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Merge remote-tracking branch 'origin/master' into doiboost

This commit is contained in:
Sandro La Bruzzo 2020-04-21 08:34:24 +02:00
parent 039f9b7871 d772d967aa
commit 3624947a7f
16 changed files with 1123 additions and 386 deletions
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30
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java
View File

@ -14,9 +14,7 @@ import java.io.StringReader;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.dom4j.Document; import org.dom4j.Document;
@ -26,9 +24,6 @@ import org.dom4j.io.SAXReader;
abstract class AbstractSparkAction implements Serializable { abstract class AbstractSparkAction implements Serializable {
protected static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
protected static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
protected static final ObjectMapper OBJECT_MAPPER = protected static final ObjectMapper OBJECT_MAPPER =
new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@ -89,29 +84,8 @@ abstract class AbstractSparkAction implements Serializable {
return SparkSession.builder().config(conf).getOrCreate(); return SparkSession.builder().config(conf).getOrCreate();
} }
protected static <T extends Oaf> void save(Dataset<T> dataset, String outPath, SaveMode mode) { protected static <T> void save(Dataset<T> dataset, String outPath, SaveMode mode) {
dataset.map( dataset.write().option("compression", "gzip").mode(mode).json(outPath);
(MapFunction<T, String>) value -> OBJECT_MAPPER.writeValueAsString(value),
Encoders.STRING())
.write()
.option("compression", "gzip")
.mode(mode)
.text(outPath);
}
protected static DataInfo getDataInfo() {
DataInfo info = new DataInfo();
info.setDeletedbyinference(false);
info.setInferred(true);
info.setInvisible(false);
Qualifier provenanceAction = new Qualifier();
provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
info.setProvenanceaction(provenanceAction);
return info;
} }
protected static void removeOutputDir(SparkSession spark, String path) { protected static void removeOutputDir(SparkSession spark, String path) {

47
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
View File

@ -5,29 +5,29 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists; import com.google.common.collect.Lists;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.pace.config.DedupConfig;
import java.util.Collection; import java.util.Collection;
import java.util.Iterator; import java.util.Iterator;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2; import scala.Tuple2;
public class DedupRecordFactory { public class DedupRecordFactory {
private static final Logger log = LoggerFactory.getLogger(DedupRecordFactory.class);
protected static final ObjectMapper OBJECT_MAPPER = protected static final ObjectMapper OBJECT_MAPPER =
new com.fasterxml.jackson.databind.ObjectMapper() new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
public static <T extends OafEntity> Dataset<T> createDedupRecord( public static <T extends OafEntity> Dataset<T> createDedupRecord(
final SparkSession spark, final SparkSession spark,
final String mergeRelsInputPath, final String mergeRelsInputPath,
final String entitiesInputPath, final String entitiesInputPath,
final Class<T> clazz, final Class<T> clazz) {
final DedupConfig dedupConf) {
long ts = System.currentTimeMillis(); long ts = System.currentTimeMillis();
@ -54,40 +54,39 @@ public class DedupRecordFactory {
r -> new Tuple2<>(r.getSource(), r.getTarget()), r -> new Tuple2<>(r.getSource(), r.getTarget()),
Encoders.tuple(Encoders.STRING(), Encoders.STRING())); Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
// <dedup_id, json_entity_merged>
return mergeRels return mergeRels
.joinWith(entities, mergeRels.col("_1").equalTo(entities.col("_1")), "left_outer") .joinWith(entities, mergeRels.col("_2").equalTo(entities.col("_1")), "inner")
.filter(
(FilterFunction<Tuple2<Tuple2<String, String>, Tuple2<String, T>>>)
value -> value._2() != null)
.map( .map(
(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, T>>, T>) (MapFunction<
value -> value._2()._2(), Tuple2<Tuple2<String, String>, Tuple2<String, T>>,
Encoders.kryo(clazz)) Tuple2<String, T>>)
.groupByKey((MapFunction<T, String>) value -> value.getId(), Encoders.STRING()) value -> new Tuple2<>(value._1()._1(), value._2()._2()),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)))
.groupByKey(
(MapFunction<Tuple2<String, T>, String>) entity -> entity._1(),
Encoders.STRING())
.mapGroups( .mapGroups(
(MapGroupsFunction<String, T, T>) (MapGroupsFunction<String, Tuple2<String, T>, T>)
(key, values) -> entityMerger(key, values, ts, clazz), (key, values) -> entityMerger(key, values, ts, clazz),
Encoders.bean(clazz)); Encoders.bean(clazz));
} }
private static <T extends OafEntity> T entityMerger( private static <T extends OafEntity> T entityMerger(
String id, Iterator<T> entities, final long ts, Class<T> clazz) { String id, Iterator<Tuple2<String, T>> entities, long ts, Class<T> clazz) {
try { try {
T entity = clazz.newInstance(); T entity = clazz.newInstance();
entity.setId(id); entity.setId(id);
if (entity.getDataInfo() == null) { entity.setDataInfo(new DataInfo());
entity.setDataInfo(new DataInfo());
}
entity.getDataInfo().setTrust("0.9"); entity.getDataInfo().setTrust("0.9");
entity.setLastupdatetimestamp(ts); entity.setLastupdatetimestamp(ts);
final Collection<String> dates = Lists.newArrayList(); final Collection<String> dates = Lists.newArrayList();
entities.forEachRemaining( entities.forEachRemaining(
e -> { t -> {
entity.mergeFrom(e); T duplicate = t._2();
if (ModelSupport.isSubClass(e, Result.class)) { entity.mergeFrom(duplicate);
Result r1 = (Result) e; if (ModelSupport.isSubClass(duplicate, Result.class)) {
Result r1 = (Result) duplicate;
Result er = (Result) entity; Result er = (Result) entity;
er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor())); er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor()));

15
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
View File

@ -11,6 +11,8 @@ import eu.dnetlib.pace.config.DedupConfig;
import java.io.IOException; import java.io.IOException;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
@ -69,11 +71,14 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
save( DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz)
DedupRecordFactory.createDedupRecord( .map(
spark, mergeRelPath, entityPath, clazz, dedupConf), (MapFunction<OafEntity, String>)
outputPath, value -> OBJECT_MAPPER.writeValueAsString(value),
SaveMode.Overwrite); Encoders.STRING())
.write()
.mode(SaveMode.Overwrite)
.json(outputPath);
} }
} }
} }

16
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java
View File

@ -6,6 +6,7 @@ import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent;
import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor; import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@ -34,7 +35,9 @@ import scala.Tuple2;
public class SparkCreateMergeRels extends AbstractSparkAction { public class SparkCreateMergeRels extends AbstractSparkAction {
public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class); private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class);
public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) { public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark); super(parser, spark);
@ -145,13 +148,22 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
r.setRelClass(relClass); r.setRelClass(relClass);
r.setSubRelType("dedup"); r.setSubRelType("dedup");
DataInfo info = getDataInfo(); DataInfo info = new DataInfo();
info.setDeletedbyinference(false);
info.setInferred(true);
info.setInvisible(false);
info.setInferenceprovenance(dedupConf.getWf().getConfigurationId()); info.setInferenceprovenance(dedupConf.getWf().getConfigurationId());
Qualifier provenanceAction = new Qualifier();
provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
info.setProvenanceaction(provenanceAction);
// TODO calculate the trust value based on the similarity score of the elements in the CC // TODO calculate the trust value based on the similarity score of the elements in the CC
// info.setTrust(); // info.setTrust();
r.setDataInfo(getDataInfo()); r.setDataInfo(info);
return r; return r;
} }

3
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java
View File

@ -2,6 +2,7 @@ package eu.dnetlib.dhp.oa.dedup;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.dedup.model.Block; import eu.dnetlib.dhp.oa.dedup.model.Block;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@ -114,7 +115,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
r.setTarget(target); r.setTarget(target);
r.setSubRelType("dedupSimilarity"); r.setSubRelType("dedupSimilarity");
r.setRelClass("isSimilarTo"); r.setRelClass("isSimilarTo");
r.setDataInfo(getDataInfo()); r.setDataInfo(new DataInfo());
switch (entity) { switch (entity) {
case "result": case "result":

7
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
View File

@ -4,6 +4,7 @@ import static org.apache.spark.sql.functions.col;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -124,7 +125,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
return value -> { return value -> {
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class); final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
if (rel.getDataInfo() == null) { if (rel.getDataInfo() == null) {
rel.setDataInfo(getDataInfo()); rel.setDataInfo(new DataInfo());
} }
return rel; return rel;
}; };
@ -148,7 +149,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
Relation r = value._1()._2(); Relation r = value._1()._2();
String id = value._2()._2(); String id = value._2()._2();
if (r.getDataInfo() == null) { if (r.getDataInfo() == null) {
r.setDataInfo(getDataInfo()); r.setDataInfo(new DataInfo());
} }
r.getDataInfo().setDeletedbyinference(false); r.getDataInfo().setDeletedbyinference(false);
switch (type) { switch (type) {
@ -172,7 +173,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
if (value._2() != null) { if (value._2() != null) {
Relation r = value._1()._2(); Relation r = value._1()._2();
if (r.getDataInfo() == null) { if (r.getDataInfo() == null) {
r.setDataInfo(getDataInfo()); r.setDataInfo(new DataInfo());
} }
r.getDataInfo().setDeletedbyinference(true); r.getDataInfo().setDeletedbyinference(true);
return r; return r;

87
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
View File

@ -8,6 +8,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.util.MapDocumentUtil;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;
import java.io.Serializable; import java.io.Serializable;
@ -16,14 +17,20 @@ import java.nio.file.Paths;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*; import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock; import org.mockito.Mock;
import org.mockito.Mockito; import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
import scala.Tuple2;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
@TestMethodOrder(MethodOrderer.OrderAnnotation.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
@ -41,7 +48,7 @@ public class SparkDedupTest implements Serializable {
private static final String testActionSetId = "test-orchestrator"; private static final String testActionSetId = "test-orchestrator";
@BeforeAll @BeforeAll
private static void cleanUp() throws IOException, URISyntaxException { public static void cleanUp() throws IOException, URISyntaxException {
testGraphBasePath = testGraphBasePath =
Paths.get( Paths.get(
@ -74,7 +81,7 @@ public class SparkDedupTest implements Serializable {
} }
@BeforeEach @BeforeEach
private void setUp() throws IOException, ISLookUpException { public void setUp() throws IOException, ISLookUpException {
lenient() lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
@ -96,6 +103,13 @@ public class SparkDedupTest implements Serializable {
IOUtils.toString( IOUtils.toString(
SparkDedupTest.class.getResourceAsStream( SparkDedupTest.class.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); "/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
.thenReturn(
IOUtils.toString(
SparkDedupTest.class.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
} }
@Test @Test
@ -109,7 +123,6 @@ public class SparkDedupTest implements Serializable {
"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
parser.parseArgument( parser.parseArgument(
new String[] { new String[] {
"-mt", "local[*]",
"-i", testGraphBasePath, "-i", testGraphBasePath,
"-asi", testActionSetId, "-asi", testActionSetId,
"-la", "lookupurl", "-la", "lookupurl",
@ -126,9 +139,14 @@ public class SparkDedupTest implements Serializable {
spark.read() spark.read()
.load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel") .load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
.count(); .count();
long sw_simrel =
spark.read()
.load(testOutputBasePath + "/" + testActionSetId + "/software_simrel")
.count();
assertEquals(3288, orgs_simrel); assertEquals(3432, orgs_simrel);
assertEquals(7260, pubs_simrel); assertEquals(7260, pubs_simrel);
assertEquals(344, sw_simrel);
} }
@Test @Test
@ -142,7 +160,6 @@ public class SparkDedupTest implements Serializable {
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
parser.parseArgument( parser.parseArgument(
new String[] { new String[] {
"-mt", "local[*]",
"-i", testGraphBasePath, "-i", testGraphBasePath,
"-asi", testActionSetId, "-asi", testActionSetId,
"-la", "lookupurl", "-la", "lookupurl",
@ -159,9 +176,14 @@ public class SparkDedupTest implements Serializable {
spark.read() spark.read()
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
.count(); .count();
long sw_mergerel =
spark.read()
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
.count();
assertEquals(1244, orgs_mergerel); assertEquals(1276, orgs_mergerel);
assertEquals(1460, pubs_mergerel); assertEquals(1460, pubs_mergerel);
assertEquals(288, sw_mergerel);
} }
@Test @Test
@ -175,7 +197,6 @@ public class SparkDedupTest implements Serializable {
"/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
parser.parseArgument( parser.parseArgument(
new String[] { new String[] {
"-mt", "local[*]",
"-i", testGraphBasePath, "-i", testGraphBasePath,
"-asi", testActionSetId, "-asi", testActionSetId,
"-la", "lookupurl", "-la", "lookupurl",
@ -198,9 +219,13 @@ public class SparkDedupTest implements Serializable {
+ testActionSetId + testActionSetId
+ "/publication_deduprecord") + "/publication_deduprecord")
.count(); .count();
long sw_deduprecord =
jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord")
.count();
assertEquals(82, orgs_deduprecord); assertEquals(82, orgs_deduprecord);
assertEquals(66, pubs_deduprecord); assertEquals(66, pubs_deduprecord);
assertEquals(51, sw_deduprecord);
} }
@Test @Test
@ -214,7 +239,6 @@ public class SparkDedupTest implements Serializable {
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
parser.parseArgument( parser.parseArgument(
new String[] { new String[] {
"-mt", "local[*]",
"-i", testGraphBasePath, "-i", testGraphBasePath,
"-w", testOutputBasePath, "-w", testOutputBasePath,
"-o", testDedupGraphBasePath "-o", testDedupGraphBasePath
@ -224,6 +248,9 @@ public class SparkDedupTest implements Serializable {
long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count(); long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count(); long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
long projects = jsc.textFile(testDedupGraphBasePath + "/project").count();
long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count();
long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count();
long mergedOrgs = long mergedOrgs =
spark.read() spark.read()
@ -245,13 +272,17 @@ public class SparkDedupTest implements Serializable {
.distinct() .distinct()
.count(); .count();
assertEquals(897, publications); assertEquals(831, publications);
assertEquals(835, organizations); assertEquals(835, organizations);
assertEquals(100, projects);
assertEquals(100, datasource);
assertEquals(200, softwares);
long deletedOrgs = long deletedOrgs =
jsc.textFile(testDedupGraphBasePath + "/organization") jsc.textFile(testDedupGraphBasePath + "/organization")
.filter(this::isDeletedByInference) .filter(this::isDeletedByInference)
.count(); .count();
long deletedPubs = long deletedPubs =
jsc.textFile(testDedupGraphBasePath + "/publication") jsc.textFile(testDedupGraphBasePath + "/publication")
.filter(this::isDeletedByInference) .filter(this::isDeletedByInference)
@ -272,7 +303,6 @@ public class SparkDedupTest implements Serializable {
"/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
parser.parseArgument( parser.parseArgument(
new String[] { new String[] {
"-mt", "local[*]",
"-i", testGraphBasePath, "-i", testGraphBasePath,
"-w", testOutputBasePath, "-w", testOutputBasePath,
"-o", testDedupGraphBasePath "-o", testDedupGraphBasePath
@ -283,6 +313,43 @@ public class SparkDedupTest implements Serializable {
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
assertEquals(826, relations); assertEquals(826, relations);
// check deletedbyinference
final Dataset<Relation> mergeRels =
spark.read()
.load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*"))
.as(Encoders.bean(Relation.class));
final JavaPairRDD<String, String> mergedIds =
mergeRels
.where("relClass == 'merges'")
.select(mergeRels.col("target"))
.distinct()
.toJavaRDD()
.mapToPair(
(PairFunction<Row, String, String>)
r -> new Tuple2<String, String>(r.getString(0), "d"));
JavaRDD<String> toCheck =
jsc.textFile(testDedupGraphBasePath + "/relation")
.mapToPair(
json ->
new Tuple2<>(
MapDocumentUtil.getJPathString("$.source", json),
json))
.join(mergedIds)
.map(t -> t._2()._1())
.mapToPair(
json ->
new Tuple2<>(
MapDocumentUtil.getJPathString("$.target", json),
json))
.join(mergedIds)
.map(t -> t._2()._1());
long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
long updated = toCheck.count();
assertEquals(updated, deletedbyinference);
} }
@AfterAll @AfterAll

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@ -0,0 +1,118 @@
{
"wf" : {
"threshold" : "0.99",
"dedupRun" : "001",
"entityType" : "result",
"subEntityType" : "resulttype",
"subEntityValue" : "dataset",
"orderField" : "title",
"queueMaxSize" : "2000",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "200",
"rootBuilder" : ["result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true"
},
"pace" : {
"clustering" : [
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree" : {
"start" : {
"fields": [
{
"field": "pid",
"comparator": "jsonListMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {
"jpath_value": "$.value",
"jpath_classid": "$.qualifier.classid"
}
}
],
"threshold": 0.5,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "layer2",
"undefined": "layer2",
"ignoreUndefined": "true"
},
"layer2" : {
"fields": [
{
"field": "title",
"comparator": "titleVersionMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {}
},
{
"field": "authors",
"comparator": "sizeMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {}
}
],
"threshold": 1.0,
"aggregation": "AND",
"positive": "layer3",
"negative": "NO_MATCH",
"undefined": "layer3",
"ignoreUndefined": "false"
},
"layer3" : {
"fields": [
{
"field": "title",
"comparator": "levensteinTitle",
"weight": 1.0,
"countIfUndefined": "true"
}
],
"threshold": 0.99,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
}
},
"model" : [
{
"name" : "doi",
"type" : "String",
"path" : "$.pid[@.qualifier.classid = 'doi'].value"
},
{
"name" : "pid",
"type" : "JSON",
"path" : "$.pid",
"overrideMatch" : "true"
},
{
"name" : "title",
"type" : "String",
"path" : "$.title[@.qualifier.classid = 'main title'].value",
"length" : 250,
"size" : 5
},
{
"name" : "authors",
"type" : "String",
"path" : "$.author[*].fullname",
"size" : 200
},
{
"name" : "resulttype",
"type" : "String",
"path" : "$.resulttype.classid"
}
],
"blacklists" : {},
"synonyms" : {}
}
}

118
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@ -0,0 +1,118 @@
{
"wf" : {
"threshold" : "0.99",
"dedupRun" : "001",
"entityType" : "result",
"subEntityType" : "resulttype",
"subEntityValue" : "otherresearchproduct",
"orderField" : "title",
"queueMaxSize" : "2000",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "200",
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true"
},
"pace" : {
"clustering" : [
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree" : {
"start" : {
"fields": [
{
"field": "pid",
"comparator": "jsonListMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {
"jpath_value": "$.value",
"jpath_classid": "$.qualifier.classid"
}
}
],
"threshold": 0.5,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "layer2",
"undefined": "layer2",
"ignoreUndefined": "true"
},
"layer2" : {
"fields": [
{
"field": "title",
"comparator": "titleVersionMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {}
},
{
"field": "authors",
"comparator": "sizeMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {}
}
],
"threshold": 1.0,
"aggregation": "AND",
"positive": "layer3",
"negative": "NO_MATCH",
"undefined": "layer3",
"ignoreUndefined": "false"
},
"layer3" : {
"fields": [
{
"field": "title",
"comparator": "levensteinTitle",
"weight": 1.0,
"countIfUndefined": "true"
}
],
"threshold": 0.99,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
}
},
"model" : [
{
"name" : "doi",
"type" : "String",
"path" : "$.pid[@.qualifier.classid = 'doi'}].value"
},
{
"name" : "pid",
"type" : "JSON",
"path" : "$.pid",
"overrideMatch" : "true"
},
{
"name" : "title",
"type" : "String",
"path" : "$.title[@.qualifier.classid = 'main title'].value",
"length" : 250,
"size" : 5
},
{
"name" : "authors",
"type" : "String",
"path" : "$.author[*].fullname",
"size" : 200
},
{
"name" : "resulttype",
"type" : "String",
"path" : "$.resulttype.classid"
}
],
"blacklists" : {},
"synonyms" : {}
}
}

92
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@ -0,0 +1,92 @@
{
"wf" : {
"threshold" : "0.99",
"dedupRun" : "001",
"entityType" : "result",
"subEntityType" : "resulttype",
"subEntityValue" : "software",
"orderField" : "title",
"queueMaxSize" : "2000",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "200",
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true"
},
"pace" : {
"clustering" : [
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi", "url" ], "params" : { } }
],
"decisionTree": {
"start": {
"fields": [
{
"field": "doi",
"comparator": "exactMatch",
"weight": 1,
"countIfUndefined": "false",
"params": {}
},
{
"field": "url",
"comparator": "exactMatch",
"weight": 1,
"countIfUndefined": "false",
"params": {}
}
],
"threshold": 1,
"aggregation": "OR",
"positive": "MATCH",
"negative": "layer2",
"undefined": "layer2",
"ignoreUndefined": "false"
},
"layer2": {
"fields": [
{
"field": "title",
"comparator": "levensteinTitleIgnoreVersion",
"weight": 1,
"countIfUndefined": "false",
"params": {}
}
],
"threshold": 0.99,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "false"
}
},
"model" : [
{
"name" : "doi",
"type" : "String",
"path" : "$.pid[?(@.qualifier.classid == 'doi')].value"
},
{
"name" : "title",
"type" : "String",
"path" : "$.title[?(@.qualifier.classid == 'main title')].value",
"length" : 250,
"size" : 5
},
{
"name" : "url",
"type" : "String",
"path" : "$.instance.url"
},
{
"name" : "resulttype",
"type" : "String",
"path" : "$.resulttype.classid"
}
],
"blacklists" : {},
"synonyms": {}
}
}

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@ -98,305 +98,305 @@
{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::21abe5a91c2949aba6ef77033a5f98f3", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eac934a34bf16c5f0de8ce743bd0b4"} {"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::21abe5a91c2949aba6ef77033a5f98f3", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eac934a34bf16c5f0de8ce743bd0b4"}
{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|dedup_wf_001::5614cb4fbc9f3be07aedd6d627470e58", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eb4e57e351343377f693ee714500b4"} {"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|dedup_wf_001::5614cb4fbc9f3be07aedd6d627470e58", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eb4e57e351343377f693ee714500b4"}
{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::c3534dbd02b4a4aa35f235671f7631aa", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eb4e57e351343377f693ee714500b4"} {"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::c3534dbd02b4a4aa35f235671f7631aa", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eb4e57e351343377f693ee714500b4"}
{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|dedup_wf_001::032546390e513e50571bf2aae948548f", "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]} {"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|dedup_wf_001::032546390e513e50571bf2aae948548f", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|dedup_wf_001::04516dab6afef5fc35f02066c192ac1c", "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]} {"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|dedup_wf_001::04516dab6afef5fc35f02066c192ac1c", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
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dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml
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@ -14,6 +14,7 @@
<SCAN_SEQUENCE> <SCAN_SEQUENCE>
<SCAN id="organization"/> <SCAN id="organization"/>
<SCAN id="publication"/> <SCAN id="publication"/>
<SCAN id="software"/>
</SCAN_SEQUENCE> </SCAN_SEQUENCE>
</DEDUPLICATION> </DEDUPLICATION>
</CONFIGURATION> </CONFIGURATION>