From 776c898c4bd281ceca5824ec2ea4fa776df36cfb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 22 Apr 2024 11:04:17 +0200 Subject: [PATCH 1/5] [WebCrawl] adding affiliation relations from web information --- .../CreateActionSetFromWebEntries.java | 272 +++++++++++++++++ .../actionmanager/webcrawl/as_parameters.json | 20 ++ .../dhp/actionmanager/webcrawl/job.properties | 2 + .../webcrawl/oozie_app/config-default.xml | 58 ++++ .../webcrawl/oozie_app/workflow.xml | 53 ++++ .../actionmanager/webcrawl/CreateASTest.java | 285 ++++++++++++++++++ .../dhp/actionmanager/webcrawl/part-00000 | 1 + .../dhp/actionmanager/webcrawl/part-00001 | 10 + .../dhp/actionmanager/webcrawl/part-00002 | 1 + 9 files changed, 702 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/part-00000 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/part-00001 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/part-00002 diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java new file mode 100644 index 0000000000..5a0be98d3e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java @@ -0,0 +1,272 @@ + +package eu.dnetlib.dhp.actionmanager.webcrawl; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.*; +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.api.java.function.FlatMapFunction; +import org.apache.spark.sql.*; +import org.apache.spark.sql.types.StructType; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; +import scala.Tuple2; + +/** + * @author miriam.baglioni + * @Date 18/04/24 + */ +public class CreateActionSetFromWebEntries implements Serializable { + private static final Logger log = LoggerFactory.getLogger(CreateActionSetFromWebEntries.class); + private static final String DOI_PREFIX = "50|doi_________::"; + + private static final String ROR_PREFIX = "20|ror_________::"; + + private static final String PMID_PREFIX = "50|pmid________::"; + + private static final String PMCID_PREFIX = "50|pmc_________::"; + private static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b"; + private static final String WEB_CRAWL_NAME = "Web Crawl"; + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + CreateActionSetFromWebEntries.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + + createActionSet(spark, inputPath, outputPath + "actionSet"); + createPlainRelations(spark, inputPath, outputPath + "relations"); + }); + } + + private static void createPlainRelations(SparkSession spark, String inputPath, String outputPath) { + final Dataset dataset = readWebCrawl(spark, inputPath); + + dataset.flatMap((FlatMapFunction>) row -> { + List> ret = new ArrayList<>(); + + final String ror = row.getAs("ror"); + ret.addAll(createAffiliationRelationPairDOI(row.getAs("publication_year"), row.getAs("doi"), ror)); + ret.addAll(createAffiliationRelationPairPMID(row.getAs("publication_year"), row.getAs("pmid"), ror)); + ret.addAll(createAffiliationRelationPairPMCID(row.getAs("publication_year"), row.getAs("pmcid"), ror)); + + return ret + .iterator(); + }, Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class))) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static Collection> createAffiliationRelationPairPMCID( + String publication_year, String pmcid, String ror) { + if (pmcid == null) + return new ArrayList<>(); + + return createAffiliatioRelationPair("PMC" + pmcid, ror) + .stream() + .map(r -> new Tuple2(publication_year, r)) + .collect(Collectors.toList()); + } + + private static Collection> createAffiliationRelationPairPMID( + String publication_year, String pmid, String ror) { + if (pmid == null) + return new ArrayList<>(); + + return createAffiliatioRelationPair(pmid, ror) + .stream() + .map(r -> new Tuple2(publication_year, r)) + .collect(Collectors.toList()); + } + + private static Collection> createAffiliationRelationPairDOI( + String publication_year, String doi, String ror) { + if (doi == null) + return new ArrayList<>(); + + return createAffiliatioRelationPair(doi, ror) + .stream() + .map(r -> new Tuple2(publication_year, r)) + .collect(Collectors.toList()); + } + + public static void createActionSet(SparkSession spark, String inputPath, + String outputPath) { + + final Dataset dataset = readWebCrawl(spark, inputPath) + .filter("publication_year <= 2020 or country_code=='IE'") + .drop("publication_year"); + + dataset.flatMap((FlatMapFunction) row -> { + List ret = new ArrayList<>(); + final String ror = ROR_PREFIX + + IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror"))); + ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror)); + ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror)); + ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror)); + + return ret + .iterator(); + }, Encoders.bean(Relation.class)) + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + + } + + private static Dataset readWebCrawl(SparkSession spark, String inputPath) { + StructType webInfo = StructType + .fromDDL( + "`id` STRING , `doi` STRING, `ids` STRUCT<`pmid` :STRING, `pmcid`: STRING >, `publication_year` STRING, " + + + "`authorships` ARRAY>>>"); + + return spark + .read() + .schema(webInfo) + .json(inputPath) + .withColumn( + "authors", functions + .explode( + functions.col("authorships"))) + .selectExpr("id", "doi", "ids", "publication_year", "authors.institutions as institutions") + .withColumn( + "institution", functions + .explode( + functions.col("institutions"))) + .selectExpr( + "id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror", + "institution.country_code as country_code", "publication_year") + // .where("country_code == 'IE'") + .distinct(); + + } + + private static List createAffiliationRelationPairPMCID(String pmcid, String ror) { + if (pmcid == null) + return new ArrayList<>(); + + return createAffiliatioRelationPair( + PMCID_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), "PMC" + pmcid.substring(43))), + ror); + } + + private static List createAffiliationRelationPairPMID(String pmid, String ror) { + if (pmid == null) + return new ArrayList<>(); + + return createAffiliatioRelationPair( + PMID_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), pmid.substring(33))), + ror); + } + + private static List createAffiliationRelationPairDOI(String doi, String ror) { + if (doi == null) + return new ArrayList<>(); + + return createAffiliatioRelationPair( + DOI_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), doi.substring(16))), + ror); + + } + + private static List createAffiliatioRelationPair(String resultId, String orgId) { + ArrayList newRelations = new ArrayList(); + + newRelations + .add( + OafMapperUtils + .getRelation( + orgId, resultId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION, + ModelConstants.IS_AUTHOR_INSTITUTION_OF, + Arrays + .asList( + OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)), + OafMapperUtils + .dataInfo( + false, null, false, false, + OafMapperUtils + .qualifier( + "sysimport:crasswalk:webcrawl", "Imported from Webcrawl", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9"), + null)); + + newRelations + .add( + OafMapperUtils + .getRelation( + resultId, orgId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION, + ModelConstants.HAS_AUTHOR_INSTITUTION, + Arrays + .asList( + OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)), + OafMapperUtils + .dataInfo( + false, null, false, false, + OafMapperUtils + .qualifier( + "sysimport:crasswalk:webcrawl", "Imported from Webcrawl", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9"), + null)); + + return newRelations; + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json new file mode 100644 index 0000000000..3f056edf77 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "sp", + "paramLongName": "sourcePath", + "paramDescription": "the zipped opencitations file", + "paramRequired": true + }, + { + "paramName": "op", + "paramLongName": "outputPath", + "paramDescription": "the working path", + "paramRequired": true + }, + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "the hdfs name node", + "paramRequired": false + } +] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties new file mode 100644 index 0000000000..f616baea70 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties @@ -0,0 +1,2 @@ +sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/ +outputPath=/tmp/miriam/webcrawlComplete/ diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/config-default.xml new file mode 100644 index 0000000000..a1755f329b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/config-default.xml @@ -0,0 +1,58 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + + + oozie.launcher.mapreduce.user.classpath.first + true + + + sparkExecutorNumber + 4 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + sparkDriverMemory + 15G + + + sparkExecutorMemory + 6G + + + sparkExecutorCores + 1 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml new file mode 100644 index 0000000000..653a7d3842 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml @@ -0,0 +1,53 @@ + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Produces the AS for WC + eu.dnetlib.dhp.actionmanager.webcrawl.CreateActionSetFromWebEntries + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${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}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${outputPath} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java new file mode 100644 index 0000000000..a1cd69dccd --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java @@ -0,0 +1,285 @@ +package eu.dnetlib.dhp.actionmanager.webcrawl; +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +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.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.Relation; + +/** + * @author miriam.baglioni + * @Date 22/04/24 + */ +public class CreateASTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(CreateASTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(CreateASTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(CreateASTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(CreateASTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + @Test + void testNumberofRelations() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/webcrawl/") + .getPath(); + + CreateActionSetFromWebEntries + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-sourcePath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet1" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + Assertions.assertEquals(64, tmp.count()); + + } + @Test + void testRelations() throws Exception { + +// , "doi":"https://doi.org/10.1126/science.1188021", "pmid":"https://pubmed.ncbi.nlm.nih.gov/20448178", https://www.ncbi.nlm.nih.gov/pmc/articles/5100745 + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/webcrawl/") + .getPath(); + + CreateActionSetFromWebEntries + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-sourcePath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet1" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getSource() + .equals( + "50|doi_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023")))) + .count()); + + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getTarget() + .equals( + "50|doi_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023")))) + .count()); + + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getSource() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue("ROR", "https://ror.org/03argrj65")))) + .count()); + + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue("ROR", "https://ror.org/03argrj65")))) + .count()); + + Assertions + .assertEquals( + 5, tmp + .filter( + r -> r + .getSource() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue("ROR", "https://ror.org/03265fv13")))) + .count()); + + Assertions + .assertEquals( + 5, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue("ROR", "https://ror.org/03265fv13")))) + .count()); + + Assertions + .assertEquals( + 2, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13"))) + && r.getSource().startsWith("50|doi")) + .count()); + + Assertions + .assertEquals( + 2, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13"))) + && r.getSource().startsWith("50|pmid")) + .count()); + + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13"))) + && r.getSource().startsWith("50|pmc")) + .count()); + } + + @Test + void testRelationsCollectedFrom() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/webcrawl") + .getPath(); + + CreateActionSetFromWebEntries + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-sourcePath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet1" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals("Web Crawl", r.getCollectedfrom().get(0).getValue()); + assertEquals("10|openaire____::fb98a192f6a055ba495ef414c330834b", r.getCollectedfrom().get(0).getKey()); + }); + + } + + + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/part-00000 b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/part-00000 new file mode 100644 index 0000000000..a94baacb4e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/part-00000 @@ -0,0 +1 @@ +{"id": "https://openalex.org/W4214628335", "doi": "https://doi.org/10.1098/rstl.1684.0023", "title": "A letter from the learned and ingenious Mr. Will. Molyneux Secrctary to the Society of Dublin, to Will. Musgrave LL. B. Fellow of New Colledge, and Secretary to the Philosophical Society of Oxford, for advertisement of natural Knowledge; concerning Lough Neagh in Ireland, and its petrifying Qualitys", "display_name": "A letter from the learned and ingenious Mr. Will. Molyneux Secrctary to the Society of Dublin, to Will. Musgrave LL. B. Fellow of New Colledge, and Secretary to the Philosophical Society of Oxford, for advertisement of natural Knowledge; concerning Lough Neagh in Ireland, and its petrifying Qualitys", "publication_year": 1684, "publication_date": "1684-04-20", "ids": {"openalex": "https://openalex.org/W4214628335", "doi": "https://doi.org/10.1098/rstl.1684.0023"}, "language": "en", "primary_location": {"is_oa": true, "landing_page_url": "https://doi.org/10.1098/rstl.1684.0023", "pdf_url": "https://royalsocietypublishing.org/doi/pdf/10.1098/rstl.1684.0023", "source": {"id": "https://openalex.org/S4210177916", "display_name": "Philosophical transactions of the Royal Society of London", "issn_l": "0261-0523", "issn": ["0261-0523", "2053-9223"], "is_oa": false, "is_in_doaj": false, "host_organization": "https://openalex.org/P4310319787", "host_organization_name": "Royal Society", "host_organization_lineage": ["https://openalex.org/P4310319787"], "host_organization_lineage_names": ["Royal Society"], "type": 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Casey", "orcid": null}, "institutions": [{"id": "https://openalex.org/I100930933", "display_name": "University College Dublin", "ror": "https://ror.org/05m7pjf47", "country_code": "IE", "type": "education", "lineage": ["https://openalex.org/I100930933", "https://openalex.org/I181231927"]}], "countries": ["IE"], "is_corresponding": false, "raw_author_name": "Jillian Casey", "raw_affiliation_string": "School of Medicine and Medical Science University College, Dublin 4, Ireland.,", "raw_affiliation_strings": ["School of Medicine and Medical Science University College, Dublin 4, Ireland.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5027881770", "display_name": "Brian Hon‐Yin Chung", "orcid": null}, "institutions": [{"id": "https://openalex.org/I2801317318", "display_name": "Hospital for Sick Children", "ror": "https://ror.org/057q4rt57", "country_code": "CA", "type": "healthcare", "lineage": ["https://openalex.org/I2801317318"]}], "countries": ["CA"], "is_corresponding": false, "raw_author_name": "Brian H.Y. Chung", "raw_affiliation_string": "The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada.,", "raw_affiliation_strings": ["The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5081922755", "display_name": "Lynne Cochrane", "orcid": null}, "institutions": [{"id": "https://openalex.org/I205274468", "display_name": "Trinity College Dublin", "ror": "https://ror.org/02tyrky19", "country_code": "IE", "type": "education", "lineage": ["https://openalex.org/I205274468"]}], "countries": ["IE"], "is_corresponding": false, "raw_author_name": "Lynne Cochrane", "raw_affiliation_string": "Department of Psychiatry, Autism Genetics Group, School of Medicine, Trinity College, Dublin 8, Ireland.,", "raw_affiliation_strings": ["Department of Psychiatry, Autism Genetics Group, School of Medicine, Trinity College, Dublin 8, Ireland.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5027303675", "display_name": "Christina Corsello", "orcid": null}, "institutions": [{"id": "https://openalex.org/I27837315", "display_name": "University of Michigan–Ann Arbor", "ror": "https://ror.org/00jmfr291", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I27837315"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Christina Corsello", "raw_affiliation_string": "Autism and Communicative Disorders Centre, University of Michigan, Ann Arbor, Michigan 48109-2054, USA.,", "raw_affiliation_strings": ["Autism and Communicative Disorders Centre, University of Michigan, Ann Arbor, Michigan 48109-2054, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5013222660", "display_name": "Emily L. Crawford", "orcid": null}, "institutions": [{"id": "https://openalex.org/I200719446", "display_name": "Vanderbilt University", "ror": "https://ror.org/02vm5rt34", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I200719446"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Emily L. Crawford", "raw_affiliation_string": "Department of Molecular Physiology and Biophysics, Vanderbilt Kennedy Center, and Centers for Human Genetics Research and Molecular Neuroscience, Vanderbilt University, Nashville, Tennessee 37232, USA.,", "raw_affiliation_strings": ["Department of Molecular Physiology and Biophysics, Vanderbilt Kennedy Center, and Centers for Human Genetics Research and Molecular Neuroscience, Vanderbilt University, Nashville, Tennessee 37232, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5071221627", "display_name": "Andrew Crossett", "orcid": null}, "institutions": [{"id": "https://openalex.org/I74973139", "display_name": "Carnegie Mellon University", "ror": "https://ror.org/05x2bcf33", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I74973139"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Andrew Crossett", "raw_affiliation_string": "Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.,", "raw_affiliation_strings": ["Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5017430701", "display_name": "Cheryl Cytrynbaum", "orcid": "https://orcid.org/0000-0002-3742-1250"}, "institutions": [{"id": "https://openalex.org/I2801317318", "display_name": "Hospital for Sick Children", "ror": "https://ror.org/057q4rt57", "country_code": "CA", "type": "healthcare", "lineage": ["https://openalex.org/I2801317318"]}], "countries": ["CA"], "is_corresponding": false, "raw_author_name": "Cheryl Cytrynbaum", "raw_affiliation_string": "The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada.,", "raw_affiliation_strings": ["The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5073522388", "display_name": "Geraldine Dawson", "orcid": "https://orcid.org/0000-0003-1410-2764"}, "institutions": [{"id": "https://openalex.org/I109266671", "display_name": "Autism Speaks", "ror": "https://ror.org/04bkad313", "country_code": "US", "type": "nonprofit", "lineage": ["https://openalex.org/I109266671"]}, {"id": "https://openalex.org/I114027177", "display_name": "University of North Carolina at Chapel Hill", "ror": "https://ror.org/0130frc33", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I114027177", "https://openalex.org/I4210158053"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Geraldine Dawson", "raw_affiliation_string": "Autism Speaks, New York 10016, USA.,; Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina 27599-3366, USA.,", "raw_affiliation_strings": ["Autism Speaks, New York 10016, USA.,", "Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina 27599-3366, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5039670828", "display_name": "Maretha de Jonge", "orcid": null}, "institutions": [{"id": "https://openalex.org/I3018483916", "display_name": "University Medical Center Utrecht", "ror": "https://ror.org/0575yy874", "country_code": "NL", "type": "healthcare", "lineage": ["https://openalex.org/I3018483916"]}], "countries": ["NL"], "is_corresponding": false, "raw_author_name": "Maretha de Jonge", "raw_affiliation_string": "Department of Child Psychiatry, University Medical Center, Utrecht 3508 GA, The Netherlands.,", "raw_affiliation_strings": ["Department of Child Psychiatry, University Medical Center, Utrecht 3508 GA, The Netherlands.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5020448299", "display_name": "Richard Delorme", "orcid": null}, "institutions": [{"id": "https://openalex.org/I4210096842", "display_name": "Fondation FondaMental", "ror": "https://ror.org/00rrhf939", "country_code": "FR", "type": "other", "lineage": ["https://openalex.org/I4210096842"]}, {"id": "https://openalex.org/I154526488", "display_name": "Inserm", "ror": "https://ror.org/02vjkv261", "country_code": "FR", "type": "government", "lineage": ["https://openalex.org/I154526488"]}, {"id": "https://openalex.org/I4210126712", "display_name": "Hôpital Robert-Debré", "ror": "https://ror.org/02dcqy320", "country_code": "FR", "type": "healthcare", "lineage": ["https://openalex.org/I4210097159", "https://openalex.org/I4210126712"]}], "countries": ["FR"], "is_corresponding": false, "raw_author_name": "Richard Delorme", "raw_affiliation_string": "INSERM U 955, Fondation FondaMental, APHP, Hôpital Robert Debré, Child and Adolescent Psychiatry, 75019 Paris, France.,", "raw_affiliation_strings": ["INSERM U 955, Fondation FondaMental, APHP, Hôpital Robert Debré, Child and Adolescent Psychiatry, 75019 Paris, France.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5081523158", "display_name": "Irene Drmic", "orcid": "https://orcid.org/0000-0002-9212-4929"}, "institutions": [{"id": "https://openalex.org/I2801420703", "display_name": "Holland Bloorview Kids Rehabilitation Hospital", "ror": "https://ror.org/03qea8398", "country_code": "CA", "type": "healthcare", "lineage": ["https://openalex.org/I2801420703"]}, {"id": "https://openalex.org/I185261750", "display_name": "University of Toronto", "ror": "https://ror.org/03dbr7087", "country_code": "CA", "type": "education", "lineage": ["https://openalex.org/I185261750"]}, {"id": "https://openalex.org/I2801317318", "display_name": "Hospital for Sick Children", "ror": "https://ror.org/057q4rt57", "country_code": "CA", "type": "healthcare", "lineage": ["https://openalex.org/I2801317318"]}, {"id": "https://openalex.org/I4210141030", "display_name": "SickKids Foundation", "ror": "https://ror.org/04374qe70", "country_code": "CA", "type": "nonprofit", "lineage": ["https://openalex.org/I4210141030"]}], "countries": ["CA"], "is_corresponding": false, "raw_author_name": "Irene Drmic", "raw_affiliation_string": "Autism Research Unit, The Hospital for Sick Children and Bloorview Kids Rehab, University of Toronto, Toronto, Ontario M5G 1X8, Canada.,", "raw_affiliation_strings": ["Autism Research Unit, The Hospital for Sick Children and Bloorview Kids Rehab, University of Toronto, Toronto, Ontario M5G 1X8, Canada.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5065665765", "display_name": "Eftichia Duketis", "orcid": null}, "institutions": [{"id": "https://openalex.org/I114090438", "display_name": "Goethe University Frankfurt", "ror": "https://ror.org/04cvxnb49", "country_code": "DE", "type": "education", "lineage": ["https://openalex.org/I114090438"]}], "countries": ["DE"], "is_corresponding": false, "raw_author_name": "Eftichia Duketis", "raw_affiliation_string": "Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany.,", "raw_affiliation_strings": ["Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5048358192", "display_name": "Frederico Duque", "orcid": null}, "institutions": [], "countries": ["PT"], "is_corresponding": false, "raw_author_name": "Frederico Duque", "raw_affiliation_string": "Hospital Pediátrico de Coimbra, 3000 – 076 Coimbra, Portugal.,", "raw_affiliation_strings": ["Hospital Pediátrico de Coimbra, 3000 – 076 Coimbra, Portugal.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5067974738", "display_name": "Annette Estes", "orcid": "https://orcid.org/0000-0003-2687-4155"}, "institutions": [{"id": "https://openalex.org/I201448701", "display_name": "University of Washington", "ror": "https://ror.org/00cvxb145", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I201448701"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Annette Estes", "raw_affiliation_string": "Department of Speech and Hearing Sciences, University of Washington, Seattle, Washington 98195, USA.,", "raw_affiliation_strings": ["Department of Speech and Hearing Sciences, University of Washington, Seattle, Washington 98195, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5034071437", "display_name": "Penny Farrar", "orcid": null}, "institutions": [{"id": "https://openalex.org/I1336263701", "display_name": "Wellcome Centre for Human Genetics", "ror": "https://ror.org/01rjnta51", "country_code": "GB", "type": "facility", "lineage": ["https://openalex.org/I1336263701", "https://openalex.org/I40120149", "https://openalex.org/I87048295"]}, {"id": "https://openalex.org/I40120149", "display_name": "University of Oxford", "ror": "https://ror.org/052gg0110", "country_code": "GB", "type": "education", "lineage": ["https://openalex.org/I40120149"]}], "countries": ["GB"], "is_corresponding": false, "raw_author_name": "Penny Farrar", "raw_affiliation_string": "Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,", "raw_affiliation_strings": ["Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5003632230", "display_name": "Bridget A. Fernandez", "orcid": "https://orcid.org/0000-0003-1265-8259"}, "institutions": [{"id": "https://openalex.org/I130438778", "display_name": "Memorial University of Newfoundland", "ror": "https://ror.org/04haebc03", "country_code": "CA", "type": "education", "lineage": ["https://openalex.org/I130438778"]}], "countries": ["CA"], "is_corresponding": false, "raw_author_name": "Bridget A. Fernandez", "raw_affiliation_string": "Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St John’s Newfoundland A1B 3V6, Canada.,", "raw_affiliation_strings": ["Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St John’s Newfoundland A1B 3V6, Canada.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5065212941", "display_name": "Susan E. Folstein", "orcid": null}, "institutions": [{"id": "https://openalex.org/I145608581", "display_name": "University of Miami", "ror": "https://ror.org/02dgjyy92", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I145608581"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Susan E. Folstein", "raw_affiliation_string": "The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida 33101, USA.,", "raw_affiliation_strings": ["The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida 33101, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5009614153", "display_name": "Éric Fombonne", "orcid": "https://orcid.org/0000-0002-8605-3538"}, "institutions": [{"id": "https://openalex.org/I5023651", "display_name": "McGill University", "ror": "https://ror.org/01pxwe438", "country_code": "CA", "type": "education", "lineage": ["https://openalex.org/I5023651"]}], "countries": ["CA"], "is_corresponding": false, "raw_author_name": "Eric Fombonne", "raw_affiliation_string": "Division of Psychiatry, McGill University, Montreal, Quebec H3A 1A1, Canada.,", "raw_affiliation_strings": ["Division of Psychiatry, McGill University, Montreal, Quebec H3A 1A1, Canada.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5050223372", "display_name": "Christine M. Freitag", "orcid": "https://orcid.org/0000-0001-9676-4782"}, "institutions": [{"id": "https://openalex.org/I114090438", "display_name": "Goethe University Frankfurt", "ror": "https://ror.org/04cvxnb49", "country_code": "DE", "type": "education", "lineage": ["https://openalex.org/I114090438"]}], "countries": ["DE"], "is_corresponding": false, "raw_author_name": "Christine M. Freitag", "raw_affiliation_string": "Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany.,", "raw_affiliation_strings": ["Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5076736767", "display_name": "John R. Gilbert", "orcid": null}, "institutions": [{"id": "https://openalex.org/I145608581", "display_name": "University of Miami", "ror": "https://ror.org/02dgjyy92", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I145608581"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "John Gilbert", "raw_affiliation_string": "The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida 33101, USA.,", "raw_affiliation_strings": ["The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida 33101, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5028456703", "display_name": "Christopher Gillberg", "orcid": "https://orcid.org/0000-0001-8848-1934"}, "institutions": [{"id": "https://openalex.org/I881427289", "display_name": "University of Gothenburg", "ror": "https://ror.org/01tm6cn81", "country_code": "SE", "type": "education", "lineage": ["https://openalex.org/I881427289"]}], "countries": ["SE"], "is_corresponding": false, "raw_author_name": "Christopher Gillberg", "raw_affiliation_string": "Department of Child and Adolescent Psychiatry, Göteborg University, Göteborg S41345, Sweden.,", "raw_affiliation_strings": ["Department of Child and Adolescent Psychiatry, Göteborg University, Göteborg S41345, Sweden.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5066789855", "display_name": "Joseph T. Glessner", "orcid": "https://orcid.org/0000-0001-5131-2811"}, "institutions": [{"id": "https://openalex.org/I1335321130", "display_name": "Children's Hospital of Philadelphia", "ror": "https://ror.org/01z7r7q48", "country_code": "US", "type": "healthcare", "lineage": ["https://openalex.org/I1335321130"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Joseph T. Glessner", "raw_affiliation_string": "Division of Human Genetics, The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,", "raw_affiliation_strings": ["Division of Human Genetics, The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5081908377", "display_name": "Jeremy Goldberg", "orcid": null}, "institutions": [{"id": "https://openalex.org/I98251732", "display_name": "McMaster University", "ror": "https://ror.org/02fa3aq29", "country_code": "CA", "type": "education", "lineage": ["https://openalex.org/I98251732"]}], "countries": ["CA"], "is_corresponding": false, "raw_author_name": "Jeremy Goldberg", "raw_affiliation_string": "Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,", "raw_affiliation_strings": ["Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5000005180", "display_name": "Andrew Green", "orcid": "https://orcid.org/0000-0002-0488-5913"}, "institutions": [{"id": "https://openalex.org/I100930933", "display_name": "University College Dublin", "ror": "https://ror.org/05m7pjf47", "country_code": "IE", "type": "education", "lineage": ["https://openalex.org/I100930933", "https://openalex.org/I181231927"]}], "countries": ["IE"], "is_corresponding": false, "raw_author_name": "Andrew Green", "raw_affiliation_string": "School of Medicine and Medical Science University College, Dublin 4, Ireland.,", "raw_affiliation_strings": ["School of Medicine and Medical Science University College, Dublin 4, Ireland.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5076431905", "display_name": "Jonathan Green", "orcid": "https://orcid.org/0000-0002-0143-181X"}, "institutions": [], "countries": ["GB"], "is_corresponding": false, "raw_author_name": "Jonathan Green", "raw_affiliation_string": "Academic Department of Child Psychiatry, Booth Hall of Children’s Hospital, Blackley, Manchester M9 7AA, UK.,", "raw_affiliation_strings": ["Academic Department of Child Psychiatry, Booth Hall of Children’s Hospital, Blackley, Manchester M9 7AA, UK.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5067479223", "display_name": "Stephen J. Guter", "orcid": null}, "institutions": [{"id": "https://openalex.org/I39422238", "display_name": "University of Illinois at Chicago", "ror": "https://ror.org/02mpq6x41", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I2801919071", "https://openalex.org/I39422238"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Stephen J. 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Klauck", "raw_affiliation_string": "Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.,", "raw_affiliation_strings": ["Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5016983099", "display_name": "Alexander Kolevzon", "orcid": "https://orcid.org/0000-0001-8129-2671"}, "institutions": [{"id": "https://openalex.org/I98704320", "display_name": "Icahn School of Medicine at Mount Sinai", "ror": "https://ror.org/04a9tmd77", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I1320796813", "https://openalex.org/I98704320"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Alexander Kolevzon", "raw_affiliation_string": "Department of Psychiatry, The Seaver Autism Center for Research and Treatment, Mount Sinai School of Medicine, New York 10029, USA.,", "raw_affiliation_strings": ["Department of Psychiatry, The Seaver Autism Center for Research and Treatment, Mount Sinai School of Medicine, New York 10029, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5020224643", "display_name": "Olena Korvatska", "orcid": null}, "institutions": [{"id": "https://openalex.org/I201448701", "display_name": "University of Washington", "ror": "https://ror.org/00cvxb145", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I201448701"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Olena Korvatska", "raw_affiliation_string": "Department of Medicine, University of Washington, Seattle, Washington 98195, USA.,", "raw_affiliation_strings": ["Department of Medicine, University of Washington, Seattle, Washington 98195, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5007111212", "display_name": "Vlad Kustanovich", "orcid": null}, "institutions": [{"id": "https://openalex.org/I109266671", "display_name": "Autism Speaks", "ror": "https://ror.org/04bkad313", "country_code": "US", "type": "nonprofit", "lineage": ["https://openalex.org/I109266671"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Vlad Kustanovich", "raw_affiliation_string": "Autism Genetic Resource Exchange, Autism Speaks, Los Angeles, California 90036-4234, USA.,", "raw_affiliation_strings": ["Autism Genetic Resource Exchange, Autism Speaks, Los Angeles, California 90036-4234, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5065072190", "display_name": "Clara Lajonchere", "orcid": "https://orcid.org/0000-0002-3190-4606"}, "institutions": [{"id": "https://openalex.org/I109266671", "display_name": "Autism Speaks", "ror": "https://ror.org/04bkad313", "country_code": "US", "type": "nonprofit", "lineage": ["https://openalex.org/I109266671"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Clara M. 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"reduction": [249], "coronary": [251], "events.": [252], "Clinical": [253], "practice": [254], "moderate": [258], "high": [260], "cardiovascular": [261, 265], "existing": [264], "disease": [266], "should": [267], "not": [268], "change.None.": [269]}, "cited_by_api_url": "https://api.openalex.org/works?filter=cites:W2115169717", "counts_by_year": [{"year": 2023, "cited_by_count": 87}, {"year": 2022, "cited_by_count": 122}, {"year": 2021, "cited_by_count": 93}, {"year": 2020, "cited_by_count": 125}, {"year": 2019, "cited_by_count": 166}, {"year": 2018, "cited_by_count": 164}, {"year": 2017, "cited_by_count": 157}, {"year": 2016, "cited_by_count": 221}, {"year": 2015, "cited_by_count": 198}, {"year": 2014, "cited_by_count": 200}, {"year": 2013, "cited_by_count": 175}, {"year": 2012, "cited_by_count": 134}], "updated_date": "2023-11-29T15:25:34.068916", "created_date": "2016-06-24"} \ No newline at end of file From 24a83fc24f438e6dd928495864f4d32897133612 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 22 Apr 2024 11:39:44 +0200 Subject: [PATCH 2/5] avoid NPEs in common Oaf merge utilities --- .../java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java index c95c31c512..62b9731dcc 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java @@ -270,8 +270,9 @@ public class MergeUtils { } HashMap values = new HashMap<>(); - left.forEach(kv -> values.put(kv.getKey(), kv)); - right.forEach(kv -> values.putIfAbsent(kv.getKey(), kv)); + + Optional.ofNullable(left).ifPresent(l -> l.forEach(kv -> values.put(kv.getKey(), kv))); + Optional.ofNullable(right).ifPresent(r -> r.forEach(kv -> values.putIfAbsent(kv.getKey(), kv))); return new ArrayList<>(values.values()); } From 7de114bda03bcf7b1e2a77e1b185bf61fd126995 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 22 Apr 2024 13:52:50 +0200 Subject: [PATCH 3/5] [WebCrawl] addressing comments from PR --- .../CreateActionSetFromWebEntries.java | 354 +++++++------- .../actionmanager/webcrawl/CreateASTest.java | 436 +++++++++--------- 2 files changed, 376 insertions(+), 414 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java index 5a0be98d3e..4035eb33a6 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java @@ -35,238 +35,198 @@ import scala.Tuple2; * @Date 18/04/24 */ public class CreateActionSetFromWebEntries implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CreateActionSetFromWebEntries.class); - private static final String DOI_PREFIX = "50|doi_________::"; + private static final Logger log = LoggerFactory.getLogger(CreateActionSetFromWebEntries.class); + private static final String DOI_PREFIX = "50|doi_________::"; - private static final String ROR_PREFIX = "20|ror_________::"; + private static final String ROR_PREFIX = "20|ror_________::"; - private static final String PMID_PREFIX = "50|pmid________::"; + private static final String PMID_PREFIX = "50|pmid________::"; - private static final String PMCID_PREFIX = "50|pmc_________::"; - private static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b"; - private static final String WEB_CRAWL_NAME = "Web Crawl"; - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final String PMCID_PREFIX = "50|pmc_________::"; + private static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b"; + private static final String WEB_CRAWL_NAME = "Web Crawl"; + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - CreateActionSetFromWebEntries.class - .getResourceAsStream( - "/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json")); + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + CreateActionSetFromWebEntries.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + 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); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); - SparkConf conf = new SparkConf(); + SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { - createActionSet(spark, inputPath, outputPath + "actionSet"); - createPlainRelations(spark, inputPath, outputPath + "relations"); - }); - } + createActionSet(spark, inputPath, outputPath ); - private static void createPlainRelations(SparkSession spark, String inputPath, String outputPath) { - final Dataset dataset = readWebCrawl(spark, inputPath); + }); + } - dataset.flatMap((FlatMapFunction>) row -> { - List> ret = new ArrayList<>(); + public static void createActionSet(SparkSession spark, String inputPath, + String outputPath) { - final String ror = row.getAs("ror"); - ret.addAll(createAffiliationRelationPairDOI(row.getAs("publication_year"), row.getAs("doi"), ror)); - ret.addAll(createAffiliationRelationPairPMID(row.getAs("publication_year"), row.getAs("pmid"), ror)); - ret.addAll(createAffiliationRelationPairPMCID(row.getAs("publication_year"), row.getAs("pmcid"), ror)); + final Dataset dataset = readWebCrawl(spark, inputPath) + .filter("publication_year <= 2020 or country_code=='IE'") + .drop("publication_year"); - return ret - .iterator(); - }, Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class))) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } + dataset.flatMap((FlatMapFunction) row -> { + List ret = new ArrayList<>(); + final String ror = ROR_PREFIX + + IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror"))); + ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror)); + ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror)); + ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror)); - private static Collection> createAffiliationRelationPairPMCID( - String publication_year, String pmcid, String ror) { - if (pmcid == null) - return new ArrayList<>(); + return ret + .iterator(); + }, Encoders.bean(Relation.class)) + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); - return createAffiliatioRelationPair("PMC" + pmcid, ror) - .stream() - .map(r -> new Tuple2(publication_year, r)) - .collect(Collectors.toList()); - } + } - private static Collection> createAffiliationRelationPairPMID( - String publication_year, String pmid, String ror) { - if (pmid == null) - return new ArrayList<>(); + private static Dataset readWebCrawl(SparkSession spark, String inputPath) { + StructType webInfo = StructType + .fromDDL( + "`id` STRING , `doi` STRING, `ids` STRUCT<`pmid` :STRING, `pmcid`: STRING >, `publication_year` STRING, " + + + "`authorships` ARRAY>>>"); - return createAffiliatioRelationPair(pmid, ror) - .stream() - .map(r -> new Tuple2(publication_year, r)) - .collect(Collectors.toList()); - } + return spark + .read() + .schema(webInfo) + .json(inputPath) + .withColumn( + "authors", functions + .explode( + functions.col("authorships"))) + .selectExpr("id", "doi", "ids", "publication_year", "authors.institutions as institutions") + .withColumn( + "institution", functions + .explode( + functions.col("institutions"))) + .selectExpr( + "id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror", + "institution.country_code as country_code", "publication_year") + .distinct(); - private static Collection> createAffiliationRelationPairDOI( - String publication_year, String doi, String ror) { - if (doi == null) - return new ArrayList<>(); + } - return createAffiliatioRelationPair(doi, ror) - .stream() - .map(r -> new Tuple2(publication_year, r)) - .collect(Collectors.toList()); - } + private static List createAffiliationRelationPairPMCID(String pmcid, String ror) { + if (pmcid == null) + return new ArrayList<>(); - public static void createActionSet(SparkSession spark, String inputPath, - String outputPath) { + return createAffiliatioRelationPair( + PMCID_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), removeResolver("PMC" , pmcid))), + ror); + } - final Dataset dataset = readWebCrawl(spark, inputPath) - .filter("publication_year <= 2020 or country_code=='IE'") - .drop("publication_year"); + private static List createAffiliationRelationPairPMID(String pmid, String ror) { + if (pmid == null) + return new ArrayList<>(); - dataset.flatMap((FlatMapFunction) row -> { - List ret = new ArrayList<>(); - final String ror = ROR_PREFIX - + IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror"))); - ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror)); - ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror)); - ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror)); + return createAffiliatioRelationPair( + PMID_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), removeResolver("PMID", pmid))), + ror); + } - return ret - .iterator(); - }, Encoders.bean(Relation.class)) - .toJavaRDD() - .map(p -> new AtomicAction(p.getClass(), p)) - .mapToPair( - aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + private static String removeResolver(String pidType, String pid) { + switch (pidType){ + case "PMID": + return pid.substring(33); + case "PMC": + return "PMC" + pid.substring(43); + case "DOI": + return pid.substring(16); + } - } + throw new RuntimeException(); - private static Dataset readWebCrawl(SparkSession spark, String inputPath) { - StructType webInfo = StructType - .fromDDL( - "`id` STRING , `doi` STRING, `ids` STRUCT<`pmid` :STRING, `pmcid`: STRING >, `publication_year` STRING, " - + - "`authorships` ARRAY>>>"); + } - return spark - .read() - .schema(webInfo) - .json(inputPath) - .withColumn( - "authors", functions - .explode( - functions.col("authorships"))) - .selectExpr("id", "doi", "ids", "publication_year", "authors.institutions as institutions") - .withColumn( - "institution", functions - .explode( - functions.col("institutions"))) - .selectExpr( - "id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror", - "institution.country_code as country_code", "publication_year") - // .where("country_code == 'IE'") - .distinct(); + private static List createAffiliationRelationPairDOI(String doi, String ror) { + if (doi == null) + return new ArrayList<>(); - } + return createAffiliatioRelationPair( + DOI_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), removeResolver("DOI" ,doi))), + ror); - private static List createAffiliationRelationPairPMCID(String pmcid, String ror) { - if (pmcid == null) - return new ArrayList<>(); + } - return createAffiliatioRelationPair( - PMCID_PREFIX - + IdentifierFactory - .md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), "PMC" + pmcid.substring(43))), - ror); - } + private static List createAffiliatioRelationPair(String resultId, String orgId) { + ArrayList newRelations = new ArrayList(); - private static List createAffiliationRelationPairPMID(String pmid, String ror) { - if (pmid == null) - return new ArrayList<>(); + newRelations + .add( + OafMapperUtils + .getRelation( + orgId, resultId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION, + ModelConstants.IS_AUTHOR_INSTITUTION_OF, + Arrays + .asList( + OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)), + OafMapperUtils + .dataInfo( + false, null, false, false, + OafMapperUtils + .qualifier( + "sysimport:crasswalk:webcrawl", "Imported from Webcrawl", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9"), + null)); - return createAffiliatioRelationPair( - PMID_PREFIX - + IdentifierFactory - .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), pmid.substring(33))), - ror); - } + newRelations + .add( + OafMapperUtils + .getRelation( + resultId, orgId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION, + ModelConstants.HAS_AUTHOR_INSTITUTION, + Arrays + .asList( + OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)), + OafMapperUtils + .dataInfo( + false, null, false, false, + OafMapperUtils + .qualifier( + "sysimport:crasswalk:webcrawl", "Imported from Webcrawl", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9"), + null)); - private static List createAffiliationRelationPairDOI(String doi, String ror) { - if (doi == null) - return new ArrayList<>(); + return newRelations; - return createAffiliatioRelationPair( - DOI_PREFIX - + IdentifierFactory - .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), doi.substring(16))), - ror); - - } - - private static List createAffiliatioRelationPair(String resultId, String orgId) { - ArrayList newRelations = new ArrayList(); - - newRelations - .add( - OafMapperUtils - .getRelation( - orgId, resultId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION, - ModelConstants.IS_AUTHOR_INSTITUTION_OF, - Arrays - .asList( - OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)), - OafMapperUtils - .dataInfo( - false, null, false, false, - OafMapperUtils - .qualifier( - "sysimport:crasswalk:webcrawl", "Imported from Webcrawl", - ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), - "0.9"), - null)); - - newRelations - .add( - OafMapperUtils - .getRelation( - resultId, orgId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION, - ModelConstants.HAS_AUTHOR_INSTITUTION, - Arrays - .asList( - OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)), - OafMapperUtils - .dataInfo( - false, null, false, false, - OafMapperUtils - .qualifier( - "sysimport:crasswalk:webcrawl", "Imported from Webcrawl", - ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), - "0.9"), - null)); - - return newRelations; - - } + } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java index a1cd69dccd..402f07d4d7 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java @@ -1,13 +1,12 @@ + package eu.dnetlib.dhp.actionmanager.webcrawl; + import static org.junit.jupiter.api.Assertions.assertEquals; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; -import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; -import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner; -import eu.dnetlib.dhp.schema.oaf.utils.PidType; import org.apache.commons.io.FileUtils; import org.apache.hadoop.io.Text; import org.apache.spark.SparkConf; @@ -25,261 +24,264 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; /** * @author miriam.baglioni * @Date 22/04/24 */ public class CreateASTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; - private static final Logger log = LoggerFactory - .getLogger(CreateASTest.class); + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(CreateASTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(CreateASTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(CreateASTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(CreateASTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(CreateASTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - 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.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(CreateASTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(CreateASTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - @Test - void testNumberofRelations() throws Exception { + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - String inputPath = getClass() - .getResource( - "/eu/dnetlib/dhp/actionmanager/webcrawl/") - .getPath(); + @Test + void testNumberofRelations() throws Exception { - CreateActionSetFromWebEntries - .main( - new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-sourcePath", - inputPath, - "-outputPath", - workingDir.toString() + "/actionSet1" - }); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/webcrawl/") + .getPath(); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + CreateActionSetFromWebEntries + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-sourcePath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet1" + }); - JavaRDD tmp = sc - .sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class) - .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) - .map(aa -> ((Relation) aa.getPayload())); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - Assertions.assertEquals(64, tmp.count()); + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); - } - @Test - void testRelations() throws Exception { + Assertions.assertEquals(64, tmp.count()); + + } + + @Test + void testRelations() throws Exception { // , "doi":"https://doi.org/10.1126/science.1188021", "pmid":"https://pubmed.ncbi.nlm.nih.gov/20448178", https://www.ncbi.nlm.nih.gov/pmc/articles/5100745 - String inputPath = getClass() - .getResource( - "/eu/dnetlib/dhp/actionmanager/webcrawl/") - .getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/webcrawl/") + .getPath(); - CreateActionSetFromWebEntries - .main( - new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-sourcePath", - inputPath, - "-outputPath", - workingDir.toString() + "/actionSet1" - }); + CreateActionSetFromWebEntries + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-sourcePath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet1" + }); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class) - .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) - .map(aa -> ((Relation) aa.getPayload())); + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); - tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - Assertions - .assertEquals( - 1, tmp - .filter( - r -> r - .getSource() - .equals( - "50|doi_________::" + IdentifierFactory - .md5( - PidCleaner - .normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023")))) - .count()); + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getSource() + .equals( + "50|doi_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023")))) + .count()); - Assertions - .assertEquals( - 1, tmp - .filter( - r -> r - .getTarget() - .equals( - "50|doi_________::" + IdentifierFactory - .md5( - PidCleaner - .normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023")))) - .count()); + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getTarget() + .equals( + "50|doi_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023")))) + .count()); - Assertions - .assertEquals( - 1, tmp - .filter( - r -> r - .getSource() - .equals( - "20|ror_________::" + IdentifierFactory - .md5( - PidCleaner - .normalizePidValue("ROR", "https://ror.org/03argrj65")))) - .count()); + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getSource() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue("ROR", "https://ror.org/03argrj65")))) + .count()); - Assertions - .assertEquals( - 1, tmp - .filter( - r -> r - .getTarget() - .equals( - "20|ror_________::" + IdentifierFactory - .md5( - PidCleaner - .normalizePidValue("ROR", "https://ror.org/03argrj65")))) - .count()); + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue("ROR", "https://ror.org/03argrj65")))) + .count()); - Assertions - .assertEquals( - 5, tmp - .filter( - r -> r - .getSource() - .equals( - "20|ror_________::" + IdentifierFactory - .md5( - PidCleaner - .normalizePidValue("ROR", "https://ror.org/03265fv13")))) - .count()); + Assertions + .assertEquals( + 5, tmp + .filter( + r -> r + .getSource() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue("ROR", "https://ror.org/03265fv13")))) + .count()); - Assertions - .assertEquals( - 5, tmp - .filter( - r -> r - .getTarget() - .equals( - "20|ror_________::" + IdentifierFactory - .md5( - PidCleaner - .normalizePidValue("ROR", "https://ror.org/03265fv13")))) - .count()); + Assertions + .assertEquals( + 5, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue("ROR", "https://ror.org/03265fv13")))) + .count()); - Assertions - .assertEquals( - 2, tmp - .filter( - r -> r - .getTarget() - .equals( - "20|ror_________::" + IdentifierFactory - .md5( - PidCleaner - .normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13"))) - && r.getSource().startsWith("50|doi")) - .count()); + Assertions + .assertEquals( + 2, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13"))) + && r.getSource().startsWith("50|doi")) + .count()); - Assertions - .assertEquals( - 2, tmp - .filter( - r -> r - .getTarget() - .equals( - "20|ror_________::" + IdentifierFactory - .md5( - PidCleaner - .normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13"))) - && r.getSource().startsWith("50|pmid")) - .count()); + Assertions + .assertEquals( + 2, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13"))) + && r.getSource().startsWith("50|pmid")) + .count()); - Assertions - .assertEquals( - 1, tmp - .filter( - r -> r - .getTarget() - .equals( - "20|ror_________::" + IdentifierFactory - .md5( - PidCleaner - .normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13"))) - && r.getSource().startsWith("50|pmc")) - .count()); - } + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13"))) + && r.getSource().startsWith("50|pmc")) + .count()); + } - @Test - void testRelationsCollectedFrom() throws Exception { + @Test + void testRelationsCollectedFrom() throws Exception { - String inputPath = getClass() - .getResource( - "/eu/dnetlib/dhp/actionmanager/webcrawl") - .getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/webcrawl") + .getPath(); - CreateActionSetFromWebEntries - .main( - new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-sourcePath", - inputPath, - "-outputPath", - workingDir.toString() + "/actionSet1" - }); + CreateActionSetFromWebEntries + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-sourcePath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet1" + }); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class) - .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) - .map(aa -> ((Relation) aa.getPayload())); - - tmp.foreach(r -> { - assertEquals("Web Crawl", r.getCollectedfrom().get(0).getValue()); - assertEquals("10|openaire____::fb98a192f6a055ba495ef414c330834b", r.getCollectedfrom().get(0).getKey()); - }); - - } + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + tmp.foreach(r -> { + assertEquals("Web Crawl", r.getCollectedfrom().get(0).getValue()); + assertEquals("10|openaire____::fb98a192f6a055ba495ef414c330834b", r.getCollectedfrom().get(0).getKey()); + }); + } } From 6189879643c6023de280231b1c6e737a5e849e4a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 23 Apr 2024 11:09:18 +0200 Subject: [PATCH 4/5] [NOAMI] removed entry for Irish Research eLibray (IReL) Care Board from the list of funders. --- .../eu/dnetlib/dhp/collection/crossref/irish_funder.json | 6 ------ 1 file changed, 6 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json index 598fe2ba58..f0275e06bc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json @@ -271,12 +271,6 @@ "name": "An Roinn Sl\u00e1inte", "synonym": [] }, - { - "id": "100018998", - "uri": "http://dx.doi.org/10.13039/100018998", - "name": "Irish Research eLibrary", - "synonym": [] - }, { "id": "100019428", "uri": "http://dx.doi.org/10.13039/100019428", From 93dd9cc639fa52cb36d617740cb097b42b805186 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 23 Apr 2024 11:28:00 +0200 Subject: [PATCH 5/5] code formatting --- .../webcrawl/CreateActionSetFromWebEntries.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java index 4035eb33a6..eb370e981a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java @@ -77,7 +77,7 @@ public class CreateActionSetFromWebEntries implements Serializable { isSparkSessionManaged, spark -> { - createActionSet(spark, inputPath, outputPath ); + createActionSet(spark, inputPath, outputPath); }); } @@ -143,7 +143,7 @@ public class CreateActionSetFromWebEntries implements Serializable { return createAffiliatioRelationPair( PMCID_PREFIX + IdentifierFactory - .md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), removeResolver("PMC" , pmcid))), + .md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), removeResolver("PMC", pmcid))), ror); } @@ -159,7 +159,7 @@ public class CreateActionSetFromWebEntries implements Serializable { } private static String removeResolver(String pidType, String pid) { - switch (pidType){ + switch (pidType) { case "PMID": return pid.substring(33); case "PMC": @@ -179,7 +179,7 @@ public class CreateActionSetFromWebEntries implements Serializable { return createAffiliatioRelationPair( DOI_PREFIX + IdentifierFactory - .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), removeResolver("DOI" ,doi))), + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), removeResolver("DOI", doi))), ror); }