diff --git a/README.md b/README.md
index 39d4d98e4..0a0bd82ab 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,2 @@
# dnet-hadoop
-Dnet-hadoop is a tool for
\ No newline at end of file
+Dnet-hadoop is the project that defined all the OOZIE workflows for the OpenAIRE Graph construction, processing, provisioning.
\ No newline at end of file
diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml
index 74f31cf35..4c7810c47 100644
--- a/dhp-common/pom.xml
+++ b/dhp-common/pom.xml
@@ -25,6 +25,11 @@
com.github.sisyphsu
dateparser
+
+ me.xuender
+ unidecode
+
+
org.apache.spark
spark-core_2.11
diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
index e5181b111..1d002ed7e 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
@@ -7,22 +7,19 @@ import java.time.format.DateTimeFormatter;
import java.time.format.DateTimeParseException;
import java.util.*;
import java.util.function.Function;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
-import org.jetbrains.annotations.NotNull;
import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Lists;
-import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
+import me.xuender.unidecode.Unidecode;
public class GraphCleaningFunctions extends CleaningFunctions {
@@ -194,11 +191,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.filter(Objects::nonNull)
.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
.filter(
- sp -> sp
- .getValue()
- .toLowerCase()
- .replaceAll(TITLE_FILTER_REGEX, "")
- .length() > TITLE_FILTER_RESIDUAL_LENGTH)
+ sp -> {
+ final String title = sp
+ .getValue()
+ .toLowerCase();
+ final String residual = Unidecode
+ .decode(title)
+ .replaceAll(TITLE_FILTER_REGEX, "");
+ return residual.length() > TITLE_FILTER_RESIDUAL_LENGTH;
+ })
.map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList()));
}
diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
index eefa1e9a3..8d519a93f 100644
--- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
+++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
@@ -4,12 +4,8 @@ package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException;
-import java.time.LocalDate;
-import java.time.format.DateTimeFormatter;
import java.util.HashSet;
import java.util.List;
-import java.util.Locale;
-import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
@@ -19,13 +15,32 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.Dataset;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import me.xuender.unidecode.Unidecode;
public class OafMapperUtilsTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+ @Test
+ public void testUnidecode() {
+
+ assertEquals("Liu Ben Mu hiruzuSen tawa", Unidecode.decode("六本木ヒルズ森タワ"));
+ assertEquals("Nan Wu A Mi Tuo Fo", Unidecode.decode("南无阿弥陀佛"));
+ assertEquals("Yi Tiao Hui Zou Lu De Yu", Unidecode.decode("一条会走路的鱼"));
+ assertEquals("amidaniyorai", Unidecode.decode("あみだにょらい"));
+ assertEquals("T`owrk`iayi", Unidecode.decode("Թուրքիայի"));
+ assertEquals("Obzor tematiki", Unidecode.decode("Обзор тематики"));
+ assertEquals("GERMANSKIE IaZYKI", Unidecode.decode("ГЕРМАНСКИЕ ЯЗЫКИ"));
+ assertEquals("Diereunese tes ikanopoieses", Unidecode.decode("Διερεύνηση της ικανοποίησης"));
+ assertEquals("lqDy l'wly@", Unidecode.decode("القضايا الأولية"));
+ assertEquals("abc def ghi", Unidecode.decode("abc def ghi"));
+ }
+
@Test
public void testDateValidation() {
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java
new file mode 100644
index 000000000..5523863ff
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java
@@ -0,0 +1,127 @@
+
+package eu.dnetlib.dhp.oa.graph.raw;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.FileNotFoundException;
+import java.util.Objects;
+import java.util.Optional;
+
+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;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.oa.graph.dump.Utils;
+import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import scala.Tuple2;
+
+public class PatchRelationsApplication {
+
+ private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class);
+
+ private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+ public static void main(final String[] args) throws Exception {
+ final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+ IOUtils
+ .toString(
+ Optional
+ .ofNullable(
+ PatchRelationsApplication.class
+ .getResourceAsStream(
+ "/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json"))
+ .orElseThrow(FileNotFoundException::new)));
+ parser.parseArgument(args);
+
+ final Boolean isSparkSessionManaged = Optional
+ .ofNullable(parser.get("isSparkSessionManaged"))
+ .map(Boolean::valueOf)
+ .orElse(Boolean.TRUE);
+ log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+ final String graphBasePath = parser.get("graphBasePath");
+ log.info("graphBasePath: {}", graphBasePath);
+
+ final String workingDir = parser.get("workingDir");
+ log.info("workingDir: {}", workingDir);
+
+ final String idMappingPath = parser.get("idMappingPath");
+ log.info("idMappingPath: {}", idMappingPath);
+
+ final SparkConf conf = new SparkConf();
+ runWithSparkSession(
+ conf,
+ isSparkSessionManaged,
+ spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath));
+ }
+
+ /**
+ * Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the
+ * mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location.
+ *
+ * @param spark the SparkSession
+ * @param graphBasePath base graph path providing the set of relations to patch
+ * @param workingDir intermediate storage location
+ * @param idMappingPath dataset providing the old -> new identifier mapping
+ */
+ private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir,
+ final String idMappingPath) {
+
+ final String relationPath = graphBasePath + "/relation";
+
+ final Dataset rels = Utils.readPath(spark, relationPath, Relation.class);
+ final Dataset idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class);
+
+ log.info("relations: {}", rels.count());
+ log.info("idMapping: {}", idMapping.count());
+
+ final Dataset bySource = rels
+ .joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left")
+ .map((MapFunction, Relation>) t -> {
+ final Relation r = t._1();
+ Optional
+ .ofNullable(t._2())
+ .map(RelationIdMapping::getNewId)
+ .ifPresent(r::setSource);
+ return r;
+ }, Encoders.bean(Relation.class));
+
+ bySource
+ .joinWith(idMapping, bySource.col("target").equalTo(idMapping.col("oldId")), "left")
+ .map((MapFunction, Relation>) t -> {
+ final Relation r = t._1();
+ Optional
+ .ofNullable(t._2())
+ .map(RelationIdMapping::getNewId)
+ .ifPresent(r::setTarget);
+ return r;
+ }, Encoders.bean(Relation.class))
+ .map(
+ (MapFunction) OBJECT_MAPPER::writeValueAsString,
+ Encoders.STRING())
+ .write()
+ .mode(SaveMode.Overwrite)
+ .option("compression", "gzip")
+ .text(workingDir);
+
+ spark
+ .read()
+ .textFile(workingDir)
+ .write()
+ .mode(SaveMode.Overwrite)
+ .option("compression", "gzip")
+ .text(relationPath);
+ }
+
+}
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java
new file mode 100644
index 000000000..d5852ab70
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java
@@ -0,0 +1,25 @@
+
+package eu.dnetlib.dhp.oa.graph.raw.common;
+
+public class RelationIdMapping {
+
+ private String oldId;
+
+ private String newId;
+
+ public String getOldId() {
+ return oldId;
+ }
+
+ public void setOldId(final String oldId) {
+ this.oldId = oldId;
+ }
+
+ public String getNewId() {
+ return newId;
+ }
+
+ public void setNewId(final String newId) {
+ this.newId = newId;
+ }
+}
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json
new file mode 100644
index 000000000..178c2d69b
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json
@@ -0,0 +1,26 @@
+[
+ {
+ "paramName": "issm",
+ "paramLongName": "isSparkSessionManaged",
+ "paramDescription": "when true will stop SparkSession after job execution",
+ "paramRequired": false
+ },
+ {
+ "paramName": "g",
+ "paramLongName": "graphBasePath",
+ "paramDescription": "base graph path providing the set of relations to patch",
+ "paramRequired": true
+ },
+ {
+ "paramName": "w",
+ "paramLongName": "workingDir",
+ "paramDescription": "intermediate storage location",
+ "paramRequired": true
+ },
+ {
+ "paramName": "i",
+ "paramLongName": "idMappingPath",
+ "paramDescription": "dataset providing the old -> new identifier mapping",
+ "paramRequired": true
+ }
+]
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
index 7f1ecb39f..321ca4090 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
@@ -100,6 +100,16 @@
a blacklist of nsprefixes (comma separeted)
+
+ shouldPatchRelations
+ false
+ activates the relation patching phase, driven by the content in ${idMappingPath}
+
+
+ idMappingPath
+
+ path pointing to the relations identifiers mapping dataset
+
sparkDriverMemory
memory for driver process
@@ -551,7 +561,6 @@
-
yarn
@@ -760,7 +769,42 @@
-
+
+
+
+
+
+ ${(shouldPatchRelations eq "true") and
+ (fs:exists(concat(concat(wf:conf('nameNode'),'/'),wf:conf('idMappingPath'))) eq "true")}
+
+
+
+
+
+
+
+ yarn
+ cluster
+ PatchRelations
+ eu.dnetlib.dhp.oa.graph.raw.PatchRelationsApplication
+ dhp-graph-mapper-${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}${spark2EventLogDir}
+ --conf spark.sql.shuffle.partitions=7680
+
+ --graphBasePath${graphOutputPath}
+ --workingDir${workingDir}/patch_relations
+ --idMappingPath${idMappingPath}
+
+
+
+
\ No newline at end of file
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 495dc4a04..ba4211a3f 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
@@ -1,11 +1,9 @@
package eu.dnetlib.dhp.oa.graph.raw;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.junit.jupiter.api.Assertions.assertNotNull;
-import static org.junit.jupiter.api.Assertions.assertNull;
-import static org.junit.jupiter.api.Assertions.assertTrue;
+import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.cleanup;
+import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.fixVocabularyNames;
+import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.lenient;
import java.io.IOException;
@@ -25,15 +23,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest;
import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Author;
-import eu.dnetlib.dhp.schema.oaf.Dataset;
-import eu.dnetlib.dhp.schema.oaf.Field;
-import eu.dnetlib.dhp.schema.oaf.Instance;
-import eu.dnetlib.dhp.schema.oaf.Oaf;
-import eu.dnetlib.dhp.schema.oaf.Publication;
-import eu.dnetlib.dhp.schema.oaf.Relation;
-import eu.dnetlib.dhp.schema.oaf.Software;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -74,7 +64,7 @@ public class MappersTest {
assertValidId(p.getId());
- assertEquals(1, p.getOriginalId().size());
+ assertEquals(2, p.getOriginalId().size());
assertTrue(p.getOriginalId().contains("10.3897/oneeco.2.e13718"));
assertValidId(p.getCollectedfrom().get(0).getKey());
@@ -261,8 +251,8 @@ public class MappersTest {
final Relation r2 = (Relation) list.get(2);
assertValidId(d.getId());
- assertEquals(1, d.getOriginalId().size());
- assertTrue(d.getOriginalId().contains("oai:zenodo.org:3234526"));
+ assertEquals(2, d.getOriginalId().size());
+ assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526")));
assertValidId(d.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
assertTrue(d.getAuthor().size() > 0);
@@ -351,8 +341,11 @@ public class MappersTest {
final Publication p = (Publication) list.get(0);
assertValidId(p.getId());
- assertTrue(p.getOriginalId().size() == 1);
- assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0));
+ assertEquals(2, p.getOriginalId().size());
+
+ assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:pub.uni-bielefeld.de:2949739")));
+ // assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0));
+
assertValidId(p.getCollectedfrom().get(0).getKey());
assertTrue(p.getAuthor().size() > 0);
@@ -413,7 +406,8 @@ public class MappersTest {
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, d.getDataInfo().getProvenanceaction().getSchemename());
assertValidId(d.getId());
- assertTrue(d.getOriginalId().size() == 1);
+ assertEquals(2, d.getOriginalId().size());
+
assertEquals("feabb67c-1fd1-423b-aec6-606d04ce53c6", d.getOriginalId().get(0));
assertValidId(d.getCollectedfrom().get(0).getKey());
@@ -567,31 +561,6 @@ public class MappersTest {
assertNotNull(d.getInstance().get(0).getUrl());
}
- @Test
- void testEnermaps() throws IOException {
- final String xml = IOUtils.toString(getClass().getResourceAsStream("enermaps.xml"));
- final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
-
- System.out.println("***************");
- System.out.println(new ObjectMapper().writeValueAsString(list));
- System.out.println("***************");
-
- assertEquals(1, list.size());
- assertTrue(list.get(0) instanceof Dataset);
-
- final Dataset d = (Dataset) list.get(0);
-
- assertValidId(d.getId());
- assertValidId(d.getCollectedfrom().get(0).getKey());
- assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
- assertEquals(1, d.getAuthor().size());
- assertEquals(1, d.getInstance().size());
- assertNotNull(d.getInstance().get(0).getUrl());
- assertNotNull(d.getContext());
- assertTrue(StringUtils.isNotBlank(d.getContext().get(0).getId()));
- assertEquals("enermaps::selection::tgs00004", d.getContext().get(0).getId());
- }
-
@Test
void testClaimFromCrossref() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_crossref.xml"));
@@ -673,6 +642,30 @@ public class MappersTest {
System.out.println(p.getTitle().get(0).getValue());
}
+ @Test
+ void testJairo() throws IOException {
+ final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_jairo.xml"));
+ final List list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
+
+ System.out.println("***************");
+ System.out.println(new ObjectMapper().writeValueAsString(list));
+ System.out.println("***************");
+
+ final Publication p = (Publication) list.get(0);
+ assertValidId(p.getId());
+ assertValidId(p.getCollectedfrom().get(0).getKey());
+
+ assertNotNull(p.getTitle());
+ assertFalse(p.getTitle().isEmpty());
+ assertTrue(p.getTitle().size() == 1);
+ assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
+
+ final Publication p_cleaned = cleanup(fixVocabularyNames(p));
+
+ assertNotNull(p_cleaned.getTitle());
+ assertFalse(p_cleaned.getTitle().isEmpty());
+ }
+
@Test
void testOdfFromHdfs() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_from_hdfs.xml"));
@@ -688,8 +681,8 @@ public class MappersTest {
final Dataset p = (Dataset) list.get(0);
assertValidId(p.getId());
- assertTrue(p.getOriginalId().size() == 1);
- assertEquals("df76e73f-0483-49a4-a9bb-63f2f985574a", p.getOriginalId().get(0));
+ assertEquals(2, p.getOriginalId().size());
+ assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("df76e73f-0483-49a4-a9bb-63f2f985574a")));
assertValidId(p.getCollectedfrom().get(0).getKey());
assertTrue(p.getAuthor().size() > 0);
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java
new file mode 100644
index 000000000..3fd365416
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java
@@ -0,0 +1,115 @@
+
+package eu.dnetlib.dhp.oa.graph.raw;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+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.oaf.Relation;
+
+public class PatchRelationApplicationTest {
+
+ private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+ public static final String ID_MAPPING_PATH = "map/id_mapping.json";
+
+ private static SparkSession spark;
+
+ private static Path workingDir;
+
+ private static final Logger log = LoggerFactory.getLogger(PatchRelationApplicationTest.class);
+
+ @BeforeAll
+ public static void beforeAll() throws IOException {
+ workingDir = Files
+ .createTempDirectory(PatchRelationApplicationTest.class.getSimpleName());
+ log.info("using work dir {}", workingDir);
+
+ SparkConf conf = new SparkConf();
+ conf.setAppName(PatchRelationApplicationTest.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(PatchRelationApplicationTest.class.getSimpleName())
+ .config(conf)
+ .getOrCreate();
+
+ FileUtils
+ .copyInputStreamToFile(
+ PatchRelationApplicationTest.class.getResourceAsStream("id_mapping.json"),
+ workingDir.resolve(ID_MAPPING_PATH).toFile());
+
+ FileUtils
+ .copyInputStreamToFile(
+ PatchRelationApplicationTest.class.getResourceAsStream("relations_to_patch.json"),
+ workingDir.resolve("graphBasePath/relation/rels.json").toFile());
+
+ }
+
+ @AfterAll
+ public static void afterAll() throws IOException {
+ FileUtils.deleteDirectory(workingDir.toFile());
+ spark.stop();
+ }
+
+ @Test
+ public void testPatchRelationApplication() throws Exception {
+
+ final String graphBasePath = workingDir.toString() + "/graphBasePath";
+ PatchRelationsApplication.main(new String[] {
+ "-isSparkSessionManaged", Boolean.FALSE.toString(),
+ "-graphBasePath", graphBasePath,
+ "-workingDir", workingDir.toString() + "/workingDir",
+ "-idMappingPath", workingDir.toString() + "/" + ID_MAPPING_PATH
+ });
+
+ final List rels = spark
+ .read()
+ .textFile(graphBasePath + "/relation")
+ .map(
+ (MapFunction) s -> OBJECT_MAPPER.readValue(s, Relation.class),
+ Encoders.bean(Relation.class))
+ .collectAsList();
+
+ assertEquals(6, rels.size());
+
+ assertEquals(0, getCount(rels, "1a"), "should be patched to 1b");
+ assertEquals(0, getCount(rels, "2a"), "should be patched to 2b");
+
+ assertEquals(2, getCount(rels, "10a"), "not included in patching");
+ assertEquals(2, getCount(rels, "20a"), "not included in patching");
+
+ assertEquals(2, getCount(rels, "15a"), "not included in patching");
+ assertEquals(2, getCount(rels, "25a"), "not included in patching");
+
+ assertEquals(2, getCount(rels, "1b"), "patched from 1a");
+ assertEquals(2, getCount(rels, "2b"), "patched from 2a");
+ }
+
+ private long getCount(List rels, final String id) {
+ return rels.stream().filter(r -> r.getSource().equals(id) || r.getTarget().equals(id)).count();
+ }
+
+}
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/id_mapping.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/id_mapping.json
new file mode 100644
index 000000000..640d042b1
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/id_mapping.json
@@ -0,0 +1,5 @@
+{"oldId": "1a", "newId": "1b"}
+{"oldId": "2a", "newId": "2b"}
+{"oldId": "3a", "newId": "3b"}
+{"oldId": "4a", "newId": "4b"}
+{"oldId": "5a", "newId": "5b"}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml
new file mode 100644
index 000000000..9ec696256
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml
@@ -0,0 +1,70 @@
+
+
+
+ jairo_______::000012e58ed836576ef2a0d38b0f726f
+ oai:irdb.nii.ac.jp:01221:0000010198
+
+
+
+
+
+ 2021-05-10T11:31:09.424Z
+ 2021-06-03T01:45:42.536Z
+ jairo_______
+
+
+ 多項式GCDを用いた復号法に関する研究
+ 上原, 剛
+ 甲斐, 博
+ 野田, 松太郎
+ application/pdf
+ http://hdl.handle.net/2433/25934
+ jpn
+ 京都大学数理解析研究所
+ 410
+ Departmental Bulletin Paper
+ 0014
+ 2004-10-01
+
+ openaire____::554c7c2873
+ OPEN
+
+
+ 2433/25934
+ AN00061013
+ http://hdl.handle.net/2433/25934
+ http://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/25934/1/1395-16.pdf
+ 数理解析研究所講究録
+
+
+
+
+ https%3A%2F%2Firdb.nii.ac.jp%2Foai
+ oai:irdb.nii.ac.jp:01221:0000010198
+ 2021-04-13T13:36:29Z
+
+
+ http://repository.kulib.kyoto-u.ac.jp/dspace-oai/request
+ oai:repository.kulib.kyoto-u.ac.jp:2433/25934
+ 2012-07-12T14:15:41Z
+ http://irdb.nii.ac.jp/oai
+
+
+
+
+ false
+ false
+ 0.9
+
+
+
+
+
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json
new file mode 100644
index 000000000..31755c53d
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json
@@ -0,0 +1,6 @@
+{"source":"1a","target":"10a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
+{"source":"10a","target":"1a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
+{"source":"2a","target":"20a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
+{"source":"20a","target":"2a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
+{"source":"15a","target":"25a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
+{"source":"25a","target":"15a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary
index 4d581044a..e1fd758b4 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary
@@ -1,20 +1,10 @@
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This paper uses the concept of hedonic price theory to investigate a range of extrinsic characteristics’ ability to predict prices for different climate regions (warm and cool) and four major wine varieties of Australian wines, two reds (shiraz and cabernet) and two whites (chardonnay and riesling). The effects of winery reputation (wine company/brand), winery size (production scale), age of the wine, and region of origin (wine grape source) contributing to the relationship between price and quality attributes of Australian wines are investigated, based on 1880 observations of bottled wines. Wine quality rating and winery/brand reputation have major effects on the price, while region and size of winery have differential effects depending on the variety of grape. Vintage has only a minor effect. 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We first unravel misconceptions as perceived on different continents and subsequently present a revised interpretation of the identity and typification of three European taxa at species level: Ruppia maritima L., Ruppia spiralis L. ex Dumortier, and Ruppia cirrhosa (Petagna) Grande. To do this, historical specimens, illustrations and original descriptions were studied. We supersede a previous choice of the figure of Buccaferrea maritima, foliis minus acutis Micheli (1729) as the lectotype of R. maritima and type species of the genus Ruppia owing to a serious conflict with the protologue. Based on a meticulous interpretation of protologues and figures in a historical context, we reject the recent view of assigning R. cirrhosa and its proposed lectotype (iconotype) as a homotypic synonym of R. maritima. We agree with an earlier lectotypification of R. spiralis, though for another reason than the above-mentioned abused homotypy. Consequently, R. cirrhosa is a synonym of neither R. maritima or R. spiralis, based on material from Petagna in the Herbarium of Naples designated as the holotype of R. cirrhosa. 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Unfortunately, conventional wave theories based on Stokes-type expansions do not consider fluid motions at levels above the unperturbed fluid level. The usual practice of extrapolating the fluid kinematics from the unperturbed free surface to higher points in the fluid is generally reasonable for narrowband waves, but for broadband ocean waves this results in dramatic (and nonphysical) overestimation of surface velocities. Consequently, practical approximations for random waves are at best empirical and are often only loosely constrained by physical principles. In the present work, the authors formulate the governing equations for water waves in an incompressible and inviscid fluid, using a boundary-fitted coordinate system (i.e., sigma or s coordinates) to derive expressions for near-surface kinematics in nonlinear random waves from first principles. Comparison to a numerical model valid for highly nonlinear waves shows that the new results 1) are consistent with second-order Stokes theory, 2) are similar to extrapolation methods in narrowband waves, and 3) greatly improve estimates of surface kinematics in random seas.","dataInfo":null}],"dateofacceptance":{"value":"2017-05-09T19:33:59Z","dataInfo":null},"publisher":{"value":"American Meteorological Society","dataInfo":null},"embargoenddate":null,"source":[{"value":"Crossref","dataInfo":null}],"fulltext":[],"format":[],"contributor":[],"resourcetype":{"classid":"0001","classname":"0001","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"RESTRICTED","classname":"Restricted","schemeid":"dnet:access_modes","schemename":"dnet:access_modes","openAccessRoute":null},"instancetype":{"classid":"0001","classname":"Article","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":null,"url":["https://journals.ametsoc.org/view/journals/phoc/47/7/jpo-d-16-0281.1.xml","http://journals.ametsoc.org/jpo/article-pdf/47/7/1657/4810788/jpo-d-16-0281_1.pdf","https://journals.ametsoc.org/downloadpdf/journals/phoc/47/7/jpo-d-16-0281.1.xml","http://dx.doi.org/10.1175/jpo-d-16-0281.1"],"distributionlocation":null,"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref","dataInfo":null},"pid":[{"value":"10.1175/jpo-d-16-0281.1","qualifier":{"classid":"doi","classname":"doi","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":null}],"alternateIdentifier":null,"dateofacceptance":{"value":"2017-05-09T19:33:59Z","dataInfo":null},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null},{"license":null,"accessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes","openAccessRoute":null},"instancetype":{"classid":"0001","classname":"Article","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository","dataInfo":null},"url":["https://dx.doi.org/10.1175/jpo-d-16-0281.1"],"distributionlocation":null,"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite","dataInfo":null},"pid":[{"value":"10.1175/jpo-d-16-0281.1","qualifier":{"classid":"doi","classname":"doi","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"alternateIdentifier":null,"dateofacceptance":{"value":"2017-01-01","dataInfo":null},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"journal":{"name":"Journal of Physical Oceanography","issnPrinted":"0022-3670","issnOnline":"1520-0485","issnLinking":null,"ep":"1673","iss":null,"sp":"1657","vol":"47","edition":null,"conferenceplace":null,"conferencedate":null,"dataInfo":null}}
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\ No newline at end of file
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 7d53d3554..b3f785492 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
@@ -10,6 +10,7 @@ import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
@@ -81,6 +82,7 @@ public class PrepareRelationsJob {
Set relationFilter = Optional
.ofNullable(parser.get("relationFilter"))
+ .map(String::toLowerCase)
.map(s -> Sets.newHashSet(Splitter.on(",").split(s)))
.orElse(new HashSet<>());
log.info("relationFilter: {}", relationFilter);
@@ -130,7 +132,7 @@ public class PrepareRelationsJob {
JavaRDD rels = readPathRelationRDD(spark, inputRelationsPath)
.filter(rel -> rel.getDataInfo().getDeletedbyinference() == false)
- .filter(rel -> relationFilter.contains(rel.getRelClass()) == false);
+ .filter(rel -> relationFilter.contains(StringUtils.lowerCase(rel.getRelClass())) == false);
JavaRDD pruned = pruneRels(
pruneRels(
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 a985d2371..2c8240290 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
@@ -16,7 +16,6 @@ import javax.xml.transform.*;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.util.LongAccumulator;
import org.dom4j.Document;
@@ -43,6 +42,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
public class XmlRecordFactory implements Serializable {
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
index a5a1563aa..897e507e1 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
@@ -7,8 +7,6 @@ import java.io.IOException;
import java.io.StringReader;
import java.util.List;
-import eu.dnetlib.dhp.oa.provision.utils.ContextDef;
-import eu.dnetlib.dhp.schema.oaf.Dataset;
import org.apache.commons.io.IOUtils;
import org.dom4j.Document;
import org.dom4j.DocumentException;
@@ -25,6 +23,7 @@ import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
+import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation;
@@ -137,17 +136,18 @@ public class XmlRecordFactoryTest {
@Test
public void testEnermapsRecord() throws IOException, DocumentException {
- String contextmap = "" +
- ""+
- ""+
- "";
+ String contextmap = ""
+ +
+ "" +
+ "" +
+ "";
ContextMapper contextMapper = ContextMapper.fromXml(contextmap);
XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation,
- otherDsTypeId);
+ otherDsTypeId);
Dataset d = OBJECT_MAPPER
- .readValue(IOUtils.toString(getClass().getResourceAsStream("enermaps.json")), Dataset.class);
+ .readValue(IOUtils.toString(getClass().getResourceAsStream("enermaps.json")), Dataset.class);
JoinedEntity je = new JoinedEntity<>(d);
diff --git a/pom.xml b/pom.xml
index 19d00d637..075a45c9f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -205,6 +205,11 @@
dateparser
1.0.7
+
+ me.xuender
+ unidecode
+ 0.0.7
+
com.google.guava