException("Unable to close client ", e); } } - } - private String getJPathString(final String jsonPath, final String json) { + private String getJPathString(final String jsonPath, final String json) { try { Object o = JsonPath.read(json, jsonPath); - if (o instanceof String) - return (String) o; + if (o instanceof String) return (String) o; return null; } catch (Exception e) { return ""; @@ -79,37 +81,36 @@ public class DataciteClientIterator implements Iterator { private List getBlobs(final String body) { JSONArray array = JsonPath.read(body, blobPath); - return array.stream().map( - o -> { - try { - return mapper.writeValueAsString(o); - } catch (Throwable e) { - throw new RuntimeException(e); - } - } - ).collect(Collectors.toList()); + return array.stream() + .map( + o -> { + try { + return mapper.writeValueAsString(o); + } catch (Throwable e) { + throw new RuntimeException(e); + } + }) + .collect(Collectors.toList()); } - @Override public boolean hasNext() { - return (buffer!= null && !buffer.isEmpty()); - + return (buffer != null && !buffer.isEmpty()); } @Override public String next() { final String nextItem = buffer.remove(0); if (buffer.isEmpty()) { - final String json_param = String.format("{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}", scrollId); - final String body =getResponse(String.format("http://%s:9200/_search/scroll", esHost), json_param); + final String json_param = + String.format("{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}", scrollId); + final String body = + getResponse(String.format("http://%s:9200/_search/scroll", esHost), json_param); try { buffer = getBlobs(body); } catch (Throwable e) { System.out.println(body); - } - } return nextItem; } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/RetrieveUpdateFromDatacite.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/RetrieveUpdateFromDatacite.java index ea659dbb1b..c8f60827c2 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/RetrieveUpdateFromDatacite.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/RetrieveUpdateFromDatacite.java @@ -4,6 +4,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.provision.scholix.Scholix; import eu.dnetlib.scholexplorer.relation.RelationMapper; +import java.net.URI; +import java.util.List; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; @@ -12,14 +14,14 @@ import org.apache.hadoop.io.IntWritable; import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; -import java.net.URI; -import java.util.List; -import java.util.concurrent.atomic.AtomicInteger; - public class RetrieveUpdateFromDatacite { - public static void main(String[] args) throws Exception{ - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(RetrieveUpdateFromDatacite.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_retrieve_update_parameters.json"))); + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + RetrieveUpdateFromDatacite.class.getResourceAsStream( + "/eu/dnetlib/dhp/provision/input_retrieve_update_parameters.json"))); parser.parseArgument(args); final String hdfsuri = parser.get("namenode"); Path hdfswritepath = new Path(parser.get("targetPath")); @@ -38,26 +40,28 @@ public class RetrieveUpdateFromDatacite { FileSystem.get(URI.create(hdfsuri), conf); final Datacite2Scholix d2s = new Datacite2Scholix(RelationMapper.load()); final ObjectMapper mapper = new ObjectMapper(); - try (SequenceFile.Writer writer = SequenceFile.createWriter(conf, - SequenceFile.Writer.file(hdfswritepath), SequenceFile.Writer.keyClass(IntWritable.class), - SequenceFile.Writer.valueClass(Text.class))) { + try (SequenceFile.Writer writer = + SequenceFile.createWriter( + conf, + SequenceFile.Writer.file(hdfswritepath), + SequenceFile.Writer.keyClass(IntWritable.class), + SequenceFile.Writer.valueClass(Text.class))) { final Text value = new Text(); final IntWritable key = new IntWritable(); int i = 0; - for(String dataset: new DataciteClient(host).getDatasetsFromTs(timestamp)) { + for (String dataset : new DataciteClient(host).getDatasetsFromTs(timestamp)) { i++; List scholix = d2s.generateScholixFromJson(dataset); - if (scholix!= null) - for(Scholix s: scholix) { + if (scholix != null) + for (Scholix s : scholix) { key.set(i); value.set(mapper.writeValueAsString(s)); writer.append(key, value); if (i % 10000 == 0) { - System.out.println("wrote "+i); + System.out.println("wrote " + i); } } } - } } } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/SparkResolveScholixTarget.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/SparkResolveScholixTarget.java index 35020ecdf3..d6f6dfeac0 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/SparkResolveScholixTarget.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/SparkResolveScholixTarget.java @@ -7,7 +7,10 @@ import eu.dnetlib.dhp.provision.scholix.ScholixIdentifier; import eu.dnetlib.dhp.provision.scholix.ScholixRelationship; import eu.dnetlib.dhp.provision.scholix.ScholixResource; import eu.dnetlib.dhp.utils.DHPUtils; -import eu.dnetlib.scholexplorer.relation.RelationMapper; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.io.IntWritable; @@ -19,116 +22,168 @@ import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; import scala.Tuple2; -import java.util.ArrayList; -import java.util.Collections; -import java.util.List; -import java.util.stream.Collectors; - public class SparkResolveScholixTarget { - public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResolveScholixTarget.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_resolve_scholix_parameters.json"))); + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkResolveScholixTarget.class.getResourceAsStream( + "/eu/dnetlib/dhp/provision/input_resolve_scholix_parameters.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); final String master = parser.get("master"); final String sourcePath = parser.get("sourcePath"); - final String workingDirPath= parser.get("workingDirPath"); - final String indexHost= parser.get("indexHost"); - try (SparkSession spark = getSession(conf, master)){ + final String workingDirPath = parser.get("workingDirPath"); + final String indexHost = parser.get("indexHost"); + try (SparkSession spark = getSession(conf, master)) { final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + spark.createDataset( + sc.sequenceFile(sourcePath, IntWritable.class, Text.class) + .map(Tuple2::_2) + .map( + s -> + new ObjectMapper() + .readValue(s.toString(), Scholix.class)) + .rdd(), + Encoders.bean(Scholix.class)) + .write() + .save(workingDirPath + "/stepA"); - spark.createDataset(sc.sequenceFile(sourcePath, IntWritable.class,Text.class) - .map(Tuple2::_2) - .map(s-> new ObjectMapper().readValue(s.toString(), Scholix.class)).rdd(), Encoders.bean(Scholix.class)) - .write().save(workingDirPath+"/stepA"); + Dataset s1 = + spark.read().load(workingDirPath + "/stepA").as(Encoders.bean(Scholix.class)); + s1.where(s1.col("target.dnetIdentifier").isNull()) + .select(s1.col("target.identifier")) + .distinct() + .map( + (MapFunction) + f -> { + final String pid = ((Row) f.getList(0).get(0)).getString(0); + ScholixResource publication = + new CrossrefClient(indexHost).getResourceByDOI(pid); + if (publication != null) { + return publication; + } + ScholixResource dataset = + new DataciteClient(indexHost).getDatasetByDOI(pid); + if (dataset != null) { + return dataset; + } + ScholixResource r = new ScholixResource(); + r.setIdentifier( + Collections.singletonList( + new ScholixIdentifier(pid, "doi"))); + r.setObjectType("unknown"); + r.setDnetIdentifier( + "70|" + + DHPUtils.md5( + String.format( + "%s::doi", + pid.toLowerCase().trim()))); + return r; + }, + Encoders.bean(ScholixResource.class)) + .write() + .mode(SaveMode.Overwrite) + .save(workingDirPath + "/stepB"); - Dataset s1 = spark.read().load(workingDirPath+"/stepA").as(Encoders.bean(Scholix.class)); + Dataset s2 = + spark.read() + .load(workingDirPath + "/stepB") + .as(Encoders.bean(ScholixResource.class)); - s1.where(s1.col("target.dnetIdentifier").isNull()).select(s1.col("target.identifier")).distinct() - .map((MapFunction) f-> { - final String pid = ((Row) f.getList(0).get(0)).getString(0); - ScholixResource publication = new CrossrefClient(indexHost).getResourceByDOI(pid); - if (publication != null) { - return publication; - } - ScholixResource dataset = new DataciteClient(indexHost).getDatasetByDOI(pid); - if (dataset!= null) { - return dataset; - } - ScholixResource r = new ScholixResource(); - r.setIdentifier(Collections.singletonList(new ScholixIdentifier(pid, "doi"))); - r.setObjectType("unknown"); - r.setDnetIdentifier("70|"+DHPUtils.md5(String.format("%s::doi", pid.toLowerCase().trim()))); + s1.joinWith( + s2, + s1.col("target.identifier.identifier") + .equalTo(s2.col("identifier.identifier")), + "left") + .flatMap( + (FlatMapFunction, Scholix>) + f -> { + final List res = new ArrayList<>(); + final Scholix s = f._1(); + final ScholixResource target = f._2(); + if (StringUtils.isNotBlank(s.getIdentifier())) res.add(s); + else if (target == null) { + ScholixResource currentTarget = s.getTarget(); + currentTarget.setObjectType("unknown"); + currentTarget.setDnetIdentifier( + Datacite2Scholix.generateId( + currentTarget + .getIdentifier() + .get(0) + .getIdentifier(), + currentTarget + .getIdentifier() + .get(0) + .getSchema(), + currentTarget.getObjectType())); - return r; - }, Encoders.bean(ScholixResource.class)).write().mode(SaveMode.Overwrite).save(workingDirPath+"/stepB"); + s.generateIdentifier(); + res.add(s); + final Scholix inverse = new Scholix(); + inverse.setTarget(s.getSource()); + inverse.setSource(s.getTarget()); + inverse.setLinkprovider(s.getLinkprovider()); + inverse.setPublicationDate(s.getPublicationDate()); + inverse.setPublisher(s.getPublisher()); + inverse.setRelationship( + new ScholixRelationship( + s.getRelationship().getInverse(), + s.getRelationship().getSchema(), + s.getRelationship().getName())); + inverse.generateIdentifier(); + res.add(inverse); + } else { + target.setIdentifier( + target.getIdentifier().stream() + .map( + d -> + new ScholixIdentifier( + d.getIdentifier() + .toLowerCase(), + d.getSchema() + .toLowerCase())) + .collect(Collectors.toList())); + s.setTarget(target); + s.generateIdentifier(); + res.add(s); + final Scholix inverse = new Scholix(); + inverse.setTarget(s.getSource()); + inverse.setSource(s.getTarget()); + inverse.setLinkprovider(s.getLinkprovider()); + inverse.setPublicationDate(s.getPublicationDate()); + inverse.setPublisher(s.getPublisher()); + inverse.setRelationship( + new ScholixRelationship( + s.getRelationship().getInverse(), + s.getRelationship().getSchema(), + s.getRelationship().getName())); + inverse.generateIdentifier(); + res.add(inverse); + } - Dataset s2 = spark.read().load(workingDirPath+"/stepB").as(Encoders.bean(ScholixResource.class)); - - - s1.joinWith(s2, s1.col("target.identifier.identifier").equalTo(s2.col("identifier.identifier")), "left") - - .flatMap((FlatMapFunction, Scholix>) f -> - { - - final List res = new ArrayList<>(); - final Scholix s = f._1(); - final ScholixResource target = f._2(); - if (StringUtils.isNotBlank(s.getIdentifier())) - res.add(s); - else if (target == null) { - ScholixResource currentTarget = s.getTarget(); - currentTarget.setObjectType("unknown"); - currentTarget.setDnetIdentifier(Datacite2Scholix.generateId(currentTarget.getIdentifier().get(0).getIdentifier(),currentTarget.getIdentifier().get(0).getSchema(), currentTarget.getObjectType())); - - s.generateIdentifier(); - res.add(s); - final Scholix inverse = new Scholix(); - inverse.setTarget(s.getSource()); - inverse.setSource(s.getTarget()); - inverse.setLinkprovider(s.getLinkprovider()); - inverse.setPublicationDate(s.getPublicationDate()); - inverse.setPublisher(s.getPublisher()); - inverse.setRelationship(new ScholixRelationship(s.getRelationship().getInverse(), s.getRelationship().getSchema(), s.getRelationship().getName())); - inverse.generateIdentifier(); - res.add(inverse); - - } else - { - target.setIdentifier(target.getIdentifier().stream().map(d -> new ScholixIdentifier(d.getIdentifier().toLowerCase(), d.getSchema().toLowerCase())).collect(Collectors.toList())); - s.setTarget(target); - s.generateIdentifier(); - res.add(s); - final Scholix inverse = new Scholix(); - inverse.setTarget(s.getSource()); - inverse.setSource(s.getTarget()); - inverse.setLinkprovider(s.getLinkprovider()); - inverse.setPublicationDate(s.getPublicationDate()); - inverse.setPublisher(s.getPublisher()); - inverse.setRelationship(new ScholixRelationship(s.getRelationship().getInverse(), s.getRelationship().getSchema(), s.getRelationship().getName())); - inverse.generateIdentifier(); - res.add(inverse); - } - - return res.iterator(); - }, Encoders.bean(Scholix.class)).javaRDD().map(s -> new ObjectMapper().writeValueAsString(s)).saveAsTextFile(workingDirPath+"/resolved_json"); + return res.iterator(); + }, + Encoders.bean(Scholix.class)) + .javaRDD() + .map(s -> new ObjectMapper().writeValueAsString(s)) + .saveAsTextFile(workingDirPath + "/resolved_json"); } } private static SparkSession getSession(SparkConf conf, String master) { - return SparkSession - .builder() + return SparkSession.builder() .config(conf) .appName(SparkResolveScholixTarget.class.getSimpleName()) .master(master) .getOrCreate(); } - } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DataciteClientTest.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DataciteClientTest.java index cc4b0047a2..cd86702beb 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DataciteClientTest.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DataciteClientTest.java @@ -5,13 +5,11 @@ import eu.dnetlib.dhp.provision.scholix.Scholix; import eu.dnetlib.dhp.provision.scholix.ScholixResource; import eu.dnetlib.dhp.provision.update.*; import eu.dnetlib.scholexplorer.relation.RelationMapper; +import java.util.List; import org.apache.commons.io.IOUtils; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; -import java.util.List; - - public class DataciteClientTest { @Test public void dataciteSCholixTest() throws Exception { @@ -23,18 +21,16 @@ public class DataciteClientTest { System.out.println(new ObjectMapper().writeValueAsString(s)); } - -// public void testS() throws Exception { -// RetrieveUpdateFromDatacite.main(new String[]{ -// "-n", "file:///data/new_s2.txt", -// "-t", "/data/new_s2.txt", -// "-ts", "1586974078", -// "-ih", "ip-90-147-167-25.ct1.garrservices.it", -// "-in", "datacite", -// }); -// -// } - + // public void testS() throws Exception { + // RetrieveUpdateFromDatacite.main(new String[]{ + // "-n", "file:///data/new_s2.txt", + // "-t", "/data/new_s2.txt", + // "-ts", "1586974078", + // "-ih", "ip-90-147-167-25.ct1.garrservices.it", + // "-in", "datacite", + // }); + // + // } public void testResolveDataset() throws Exception { DataciteClient dc = new DataciteClient("ip-90-147-167-25.ct1.garrservices.it"); @@ -42,9 +38,9 @@ public class DataciteClientTest { Assertions.assertNotNull(datasetByDOI); System.out.println(new ObjectMapper().writeValueAsString(datasetByDOI)); - CrossrefClient cr = new CrossrefClient("ip-90-147-167-25.ct1.garrservices.it"); - ScholixResource crossrefByDOI = cr.getResourceByDOI("10.26850/1678-4618eqj.v35.1.2010.p41-46"); + ScholixResource crossrefByDOI = + cr.getResourceByDOI("10.26850/1678-4618eqj.v35.1.2010.p41-46"); Assertions.assertNotNull(crossrefByDOI); System.out.println(new ObjectMapper().writeValueAsString(crossrefByDOI)); } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/ExtractInfoTest.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/ExtractInfoTest.java index b5142447d1..b85dd17099 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/ExtractInfoTest.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/ExtractInfoTest.java @@ -21,8 +21,8 @@ public class ExtractInfoTest { @Test public void testScholix() throws Exception { final String jsonSummary = IOUtils.toString(getClass().getResourceAsStream("summary.json")); - final String jsonRelation = IOUtils.toString(getClass().getResourceAsStream("relation.json")); + final String jsonRelation = + IOUtils.toString(getClass().getResourceAsStream("relation.json")); Scholix.generateScholixWithSource(jsonSummary, jsonRelation); } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java index 8162927b80..27f99433c6 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java @@ -1,11 +1,16 @@ package eu.dnetlib.dhp.oa.provision; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.oa.provision.model.EntityRelEntity; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; import eu.dnetlib.dhp.oa.provision.model.Tuple2; import eu.dnetlib.dhp.schema.common.ModelSupport; +import java.util.ArrayList; +import java.util.List; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -16,42 +21,29 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.ArrayList; -import java.util.List; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - /** - * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects. - * The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization, - * and all the possible relationships (similarity links produced by the Dedup process are excluded). + * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of + * linked objects. The operation considers all the entity types (publication, dataset, software, + * ORP, project, datasource, organization, and all the possible relationships (similarity links + * produced by the Dedup process are excluded). * - * The operation is implemented by sequentially joining one entity type at time (E) with the relationships (R), and again - * by E, finally grouped by E.id; + *

The operation is implemented by sequentially joining one entity type at time (E) with the + * relationships (R), and again by E, finally grouped by E.id; * - * The workflow is organized in different parts aimed to to reduce the complexity of the operation - * 1) PrepareRelationsJob: - * only consider relationships that are not virtually deleted ($.dataInfo.deletedbyinference == false), each entity - * can be linked at most to 100 other objects + *

The workflow is organized in different parts aimed to to reduce the complexity of the + * operation 1) PrepareRelationsJob: only consider relationships that are not virtually deleted + * ($.dataInfo.deletedbyinference == false), each entity can be linked at most to 100 other objects * - * 2) JoinRelationEntityByTargetJob: - * (phase 1): prepare tuples [relation - target entity] (R - T): - * for each entity type E_i - * map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information - * join (R.target = T_i.id) - * save the tuples (R_i, T_i) - * (phase 2): - * create the union of all the entity types E, hash by id - * read the tuples (R, T), hash by R.source - * join E.id = (R, T).source, where E becomes the Source Entity S - * save the tuples (S, R, T) + *

2) JoinRelationEntityByTargetJob: (phase 1): prepare tuples [relation - target entity] (R - + * T): for each entity type E_i map E_i as RelatedEntity T_i to simplify the model and extracting + * only the necessary information join (R.target = T_i.id) save the tuples (R_i, T_i) (phase 2): + * create the union of all the entity types E, hash by id read the tuples (R, T), hash by R.source + * join E.id = (R, T).source, where E becomes the Source Entity S save the tuples (S, R, T) * - * 3) AdjacencyListBuilderJob: - * given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping the result as JoinedEntity + *

3) AdjacencyListBuilderJob: given the tuple (S - R - T) we need to group by S.id -> List [ R - + * T ], mapping the result as JoinedEntity * - * 4) XmlConverterJob: - * convert the JoinedEntities as XML records + *

4) XmlConverterJob: convert the JoinedEntities as XML records */ public class AdjacencyListBuilderJob { @@ -61,16 +53,17 @@ public class AdjacencyListBuilderJob { public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - AdjacencyListBuilderJob.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + AdjacencyListBuilderJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json"))); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); String inputPath = parser.get("inputPath"); @@ -83,33 +76,41 @@ public class AdjacencyListBuilderJob { conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - runWithSparkSession(conf, isSparkSessionManaged, + runWithSparkSession( + conf, + isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); createAdjacencyLists(spark, inputPath, outputPath); }); } - private static void createAdjacencyLists(SparkSession spark, String inputPath, String outputPath) { + private static void createAdjacencyLists( + SparkSession spark, String inputPath, String outputPath) { log.info("Reading joined entities from: {}", inputPath); spark.read() .load(inputPath) .as(Encoders.bean(EntityRelEntity.class)) - .groupByKey((MapFunction) value -> value.getEntity().getId(), Encoders.STRING()) - .mapGroups((MapGroupsFunction) (key, values) -> { - JoinedEntity j = new JoinedEntity(); - List links = new ArrayList<>(); - while (values.hasNext() && links.size() < MAX_LINKS) { - EntityRelEntity curr = values.next(); - if (j.getEntity() == null) { - j.setEntity(curr.getEntity()); - } - links.add(new Tuple2(curr.getRelation(), curr.getTarget())); - } - j.setLinks(links); - return j; - }, Encoders.bean(JoinedEntity.class)) + .groupByKey( + (MapFunction) value -> value.getEntity().getId(), + Encoders.STRING()) + .mapGroups( + (MapGroupsFunction) + (key, values) -> { + JoinedEntity j = new JoinedEntity(); + List links = new ArrayList<>(); + while (values.hasNext() && links.size() < MAX_LINKS) { + EntityRelEntity curr = values.next(); + if (j.getEntity() == null) { + j.setEntity(curr.getEntity()); + } + links.add(new Tuple2(curr.getRelation(), curr.getTarget())); + } + j.setLinks(links); + return j; + }, + Encoders.bean(JoinedEntity.class)) .write() .mode(SaveMode.Overwrite) .parquet(outputPath); @@ -118,5 +119,4 @@ public class AdjacencyListBuilderJob { private static void removeOutputDir(SparkSession spark, String path) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java index d0035fa78a..6b1dd52ced 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java @@ -1,5 +1,8 @@ package eu.dnetlib.dhp.oa.provision; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.*; + import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; @@ -9,6 +12,7 @@ import eu.dnetlib.dhp.oa.provision.model.SortableRelation; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.OafEntity; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -21,60 +25,50 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import scala.Tuple2; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.*; - /** - * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects. - * The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization, - * and all the possible relationships (similarity links produced by the Dedup process are excluded). + * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of + * linked objects. The operation considers all the entity types (publication, dataset, software, + * ORP, project, datasource, organization, and all the possible relationships (similarity links + * produced by the Dedup process are excluded). * - * The operation is implemented by sequentially joining one entity type at time (E) with the relationships (R), and again - * by E, finally grouped by E.id; + *

The operation is implemented by sequentially joining one entity type at time (E) with the + * relationships (R), and again by E, finally grouped by E.id; * - * The workflow is organized in different parts aimed to to reduce the complexity of the operation - * 1) PrepareRelationsJob: - * only consider relationships that are not virtually deleted ($.dataInfo.deletedbyinference == false), each entity - * can be linked at most to 100 other objects + *

The workflow is organized in different parts aimed to to reduce the complexity of the + * operation 1) PrepareRelationsJob: only consider relationships that are not virtually deleted + * ($.dataInfo.deletedbyinference == false), each entity can be linked at most to 100 other objects * - * 2) JoinRelationEntityByTargetJob: - * (phase 1): prepare tuples [relation - target entity] (R - T): - * for each entity type E_i - * map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information - * join (R.target = T_i.id) - * save the tuples (R_i, T_i) - * (phase 2): - * create the union of all the entity types E, hash by id - * read the tuples (R, T), hash by R.source - * join E.id = (R, T).source, where E becomes the Source Entity S - * save the tuples (S, R, T) + *

2) JoinRelationEntityByTargetJob: (phase 1): prepare tuples [relation - target entity] (R - + * T): for each entity type E_i map E_i as RelatedEntity T_i to simplify the model and extracting + * only the necessary information join (R.target = T_i.id) save the tuples (R_i, T_i) (phase 2): + * create the union of all the entity types E, hash by id read the tuples (R, T), hash by R.source + * join E.id = (R, T).source, where E becomes the Source Entity S save the tuples (S, R, T) * - * 3) AdjacencyListBuilderJob: - * given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping the result as JoinedEntity + *

3) AdjacencyListBuilderJob: given the tuple (S - R - T) we need to group by S.id -> List [ R - + * T ], mapping the result as JoinedEntity * - * 4) XmlConverterJob: - * convert the JoinedEntities as XML records + *

4) XmlConverterJob: convert the JoinedEntities as XML records */ public class CreateRelatedEntitiesJob_phase1 { - private static final Logger log = LoggerFactory.getLogger(CreateRelatedEntitiesJob_phase1.class); + private static final Logger log = + LoggerFactory.getLogger(CreateRelatedEntitiesJob_phase1.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils.toString( - PrepareRelationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.json")); + String jsonConfiguration = + IOUtils.toString( + PrepareRelationsJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); String inputRelationsPath = parser.get("inputRelationsPath"); @@ -89,70 +83,100 @@ public class CreateRelatedEntitiesJob_phase1 { String graphTableClassName = parser.get("graphTableClassName"); log.info("graphTableClassName: {}", graphTableClassName); - Class entityClazz = (Class) Class.forName(graphTableClassName); + Class entityClazz = + (Class) Class.forName(graphTableClassName); SparkConf conf = new SparkConf(); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - runWithSparkSession(conf, isSparkSessionManaged, + runWithSparkSession( + conf, + isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - joinRelationEntity(spark, inputRelationsPath, inputEntityPath, entityClazz, outputPath); + joinRelationEntity( + spark, inputRelationsPath, inputEntityPath, entityClazz, outputPath); }); } - private static void joinRelationEntity(SparkSession spark, String inputRelationsPath, String inputEntityPath, Class entityClazz, String outputPath) { + private static void joinRelationEntity( + SparkSession spark, + String inputRelationsPath, + String inputEntityPath, + Class entityClazz, + String outputPath) { - Dataset> relsByTarget = readPathRelation(spark, inputRelationsPath) - .filter((FilterFunction) value -> value.getDataInfo().getDeletedbyinference() == false) - .map((MapFunction>) r -> new Tuple2<>(r.getTarget(), r), - Encoders.tuple(Encoders.STRING(), Encoders.kryo(SortableRelation.class))) - .cache(); + Dataset> relsByTarget = + readPathRelation(spark, inputRelationsPath) + .filter( + (FilterFunction) + value -> + value.getDataInfo().getDeletedbyinference() + == false) + .map( + (MapFunction>) + r -> new Tuple2<>(r.getTarget(), r), + Encoders.tuple( + Encoders.STRING(), Encoders.kryo(SortableRelation.class))) + .cache(); - Dataset> entities = readPathEntity(spark, inputEntityPath, entityClazz) - .map((MapFunction) value -> asRelatedEntity(value, entityClazz), Encoders.bean(RelatedEntity.class)) - .map((MapFunction>) e -> new Tuple2<>(e.getId(), e), - Encoders.tuple(Encoders.STRING(), Encoders.kryo(RelatedEntity.class))) - .cache(); + Dataset> entities = + readPathEntity(spark, inputEntityPath, entityClazz) + .map( + (MapFunction) + value -> asRelatedEntity(value, entityClazz), + Encoders.bean(RelatedEntity.class)) + .map( + (MapFunction>) + e -> new Tuple2<>(e.getId(), e), + Encoders.tuple( + Encoders.STRING(), Encoders.kryo(RelatedEntity.class))) + .cache(); relsByTarget .joinWith(entities, entities.col("_1").equalTo(relsByTarget.col("_1")), "inner") - .map((MapFunction, Tuple2>, EntityRelEntity>) - t -> new EntityRelEntity(t._1()._2(), t._2()._2()), + .map( + (MapFunction< + Tuple2< + Tuple2, + Tuple2>, + EntityRelEntity>) + t -> new EntityRelEntity(t._1()._2(), t._2()._2()), Encoders.bean(EntityRelEntity.class)) .write() .mode(SaveMode.Overwrite) .parquet(outputPath + "/" + EntityType.fromClass(entityClazz)); } - private static Dataset readPathEntity(SparkSession spark, String inputEntityPath, Class entityClazz) { + private static Dataset readPathEntity( + SparkSession spark, String inputEntityPath, Class entityClazz) { log.info("Reading Graph table from: {}", inputEntityPath); - return spark - .read() + return spark.read() .textFile(inputEntityPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), Encoders.bean(entityClazz)); + .map( + (MapFunction) + value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)); } /** - * Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text file, + * Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline + * delimited json text file, * * @param spark * @param relationPath * @return the Dataset containing all the relationships */ - private static Dataset readPathRelation(SparkSession spark, final String relationPath) { + private static Dataset readPathRelation( + SparkSession spark, final String relationPath) { log.info("Reading relations from: {}", relationPath); - return spark.read() - .load(relationPath) - .as(Encoders.bean(SortableRelation.class)); + return spark.read().load(relationPath).as(Encoders.bean(SortableRelation.class)); } private static void removeOutputDir(SparkSession spark, String path) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } - - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java index 0a9235cc99..20786582f8 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java @@ -1,5 +1,7 @@ package eu.dnetlib.dhp.oa.provision; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; @@ -8,6 +10,8 @@ import eu.dnetlib.dhp.oa.provision.model.EntityRelEntity; import eu.dnetlib.dhp.oa.provision.model.TypedRow; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; +import java.util.List; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; @@ -23,60 +27,50 @@ import scala.Tuple2; import scala.collection.JavaConverters; import scala.collection.Seq; -import java.util.List; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - /** - * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects. - * The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization, - * and all the possible relationships (similarity links produced by the Dedup process are excluded). + * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of + * linked objects. The operation considers all the entity types (publication, dataset, software, + * ORP, project, datasource, organization, and all the possible relationships (similarity links + * produced by the Dedup process are excluded). * - * The operation is implemented by sequentially joining one entity type at time (E) with the relationships (R), and again - * by E, finally grouped by E.id; + *

The operation is implemented by sequentially joining one entity type at time (E) with the + * relationships (R), and again by E, finally grouped by E.id; * - * The workflow is organized in different parts aimed to to reduce the complexity of the operation - * 1) PrepareRelationsJob: - * only consider relationships that are not virtually deleted ($.dataInfo.deletedbyinference == false), each entity - * can be linked at most to 100 other objects + *

The workflow is organized in different parts aimed to to reduce the complexity of the + * operation 1) PrepareRelationsJob: only consider relationships that are not virtually deleted + * ($.dataInfo.deletedbyinference == false), each entity can be linked at most to 100 other objects * - * 2) JoinRelationEntityByTargetJob: - * (phase 1): prepare tuples [relation - target entity] (R - T): - * for each entity type E_i - * map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information - * join (R.target = T_i.id) - * save the tuples (R_i, T_i) - * (phase 2): - * create the union of all the entity types E, hash by id - * read the tuples (R, T), hash by R.source - * join E.id = (R, T).source, where E becomes the Source Entity S - * save the tuples (S, R, T) + *

2) JoinRelationEntityByTargetJob: (phase 1): prepare tuples [relation - target entity] (R - + * T): for each entity type E_i map E_i as RelatedEntity T_i to simplify the model and extracting + * only the necessary information join (R.target = T_i.id) save the tuples (R_i, T_i) (phase 2): + * create the union of all the entity types E, hash by id read the tuples (R, T), hash by R.source + * join E.id = (R, T).source, where E becomes the Source Entity S save the tuples (S, R, T) * - * 3) AdjacencyListBuilderJob: - * given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping the result as JoinedEntity + *

3) AdjacencyListBuilderJob: given the tuple (S - R - T) we need to group by S.id -> List [ R - + * T ], mapping the result as JoinedEntity * - * 4) XmlConverterJob: - * convert the JoinedEntities as XML records + *

4) XmlConverterJob: convert the JoinedEntities as XML records */ public class CreateRelatedEntitiesJob_phase2 { - private static final Logger log = LoggerFactory.getLogger(CreateRelatedEntitiesJob_phase2.class); + private static final Logger log = + LoggerFactory.getLogger(CreateRelatedEntitiesJob_phase2.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils.toString( - PrepareRelationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase2.json")); + String jsonConfiguration = + IOUtils.toString( + PrepareRelationsJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase2.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); String inputRelatedEntitiesPath = parser.get("inputRelatedEntitiesPath"); @@ -95,45 +89,88 @@ public class CreateRelatedEntitiesJob_phase2 { conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - runWithSparkSession(conf, isSparkSessionManaged, + runWithSparkSession( + conf, + isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - joinAllEntities(spark, inputRelatedEntitiesPath, inputGraphRootPath, outputPath, numPartitions); + joinAllEntities( + spark, + inputRelatedEntitiesPath, + inputGraphRootPath, + outputPath, + numPartitions); }); } - private static void joinAllEntities(SparkSession spark, String inputRelatedEntitiesPath, String inputGraphRootPath, String outputPath, int numPartitions) { + private static void joinAllEntities( + SparkSession spark, + String inputRelatedEntitiesPath, + String inputGraphRootPath, + String outputPath, + int numPartitions) { - Dataset> entities = readAllEntities(spark, inputGraphRootPath, numPartitions); - Dataset> relsBySource = readRelatedEntities(spark, inputRelatedEntitiesPath); + Dataset> entities = + readAllEntities(spark, inputGraphRootPath, numPartitions); + Dataset> relsBySource = + readRelatedEntities(spark, inputRelatedEntitiesPath); - entities - .joinWith(relsBySource, entities.col("_1").equalTo(relsBySource.col("_1")), "left_outer") - .map((MapFunction, Tuple2>, EntityRelEntity>) value -> { - EntityRelEntity re = new EntityRelEntity(); - re.setEntity(value._1()._2()); - Optional related = Optional.ofNullable(value._2()).map(Tuple2::_2); - if (related.isPresent()) { - re.setRelation(related.get().getRelation()); - re.setTarget(related.get().getTarget()); - } - return re; - }, Encoders.bean(EntityRelEntity.class)) + entities.joinWith( + relsBySource, + entities.col("_1").equalTo(relsBySource.col("_1")), + "left_outer") + .map( + (MapFunction< + Tuple2< + Tuple2, + Tuple2>, + EntityRelEntity>) + value -> { + EntityRelEntity re = new EntityRelEntity(); + re.setEntity(value._1()._2()); + Optional related = + Optional.ofNullable(value._2()).map(Tuple2::_2); + if (related.isPresent()) { + re.setRelation(related.get().getRelation()); + re.setTarget(related.get().getTarget()); + } + return re; + }, + Encoders.bean(EntityRelEntity.class)) .repartition(numPartitions) - .filter((FilterFunction) value -> value.getEntity() != null && StringUtils.isNotBlank(value.getEntity().getId())) + .filter( + (FilterFunction) + value -> + value.getEntity() != null + && StringUtils.isNotBlank( + value.getEntity().getId())) .write() .mode(SaveMode.Overwrite) .parquet(outputPath); } - private static Dataset> readAllEntities(SparkSession spark, String inputGraphPath, int numPartitions) { - Dataset publication = readPathEntity(spark, inputGraphPath + "/publication", Publication.class); - Dataset dataset = readPathEntity(spark, inputGraphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); - Dataset other = readPathEntity(spark, inputGraphPath + "/otherresearchproduct", OtherResearchProduct.class); - Dataset software = readPathEntity(spark, inputGraphPath + "/software", Software.class); - Dataset datasource = readPathEntity(spark, inputGraphPath + "/datasource", Datasource.class); - Dataset organization = readPathEntity(spark, inputGraphPath + "/organization", Organization.class); - Dataset project = readPathEntity(spark, inputGraphPath + "/project", Project.class); + private static Dataset> readAllEntities( + SparkSession spark, String inputGraphPath, int numPartitions) { + Dataset publication = + readPathEntity(spark, inputGraphPath + "/publication", Publication.class); + Dataset dataset = + readPathEntity( + spark, + inputGraphPath + "/dataset", + eu.dnetlib.dhp.schema.oaf.Dataset.class); + Dataset other = + readPathEntity( + spark, + inputGraphPath + "/otherresearchproduct", + OtherResearchProduct.class); + Dataset software = + readPathEntity(spark, inputGraphPath + "/software", Software.class); + Dataset datasource = + readPathEntity(spark, inputGraphPath + "/datasource", Datasource.class); + Dataset organization = + readPathEntity(spark, inputGraphPath + "/organization", Organization.class); + Dataset project = + readPathEntity(spark, inputGraphPath + "/project", Project.class); return publication .union(dataset) @@ -142,39 +179,55 @@ public class CreateRelatedEntitiesJob_phase2 { .union(datasource) .union(organization) .union(project) - .map((MapFunction>) + .map( + (MapFunction>) value -> new Tuple2<>(value.getId(), value), Encoders.tuple(Encoders.STRING(), Encoders.kryo(TypedRow.class))) .repartition(numPartitions); } - private static Dataset> readRelatedEntities(SparkSession spark, String inputRelatedEntitiesPath) { + private static Dataset> readRelatedEntities( + SparkSession spark, String inputRelatedEntitiesPath) { log.info("Reading related entities from: {}", inputRelatedEntitiesPath); - final List paths = HdfsSupport.listFiles(inputRelatedEntitiesPath, spark.sparkContext().hadoopConfiguration()); + final List paths = + HdfsSupport.listFiles( + inputRelatedEntitiesPath, spark.sparkContext().hadoopConfiguration()); log.info("Found paths: {}", String.join(",", paths)); return spark.read() .load(toSeq(paths)) .as(Encoders.bean(EntityRelEntity.class)) - .map((MapFunction>) + .map( + (MapFunction>) value -> new Tuple2<>(value.getRelation().getSource(), value), Encoders.tuple(Encoders.STRING(), Encoders.kryo(EntityRelEntity.class))); } - private static Dataset readPathEntity(SparkSession spark, String inputEntityPath, Class entityClazz) { + private static Dataset readPathEntity( + SparkSession spark, String inputEntityPath, Class entityClazz) { log.info("Reading Graph table from: {}", inputEntityPath); - return spark - .read() + return spark.read() .textFile(inputEntityPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), Encoders.bean(entityClazz)) - .map((MapFunction) value -> getTypedRow(StringUtils.substringAfterLast(inputEntityPath, "/"), value), Encoders.bean(TypedRow.class)); + .map( + (MapFunction) + value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + .map( + (MapFunction) + value -> + getTypedRow( + StringUtils.substringAfterLast( + inputEntityPath, "/"), + value), + Encoders.bean(TypedRow.class)); } - private static TypedRow getTypedRow(String type, OafEntity entity) throws JsonProcessingException { + private static TypedRow getTypedRow(String type, OafEntity entity) + throws JsonProcessingException { TypedRow t = new TypedRow(); t.setType(type); t.setDeleted(entity.getDataInfo().getDeletedbyinference()); @@ -190,5 +243,4 @@ public class CreateRelatedEntitiesJob_phase2 { private static Seq toSeq(List list) { return JavaConverters.asScalaIteratorConverter(list.iterator()).asScala().toSeq(); } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java index 95d2263b5e..a6c261ec72 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java @@ -1,5 +1,7 @@ package eu.dnetlib.dhp.oa.provision; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Iterables; import com.google.common.collect.Iterators; @@ -7,8 +9,8 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.oa.provision.model.SortableRelation; import eu.dnetlib.dhp.oa.provision.utils.RelationPartitioner; +import java.util.Optional; import org.apache.commons.io.IOUtils; -import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -22,40 +24,29 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import scala.Tuple2; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - /** - * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects. - * The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization, - * and all the possible relationships (similarity links produced by the Dedup process are excluded). + * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of + * linked objects. The operation considers all the entity types (publication, dataset, software, + * ORP, project, datasource, organization, and all the possible relationships (similarity links + * produced by the Dedup process are excluded). * - * The operation is implemented by sequentially joining one entity type at time (E) with the relationships (R), and again - * by E, finally grouped by E.id; + *

The operation is implemented by sequentially joining one entity type at time (E) with the + * relationships (R), and again by E, finally grouped by E.id; * - * The workflow is organized in different parts aimed to to reduce the complexity of the operation - * 1) PrepareRelationsJob: - * only consider relationships that are not virtually deleted ($.dataInfo.deletedbyinference == false), each entity - * can be linked at most to 100 other objects + *

The workflow is organized in different parts aimed to to reduce the complexity of the + * operation 1) PrepareRelationsJob: only consider relationships that are not virtually deleted + * ($.dataInfo.deletedbyinference == false), each entity can be linked at most to 100 other objects * - * 2) JoinRelationEntityByTargetJob: - * (phase 1): prepare tuples [relation - target entity] (R - T): - * for each entity type E_i - * map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information - * join (R.target = T_i.id) - * save the tuples (R_i, T_i) - * (phase 2): - * create the union of all the entity types E, hash by id - * read the tuples (R, T), hash by R.source - * join E.id = (R, T).source, where E becomes the Source Entity S - * save the tuples (S, R, T) + *

2) JoinRelationEntityByTargetJob: (phase 1): prepare tuples [relation - target entity] (R - + * T): for each entity type E_i map E_i as RelatedEntity T_i to simplify the model and extracting + * only the necessary information join (R.target = T_i.id) save the tuples (R_i, T_i) (phase 2): + * create the union of all the entity types E, hash by id read the tuples (R, T), hash by R.source + * join E.id = (R, T).source, where E becomes the Source Entity S save the tuples (S, R, T) * - * 3) AdjacencyListBuilderJob: - * given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping the result as JoinedEntity + *

3) AdjacencyListBuilderJob: given the tuple (S - R - T) we need to group by S.id -> List [ R - + * T ], mapping the result as JoinedEntity * - * 4) XmlConverterJob: - * convert the JoinedEntities as XML records + *

4) XmlConverterJob: convert the JoinedEntities as XML records */ public class PrepareRelationsJob { @@ -66,16 +57,17 @@ public class PrepareRelationsJob { public static final int MAX_RELS = 100; public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils.toString( - PrepareRelationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json")); + String jsonConfiguration = + IOUtils.toString( + PrepareRelationsJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); String inputRelationsPath = parser.get("inputRelationsPath"); @@ -89,18 +81,28 @@ public class PrepareRelationsJob { SparkConf conf = new SparkConf(); - runWithSparkSession(conf, isSparkSessionManaged, + runWithSparkSession( + conf, + isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); prepareRelationsFromPaths(spark, inputRelationsPath, outputPath, numPartitions); }); } - private static void prepareRelationsFromPaths(SparkSession spark, String inputRelationsPath, String outputPath, int numPartitions) { + private static void prepareRelationsFromPaths( + SparkSession spark, String inputRelationsPath, String outputPath, int numPartitions) { readPathRelation(spark, inputRelationsPath) - .filter((FilterFunction) value -> value.getDataInfo().getDeletedbyinference() == false) - .groupByKey((MapFunction) value -> value.getSource(), Encoders.STRING()) - .flatMapGroups((FlatMapGroupsFunction) (key, values) -> Iterators.limit(values, MAX_RELS), Encoders.bean(SortableRelation.class)) + .filter( + (FilterFunction) + value -> value.getDataInfo().getDeletedbyinference() == false) + .groupByKey( + (MapFunction) value -> value.getSource(), + Encoders.STRING()) + .flatMapGroups( + (FlatMapGroupsFunction) + (key, values) -> Iterators.limit(values, MAX_RELS), + Encoders.bean(SortableRelation.class)) .repartition(numPartitions) .write() .mode(SaveMode.Overwrite) @@ -108,30 +110,43 @@ public class PrepareRelationsJob { } /** - * Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text file, + * Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline + * delimited json text file, * * @param spark * @param inputPath * @return the Dataset containing all the relationships */ - private static Dataset readPathRelation(SparkSession spark, final String inputPath) { + private static Dataset readPathRelation( + SparkSession spark, final String inputPath) { return spark.read() .textFile(inputPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, SortableRelation.class), Encoders.bean(SortableRelation.class)); + .map( + (MapFunction) + value -> OBJECT_MAPPER.readValue(value, SortableRelation.class), + Encoders.bean(SortableRelation.class)); } - //TODO work in progress - private static void prepareRelationsRDDFromPaths(SparkSession spark, String inputRelationsPath, String outputPath, int numPartitions) { - JavaRDD rels = readPathRelationRDD(spark, inputRelationsPath) - .repartition(numPartitions); + // TODO work in progress + private static void prepareRelationsRDDFromPaths( + SparkSession spark, String inputRelationsPath, String outputPath, int numPartitions) { + JavaRDD rels = + readPathRelationRDD(spark, inputRelationsPath).repartition(numPartitions); - RDD d = rels - .filter(rel -> !rel.getDataInfo().getDeletedbyinference()) //only consider those that are not virtually deleted - .mapToPair((PairFunction) rel -> new Tuple2<>(rel, rel)) - .groupByKey(new RelationPartitioner(rels.getNumPartitions())) - .map(p -> Iterables.limit(p._2(), MAX_RELS)) - .flatMap(p -> p.iterator()) - .rdd(); + RDD d = + rels.filter( + rel -> + !rel.getDataInfo() + .getDeletedbyinference()) // only consider those + // that are not virtually + // deleted + .mapToPair( + (PairFunction) + rel -> new Tuple2<>(rel, rel)) + .groupByKey(new RelationPartitioner(rels.getNumPartitions())) + .map(p -> Iterables.limit(p._2(), MAX_RELS)) + .flatMap(p -> p.iterator()) + .rdd(); spark.createDataset(d, Encoders.bean(SortableRelation.class)) .write() @@ -139,14 +154,13 @@ public class PrepareRelationsJob { .parquet(outputPath); } - private static JavaRDD readPathRelationRDD(SparkSession spark, final String inputPath) { + private static JavaRDD readPathRelationRDD( + SparkSession spark, final String inputPath) { JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - return sc.textFile(inputPath) - .map(s -> OBJECT_MAPPER.readValue(s, SortableRelation.class)); + return sc.textFile(inputPath).map(s -> OBJECT_MAPPER.readValue(s, SortableRelation.class)); } private static void removeOutputDir(SparkSession spark, String path) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java index 059cb31f25..5ea267d629 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java @@ -1,68 +1,54 @@ package eu.dnetlib.dhp.oa.provision; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Maps; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.oa.provision.model.*; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; -import eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; import eu.dnetlib.dhp.schema.oaf.*; +import java.util.ArrayList; +import java.util.Map; +import java.util.Optional; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.SparkContext; -import org.apache.spark.api.java.function.Function; -import org.apache.spark.api.java.function.Function2; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.PairFunction; -import org.apache.spark.rdd.RDD; import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.apache.spark.util.LongAccumulator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import scala.Tuple2; -import java.util.ArrayList; -import java.util.List; -import java.util.Map; -import java.util.Optional; -import java.util.stream.Collectors; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - /** - * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects. - * The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization, - * and all the possible relationships (similarity links produced by the Dedup process are excluded). + * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of + * linked objects. The operation considers all the entity types (publication, dataset, software, + * ORP, project, datasource, organization, and all the possible relationships (similarity links + * produced by the Dedup process are excluded). * - * The workflow is organized in different parts aimed to to reduce the complexity of the operation - * 1) PrepareRelationsJob: - * only consider relationships that are not virtually deleted ($.dataInfo.deletedbyinference == false), each entity - * can be linked at most to 100 other objects + *

The workflow is organized in different parts aimed to to reduce the complexity of the + * operation 1) PrepareRelationsJob: only consider relationships that are not virtually deleted + * ($.dataInfo.deletedbyinference == false), each entity can be linked at most to 100 other objects * - * 2) JoinRelationEntityByTargetJob: - * (phase 1): prepare tuples [relation - target entity] (R - T): - * for each entity type E_i - * map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information - * join (R.target = T_i.id) - * save the tuples (R_i, T_i) - * (phase 2): - * create the union of all the entity types E, hash by id - * read the tuples (R, T), hash by R.source - * join E.id = (R, T).source, where E becomes the Source Entity S - * save the tuples (S, R, T) + *

2) JoinRelationEntityByTargetJob: (phase 1): prepare tuples [relation - target entity] (R - + * T): for each entity type E_i map E_i as RelatedEntity T_i to simplify the model and extracting + * only the necessary information join (R.target = T_i.id) save the tuples (R_i, T_i) (phase 2): + * create the union of all the entity types E, hash by id read the tuples (R, T), hash by R.source + * join E.id = (R, T).source, where E becomes the Source Entity S save the tuples (S, R, T) * - * 3) AdjacencyListBuilderJob: - * given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping the result as JoinedEntity + *

3) AdjacencyListBuilderJob: given the tuple (S - R - T) we need to group by S.id -> List [ R - + * T ], mapping the result as JoinedEntity * - * 4) XmlConverterJob: - * convert the JoinedEntities as XML records + *

4) XmlConverterJob: convert the JoinedEntities as XML records */ public class XmlConverterJob { @@ -74,16 +60,17 @@ public class XmlConverterJob { public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - XmlConverterJob.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + XmlConverterJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json"))); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); String inputPath = parser.get("inputPath"); @@ -100,37 +87,71 @@ public class XmlConverterJob { SparkConf conf = new SparkConf(); - runWithSparkSession(conf, isSparkSessionManaged, + runWithSparkSession( + conf, + isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - convertToXml(spark, inputPath, outputPath, ContextMapper.fromIS(isLookupUrl), otherDsTypeId); + convertToXml( + spark, + inputPath, + outputPath, + ContextMapper.fromIS(isLookupUrl), + otherDsTypeId); }); - } - private static void convertToXml(SparkSession spark, String inputPath, String outputPath, ContextMapper contextMapper, String otherDsTypeId) { + private static void convertToXml( + SparkSession spark, + String inputPath, + String outputPath, + ContextMapper contextMapper, + String otherDsTypeId) { - final XmlRecordFactory recordFactory = new XmlRecordFactory(prepareAccumulators(spark.sparkContext()), contextMapper, false, schemaLocation, otherDsTypeId); + final XmlRecordFactory recordFactory = + new XmlRecordFactory( + prepareAccumulators(spark.sparkContext()), + contextMapper, + false, + schemaLocation, + otherDsTypeId); spark.read() .load(inputPath) .as(Encoders.bean(JoinedEntity.class)) - .map((MapFunction) j -> { - if (j.getLinks() != null) { - j.setLinks(j.getLinks() - .stream() - .filter(t -> t.getRelation() != null & t.getRelatedEntity() != null) - .collect(Collectors.toCollection(ArrayList::new))); - } - return j; - }, Encoders.bean(JoinedEntity.class)) - .map((MapFunction>) je -> new Tuple2<>( - je.getEntity().getId(), - recordFactory.build(je) - ), Encoders.tuple(Encoders.STRING(), Encoders.STRING())) + .map( + (MapFunction) + j -> { + if (j.getLinks() != null) { + j.setLinks( + j.getLinks().stream() + .filter( + t -> + t.getRelation() != null + & t + .getRelatedEntity() + != null) + .collect( + Collectors.toCollection( + ArrayList::new))); + } + return j; + }, + Encoders.bean(JoinedEntity.class)) + .map( + (MapFunction>) + je -> new Tuple2<>(je.getEntity().getId(), recordFactory.build(je)), + Encoders.tuple(Encoders.STRING(), Encoders.STRING())) .javaRDD() - .mapToPair((PairFunction, Text, Text>) t -> new Tuple2<>(new Text(t._1()), new Text(t._2()))) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + .mapToPair( + (PairFunction, Text, Text>) + t -> new Tuple2<>(new Text(t._1()), new Text(t._2()))) + .saveAsHadoopFile( + outputPath, + Text.class, + Text.class, + SequenceFileOutputFormat.class, + GzipCodec.class); } private static void removeOutputDir(SparkSession spark, String path) { @@ -139,28 +160,62 @@ public class XmlConverterJob { private static Map prepareAccumulators(SparkContext sc) { Map accumulators = Maps.newHashMap(); - accumulators.put("resultResult_similarity_isAmongTopNSimilarDocuments", sc.longAccumulator("resultResult_similarity_isAmongTopNSimilarDocuments")); - accumulators.put("resultResult_similarity_hasAmongTopNSimilarDocuments", sc.longAccumulator("resultResult_similarity_hasAmongTopNSimilarDocuments")); - accumulators.put("resultResult_supplement_isSupplementTo", sc.longAccumulator("resultResult_supplement_isSupplementTo")); - accumulators.put("resultResult_supplement_isSupplementedBy", sc.longAccumulator("resultResult_supplement_isSupplementedBy")); - accumulators.put("resultResult_dedup_isMergedIn", sc.longAccumulator("resultResult_dedup_isMergedIn")); - accumulators.put("resultResult_dedup_merges", sc.longAccumulator("resultResult_dedup_merges")); + accumulators.put( + "resultResult_similarity_isAmongTopNSimilarDocuments", + sc.longAccumulator("resultResult_similarity_isAmongTopNSimilarDocuments")); + accumulators.put( + "resultResult_similarity_hasAmongTopNSimilarDocuments", + sc.longAccumulator("resultResult_similarity_hasAmongTopNSimilarDocuments")); + accumulators.put( + "resultResult_supplement_isSupplementTo", + sc.longAccumulator("resultResult_supplement_isSupplementTo")); + accumulators.put( + "resultResult_supplement_isSupplementedBy", + sc.longAccumulator("resultResult_supplement_isSupplementedBy")); + accumulators.put( + "resultResult_dedup_isMergedIn", + sc.longAccumulator("resultResult_dedup_isMergedIn")); + accumulators.put( + "resultResult_dedup_merges", sc.longAccumulator("resultResult_dedup_merges")); - accumulators.put("resultResult_publicationDataset_isRelatedTo", sc.longAccumulator("resultResult_publicationDataset_isRelatedTo")); - accumulators.put("resultResult_relationship_isRelatedTo", sc.longAccumulator("resultResult_relationship_isRelatedTo")); - accumulators.put("resultProject_outcome_isProducedBy", sc.longAccumulator("resultProject_outcome_isProducedBy")); - accumulators.put("resultProject_outcome_produces", sc.longAccumulator("resultProject_outcome_produces")); - accumulators.put("resultOrganization_affiliation_isAuthorInstitutionOf", sc.longAccumulator("resultOrganization_affiliation_isAuthorInstitutionOf")); + accumulators.put( + "resultResult_publicationDataset_isRelatedTo", + sc.longAccumulator("resultResult_publicationDataset_isRelatedTo")); + accumulators.put( + "resultResult_relationship_isRelatedTo", + sc.longAccumulator("resultResult_relationship_isRelatedTo")); + accumulators.put( + "resultProject_outcome_isProducedBy", + sc.longAccumulator("resultProject_outcome_isProducedBy")); + accumulators.put( + "resultProject_outcome_produces", + sc.longAccumulator("resultProject_outcome_produces")); + accumulators.put( + "resultOrganization_affiliation_isAuthorInstitutionOf", + sc.longAccumulator("resultOrganization_affiliation_isAuthorInstitutionOf")); - accumulators.put("resultOrganization_affiliation_hasAuthorInstitution", sc.longAccumulator("resultOrganization_affiliation_hasAuthorInstitution")); - accumulators.put("projectOrganization_participation_hasParticipant", sc.longAccumulator("projectOrganization_participation_hasParticipant")); - accumulators.put("projectOrganization_participation_isParticipant", sc.longAccumulator("projectOrganization_participation_isParticipant")); - accumulators.put("organizationOrganization_dedup_isMergedIn", sc.longAccumulator("organizationOrganization_dedup_isMergedIn")); - accumulators.put("organizationOrganization_dedup_merges", sc.longAccumulator("resultProject_outcome_produces")); - accumulators.put("datasourceOrganization_provision_isProvidedBy", sc.longAccumulator("datasourceOrganization_provision_isProvidedBy")); - accumulators.put("datasourceOrganization_provision_provides", sc.longAccumulator("datasourceOrganization_provision_provides")); + accumulators.put( + "resultOrganization_affiliation_hasAuthorInstitution", + sc.longAccumulator("resultOrganization_affiliation_hasAuthorInstitution")); + accumulators.put( + "projectOrganization_participation_hasParticipant", + sc.longAccumulator("projectOrganization_participation_hasParticipant")); + accumulators.put( + "projectOrganization_participation_isParticipant", + sc.longAccumulator("projectOrganization_participation_isParticipant")); + accumulators.put( + "organizationOrganization_dedup_isMergedIn", + sc.longAccumulator("organizationOrganization_dedup_isMergedIn")); + accumulators.put( + "organizationOrganization_dedup_merges", + sc.longAccumulator("resultProject_outcome_produces")); + accumulators.put( + "datasourceOrganization_provision_isProvidedBy", + sc.longAccumulator("datasourceOrganization_provision_isProvidedBy")); + accumulators.put( + "datasourceOrganization_provision_provides", + sc.longAccumulator("datasourceOrganization_provision_provides")); return accumulators; } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java index 84538c924a..2215eaad2f 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java @@ -1,5 +1,7 @@ package eu.dnetlib.dhp.oa.provision; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import com.lucidworks.spark.util.SolrSupport; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory; @@ -8,6 +10,16 @@ import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpDocumentNotFoundException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import java.io.IOException; +import java.io.StringReader; +import java.io.StringWriter; +import java.text.SimpleDateFormat; +import java.util.Date; +import java.util.Optional; +import javax.xml.transform.Transformer; +import javax.xml.transform.TransformerException; +import javax.xml.transform.stream.StreamResult; +import javax.xml.transform.stream.StreamSource; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.io.Text; @@ -18,19 +30,6 @@ import org.apache.spark.rdd.RDD; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.xml.transform.Transformer; -import javax.xml.transform.TransformerException; -import javax.xml.transform.stream.StreamResult; -import javax.xml.transform.stream.StreamSource; -import java.io.IOException; -import java.io.StringReader; -import java.io.StringWriter; -import java.text.SimpleDateFormat; -import java.util.Date; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - public class XmlIndexingJob { private static final Logger log = LoggerFactory.getLogger(XmlIndexingJob.class); @@ -44,16 +43,17 @@ public class XmlIndexingJob { public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - XmlIndexingJob.class.getResourceAsStream( - "/eu/dnetlib/dhp/oa/provision/input_params_update_index.json"))); + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + XmlIndexingJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/provision/input_params_update_index.json"))); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("inputPath"); @@ -65,7 +65,10 @@ public class XmlIndexingJob { final String format = parser.get("format"); log.info("format: {}", format); - final Integer batchSize = parser.getObjectMap().containsKey("batchSize") ? Integer.valueOf(parser.get("batchSize")) : DEFAULT_BATCH_SIZE; + final Integer batchSize = + parser.getObjectMap().containsKey("batchSize") + ? Integer.valueOf(parser.get("batchSize")) + : DEFAULT_BATCH_SIZE; log.info("batchSize: {}", batchSize); final ISLookUpService isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl); @@ -87,17 +90,30 @@ public class XmlIndexingJob { final SparkConf conf = new SparkConf(); - runWithSparkSession(conf, isSparkSessionManaged, + runWithSparkSession( + conf, + isSparkSessionManaged, spark -> { - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + final JavaSparkContext sc = + JavaSparkContext.fromSparkContext(spark.sparkContext()); - RDD docs = sc.sequenceFile(inputPath, Text.class, Text.class) - .map(t -> t._2().toString()) - .map(s -> toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), s)) - .map(s -> new StreamingInputDocumentFactory(version, dsId).parseDocument(s)) - .rdd(); + RDD docs = + sc.sequenceFile(inputPath, Text.class, Text.class) + .map(t -> t._2().toString()) + .map( + s -> + toIndexRecord( + SaxonTransformerFactory.newInstance( + indexRecordXslt), + s)) + .map( + s -> + new StreamingInputDocumentFactory(version, dsId) + .parseDocument(s)) + .rdd(); - final String collection = format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION; + final String collection = + format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION; SolrSupport.indexDocs(zkHost, collection, batchSize, docs); }); } @@ -116,15 +132,16 @@ public class XmlIndexingJob { /** * Creates the XSLT responsible for building the index xml records. * - * @param format Metadata format name (DMF|TMF) - * @param xslt xslt for building the index record transformer - * @param fields the list of fields + * @param format Metadata format name (DMF|TMF) + * @param xslt xslt for building the index record transformer + * @param fields the list of fields * @return the javax.xml.transform.Transformer - * @throws ISLookUpException could happen - * @throws IOException could happen + * @throws ISLookUpException could happen + * @throws IOException could happen * @throws TransformerException could happen */ - private static String getLayoutTransformer(String format, String fields, String xslt) throws TransformerException { + private static String getLayoutTransformer(String format, String fields, String xslt) + throws TransformerException { final Transformer layoutTransformer = SaxonTransformerFactory.newInstance(xslt); final StreamResult layoutToXsltXslt = new StreamResult(new StringWriter()); @@ -136,7 +153,9 @@ public class XmlIndexingJob { } /** - * method return a solr-compatible string representation of a date, used to mark all records as indexed today + * method return a solr-compatible string representation of a date, used to mark all records as + * indexed today + * * @return the parsed date */ public static String getRecordDatestamp() { @@ -144,18 +163,22 @@ public class XmlIndexingJob { } /** - * Method retrieves from the information system the list of fields associated to the given MDFormat name + * Method retrieves from the information system the list of fields associated to the given + * MDFormat name * * @param isLookup the ISLookup service stub * @param format the Metadata format name * @return the string representation of the list of fields to be indexed - * * @throws ISLookUpDocumentNotFoundException * @throws ISLookUpException */ - private static String getLayoutSource(final ISLookUpService isLookup, final String format) throws ISLookUpDocumentNotFoundException, ISLookUpException { - return doLookup(isLookup, String.format( - "collection('')//RESOURCE_PROFILE[.//RESOURCE_TYPE/@value = 'MDFormatDSResourceType' and .//NAME='%s']//LAYOUT[@name='%s']", format, LAYOUT)); + private static String getLayoutSource(final ISLookUpService isLookup, final String format) + throws ISLookUpDocumentNotFoundException, ISLookUpException { + return doLookup( + isLookup, + String.format( + "collection('')//RESOURCE_PROFILE[.//RESOURCE_TYPE/@value = 'MDFormatDSResourceType' and .//NAME='%s']//LAYOUT[@name='%s']", + format, LAYOUT)); } /** @@ -163,42 +186,54 @@ public class XmlIndexingJob { * * @param isLookup the ISLookup service stub * @return the string representation of the XSLT contained in the transformation rule profile - * * @throws ISLookUpDocumentNotFoundException * @throws ISLookUpException */ private static String getLayoutTransformer(ISLookUpService isLookup) throws ISLookUpException { - return doLookup(isLookup, "collection('/db/DRIVER/TransformationRuleDSResources/TransformationRuleDSResourceType')" + - "//RESOURCE_PROFILE[./BODY/CONFIGURATION/SCRIPT/TITLE/text() = 'openaireLayoutToRecordStylesheet']//CODE/node()"); + return doLookup( + isLookup, + "collection('/db/DRIVER/TransformationRuleDSResources/TransformationRuleDSResourceType')" + + "//RESOURCE_PROFILE[./BODY/CONFIGURATION/SCRIPT/TITLE/text() = 'openaireLayoutToRecordStylesheet']//CODE/node()"); } /** - * Method retrieves from the information system the IndexDS profile ID associated to the given MDFormat name + * Method retrieves from the information system the IndexDS profile ID associated to the given + * MDFormat name + * * @param format * @param isLookup * @return the IndexDS identifier * @throws ISLookUpException */ - private static String getDsId(String format, ISLookUpService isLookup) throws ISLookUpException { - return doLookup(isLookup, String.format("collection('/db/DRIVER/IndexDSResources/IndexDSResourceType')" + - "//RESOURCE_PROFILE[./BODY/CONFIGURATION/METADATA_FORMAT/text() = '%s']//RESOURCE_IDENTIFIER/@value/string()", format)); + private static String getDsId(String format, ISLookUpService isLookup) + throws ISLookUpException { + return doLookup( + isLookup, + String.format( + "collection('/db/DRIVER/IndexDSResources/IndexDSResourceType')" + + "//RESOURCE_PROFILE[./BODY/CONFIGURATION/METADATA_FORMAT/text() = '%s']//RESOURCE_IDENTIFIER/@value/string()", + format)); } /** * Method retrieves from the information system the zookeeper quorum of the Solr server + * * @param isLookup * @return the zookeeper quorum of the Solr server * @throws ISLookUpException */ private static String getZkHost(ISLookUpService isLookup) throws ISLookUpException { - return doLookup(isLookup, "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='IndexServiceResourceType'] return $x//PROTOCOL[./@name='solr']/@address/string()"); + return doLookup( + isLookup, + "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='IndexServiceResourceType'] return $x//PROTOCOL[./@name='solr']/@address/string()"); } - private static String doLookup(ISLookUpService isLookup, String xquery) throws ISLookUpException { + private static String doLookup(ISLookUpService isLookup, String xquery) + throws ISLookUpException { log.info(String.format("running xquery: %s", xquery)); final String res = isLookup.getResourceProfileByQuery(xquery); - log.info(String.format("got response (100 chars): %s", StringUtils.left(res, 100) + " ...")); + log.info( + String.format("got response (100 chars): %s", StringUtils.left(res, 100) + " ...")); return res; } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/EntityRelEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/EntityRelEntity.java index e1ca8e3164..5873155cfe 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/EntityRelEntity.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/EntityRelEntity.java @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.oa.provision.model; import com.google.common.base.Objects; - import java.io.Serializable; public class EntityRelEntity implements Serializable { @@ -10,8 +9,7 @@ public class EntityRelEntity implements Serializable { private SortableRelation relation; private RelatedEntity target; - public EntityRelEntity() { - } + public EntityRelEntity() {} public EntityRelEntity(SortableRelation relation, RelatedEntity target) { this(null, relation, target); @@ -52,9 +50,9 @@ public class EntityRelEntity implements Serializable { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; EntityRelEntity that = (EntityRelEntity) o; - return Objects.equal(entity, that.entity) && - Objects.equal(relation, that.relation) && - Objects.equal(target, that.target); + return Objects.equal(entity, that.entity) + && Objects.equal(relation, that.relation) + && Objects.equal(target, that.target); } @Override diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java index b6e97a503f..519d7f2bd7 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java @@ -9,8 +9,7 @@ public class JoinedEntity implements Serializable { private List links; - public JoinedEntity() { - } + public JoinedEntity() {} public TypedRow getEntity() { return entity; diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java index 011d9276d3..2964c51eef 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java @@ -5,7 +5,6 @@ import eu.dnetlib.dhp.schema.oaf.Instance; import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; - import java.io.Serializable; import java.util.List; @@ -32,7 +31,7 @@ public class RelatedEntity implements Serializable { private Qualifier datasourcetype; private Qualifier datasourcetypeui; private Qualifier openairecompatibility; - //private String aggregatortype; + // private String aggregatortype; // organization private String legalname; @@ -235,33 +234,56 @@ public class RelatedEntity implements Serializable { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; RelatedEntity that = (RelatedEntity) o; - return Objects.equal(id, that.id) && - Objects.equal(type, that.type) && - Objects.equal(title, that.title) && - Objects.equal(websiteurl, that.websiteurl) && - Objects.equal(dateofacceptance, that.dateofacceptance) && - Objects.equal(publisher, that.publisher) && - Objects.equal(pid, that.pid) && - Objects.equal(codeRepositoryUrl, that.codeRepositoryUrl) && - Objects.equal(resulttype, that.resulttype) && - Objects.equal(collectedfrom, that.collectedfrom) && - Objects.equal(instances, that.instances) && - Objects.equal(officialname, that.officialname) && - Objects.equal(datasourcetype, that.datasourcetype) && - Objects.equal(datasourcetypeui, that.datasourcetypeui) && - Objects.equal(openairecompatibility, that.openairecompatibility) && - Objects.equal(legalname, that.legalname) && - Objects.equal(legalshortname, that.legalshortname) && - Objects.equal(country, that.country) && - Objects.equal(projectTitle, that.projectTitle) && - Objects.equal(code, that.code) && - Objects.equal(acronym, that.acronym) && - Objects.equal(contracttype, that.contracttype) && - Objects.equal(fundingtree, that.fundingtree); + return Objects.equal(id, that.id) + && Objects.equal(type, that.type) + && Objects.equal(title, that.title) + && Objects.equal(websiteurl, that.websiteurl) + && Objects.equal(dateofacceptance, that.dateofacceptance) + && Objects.equal(publisher, that.publisher) + && Objects.equal(pid, that.pid) + && Objects.equal(codeRepositoryUrl, that.codeRepositoryUrl) + && Objects.equal(resulttype, that.resulttype) + && Objects.equal(collectedfrom, that.collectedfrom) + && Objects.equal(instances, that.instances) + && Objects.equal(officialname, that.officialname) + && Objects.equal(datasourcetype, that.datasourcetype) + && Objects.equal(datasourcetypeui, that.datasourcetypeui) + && Objects.equal(openairecompatibility, that.openairecompatibility) + && Objects.equal(legalname, that.legalname) + && Objects.equal(legalshortname, that.legalshortname) + && Objects.equal(country, that.country) + && Objects.equal(projectTitle, that.projectTitle) + && Objects.equal(code, that.code) + && Objects.equal(acronym, that.acronym) + && Objects.equal(contracttype, that.contracttype) + && Objects.equal(fundingtree, that.fundingtree); } @Override public int hashCode() { - return Objects.hashCode(id, type, title, websiteurl, dateofacceptance, publisher, pid, codeRepositoryUrl, resulttype, collectedfrom, instances, officialname, datasourcetype, datasourcetypeui, openairecompatibility, legalname, legalshortname, country, projectTitle, code, acronym, contracttype, fundingtree); + return Objects.hashCode( + id, + type, + title, + websiteurl, + dateofacceptance, + publisher, + pid, + codeRepositoryUrl, + resulttype, + collectedfrom, + instances, + officialname, + datasourcetype, + datasourcetypeui, + openairecompatibility, + legalname, + legalshortname, + country, + projectTitle, + code, + acronym, + contracttype, + fundingtree); } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelation.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelation.java index b294a66334..467bd20d51 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelation.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelation.java @@ -3,13 +3,12 @@ package eu.dnetlib.dhp.oa.provision.model; import com.google.common.collect.ComparisonChain; import com.google.common.collect.Maps; import eu.dnetlib.dhp.schema.oaf.Relation; - import java.io.Serializable; import java.util.Map; public class SortableRelation extends Relation implements Comparable, Serializable { - private final static Map weights = Maps.newHashMap(); + private static final Map weights = Maps.newHashMap(); static { weights.put("outcome", 0); diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Tuple2.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Tuple2.java index 942acaea1d..30de29038d 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Tuple2.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Tuple2.java @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.oa.provision.model; import eu.dnetlib.dhp.schema.oaf.Relation; - import java.io.Serializable; import java.util.Objects; @@ -11,8 +10,7 @@ public class Tuple2 implements Serializable { private RelatedEntity relatedEntity; - public Tuple2() { - } + public Tuple2() {} public Tuple2(Relation relation, RelatedEntity relatedEntity) { this.relation = relation; @@ -47,5 +45,4 @@ public class Tuple2 implements Serializable { public int hashCode() { return Objects.hash(getRelation().hashCode()); } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TypedRow.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TypedRow.java index 54f34802f0..01467ab7c5 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TypedRow.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TypedRow.java @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.oa.provision.model; import com.google.common.base.Objects; - import java.io.Serializable; public class TypedRow implements Serializable { diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextDef.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextDef.java index fba3a8e7bb..f85606b2ee 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextDef.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextDef.java @@ -48,4 +48,4 @@ public class ContextDef implements Serializable { public void setType(final String type) { this.type = type; } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextMapper.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextMapper.java index bdeacf45e3..fc71d8861d 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextMapper.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextMapper.java @@ -4,22 +4,23 @@ import com.google.common.base.Joiner; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import java.io.Serializable; +import java.io.StringReader; +import java.util.HashMap; import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.Node; import org.dom4j.io.SAXReader; -import java.io.Serializable; -import java.io.StringReader; -import java.util.HashMap; - public class ContextMapper extends HashMap implements Serializable { private static final long serialVersionUID = 2159682308502487305L; - private final static String XQUERY = "for $x in //RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ContextDSResourceType']//*[name()='context' or name()='category' or name()='concept'] return "; + private static final String XQUERY = + "for $x in //RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ContextDSResourceType']//*[name()='context' or name()='category' or name()='concept'] return "; - public static ContextMapper fromIS(final String isLookupUrl) throws DocumentException, ISLookUpException { + public static ContextMapper fromIS(final String isLookupUrl) + throws DocumentException, ISLookUpException { ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); StringBuilder sb = new StringBuilder(""); Joiner.on("").appendTo(sb, isLookUp.quickSearchProfile(XQUERY)); @@ -42,5 +43,4 @@ public class ContextMapper extends HashMap implements Serial } return contextMapper; } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java index 42174ac94d..cea3539bce 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java @@ -1,18 +1,17 @@ package eu.dnetlib.dhp.oa.provision.utils; +import static org.apache.commons.lang3.StringUtils.substringAfter; + import com.google.common.collect.Sets; import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.oaf.*; - import java.util.List; import java.util.Objects; import java.util.Optional; import java.util.Set; import java.util.stream.Collectors; -import static org.apache.commons.lang3.StringUtils.substringAfter; - public class GraphMappingUtils { public static final String SEPARATOR = "_"; @@ -33,7 +32,6 @@ public class GraphMappingUtils { case dataset: case otherresearchproduct: case software: - Result result = (Result) entity; if (result.getTitle() == null && !result.getTitle().isEmpty()) { @@ -45,8 +43,8 @@ public class GraphMappingUtils { re.setResulttype(result.getResulttype()); re.setInstances(result.getInstance()); - //TODO still to be mapped - //re.setCodeRepositoryUrl(j.read("$.coderepositoryurl")); + // TODO still to be mapped + // re.setCodeRepositoryUrl(j.read("$.coderepositoryurl")); break; case datasource: @@ -76,9 +74,8 @@ public class GraphMappingUtils { List> f = p.getFundingtree(); if (!f.isEmpty()) { - re.setFundingtree(f.stream() - .map(s -> s.getValue()) - .collect(Collectors.toList())); + re.setFundingtree( + f.stream().map(s -> s.getValue()).collect(Collectors.toList())); } break; } @@ -104,5 +101,4 @@ public class GraphMappingUtils { public static String getRelDescriptor(String relType, String subRelType, String relClass) { return relType + SEPARATOR + subRelType + SEPARATOR + relClass; } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/LicenseComparator.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/LicenseComparator.java index 17073038de..9415cbd062 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/LicenseComparator.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/LicenseComparator.java @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.oa.provision.utils; import eu.dnetlib.dhp.schema.oaf.Qualifier; - import java.util.Comparator; public class LicenseComparator implements Comparator { @@ -45,5 +44,4 @@ public class LicenseComparator implements Comparator { // Else (but unlikely), lexicographical ordering will do. return lClass.compareTo(rClass); } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/RelationPartitioner.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/RelationPartitioner.java index c8e7a24292..ca0a4ca513 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/RelationPartitioner.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/RelationPartitioner.java @@ -5,8 +5,9 @@ import org.apache.spark.Partitioner; import org.apache.spark.util.Utils; /** - * Used in combination with SortableRelationKey, allows to partition the records by source id, therefore - * allowing to sort relations sharing the same source id by the ordering defined in SortableRelationKey. + * Used in combination with SortableRelationKey, allows to partition the records by source id, + * therefore allowing to sort relations sharing the same source id by the ordering defined in + * SortableRelationKey. */ public class RelationPartitioner extends Partitioner { @@ -23,7 +24,7 @@ public class RelationPartitioner extends Partitioner { @Override public int getPartition(Object key) { - return Utils.nonNegativeMod(((SortableRelation) key).getSource().hashCode(), numPartitions()); + return Utils.nonNegativeMod( + ((SortableRelation) key).getSource().hashCode(), numPartitions()); } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/StreamingInputDocumentFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/StreamingInputDocumentFactory.java index f0499781f1..e86d37fa1f 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/StreamingInputDocumentFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/StreamingInputDocumentFactory.java @@ -1,5 +1,6 @@ package eu.dnetlib.dhp.oa.provision.utils; +import com.google.common.collect.Lists; import java.io.StringReader; import java.io.StringWriter; import java.util.Arrays; @@ -10,29 +11,23 @@ import javax.xml.stream.*; import javax.xml.stream.events.Namespace; import javax.xml.stream.events.StartElement; import javax.xml.stream.events.XMLEvent; - -import com.google.common.collect.Lists; import org.apache.solr.common.SolrInputDocument; /** * Optimized version of the document parser, drop in replacement of InputDocumentFactory. * - *

- * Faster because: - *

+ *

Faster because: + * *

    - *
  • Doesn't create a DOM for the full document
    • - *
  • Doesn't execute xpaths agains the DOM
    • - *
  • Quickly serialize the 'result' element directly in a string.
    • - *
  • Uses less memory: less pressure on GC and allows more threads to process this in parallel
    • + *
  • Doesn't create a DOM for the full document + *
  • Doesn't execute xpaths agains the DOM + *
  • Quickly serialize the 'result' element directly in a string. + *
  • Uses less memory: less pressure on GC and allows more threads to process this in parallel *
* - *

- * This class is fully reentrant and can be invoked in parallel. - *

+ *

This class is fully reentrant and can be invoked in parallel. * * @author claudio - * */ public class StreamingInputDocumentFactory { @@ -50,7 +45,9 @@ public class StreamingInputDocumentFactory { private static final String outFormat = new String("yyyy-MM-dd'T'hh:mm:ss'Z'"); - private final static List dateFormats = Arrays.asList("yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "dd-MM-yyyy", "dd/MM/yyyy", "yyyy"); + private static final List dateFormats = + Arrays.asList( + "yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "dd-MM-yyyy", "dd/MM/yyyy", "yyyy"); private static final String DEFAULTDNETRESULT = "dnetResult"; @@ -62,11 +59,14 @@ public class StreamingInputDocumentFactory { private static final int MAX_FIELD_LENGTH = 25000; - private ThreadLocal inputFactory = ThreadLocal.withInitial(() -> XMLInputFactory.newInstance()); + private ThreadLocal inputFactory = + ThreadLocal.withInitial(() -> XMLInputFactory.newInstance()); - private ThreadLocal outputFactory = ThreadLocal.withInitial(() -> XMLOutputFactory.newInstance()); + private ThreadLocal outputFactory = + ThreadLocal.withInitial(() -> XMLOutputFactory.newInstance()); - private ThreadLocal eventFactory = ThreadLocal.withInitial(() -> XMLEventFactory.newInstance()); + private ThreadLocal eventFactory = + ThreadLocal.withInitial(() -> XMLEventFactory.newInstance()); private String version; @@ -78,7 +78,8 @@ public class StreamingInputDocumentFactory { this(version, dsId, DEFAULTDNETRESULT); } - public StreamingInputDocumentFactory(final String version, final String dsId, final String resultName) { + public StreamingInputDocumentFactory( + final String version, final String dsId, final String resultName) { this.version = version; this.dsId = dsId; this.resultName = resultName; @@ -90,7 +91,8 @@ public class StreamingInputDocumentFactory { final List nsList = Lists.newLinkedList(); try { - XMLEventReader parser = inputFactory.get().createXMLEventReader(new StringReader(inputDocument)); + XMLEventReader parser = + inputFactory.get().createXMLEventReader(new StringReader(inputDocument)); final SolrInputDocument indexDocument = new SolrInputDocument(new HashMap<>()); @@ -150,13 +152,16 @@ public class StreamingInputDocumentFactory { * @param parser * @throws XMLStreamException */ - protected void parseTargetFields(final SolrInputDocument indexDocument, final XMLEventReader parser) throws XMLStreamException { + protected void parseTargetFields( + final SolrInputDocument indexDocument, final XMLEventReader parser) + throws XMLStreamException { boolean hasFields = false; while (parser.hasNext()) { final XMLEvent targetEvent = parser.nextEvent(); - if (targetEvent.isEndElement() && targetEvent.asEndElement().getName().getLocalPart().equals(TARGETFIELDS)) { + if (targetEvent.isEndElement() + && targetEvent.asEndElement().getName().getLocalPart().equals(TARGETFIELDS)) { break; } @@ -185,18 +190,21 @@ public class StreamingInputDocumentFactory { * @param nsList * @throws XMLStreamException */ - protected void copyResult(final SolrInputDocument indexDocument, - final StringWriter results, - final XMLEventReader parser, - final List nsList, - final String dnetResult) throws XMLStreamException { + protected void copyResult( + final SolrInputDocument indexDocument, + final StringWriter results, + final XMLEventReader parser, + final List nsList, + final String dnetResult) + throws XMLStreamException { final XMLEventWriter writer = outputFactory.get().createXMLEventWriter(results); for (Namespace ns : nsList) { eventFactory.get().createNamespace(ns.getPrefix(), ns.getNamespaceURI()); } - StartElement newRecord = eventFactory.get().createStartElement("", null, RESULT, null, nsList.iterator()); + StartElement newRecord = + eventFactory.get().createStartElement("", null, RESULT, null, nsList.iterator()); // new root record writer.add(newRecord); @@ -206,7 +214,8 @@ public class StreamingInputDocumentFactory { final XMLEvent resultEvent = parser.nextEvent(); // TODO: replace with depth tracking instead of close tag tracking. - if (resultEvent.isEndElement() && resultEvent.asEndElement().getName().getLocalPart().equals(dnetResult)) { + if (resultEvent.isEndElement() + && resultEvent.asEndElement().getName().getLocalPart().equals(dnetResult)) { writer.add(eventFactory.get().createEndElement("", null, RESULT)); break; } @@ -224,7 +233,8 @@ public class StreamingInputDocumentFactory { * @param field * @param value */ - private final void addField(final SolrInputDocument indexDocument, final String field, final String value) { + private final void addField( + final SolrInputDocument indexDocument, final String field, final String value) { String cleaned = value.trim(); if (!cleaned.isEmpty()) { // log.info("\n\n adding field " + field.toLowerCase() + " value: " + cleaned + "\n"); @@ -239,7 +249,8 @@ public class StreamingInputDocumentFactory { * @return the */ protected final String getText(final XMLEvent text) { - if (text.isEndElement()) // log.warn("skipping because isEndOfElement " + text.asEndElement().getName().getLocalPart()); + if (text.isEndElement()) // log.warn("skipping because isEndOfElement " + + // text.asEndElement().getName().getLocalPart()); return ""; final String data = text.asCharacters().getData(); @@ -249,5 +260,4 @@ public class StreamingInputDocumentFactory { return data; } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java index c9d623a486..efb1dac6c8 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java @@ -1,23 +1,22 @@ package eu.dnetlib.dhp.oa.provision.utils; +import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.removePrefix; +import static eu.dnetlib.dhp.oa.provision.utils.XmlSerializationUtils.escapeXml; + import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.OafEntity; -import org.apache.commons.lang3.StringUtils; -import org.stringtemplate.v4.ST; - import java.io.IOException; import java.util.Collection; import java.util.List; import java.util.stream.Collectors; - -import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.removePrefix; -import static eu.dnetlib.dhp.oa.provision.utils.XmlSerializationUtils.escapeXml; +import org.apache.commons.lang3.StringUtils; +import org.stringtemplate.v4.ST; public class TemplateFactory { private TemplateResources resources; - private final static char DELIMITER = '$'; + private static final char DELIMITER = '$'; public TemplateFactory() { try { @@ -27,7 +26,12 @@ public class TemplateFactory { } } - public String buildBody(final String type, final List metadata, final List rels, final List children, final List extraInfo) { + public String buildBody( + final String type, + final List metadata, + final List rels, + final List children, + final List extraInfo) { ST body = getTemplate(resources.getEntity()); body.add("name", type); @@ -41,61 +45,68 @@ public class TemplateFactory { public String getChild(final String name, final String id, final List metadata) { return getTemplate(resources.getChild()) - .add("name", name) - .add("hasId", !(id == null)) - .add("id", id != null ? escapeXml(removePrefix(id)) : "") - .add("metadata", metadata) - .render(); + .add("name", name) + .add("hasId", !(id == null)) + .add("id", id != null ? escapeXml(removePrefix(id)) : "") + .add("metadata", metadata) + .render(); } public String buildRecord( - final OafEntity entity, - final String schemaLocation, - final String body) { + final OafEntity entity, final String schemaLocation, final String body) { return getTemplate(resources.getRecord()) - .add("id", escapeXml(removePrefix(entity.getId()))) - .add("dateofcollection", entity.getDateofcollection()) - .add("dateoftransformation", entity.getDateoftransformation()) - .add("schemaLocation", schemaLocation) - .add("it", body) - .render(); + .add("id", escapeXml(removePrefix(entity.getId()))) + .add("dateofcollection", entity.getDateofcollection()) + .add("dateoftransformation", entity.getDateoftransformation()) + .add("schemaLocation", schemaLocation) + .add("it", body) + .render(); } - public String getRel(final String type, - final String objIdentifier, - final Collection fields, - final String semanticclass, - final String semantischeme, - final DataInfo info) { + public String getRel( + final String type, + final String objIdentifier, + final Collection fields, + final String semanticclass, + final String semantischeme, + final DataInfo info) { return getTemplate(resources.getRel()) - .add("type", type) - .add("objIdentifier", escapeXml(removePrefix(objIdentifier))) - .add("class", semanticclass) - .add("scheme", semantischeme) - .add("metadata", fields) - .add("inferred", info.getInferred()) - .add("trust", info.getTrust()) - .add("inferenceprovenance", info.getInferenceprovenance()) - .add("provenanceaction", info.getProvenanceaction() != null ? info.getProvenanceaction().getClassid() : "") - .render(); + .add("type", type) + .add("objIdentifier", escapeXml(removePrefix(objIdentifier))) + .add("class", semanticclass) + .add("scheme", semantischeme) + .add("metadata", fields) + .add("inferred", info.getInferred()) + .add("trust", info.getTrust()) + .add("inferenceprovenance", info.getInferenceprovenance()) + .add( + "provenanceaction", + info.getProvenanceaction() != null + ? info.getProvenanceaction().getClassid() + : "") + .render(); } - public String getInstance(final String resultId, final List instancemetadata, final List webresources) { + public String getInstance( + final String resultId, + final List instancemetadata, + final List webresources) { return getTemplate(resources.getInstance()) - .add("instanceId", escapeXml(removePrefix(resultId))) - .add("metadata", instancemetadata) - .add("webresources", webresources - .stream() - .filter(StringUtils::isNotBlank) - .map(w -> getWebResource(w)) - .collect(Collectors.toList())) - .render(); + .add("instanceId", escapeXml(removePrefix(resultId))) + .add("metadata", instancemetadata) + .add( + "webresources", + webresources.stream() + .filter(StringUtils::isNotBlank) + .map(w -> getWebResource(w)) + .collect(Collectors.toList())) + .render(); } private String getWebResource(final String identifier) { return getTemplate(resources.getWebresource()) - .add("identifier", escapeXml(identifier)) - .render(); + .add("identifier", escapeXml(identifier)) + .render(); } // HELPERS @@ -103,5 +114,4 @@ public class TemplateFactory { private ST getTemplate(final String res) { return new ST(res, DELIMITER, DELIMITER); } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateResources.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateResources.java index b22e083ce3..ff7d9e3220 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateResources.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateResources.java @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.oa.provision.utils; import com.google.common.io.Resources; - import java.io.IOException; import java.nio.charset.StandardCharsets; @@ -23,9 +22,7 @@ public class TemplateResources { return Resources.toString(Resources.getResource(classpathResource), StandardCharsets.UTF_8); } - public TemplateResources() throws IOException { - - } + public TemplateResources() throws IOException {} public String getEntity() { return entity; @@ -50,5 +47,4 @@ public class TemplateResources { public String getChild() { return child; } - } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index aced9ac0a6..3455cb5f3b 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -1,5 +1,9 @@ package eu.dnetlib.dhp.oa.provision.utils; +import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.*; +import static org.apache.commons.lang3.StringUtils.isNotBlank; +import static org.apache.commons.lang3.StringUtils.substringBefore; + import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.base.Joiner; import com.google.common.base.Splitter; @@ -12,22 +16,8 @@ import eu.dnetlib.dhp.oa.provision.model.*; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.MainEntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.commons.lang3.StringUtils; -import org.apache.spark.util.LongAccumulator; -import org.codehaus.janino.Mod; -import org.dom4j.Document; -import org.dom4j.DocumentException; -import org.dom4j.Element; -import org.dom4j.Node; -import org.dom4j.io.OutputFormat; -import org.dom4j.io.SAXReader; -import org.dom4j.io.XMLWriter; - -import javax.xml.transform.*; -import javax.xml.transform.dom.DOMSource; -import javax.xml.transform.stream.StreamResult; +import eu.dnetlib.dhp.schema.oaf.Result; import java.io.IOException; import java.io.Serializable; import java.io.StringReader; @@ -36,14 +26,22 @@ import java.util.List; import java.util.Map; import java.util.Set; import java.util.stream.Collectors; - -import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.*; -import static org.apache.commons.lang3.StringUtils.isNotBlank; -import static org.apache.commons.lang3.StringUtils.substringBefore; +import javax.xml.transform.*; +import javax.xml.transform.dom.DOMSource; +import javax.xml.transform.stream.StreamResult; +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.util.LongAccumulator; +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.Element; +import org.dom4j.Node; +import org.dom4j.io.OutputFormat; +import org.dom4j.io.SAXReader; +import org.dom4j.io.XMLWriter; public class XmlRecordFactory implements Serializable { - private Map accumulators; + private Map accumulators; private Set specialDatasourceTypes; @@ -56,21 +54,26 @@ public class XmlRecordFactory implements Serializable { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public XmlRecordFactory( - final ContextMapper contextMapper, final boolean indent, - final String schemaLocation, final String otherDatasourceTypesUForUI) { + final ContextMapper contextMapper, + final boolean indent, + final String schemaLocation, + final String otherDatasourceTypesUForUI) { this(Maps.newHashMap(), contextMapper, indent, schemaLocation, otherDatasourceTypesUForUI); } public XmlRecordFactory( - final Map accumulators, - final ContextMapper contextMapper, final boolean indent, - final String schemaLocation, final String otherDatasourceTypesUForUI) { + final Map accumulators, + final ContextMapper contextMapper, + final boolean indent, + final String schemaLocation, + final String otherDatasourceTypesUForUI) { this.accumulators = accumulators; this.contextMapper = contextMapper; this.schemaLocation = schemaLocation; - this.specialDatasourceTypes = Sets.newHashSet(Splitter.on(",").trimResults().split(otherDatasourceTypesUForUI)); + this.specialDatasourceTypes = + Sets.newHashSet(Splitter.on(",").trimResults().split(otherDatasourceTypesUForUI)); this.indent = indent; } @@ -85,22 +88,27 @@ public class XmlRecordFactory implements Serializable { final EntityType type = EntityType.valueOf(je.getEntity().getType()); final List metadata = metadata(type, entity, contexts); - // rels has to be processed before the contexts because they enrich the contextMap with the funding info. + // rels has to be processed before the contexts because they enrich the contextMap with + // the + // funding info. final List relations = listRelations(je, templateFactory, contexts); final String mainType = ModelSupport.getMainType(type); metadata.addAll(buildContexts(mainType, contexts)); metadata.add(XmlSerializationUtils.parseDataInfo(entity.getDataInfo())); - final String body = templateFactory.buildBody( - mainType, - metadata, - relations, - listChildren(entity, je.getEntity().getType(), templateFactory), listExtraInfo(entity)); + final String body = + templateFactory.buildBody( + mainType, + metadata, + relations, + listChildren(entity, je.getEntity().getType(), templateFactory), + listExtraInfo(entity)); return printXML(templateFactory.buildRecord(entity, schemaLocation, body), indent); } catch (final Throwable e) { - throw new RuntimeException(String.format("error building record '%s'", entity.getId()), e); + throw new RuntimeException( + String.format("error building record '%s'", entity.getId()), e); } } @@ -136,7 +144,8 @@ public class XmlRecordFactory implements Serializable { private String printXML(String xml, boolean indent) { try { final Document doc = new SAXReader().read(new StringReader(xml)); - OutputFormat format = indent ? OutputFormat.createPrettyPrint() : OutputFormat.createCompactFormat(); + OutputFormat format = + indent ? OutputFormat.createPrettyPrint() : OutputFormat.createCompactFormat(); format.setExpandEmptyElements(false); format.setSuppressDeclaration(true); StringWriter sw = new StringWriter(); @@ -148,38 +157,36 @@ public class XmlRecordFactory implements Serializable { } } - private List metadata(final EntityType type, final OafEntity entity, final Set contexts) { + private List metadata( + final EntityType type, final OafEntity entity, final Set contexts) { final List metadata = Lists.newArrayList(); - if (entity.getCollectedfrom() != null) { - metadata.addAll(entity.getCollectedfrom() - .stream() - .map(kv -> XmlSerializationUtils.mapKeyValue("collectedfrom", kv)) - .collect(Collectors.toList())); + metadata.addAll( + entity.getCollectedfrom().stream() + .map(kv -> XmlSerializationUtils.mapKeyValue("collectedfrom", kv)) + .collect(Collectors.toList())); } if (entity.getOriginalId() != null) { - metadata.addAll(entity.getOriginalId() - .stream() - .map(s -> XmlSerializationUtils.asXmlElement("originalId", s)) - .collect(Collectors.toList())); + metadata.addAll( + entity.getOriginalId().stream() + .map(s -> XmlSerializationUtils.asXmlElement("originalId", s)) + .collect(Collectors.toList())); } if (entity.getPid() != null) { - metadata.addAll(entity.getPid() - .stream() - .map(p -> XmlSerializationUtils.mapStructuredProperty("pid", p)) - .collect(Collectors.toList())); + metadata.addAll( + entity.getPid().stream() + .map(p -> XmlSerializationUtils.mapStructuredProperty("pid", p)) + .collect(Collectors.toList())); } if (ModelSupport.isResult(type)) { final Result r = (Result) entity; if (r.getContext() != null) { - contexts.addAll(r.getContext() - .stream() - .map(c -> c.getId()) - .collect(Collectors.toList())); + contexts.addAll( + r.getContext().stream().map(c -> c.getId()).collect(Collectors.toList())); /* FIXME: Workaround for CLARIN mining issue: #3670#note-29 */ if (contexts.contains("dh-ch::subcommunity::2")) { contexts.add("clarin"); @@ -187,114 +194,197 @@ public class XmlRecordFactory implements Serializable { } if (r.getTitle() != null) { - metadata.addAll(r.getTitle() - .stream() - .map(t -> XmlSerializationUtils.mapStructuredProperty("title", t)) - .collect(Collectors.toList())); + metadata.addAll( + r.getTitle().stream() + .map(t -> XmlSerializationUtils.mapStructuredProperty("title", t)) + .collect(Collectors.toList())); } if (r.getBestaccessright() != null) { - metadata.add(XmlSerializationUtils.mapQualifier("bestaccessright", r.getBestaccessright())); + metadata.add( + XmlSerializationUtils.mapQualifier( + "bestaccessright", r.getBestaccessright())); } if (r.getAuthor() != null) { - metadata.addAll(r.getAuthor() - .stream() - .map(a -> { - final StringBuilder sb = new StringBuilder(" isNotBlank(sp.getQualifier().getClassid()) && isNotBlank(sp.getValue())) - .forEach(sp -> { - String pidType = XmlSerializationUtils.escapeXml(sp.getQualifier().getClassid()).replaceAll("\\W", ""); - String pidValue = XmlSerializationUtils.escapeXml(sp.getValue()); - - // ugly hack: some records provide swapped pidtype and pidvalue - if (authorPidTypes.contains(pidValue.toLowerCase().trim())) { - sb.append(String.format(" %s=\"%s\"", pidValue, pidType)); - } else { - pidType = pidType.replaceAll("\\W", "").replaceAll("\\d", ""); - if (isNotBlank(pidType)) { - sb.append(String.format(" %s=\"%s\"", - pidType, - pidValue.toLowerCase().replaceAll("orcid", ""))); + metadata.addAll( + r.getAuthor().stream() + .map( + a -> { + final StringBuilder sb = + new StringBuilder( + "" + XmlSerializationUtils.escapeXml(a.getFullname()) + ""); - return sb.toString(); - }).collect(Collectors.toList())); + if (isNotBlank(a.getSurname())) { + sb.append( + " surname=\"" + + XmlSerializationUtils.escapeXml( + a.getSurname()) + + "\""); + } + if (a.getPid() != null) { + a.getPid().stream() + .filter( + sp -> + isNotBlank( + sp.getQualifier() + .getClassid()) + && isNotBlank( + sp + .getValue())) + .forEach( + sp -> { + String pidType = + XmlSerializationUtils + .escapeXml( + sp.getQualifier() + .getClassid()) + .replaceAll( + "\\W", + ""); + String pidValue = + XmlSerializationUtils + .escapeXml( + sp + .getValue()); + + // ugly hack: some records + // provide swapped pidtype and + // pidvalue + if (authorPidTypes.contains( + pidValue.toLowerCase() + .trim())) { + sb.append( + String.format( + " %s=\"%s\"", + pidValue, + pidType)); + } else { + pidType = + pidType.replaceAll( + "\\W", + "") + .replaceAll( + "\\d", + ""); + if (isNotBlank(pidType)) { + sb.append( + String.format( + " %s=\"%s\"", + pidType, + pidValue.toLowerCase() + .replaceAll( + "orcid", + ""))); + } + } + }); + } + sb.append( + ">" + + XmlSerializationUtils.escapeXml( + a.getFullname()) + + ""); + return sb.toString(); + }) + .collect(Collectors.toList())); } if (r.getContributor() != null) { - metadata.addAll(r.getContributor() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("contributor", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + r.getContributor().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "contributor", c.getValue())) + .collect(Collectors.toList())); } if (r.getCountry() != null) { - metadata.addAll(r.getCountry() - .stream() - .map(c -> XmlSerializationUtils.mapQualifier("country", c)) - .collect(Collectors.toList())); + metadata.addAll( + r.getCountry().stream() + .map(c -> XmlSerializationUtils.mapQualifier("country", c)) + .collect(Collectors.toList())); } if (r.getCoverage() != null) { - metadata.addAll(r.getCoverage() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("coverage", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + r.getCoverage().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "coverage", c.getValue())) + .collect(Collectors.toList())); } if (r.getDateofacceptance() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("dateofacceptance", r.getDateofacceptance().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "dateofacceptance", r.getDateofacceptance().getValue())); } if (r.getDescription() != null) { - metadata.addAll(r.getDescription() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("description", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + r.getDescription().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "description", c.getValue())) + .collect(Collectors.toList())); } if (r.getEmbargoenddate() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("embargoenddate", r.getEmbargoenddate().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "embargoenddate", r.getEmbargoenddate().getValue())); } if (r.getSubject() != null) { - metadata.addAll(r.getSubject() - .stream() - .map(s -> XmlSerializationUtils.mapStructuredProperty("subject", s)) - .collect(Collectors.toList())); + metadata.addAll( + r.getSubject().stream() + .map(s -> XmlSerializationUtils.mapStructuredProperty("subject", s)) + .collect(Collectors.toList())); } if (r.getLanguage() != null) { metadata.add(XmlSerializationUtils.mapQualifier("language", r.getLanguage())); } if (r.getRelevantdate() != null) { - metadata.addAll(r.getRelevantdate() - .stream() - .map(s -> XmlSerializationUtils.mapStructuredProperty("relevantdate", s)) - .collect(Collectors.toList())); + metadata.addAll( + r.getRelevantdate().stream() + .map( + s -> + XmlSerializationUtils.mapStructuredProperty( + "relevantdate", s)) + .collect(Collectors.toList())); } if (r.getPublisher() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("publisher", r.getPublisher().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "publisher", r.getPublisher().getValue())); } if (r.getSource() != null) { - metadata.addAll(r.getSource() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("source", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + r.getSource().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "source", c.getValue())) + .collect(Collectors.toList())); } if (r.getFormat() != null) { - metadata.addAll(r.getFormat() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("format", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + r.getFormat().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "format", c.getValue())) + .collect(Collectors.toList())); } if (r.getResulttype() != null) { metadata.add(XmlSerializationUtils.mapQualifier("resulttype", r.getResulttype())); } if (r.getResourcetype() != null) { - metadata.add(XmlSerializationUtils.mapQualifier("resourcetype", r.getResourcetype())); + metadata.add( + XmlSerializationUtils.mapQualifier("resourcetype", r.getResourcetype())); } } @@ -311,69 +401,99 @@ public class XmlRecordFactory implements Serializable { case dataset: final Dataset d = (Dataset) entity; if (d.getDevice() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("device", d.getDevice().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement("device", d.getDevice().getValue())); } if (d.getLastmetadataupdate() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("lastmetadataupdate", d.getLastmetadataupdate().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "lastmetadataupdate", d.getLastmetadataupdate().getValue())); } if (d.getMetadataversionnumber() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("metadataversionnumber", d.getMetadataversionnumber().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "metadataversionnumber", + d.getMetadataversionnumber().getValue())); } if (d.getSize() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("size", d.getSize().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement("size", d.getSize().getValue())); } if (d.getStoragedate() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("storagedate", d.getStoragedate().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "storagedate", d.getStoragedate().getValue())); } if (d.getVersion() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("version", d.getVersion().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "version", d.getVersion().getValue())); } - //TODO d.getGeolocation() + // TODO d.getGeolocation() break; case otherresearchproduct: final OtherResearchProduct orp = (OtherResearchProduct) entity; if (orp.getContactperson() != null) { - metadata.addAll(orp.getContactperson() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("contactperson", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + orp.getContactperson().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "contactperson", c.getValue())) + .collect(Collectors.toList())); } if (orp.getContactgroup() != null) { - metadata.addAll(orp.getContactgroup() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("contactgroup", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + orp.getContactgroup().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "contactgroup", c.getValue())) + .collect(Collectors.toList())); } if (orp.getTool() != null) { - metadata.addAll(orp.getTool() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("tool", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + orp.getTool().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "tool", c.getValue())) + .collect(Collectors.toList())); } break; case software: final Software s = (Software) entity; if (s.getDocumentationUrl() != null) { - metadata.addAll(s.getDocumentationUrl() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("documentationUrl", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + s.getDocumentationUrl().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "documentationUrl", c.getValue())) + .collect(Collectors.toList())); } if (s.getLicense() != null) { - metadata.addAll(s.getLicense() - .stream() - .map(l -> XmlSerializationUtils.mapStructuredProperty("license", l)) - .collect(Collectors.toList())); + metadata.addAll( + s.getLicense().stream() + .map( + l -> + XmlSerializationUtils.mapStructuredProperty( + "license", l)) + .collect(Collectors.toList())); } if (s.getCodeRepositoryUrl() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("codeRepositoryUrl", s.getCodeRepositoryUrl().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "codeRepositoryUrl", s.getCodeRepositoryUrl().getValue())); } if (s.getProgrammingLanguage() != null) { - metadata.add(XmlSerializationUtils.mapQualifier("programmingLanguage", s.getProgrammingLanguage())); + metadata.add( + XmlSerializationUtils.mapQualifier( + "programmingLanguage", s.getProgrammingLanguage())); } break; case datasource: @@ -383,121 +503,194 @@ public class XmlRecordFactory implements Serializable { mapDatasourceType(metadata, ds.getDatasourcetype()); } if (ds.getOpenairecompatibility() != null) { - metadata.add(XmlSerializationUtils.mapQualifier("openairecompatibility", ds.getOpenairecompatibility())); + metadata.add( + XmlSerializationUtils.mapQualifier( + "openairecompatibility", ds.getOpenairecompatibility())); } if (ds.getOfficialname() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("officialname", ds.getOfficialname().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "officialname", ds.getOfficialname().getValue())); } if (ds.getEnglishname() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("englishname", ds.getEnglishname().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "englishname", ds.getEnglishname().getValue())); } if (ds.getWebsiteurl() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("websiteurl", ds.getWebsiteurl().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "websiteurl", ds.getWebsiteurl().getValue())); } if (ds.getLogourl() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("logourl", ds.getLogourl().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "logourl", ds.getLogourl().getValue())); } if (ds.getContactemail() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("contactemail", ds.getContactemail().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "contactemail", ds.getContactemail().getValue())); } if (ds.getNamespaceprefix() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("namespaceprefix", ds.getNamespaceprefix().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "namespaceprefix", ds.getNamespaceprefix().getValue())); } if (ds.getLatitude() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("latitude", ds.getLatitude().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "latitude", ds.getLatitude().getValue())); } if (ds.getLongitude() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("longitude", ds.getLongitude().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "longitude", ds.getLongitude().getValue())); } if (ds.getDateofvalidation() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("dateofvalidation", ds.getDateofvalidation().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "dateofvalidation", ds.getDateofvalidation().getValue())); } if (ds.getDescription() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("description", ds.getDescription().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "description", ds.getDescription().getValue())); } if (ds.getOdnumberofitems() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("odnumberofitems", ds.getOdnumberofitems().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "odnumberofitems", ds.getOdnumberofitems().getValue())); } if (ds.getOdnumberofitemsdate() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("odnumberofitemsdate", ds.getOdnumberofitemsdate().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "odnumberofitemsdate", ds.getOdnumberofitemsdate().getValue())); } if (ds.getOdpolicies() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("odpolicies", ds.getOdpolicies().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "odpolicies", ds.getOdpolicies().getValue())); } if (ds.getOdlanguages() != null) { - metadata.addAll(ds.getOdlanguages() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("odlanguages", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + ds.getOdlanguages().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "odlanguages", c.getValue())) + .collect(Collectors.toList())); } if (ds.getOdcontenttypes() != null) { - metadata.addAll(ds.getOdcontenttypes() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("odcontenttypes", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + ds.getOdcontenttypes().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "odcontenttypes", c.getValue())) + .collect(Collectors.toList())); } if (ds.getAccessinfopackage() != null) { - metadata.addAll(ds.getAccessinfopackage() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("accessinfopackage", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + ds.getAccessinfopackage().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "accessinfopackage", c.getValue())) + .collect(Collectors.toList())); } if (ds.getReleaseenddate() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("releasestartdate", ds.getReleaseenddate().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "releasestartdate", ds.getReleaseenddate().getValue())); } if (ds.getReleaseenddate() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("releaseenddate", ds.getReleaseenddate().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "releaseenddate", ds.getReleaseenddate().getValue())); } if (ds.getMissionstatementurl() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("missionstatementurl", ds.getMissionstatementurl().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "missionstatementurl", ds.getMissionstatementurl().getValue())); } if (ds.getDataprovider() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("dataprovider", ds.getDataprovider().getValue().toString())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "dataprovider", ds.getDataprovider().getValue().toString())); } if (ds.getServiceprovider() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("serviceprovider", ds.getServiceprovider().getValue().toString())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "serviceprovider", + ds.getServiceprovider().getValue().toString())); } if (ds.getDatabaseaccesstype() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("databaseaccesstype", ds.getDatabaseaccesstype().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "databaseaccesstype", ds.getDatabaseaccesstype().getValue())); } if (ds.getDatauploadtype() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("datauploadtype", ds.getDatauploadtype().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "datauploadtype", ds.getDatauploadtype().getValue())); } if (ds.getDatabaseaccessrestriction() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("databaseaccessrestriction", ds.getDatabaseaccessrestriction().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "databaseaccessrestriction", + ds.getDatabaseaccessrestriction().getValue())); } if (ds.getDatauploadrestriction() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("datauploadrestriction", ds.getDatauploadrestriction().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "datauploadrestriction", + ds.getDatauploadrestriction().getValue())); } if (ds.getVersioning() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("versioning", ds.getVersioning().getValue().toString())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "versioning", ds.getVersioning().getValue().toString())); } if (ds.getCitationguidelineurl() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("citationguidelineurl", ds.getCitationguidelineurl().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "citationguidelineurl", + ds.getCitationguidelineurl().getValue())); } if (ds.getQualitymanagementkind() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("qualitymanagementkind", ds.getQualitymanagementkind().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "qualitymanagementkind", + ds.getQualitymanagementkind().getValue())); } if (ds.getPidsystems() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("pidsystems", ds.getPidsystems().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "pidsystems", ds.getPidsystems().getValue())); } if (ds.getCertificates() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("certificates", ds.getCertificates().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "certificates", ds.getCertificates().getValue())); } if (ds.getPolicies() != null) { - metadata.addAll(ds.getPolicies() - .stream() - .map(kv -> XmlSerializationUtils.mapKeyValue("policies", kv)) - .collect(Collectors.toList())); + metadata.addAll( + ds.getPolicies().stream() + .map(kv -> XmlSerializationUtils.mapKeyValue("policies", kv)) + .collect(Collectors.toList())); } if (ds.getJournal() != null) { metadata.add(XmlSerializationUtils.mapJournal(ds.getJournal())); } if (ds.getSubjects() != null) { - metadata.addAll(ds.getSubjects() - .stream() - .map(sp -> XmlSerializationUtils.mapStructuredProperty("subjects", sp)) - .collect(Collectors.toList())); + metadata.addAll( + ds.getSubjects().stream() + .map( + sp -> + XmlSerializationUtils.mapStructuredProperty( + "subjects", sp)) + .collect(Collectors.toList())); } break; @@ -505,53 +698,87 @@ public class XmlRecordFactory implements Serializable { final Organization o = (Organization) entity; if (o.getLegalshortname() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("legalshortname", o.getLegalshortname().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "legalshortname", o.getLegalshortname().getValue())); } if (o.getLegalname() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("legalname", o.getLegalname().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "legalname", o.getLegalname().getValue())); } if (o.getAlternativeNames() != null) { - metadata.addAll(o.getAlternativeNames() - .stream() - .map(c -> XmlSerializationUtils.asXmlElement("alternativeNames", c.getValue())) - .collect(Collectors.toList())); + metadata.addAll( + o.getAlternativeNames().stream() + .map( + c -> + XmlSerializationUtils.asXmlElement( + "alternativeNames", c.getValue())) + .collect(Collectors.toList())); } if (o.getWebsiteurl() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("websiteurl", o.getWebsiteurl().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "websiteurl", o.getWebsiteurl().getValue())); } if (o.getLogourl() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("websiteurl", o.getLogourl().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "websiteurl", o.getLogourl().getValue())); } if (o.getEclegalbody() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("eclegalbody", o.getEclegalbody().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "eclegalbody", o.getEclegalbody().getValue())); } if (o.getEclegalperson() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("eclegalperson", o.getEclegalperson().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "eclegalperson", o.getEclegalperson().getValue())); } if (o.getEcnonprofit() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("ecnonprofit", o.getEcnonprofit().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "ecnonprofit", o.getEcnonprofit().getValue())); } if (o.getEcresearchorganization() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("ecresearchorganization", o.getEcresearchorganization().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "ecresearchorganization", + o.getEcresearchorganization().getValue())); } if (o.getEchighereducation() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("echighereducation", o.getEchighereducation().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "echighereducation", o.getEchighereducation().getValue())); } if (o.getEcinternationalorganization() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("ecinternationalorganizationeurinterests", o.getEcinternationalorganization().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "ecinternationalorganizationeurinterests", + o.getEcinternationalorganization().getValue())); } if (o.getEcinternationalorganization() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("ecinternationalorganization", o.getEcinternationalorganization().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "ecinternationalorganization", + o.getEcinternationalorganization().getValue())); } if (o.getEcenterprise() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("ecenterprise", o.getEcenterprise().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "ecenterprise", o.getEcenterprise().getValue())); } if (o.getEcsmevalidated() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("ecsmevalidated", o.getEcsmevalidated().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "ecsmevalidated", o.getEcsmevalidated().getValue())); } if (o.getEcnutscode() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("ecnutscode", o.getEcnutscode().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "ecnutscode", o.getEcnutscode().getValue())); } if (o.getCountry() != null) { metadata.add(XmlSerializationUtils.mapQualifier("country", o.getCountry())); @@ -559,80 +786,119 @@ public class XmlRecordFactory implements Serializable { break; case project: - final Project p = (Project) entity; if (p.getWebsiteurl() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("websiteurl", p.getWebsiteurl().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "websiteurl", p.getWebsiteurl().getValue())); } if (p.getCode() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("code", p.getCode().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement("code", p.getCode().getValue())); } if (p.getAcronym() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("acronym", p.getAcronym().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "acronym", p.getAcronym().getValue())); } if (p.getTitle() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("title", p.getTitle().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement("title", p.getTitle().getValue())); } if (p.getStartdate() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("startdate", p.getStartdate().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "startdate", p.getStartdate().getValue())); } if (p.getEnddate() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("enddate", p.getEnddate().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "enddate", p.getEnddate().getValue())); } if (p.getCallidentifier() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("callidentifier", p.getCallidentifier().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "callidentifier", p.getCallidentifier().getValue())); } if (p.getKeywords() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("keywords", p.getKeywords().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "keywords", p.getKeywords().getValue())); } if (p.getDuration() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("duration", p.getDuration().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "duration", p.getDuration().getValue())); } if (p.getEcarticle29_3() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("ecarticle29_3", p.getEcarticle29_3().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "ecarticle29_3", p.getEcarticle29_3().getValue())); } if (p.getSubjects() != null) { - metadata.addAll(p.getSubjects() - .stream() - .map(sp -> XmlSerializationUtils.mapStructuredProperty("subject", sp)) - .collect(Collectors.toList())); + metadata.addAll( + p.getSubjects().stream() + .map( + sp -> + XmlSerializationUtils.mapStructuredProperty( + "subject", sp)) + .collect(Collectors.toList())); } if (p.getContracttype() != null) { - metadata.add(XmlSerializationUtils.mapQualifier("contracttype", p.getContracttype())); + metadata.add( + XmlSerializationUtils.mapQualifier( + "contracttype", p.getContracttype())); } if (p.getEcsc39() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("ecsc39", p.getEcsc39().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement("ecsc39", p.getEcsc39().getValue())); } if (p.getContactfullname() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("contactfullname", p.getContactfullname().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "contactfullname", p.getContactfullname().getValue())); } if (p.getContactfax() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("contactfax", p.getContactfax().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "contactfax", p.getContactfax().getValue())); } if (p.getContactphone() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("contactphone", p.getContactphone().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "contactphone", p.getContactphone().getValue())); } if (p.getContactemail() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("contactemail", p.getContactemail().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "contactemail", p.getContactemail().getValue())); } if (p.getSummary() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("summary", p.getSummary().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "summary", p.getSummary().getValue())); } if (p.getCurrency() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("currency", p.getCurrency().getValue())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "currency", p.getCurrency().getValue())); } if (p.getTotalcost() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("totalcost", p.getTotalcost().toString())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "totalcost", p.getTotalcost().toString())); } if (p.getFundedamount() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("fundedamount", p.getFundedamount().toString())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "fundedamount", p.getFundedamount().toString())); } if (p.getFundingtree() != null) { - metadata.addAll(p.getFundingtree() - .stream() - .map(ft -> ft.getValue()) - .collect(Collectors.toList())); + metadata.addAll( + p.getFundingtree().stream() + .map(ft -> ft.getValue()) + .collect(Collectors.toList())); } break; @@ -669,7 +935,8 @@ public class XmlRecordFactory implements Serializable { return bestAccessRight; } - private List listRelations(final JoinedEntity je, TemplateFactory templateFactory, final Set contexts) { + private List listRelations( + final JoinedEntity je, TemplateFactory templateFactory, final Set contexts) { final List rels = Lists.newArrayList(); for (final Tuple2 link : je.getLinks()) { @@ -685,104 +952,135 @@ public class XmlRecordFactory implements Serializable { case otherresearchproduct: case software: if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) { - metadata.add(XmlSerializationUtils.mapStructuredProperty("title", re.getTitle())); + metadata.add( + XmlSerializationUtils.mapStructuredProperty( + "title", re.getTitle())); } if (isNotBlank(re.getDateofacceptance())) { - metadata.add(XmlSerializationUtils.asXmlElement("dateofacceptance", re.getDateofacceptance())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "dateofacceptance", re.getDateofacceptance())); } if (isNotBlank(re.getPublisher())) { - metadata.add(XmlSerializationUtils.asXmlElement("publisher", re.getPublisher())); + metadata.add( + XmlSerializationUtils.asXmlElement("publisher", re.getPublisher())); } if (isNotBlank(re.getCodeRepositoryUrl())) { - metadata.add(XmlSerializationUtils.asXmlElement("coderepositoryurl", re.getCodeRepositoryUrl())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "coderepositoryurl", re.getCodeRepositoryUrl())); } if (re.getResulttype() != null & re.getResulttype().isBlank()) { - metadata.add(XmlSerializationUtils.mapQualifier("resulttype", re.getResulttype())); + metadata.add( + XmlSerializationUtils.mapQualifier( + "resulttype", re.getResulttype())); } if (re.getCollectedfrom() != null) { - metadata.addAll(re.getCollectedfrom() - .stream() - .map(kv -> XmlSerializationUtils.mapKeyValue("collectedfrom", kv)) - .collect(Collectors.toList())); + metadata.addAll( + re.getCollectedfrom().stream() + .map( + kv -> + XmlSerializationUtils.mapKeyValue( + "collectedfrom", kv)) + .collect(Collectors.toList())); } if (re.getPid() != null) { - metadata.addAll(re.getPid() - .stream() - .map(p -> XmlSerializationUtils.mapStructuredProperty("pid", p)) - .collect(Collectors.toList())); + metadata.addAll( + re.getPid().stream() + .map( + p -> + XmlSerializationUtils.mapStructuredProperty( + "pid", p)) + .collect(Collectors.toList())); } break; case datasource: if (isNotBlank(re.getOfficialname())) { - metadata.add(XmlSerializationUtils.asXmlElement("officialname", re.getOfficialname())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "officialname", re.getOfficialname())); } if (re.getDatasourcetype() != null & !re.getDatasourcetype().isBlank()) { mapDatasourceType(metadata, re.getDatasourcetype()); } - if (re.getOpenairecompatibility() != null & !re.getOpenairecompatibility().isBlank()) { - metadata.add(XmlSerializationUtils.mapQualifier("openairecompatibility", re.getOpenairecompatibility())); + if (re.getOpenairecompatibility() != null + & !re.getOpenairecompatibility().isBlank()) { + metadata.add( + XmlSerializationUtils.mapQualifier( + "openairecompatibility", re.getOpenairecompatibility())); } break; case organization: if (isNotBlank(re.getLegalname())) { - metadata.add(XmlSerializationUtils.asXmlElement("legalname", re.getLegalname())); + metadata.add( + XmlSerializationUtils.asXmlElement("legalname", re.getLegalname())); } if (isNotBlank(re.getLegalshortname())) { - metadata.add(XmlSerializationUtils.asXmlElement("legalshortname", re.getLegalshortname())); + metadata.add( + XmlSerializationUtils.asXmlElement( + "legalshortname", re.getLegalshortname())); } if (re.getCountry() != null & !re.getCountry().isBlank()) { - metadata.add(XmlSerializationUtils.mapQualifier("country", re.getCountry())); + metadata.add( + XmlSerializationUtils.mapQualifier("country", re.getCountry())); } break; case project: if (isNotBlank(re.getProjectTitle())) { - metadata.add(XmlSerializationUtils.asXmlElement("title", re.getProjectTitle())); + metadata.add( + XmlSerializationUtils.asXmlElement("title", re.getProjectTitle())); } if (isNotBlank(re.getCode())) { metadata.add(XmlSerializationUtils.asXmlElement("code", re.getCode())); } if (isNotBlank(re.getAcronym())) { - metadata.add(XmlSerializationUtils.asXmlElement("acronym", re.getAcronym())); + metadata.add( + XmlSerializationUtils.asXmlElement("acronym", re.getAcronym())); } if (re.getContracttype() != null & !re.getContracttype().isBlank()) { - metadata.add(XmlSerializationUtils.mapQualifier("contracttype", re.getContracttype())); + metadata.add( + XmlSerializationUtils.mapQualifier( + "contracttype", re.getContracttype())); } if (re.getFundingtree() != null) { - metadata.addAll(re.getFundingtree() - .stream() - .peek(ft -> fillContextMap(ft, contexts)) - .map(ft -> getRelFundingTree(ft)) - .collect(Collectors.toList())); + metadata.addAll( + re.getFundingtree().stream() + .peek(ft -> fillContextMap(ft, contexts)) + .map(ft -> getRelFundingTree(ft)) + .collect(Collectors.toList())); } break; default: throw new IllegalArgumentException("invalid target type: " + targetType); - } final DataInfo info = rel.getDataInfo(); final String scheme = ModelSupport.getScheme(re.getType(), targetType); if (StringUtils.isBlank(scheme)) { - throw new IllegalArgumentException(String.format("missing scheme for: <%s - %s>", re.getType(), targetType)); + throw new IllegalArgumentException( + String.format("missing scheme for: <%s - %s>", re.getType(), targetType)); } - final String accumulatorName = getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass()); + final String accumulatorName = + getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass()); if (accumulators.containsKey(accumulatorName)) { accumulators.get(accumulatorName).add(1); } - rels.add(templateFactory.getRel( - targetType, - rel.getTarget(), - Sets.newHashSet(metadata), - rel.getRelClass(), - scheme, - info)); + rels.add( + templateFactory.getRel( + targetType, + rel.getTarget(), + Sets.newHashSet(metadata), + rel.getRelClass(), + scheme, + info)); } return rels; } - private List listChildren(final OafEntity entity, String type, TemplateFactory templateFactory) { + private List listChildren( + final OafEntity entity, String type, TemplateFactory templateFactory) { final List children = Lists.newArrayList(); EntityType entityType = EntityType.valueOf(type); @@ -794,34 +1092,63 @@ public class XmlRecordFactory implements Serializable { final List fields = Lists.newArrayList(); if (instance.getAccessright() != null && !instance.getAccessright().isBlank()) { - fields.add(XmlSerializationUtils.mapQualifier("accessright", instance.getAccessright())); + fields.add( + XmlSerializationUtils.mapQualifier( + "accessright", instance.getAccessright())); } if (instance.getCollectedfrom() != null) { - fields.add(XmlSerializationUtils.mapKeyValue("collectedfrom", instance.getCollectedfrom())); + fields.add( + XmlSerializationUtils.mapKeyValue( + "collectedfrom", instance.getCollectedfrom())); } if (instance.getHostedby() != null) { - fields.add(XmlSerializationUtils.mapKeyValue("hostedby", instance.getHostedby())); + fields.add( + XmlSerializationUtils.mapKeyValue( + "hostedby", instance.getHostedby())); } - if (instance.getDateofacceptance() != null && isNotBlank(instance.getDateofacceptance().getValue())) { - fields.add(XmlSerializationUtils.asXmlElement("dateofacceptance", instance.getDateofacceptance().getValue())); + if (instance.getDateofacceptance() != null + && isNotBlank(instance.getDateofacceptance().getValue())) { + fields.add( + XmlSerializationUtils.asXmlElement( + "dateofacceptance", + instance.getDateofacceptance().getValue())); } - if (instance.getInstancetype() != null && !instance.getInstancetype().isBlank()) { - fields.add(XmlSerializationUtils.mapQualifier("instancetype", instance.getInstancetype())); + if (instance.getInstancetype() != null + && !instance.getInstancetype().isBlank()) { + fields.add( + XmlSerializationUtils.mapQualifier( + "instancetype", instance.getInstancetype())); } if (isNotBlank(instance.getDistributionlocation())) { - fields.add(XmlSerializationUtils.asXmlElement("distributionlocation", instance.getDistributionlocation())); + fields.add( + XmlSerializationUtils.asXmlElement( + "distributionlocation", + instance.getDistributionlocation())); } - if (instance.getRefereed() != null && isNotBlank(instance.getRefereed().getValue())) { - fields.add(XmlSerializationUtils.asXmlElement("refereed", instance.getRefereed().getValue())); + if (instance.getRefereed() != null + && isNotBlank(instance.getRefereed().getValue())) { + fields.add( + XmlSerializationUtils.asXmlElement( + "refereed", instance.getRefereed().getValue())); } - if (instance.getProcessingchargeamount() != null && isNotBlank(instance.getProcessingchargeamount().getValue())) { - fields.add(XmlSerializationUtils.asXmlElement("processingchargeamount", instance.getProcessingchargeamount().getValue())); + if (instance.getProcessingchargeamount() != null + && isNotBlank(instance.getProcessingchargeamount().getValue())) { + fields.add( + XmlSerializationUtils.asXmlElement( + "processingchargeamount", + instance.getProcessingchargeamount().getValue())); } - if (instance.getProcessingchargecurrency() != null && isNotBlank(instance.getProcessingchargecurrency().getValue())) { - fields.add(XmlSerializationUtils.asXmlElement("processingchargecurrency", instance.getProcessingchargecurrency().getValue())); + if (instance.getProcessingchargecurrency() != null + && isNotBlank(instance.getProcessingchargecurrency().getValue())) { + fields.add( + XmlSerializationUtils.asXmlElement( + "processingchargecurrency", + instance.getProcessingchargecurrency().getValue())); } - children.add(templateFactory.getInstance(instance.getHostedby().getKey(), fields, instance.getUrl())); + children.add( + templateFactory.getInstance( + instance.getHostedby().getKey(), fields, instance.getUrl())); } } final List ext = ((Result) entity).getExternalReference(); @@ -831,7 +1158,8 @@ public class XmlRecordFactory implements Serializable { final List fields = Lists.newArrayList(); if (isNotBlank(er.getSitename())) { - fields.add(XmlSerializationUtils.asXmlElement("sitename", er.getSitename())); + fields.add( + XmlSerializationUtils.asXmlElement("sitename", er.getSitename())); } if (isNotBlank(er.getLabel())) { fields.add(XmlSerializationUtils.asXmlElement("label", er.getLabel())); @@ -840,13 +1168,18 @@ public class XmlRecordFactory implements Serializable { fields.add(XmlSerializationUtils.asXmlElement("url", er.getUrl())); } if (isNotBlank(er.getDescription())) { - fields.add(XmlSerializationUtils.asXmlElement("description", er.getDescription())); + fields.add( + XmlSerializationUtils.asXmlElement( + "description", er.getDescription())); } if (isNotBlank(er.getUrl())) { - fields.add(XmlSerializationUtils.mapQualifier("qualifier", er.getQualifier())); + fields.add( + XmlSerializationUtils.mapQualifier("qualifier", er.getQualifier())); } if (isNotBlank(er.getRefidentifier())) { - fields.add(XmlSerializationUtils.asXmlElement("refidentifier", er.getRefidentifier())); + fields.add( + XmlSerializationUtils.asXmlElement( + "refidentifier", er.getRefidentifier())); } if (isNotBlank(er.getQuery())) { fields.add(XmlSerializationUtils.asXmlElement("query", er.getQuery())); @@ -862,16 +1195,19 @@ public class XmlRecordFactory implements Serializable { private List listExtraInfo(OafEntity entity) { final List extraInfo = entity.getExtraInfo(); - return extraInfo != null ? extraInfo - .stream() - .map(e -> XmlSerializationUtils.mapExtraInfo(e)) - .collect(Collectors.toList()) : Lists.newArrayList(); + return extraInfo != null + ? extraInfo.stream() + .map(e -> XmlSerializationUtils.mapExtraInfo(e)) + .collect(Collectors.toList()) + : Lists.newArrayList(); } private List buildContexts(final String type, final Set contexts) { final List res = Lists.newArrayList(); - if ((contextMapper != null) && !contextMapper.isEmpty() && MainEntityType.result.toString().equals(type)) { + if ((contextMapper != null) + && !contextMapper.isEmpty() + && MainEntityType.result.toString().equals(type)) { XMLTag document = XMLDoc.newDocument(true).addRoot("contextRoot"); @@ -885,7 +1221,9 @@ public class XmlRecordFactory implements Serializable { if (def == null) { continue; - // throw new IllegalStateException(String.format("cannot find context for id '%s'", id)); + // throw new IllegalStateException(String.format("cannot find context for id + // '%s'", + // id)); } if (def.getName().equals("context")) { @@ -897,7 +1235,13 @@ public class XmlRecordFactory implements Serializable { if (def.getName().equals("category")) { final String rootId = substringBefore(def.getId(), "::"); - document = addContextDef(document.gotoRoot().gotoTag("//context[./@id='" + rootId + "']", new Object()), def); + document = + addContextDef( + document.gotoRoot() + .gotoTag( + "//context[./@id='" + rootId + "']", + new Object()), + def); } if (def.getName().equals("concept")) { @@ -930,14 +1274,17 @@ public class XmlRecordFactory implements Serializable { } private XMLTag addContextDef(final XMLTag tag, final ContextDef def) { - tag.addTag(def.getName()).addAttribute("id", def.getId()).addAttribute("label", def.getLabel()); + tag.addTag(def.getName()) + .addAttribute("id", def.getId()) + .addAttribute("label", def.getLabel()); if ((def.getType() != null) && !def.getType().isEmpty()) { tag.addAttribute("type", def.getType()); } return tag; } - private String asStringElement(final org.w3c.dom.Element element, final Transformer transformer) throws TransformerException { + private String asStringElement(final org.w3c.dom.Element element, final Transformer transformer) + throws TransformerException { final StringWriter buffer = new StringWriter(); transformer.transform(new DOMSource(element), new StreamResult(buffer)); return buffer.toString(); @@ -959,23 +1306,41 @@ public class XmlRecordFactory implements Serializable { final String funderShortName = funder.valueOf("./shortname"); contexts.add(funderShortName); - contextMapper.put(funderShortName, new ContextDef(funderShortName, funder.valueOf("./name"), "context", "funding")); + contextMapper.put( + funderShortName, + new ContextDef( + funderShortName, funder.valueOf("./name"), "context", "funding")); final Node level0 = fundingPath.selectSingleNode("//funding_level_0"); if (level0 != null) { - final String level0Id = Joiner.on("::").join(funderShortName, level0.valueOf("./name")); - contextMapper.put(level0Id, new ContextDef(level0Id, level0.valueOf("./description"), "category", "")); + final String level0Id = + Joiner.on("::").join(funderShortName, level0.valueOf("./name")); + contextMapper.put( + level0Id, + new ContextDef( + level0Id, level0.valueOf("./description"), "category", "")); final Node level1 = fundingPath.selectSingleNode("//funding_level_1"); if (level1 == null) { contexts.add(level0Id); } else { - final String level1Id = Joiner.on("::").join(level0Id, level1.valueOf("./name")); - contextMapper.put(level1Id, new ContextDef(level1Id, level1.valueOf("./description"), "concept", "")); + final String level1Id = + Joiner.on("::").join(level0Id, level1.valueOf("./name")); + contextMapper.put( + level1Id, + new ContextDef( + level1Id, level1.valueOf("./description"), "concept", "")); final Node level2 = fundingPath.selectSingleNode("//funding_level_2"); if (level2 == null) { contexts.add(level1Id); } else { - final String level2Id = Joiner.on("::").join(level1Id, level2.valueOf("./name")); - contextMapper.put(level2Id, new ContextDef(level2Id, level2.valueOf("./description"), "concept", "")); + final String level2Id = + Joiner.on("::").join(level1Id, level2.valueOf("./name")); + contextMapper.put( + level2Id, + new ContextDef( + level2Id, + level2.valueOf("./description"), + "concept", + "")); contexts.add(level2Id); } } @@ -986,8 +1351,6 @@ public class XmlRecordFactory implements Serializable { } } - - @SuppressWarnings("unchecked") protected static String getRelFundingTree(final String xmlTree) { String funding = ""; @@ -997,13 +1360,26 @@ public class XmlRecordFactory implements Serializable { funding += getFunderElement(ftree); - for (final Object o : Lists.reverse(ftree.selectNodes("//fundingtree//*[starts-with(local-name(),'funding_level_')]"))) { + for (final Object o : + Lists.reverse( + ftree.selectNodes( + "//fundingtree//*[starts-with(local-name(),'funding_level_')]"))) { final Element e = (Element) o; final String _id = e.valueOf("./id"); - funding += "<" + e.getName() + " name=\"" + XmlSerializationUtils.escapeXml(e.valueOf("./name")) + "\">" + XmlSerializationUtils.escapeXml(_id) + ""; + funding += + "<" + + e.getName() + + " name=\"" + + XmlSerializationUtils.escapeXml(e.valueOf("./name")) + + "\">" + + XmlSerializationUtils.escapeXml(_id) + + ""; } } catch (final DocumentException e) { - throw new IllegalArgumentException("unable to parse funding tree: " + xmlTree + "\n" + e.getMessage()); + throw new IllegalArgumentException( + "unable to parse funding tree: " + xmlTree + "\n" + e.getMessage()); } finally { funding += ""; } @@ -1016,8 +1392,14 @@ public class XmlRecordFactory implements Serializable { final String funderName = ftree.valueOf("//fundingtree/funder/name"); final String funderJurisdiction = ftree.valueOf("//fundingtree/funder/jurisdiction"); - return ""; + return ""; } - -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java index bc183d0b3b..4dacce7b9b 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java @@ -1,41 +1,43 @@ package eu.dnetlib.dhp.oa.provision.utils; -import eu.dnetlib.dhp.schema.oaf.*; - import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.removePrefix; import static org.apache.commons.lang3.StringUtils.isBlank; import static org.apache.commons.lang3.StringUtils.isNotBlank; +import eu.dnetlib.dhp.schema.oaf.*; + public class XmlSerializationUtils { // XML 1.0 // #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] | [#x10000-#x10FFFF] - private final static String xml10pattern = "[^" - + "\u0009\r\n" - + "\u0020-\uD7FF" - + "\uE000-\uFFFD" - + "\ud800\udc00-\udbff\udfff" - + "]"; + private static final String xml10pattern = + "[^" + + "\u0009\r\n" + + "\u0020-\uD7FF" + + "\uE000-\uFFFD" + + "\ud800\udc00-\udbff\udfff" + + "]"; public static String mapJournal(Journal j) { - final String attrs = new StringBuilder() - .append(attr("issn", j.getIssnPrinted())) - .append(attr("eissn", j.getIssnOnline())) - .append(attr("lissn", j.getIssnLinking())) - .append(attr("ep", j.getEp())) - .append(attr("iss", j.getIss())) - .append(attr("sp", j.getSp())) - .append(attr("vol", j.getVol())) - .toString() - .trim(); + final String attrs = + new StringBuilder() + .append(attr("issn", j.getIssnPrinted())) + .append(attr("eissn", j.getIssnOnline())) + .append(attr("lissn", j.getIssnLinking())) + .append(attr("ep", j.getEp())) + .append(attr("iss", j.getIss())) + .append(attr("sp", j.getSp())) + .append(attr("vol", j.getVol())) + .toString() + .trim(); return new StringBuilder() - .append("") - .append(escapeXml(j.getName())) - .append("") - .toString(); + .append("") + .append(escapeXml(j.getName())) + .append("") + .toString(); } private static String attr(final String name, final String value) { @@ -43,7 +45,11 @@ public class XmlSerializationUtils { } public static String mapStructuredProperty(String name, StructuredProperty t) { - return asXmlElement(name, t.getValue(), t.getQualifier(), t.getDataInfo() != null ? t.getDataInfo() : null); + return asXmlElement( + name, + t.getValue(), + t.getQualifier(), + t.getDataInfo() != null ? t.getDataInfo() : null); } public static String mapQualifier(String name, Qualifier q) { @@ -51,8 +57,7 @@ public class XmlSerializationUtils { } public static String escapeXml(final String value) { - return value - .replaceAll("&", "&") + return value.replaceAll("&", "&") .replaceAll("<", "<") .replaceAll(">", ">") .replaceAll("\"", """) @@ -67,16 +72,25 @@ public class XmlSerializationUtils { .append(asXmlElement("deletedbyinference", dataInfo.getDeletedbyinference() + "")) .append(asXmlElement("trust", dataInfo.getTrust() + "")) .append(asXmlElement("inferenceprovenance", dataInfo.getInferenceprovenance() + "")) - .append(asXmlElement("provenanceaction", null, dataInfo.getProvenanceaction(), null)) + .append( + asXmlElement( + "provenanceaction", null, dataInfo.getProvenanceaction(), null)) .append("") .toString(); } private static StringBuilder dataInfoAsAttributes(final StringBuilder sb, final DataInfo info) { - return sb - .append(attr("inferred", info.getInferred() != null ? info.getInferred().toString() : "")) + return sb.append( + attr( + "inferred", + info.getInferred() != null ? info.getInferred().toString() : "")) .append(attr("inferenceprovenance", info.getInferenceprovenance())) - .append(attr("provenanceaction", info.getProvenanceaction() != null ? info.getProvenanceaction().getClassid() : "")) + .append( + attr( + "provenanceaction", + info.getProvenanceaction() != null + ? info.getProvenanceaction().getClassid() + : "")) .append(attr("trust", info.getTrust())); } @@ -108,7 +122,8 @@ public class XmlSerializationUtils { return asXmlElement(name, value, null, null); } - public static String asXmlElement(final String name, final String value, final Qualifier q, final DataInfo info) { + public static String asXmlElement( + final String name, final String value, final Qualifier q, final DataInfo info) { StringBuilder sb = new StringBuilder(); sb.append("<"); sb.append(name); @@ -116,12 +131,21 @@ public class XmlSerializationUtils { sb.append(getAttributes(q)); } if (info != null) { - sb - .append(" ") - .append(attr("inferred", info.getInferred() != null ? info.getInferred().toString() : "")) - .append(attr("inferenceprovenance", info.getInferenceprovenance())) - .append(attr("provenanceaction", info.getProvenanceaction() != null ? info.getProvenanceaction().getClassid() : "")) - .append(attr("trust", info.getTrust())); + sb.append(" ") + .append( + attr( + "inferred", + info.getInferred() != null + ? info.getInferred().toString() + : "")) + .append(attr("inferenceprovenance", info.getInferenceprovenance())) + .append( + attr( + "provenanceaction", + info.getProvenanceaction() != null + ? info.getProvenanceaction().getClassid() + : "")) + .append(attr("trust", info.getTrust())); } if (isBlank(value)) { sb.append("/>"); @@ -147,5 +171,4 @@ public class XmlSerializationUtils { .append(attr("schemename", q.getSchemename())) .toString(); } - } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java index d1456d8321..e1c0af7adb 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java @@ -1,10 +1,9 @@ package eu.dnetlib.dhp.oa.provision; -import org.junit.jupiter.api.BeforeEach; - import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import org.junit.jupiter.api.BeforeEach; public class GraphJoinerTest { @@ -21,18 +20,22 @@ public class GraphJoinerTest { } private static void copyFiles(Path source, Path target) throws IOException { - Files.list(source).forEach(f -> { - try { - if (Files.isDirectory(f)) { - Path subTarget = Files.createDirectories(target.resolve(f.getFileName())); - copyFiles(f, subTarget); - } else { - Files.copy(f, target.resolve(f.getFileName())); - } - } catch (IOException e) { - e.printStackTrace(); - throw new RuntimeException(e); - } - }); + Files.list(source) + .forEach( + f -> { + try { + if (Files.isDirectory(f)) { + Path subTarget = + Files.createDirectories( + target.resolve(f.getFileName())); + copyFiles(f, subTarget); + } else { + Files.copy(f, target.resolve(f.getFileName())); + } + } catch (IOException e) { + e.printStackTrace(); + throw new RuntimeException(e); + } + }); } } diff --git a/pom.xml b/pom.xml index 1d36d42f91..f4dfc2c0db 100644 --- a/pom.xml +++ b/pom.xml @@ -462,6 +462,36 @@ + + com.cosium.code + git-code-format-maven-plugin + ${git-code-format-maven-plugin.version} + + + + install-formatter-hook + + install-hooks + + + + + validate-code-format + + validate-code-format + + + + + + true + false + false + false + + + org.apache.maven.plugins maven-release-plugin @@ -535,6 +565,7 @@ UTF-8 3.6.0 2.22.2 + 2.4 cdh5.9.2 2.6.0-${dhp.cdh.version} 4.1.0-${dhp.cdh.version}