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dnet-hadoop
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merge branch with fork master

This commit is contained in:
Miriam Baglioni 2020-05-28 10:09:51 +02:00
parent df44db686a aac1515b58
commit 37c155b86a
15 changed files with 1911 additions and 127 deletions
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76
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -10,10 +10,27 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASET_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY;
import static eu.dnetlib.dhp.schema.common.ModelConstants.NOT_AVAILABLE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.ORP_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.REPOSITORY_PROVENANCE_ACTIONS;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.UNKNOWN;
import java.util.*; import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document; import org.dom4j.Document;
@ -21,6 +38,7 @@ import org.dom4j.DocumentFactory;
import org.dom4j.DocumentHelper; import org.dom4j.DocumentHelper;
import org.dom4j.Node; import org.dom4j.Node;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.LicenseComparator; import eu.dnetlib.dhp.schema.common.LicenseComparator;
import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.Context;
@ -43,7 +61,7 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public abstract class AbstractMdRecordToOafMapper { public abstract class AbstractMdRecordToOafMapper {
protected final Map<String, String> code2name; protected final VocabularyGroup vocs;
protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4"; protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4";
protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3";
@ -67,8 +85,8 @@ public abstract class AbstractMdRecordToOafMapper {
protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier( protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
"main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); "main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) { protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs) {
this.code2name = code2name; this.vocs = vocs;
} }
public List<Oaf> processMdRecord(final String xml) { public List<Oaf> processMdRecord(final String xml) {
@ -247,10 +265,7 @@ public abstract class AbstractMdRecordToOafMapper {
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
r.setCollectedfrom(Arrays.asList(collectedFrom)); r.setCollectedfrom(Arrays.asList(collectedFrom));
r r.setPid(prepareResultPids(doc, info));
.setPid(
prepareListStructProps(
doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
@ -278,6 +293,8 @@ public abstract class AbstractMdRecordToOafMapper {
r.setBestaccessright(getBestAccessRights(instances)); r.setBestaccessright(getBestAccessRights(instances));
} }
protected abstract List<StructuredProperty> prepareResultPids(Document doc, DataInfo info);
private List<Context> prepareContexts(final Document doc, final DataInfo info) { private List<Context> prepareContexts(final Document doc, final DataInfo info) {
final List<Context> list = new ArrayList<>(); final List<Context> list = new ArrayList<>();
for (final Object o : doc.selectNodes("//oaf:concept")) { for (final Object o : doc.selectNodes("//oaf:concept")) {
@ -358,7 +375,7 @@ public abstract class AbstractMdRecordToOafMapper {
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info); protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
protected static Qualifier getBestAccessRights(List<Instance> instanceList) { protected static Qualifier getBestAccessRights(final List<Instance> instanceList) {
if (instanceList != null) { if (instanceList != null) {
final Optional<Qualifier> min = instanceList final Optional<Qualifier> min = instanceList
.stream() .stream()
@ -405,14 +422,12 @@ public abstract class AbstractMdRecordToOafMapper {
return null; return null;
} }
protected Qualifier prepareQualifier( protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId) {
final Node node, return prepareQualifier(node.valueOf(xpath).trim(), schemeId);
final String xpath, }
final String schemeId,
final String schemeName) { protected Qualifier prepareQualifier(final String classId, final String schemeId) {
final String classId = node.valueOf(xpath); return vocs.getTermAsQualifier(schemeId, classId);
final String className = code2name.get(classId);
return qualifier(classId, className, schemeId, schemeName);
} }
protected List<StructuredProperty> prepareListStructProps( protected List<StructuredProperty> prepareListStructProps(
@ -420,14 +435,31 @@ public abstract class AbstractMdRecordToOafMapper {
final String xpath, final String xpath,
final String xpathClassId, final String xpathClassId,
final String schemeId, final String schemeId,
final String schemeName,
final DataInfo info) { final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>(); final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) { for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o; final Node n = (Node) o;
final String classId = n.valueOf(xpathClassId); final String classId = n.valueOf(xpathClassId).trim();
final String className = code2name.get(classId); res.add(structuredProperty(n.getText(), prepareQualifier(classId, schemeId), info));
res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info)); }
return res;
}
protected List<StructuredProperty> prepareListStructPropsWithValidQualifier(
final Node node,
final String xpath,
final String xpathClassId,
final String schemeId,
final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
final String classId = n.valueOf(xpathClassId).trim();
if (vocs.termExists(schemeId, classId)) {
res.add(structuredProperty(n.getText(), vocs.getTermAsQualifier(schemeId, classId), info));
}
} }
return res; return res;
} }

110
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
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@ -4,8 +4,10 @@ package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException; import java.io.IOException;
import java.sql.SQLException; import java.util.Arrays;
import java.util.*; import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
@ -24,10 +26,22 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.DbClient;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
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.Dataset;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Project;
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.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import scala.Tuple2; import scala.Tuple2;
public class GenerateEntitiesApplication { public class GenerateEntitiesApplication {
@ -40,13 +54,12 @@ public class GenerateEntitiesApplication {
final ArgumentApplicationParser parser = new ArgumentApplicationParser( final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils IOUtils
.toString( .toString(
MigrateMongoMdstoresApplication.class GenerateEntitiesApplication.class
.getResourceAsStream( .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json")));
"/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json")));
parser.parseArgument(args); parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional final Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged")) .ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf) .map(Boolean::valueOf)
.orElse(Boolean.TRUE); .orElse(Boolean.TRUE);
@ -55,29 +68,28 @@ public class GenerateEntitiesApplication {
final String sourcePaths = parser.get("sourcePaths"); final String sourcePaths = parser.get("sourcePaths");
final String targetPath = parser.get("targetPath"); final String targetPath = parser.get("targetPath");
final String dbUrl = parser.get("postgresUrl"); // final String dbUrl = parser.get("postgresUrl");
final String dbUser = parser.get("postgresUser"); // final String dbUser = parser.get("postgresUser");
final String dbPassword = parser.get("postgresPassword"); // final String dbPassword = parser.get("postgresPassword");
final Map<String, String> code2name = loadClassNames(dbUrl, dbUser, dbPassword); final String isLookupUrl = parser.get("isLookupUrl");
SparkConf conf = new SparkConf(); final VocabularyGroup vocs = loadVocsFromIS(isLookupUrl); // MAP: vocId -> voc
runWithSparkSession(
conf, final SparkConf conf = new SparkConf();
isSparkSessionManaged, runWithSparkSession(conf, isSparkSessionManaged, spark -> {
spark -> { removeOutputDir(spark, targetPath);
removeOutputDir(spark, targetPath); generateEntities(spark, vocs, sourcePaths, targetPath);
generateEntities(spark, code2name, sourcePaths, targetPath); });
});
} }
private static void generateEntities( private static void generateEntities(
final SparkSession spark, final SparkSession spark,
final Map<String, String> code2name, final VocabularyGroup vocs,
final String sourcePaths, final String sourcePaths,
final String targetPath) { final String targetPath) {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final List<String> existingSourcePaths = Arrays final List<String> existingSourcePaths = Arrays
.stream(sourcePaths.split(",")) .stream(sourcePaths.split(","))
.filter(p -> exists(sc, p)) .filter(p -> exists(sc, p))
@ -94,7 +106,7 @@ public class GenerateEntitiesApplication {
sc sc
.sequenceFile(sp, Text.class, Text.class) .sequenceFile(sp, Text.class, Text.class)
.map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) .map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
.map(k -> convertToListOaf(k._1(), k._2(), code2name)) .map(k -> convertToListOaf(k._1(), k._2(), vocs))
.filter(Objects::nonNull) .filter(Objects::nonNull)
.flatMap(list -> list.iterator())); .flatMap(list -> list.iterator()));
} }
@ -110,7 +122,7 @@ public class GenerateEntitiesApplication {
.saveAsTextFile(targetPath, GzipCodec.class); .saveAsTextFile(targetPath, GzipCodec.class);
} }
private static Oaf merge(Oaf o1, Oaf o2) { private static Oaf merge(final Oaf o1, final Oaf o2) {
if (ModelSupport.isSubClass(o1, OafEntity.class)) { if (ModelSupport.isSubClass(o1, OafEntity.class)) {
((OafEntity) o1).mergeFrom((OafEntity) o2); ((OafEntity) o1).mergeFrom((OafEntity) o2);
} else if (ModelSupport.isSubClass(o1, Relation.class)) { } else if (ModelSupport.isSubClass(o1, Relation.class)) {
@ -122,14 +134,16 @@ public class GenerateEntitiesApplication {
} }
private static List<Oaf> convertToListOaf( private static List<Oaf> convertToListOaf(
final String id, final String s, final Map<String, String> code2name) { final String id,
final String s,
final VocabularyGroup vocs) {
final String type = StringUtils.substringAfter(id, ":"); final String type = StringUtils.substringAfter(id, ":");
switch (type.toLowerCase()) { switch (type.toLowerCase()) {
case "native_oaf": case "native_oaf":
return new OafToOafMapper(code2name).processMdRecord(s); return new OafToOafMapper(vocs).processMdRecord(s);
case "native_odf": case "native_odf":
return new OdfToOafMapper(code2name).processMdRecord(s); return new OdfToOafMapper(vocs).processMdRecord(s);
case "datasource": case "datasource":
return Arrays.asList(convertFromJson(s, Datasource.class)); return Arrays.asList(convertFromJson(s, Datasource.class));
case "organization": case "organization":
@ -151,29 +165,33 @@ public class GenerateEntitiesApplication {
} }
} }
private static Map<String, String> loadClassNames( private static VocabularyGroup loadVocsFromIS(final String isLookupUrl) throws IOException, ISLookUpException {
final String dbUrl, final String dbUser, final String dbPassword) throws IOException { final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl);
log.info("Loading vocabulary terms from db..."); final String xquery = IOUtils
.toString(
GenerateEntitiesApplication.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery"));
final Map<String, String> map = new HashMap<>(); final VocabularyGroup vocs = new VocabularyGroup();
try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) { for (final String s : isLookUpService.quickSearchProfile(xquery)) {
dbClient final String[] arr = s.split("@=@");
.processResults( if (arr.length == 4) {
"select code, name from class", final String vocId = arr[0].trim();
rs -> { final String vocName = arr[1].trim();
try { final String termId = arr[2].trim();
map.put(rs.getString("code"), rs.getString("name")); final String termName = arr[3].trim();
} catch (final SQLException e) {
e.printStackTrace(); if (!vocs.vocabularyExists(vocId)) {
} vocs.addVocabulary(vocId, vocName);
}); }
vocs.addTerm(vocId, termId, termName);
}
} }
log.info("Found " + map.size() + " terms."); return vocs;
return map;
} }
private static Oaf convertFromJson(final String s, final Class<? extends Oaf> clazz) { private static Oaf convertFromJson(final String s, final Class<? extends Oaf> clazz) {
@ -196,7 +214,7 @@ public class GenerateEntitiesApplication {
} }
} }
private static void removeOutputDir(SparkSession spark, String path) { private static void removeOutputDir(final SparkSession spark, final String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
} }
} }

20
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
View File

@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO; import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DATASET; import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DATASET;
@ -13,7 +14,6 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Map;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
@ -24,6 +24,7 @@ import org.dom4j.Node;
import com.google.common.collect.Lists; import com.google.common.collect.Lists;
import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.common.PacePerson;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.dhp.schema.oaf.Field;
@ -36,8 +37,8 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class OafToOafMapper extends AbstractMdRecordToOafMapper { public class OafToOafMapper extends AbstractMdRecordToOafMapper {
public OafToOafMapper(final Map<String, String> code2name) { public OafToOafMapper(final VocabularyGroup vocs) {
super(code2name); super(vocs);
} }
@Override @Override
@ -83,7 +84,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
@Override @Override
protected Qualifier prepareLanguages(final Document doc) { protected Qualifier prepareLanguages(final Document doc) {
return prepareQualifier(doc, "//dc:language", DNET_LANGUAGES, DNET_LANGUAGES); return prepareQualifier(doc, "//dc:language", DNET_LANGUAGES);
} }
@Override @Override
@ -130,14 +131,13 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
final Instance instance = new Instance(); final Instance instance = new Instance();
instance instance
.setInstancetype( .setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE));
prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
instance.setCollectedfrom(collectedfrom); instance.setCollectedfrom(collectedfrom);
instance.setHostedby(hostedby); instance.setHostedby(hostedby);
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
instance instance
.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES)); .setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
instance.setLicense(field(doc.valueOf("//oaf:license"), info)); instance.setLicense(field(doc.valueOf("//oaf:license"), info));
instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
instance instance
@ -297,4 +297,10 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
return null; // NOT PRESENT IN OAF return null; // NOT PRESENT IN OAF
} }
@Override
protected List<StructuredProperty> prepareResultPids(final Document doc, final DataInfo info) {
return prepareListStructPropsWithValidQualifier(
doc, "//oaf:identifier", "@identifierType", DNET_PID_TYPES, info);
}
} }

39
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
View File

@ -8,6 +8,7 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_DATE; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_DATE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_RESOURCE; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_RESOURCE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTS; import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTS;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PART_OF; import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PART_OF;
@ -21,7 +22,6 @@ import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashSet; import java.util.HashSet;
import java.util.List; import java.util.List;
import java.util.Map;
import java.util.Set; import java.util.Set;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
@ -29,6 +29,7 @@ import org.dom4j.Document;
import org.dom4j.Node; import org.dom4j.Node;
import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.common.PacePerson;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.dhp.schema.oaf.Field;
@ -43,8 +44,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
public static final String HTTP_DX_DOI_PREIFX = "http://dx.doi.org/"; public static final String HTTP_DX_DOI_PREIFX = "http://dx.doi.org/";
public OdfToOafMapper(final Map<String, String> code2name) { public OdfToOafMapper(final VocabularyGroup vocs) {
super(code2name); super(vocs);
} }
@Override @Override
@ -120,14 +121,13 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
final Instance instance = new Instance(); final Instance instance = new Instance();
instance instance
.setInstancetype( .setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE));
prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
instance.setCollectedfrom(collectedfrom); instance.setCollectedfrom(collectedfrom);
instance.setHostedby(hostedby); instance.setHostedby(hostedby);
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
instance instance
.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES)); .setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
instance.setLicense(field(doc.valueOf("//oaf:license"), info)); instance.setLicense(field(doc.valueOf("//oaf:license"), info));
instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
@ -211,7 +211,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@Override @Override
protected Qualifier prepareLanguages(final Document doc) { protected Qualifier prepareLanguages(final Document doc) {
return prepareQualifier(doc, "//datacite:language", DNET_LANGUAGES, DNET_LANGUAGES); return prepareQualifier(doc, "//datacite:language", DNET_LANGUAGES);
} }
@Override @Override
@ -239,7 +239,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@Override @Override
protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) { protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) {
return prepareQualifier(doc, "//datacite:format", "dnet:programming_languages", "dnet:programming_languages"); return prepareQualifier(doc, "//datacite:format", "dnet:programming_languages");
} }
@Override @Override
@ -366,7 +366,26 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@Override @Override
protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
return prepareQualifier( return prepareQualifier(
doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE, doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE);
DNET_DATA_CITE_RESOURCE);
} }
@Override
protected List<StructuredProperty> prepareResultPids(final Document doc, final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
res
.addAll(
prepareListStructPropsWithValidQualifier(
doc, "//oaf:identifier", "@identifierType", DNET_PID_TYPES, info));
res
.addAll(
prepareListStructPropsWithValidQualifier(
doc, "//datacite:identifier[@identifierType != 'URL']", "@identifierType", DNET_PID_TYPES, info));
res
.addAll(
prepareListStructPropsWithValidQualifier(
doc, "//datacite:alternateIdentifier[@alternateIdentifierType != 'URL']",
"@alternateIdentifierType", DNET_PID_TYPES, info));
return res;
}
} }

42
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java Normal file
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@ -0,0 +1,42 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
import java.util.HashMap;
import java.util.Map;
public class Vocabulary {
private final String id;
private final String name;
private final Map<String, VocabularyTerm> terms = new HashMap<>();
public Vocabulary(final String id, final String name) {
this.id = id;
this.name = name;
}
public String getId() {
return id;
}
public String getName() {
return name;
}
protected Map<String, VocabularyTerm> getTerms() {
return terms;
}
public VocabularyTerm getTerm(final String id) {
return terms.get(id.toLowerCase());
}
protected void addTerm(final String id, final String name) {
terms.put(id.toLowerCase(), new VocabularyTerm(id, name));
}
protected boolean termExists(final String id) {
return terms.containsKey(id.toLowerCase());
}
}

49
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java Normal file
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@ -0,0 +1,49 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
import java.util.HashMap;
import java.util.Map;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class VocabularyGroup {
private final Map<String, Vocabulary> vocs = new HashMap<>();
public void addVocabulary(final String id, final String name) {
vocs.put(id.toLowerCase(), new Vocabulary(id, name));
}
public void addTerm(final String vocId, final String id, final String name) {
if (vocabularyExists(vocId)) {
vocs.get(vocId.toLowerCase()).addTerm(id, name);
}
}
public VocabularyTerm getTerm(final String vocId, final String id) {
if (termExists(vocId, id)) {
return vocs.get(vocId.toLowerCase()).getTerm(id);
} else {
return new VocabularyTerm(id, id);
}
}
public Qualifier getTermAsQualifier(final String vocId, final String id) {
if (termExists(vocId, id)) {
final Vocabulary v = vocs.get(vocId.toLowerCase());
final VocabularyTerm t = v.getTerm(id);
return OafMapperUtils.qualifier(t.getId(), t.getName(), v.getId(), v.getName());
} else {
return OafMapperUtils.qualifier(id, id, vocId, vocId);
}
}
public boolean termExists(final String vocId, final String id) {
return vocabularyExists(vocId) && vocs.get(vocId.toLowerCase()).termExists(id);
}
public boolean vocabularyExists(final String vocId) {
return vocs.containsKey(vocId.toLowerCase());
}
}

22
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyTerm.java Normal file
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@ -0,0 +1,22 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
public class VocabularyTerm {
private final String id;
private final String name;
public VocabularyTerm(final String id, final String name) {
this.id = id;
this.name = name;
}
public String getId() {
return id;
}
public String getName() {
return name;
}
}

19
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json
View File

@ -18,22 +18,9 @@
"paramRequired": true "paramRequired": true
}, },
{ {
"paramName": "pgurl", "paramName": "islookup",
"paramLongName": "postgresUrl", "paramLongName": "islookup",
"paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb", "paramDescription": "the url of the ISLookupService",
"paramRequired": true "paramRequired": true
},
{
"paramName": "pguser",
"paramLongName": "postgresUser",
"paramDescription": "postgres user",
"paramRequired": false
},
{
"paramName": "pgpasswd",
"paramLongName": "postgresPassword",
"paramDescription": "postgres password",
"paramRequired": false
} }
] ]

12
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
View File

@ -34,6 +34,10 @@
<name>mongoDb</name> <name>mongoDb</name>
<description>mongo database</description> <description>mongo database</description>
</property> </property>
<property>
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property> <property>
<name>sparkDriverMemory</name> <name>sparkDriverMemory</name>
@ -233,9 +237,7 @@
</spark-opts> </spark-opts>
<arg>--sourcePaths</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims</arg> <arg>--sourcePaths</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims</arg>
<arg>--targetPath</arg><arg>${workingDir}/entities_claim</arg> <arg>--targetPath</arg><arg>${workingDir}/entities_claim</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg> <arg>--islookup</arg><arg>${isLookupUrl}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
</spark> </spark>
<ok to="GenerateGraph_claims"/> <ok to="GenerateGraph_claims"/>
<error to="Kill"/> <error to="Kill"/>
@ -282,9 +284,7 @@
</spark-opts> </spark-opts>
<arg>--sourcePaths</arg><arg>${contentPath}/db_records,${contentPath}/oaf_records,${contentPath}/odf_records</arg> <arg>--sourcePaths</arg><arg>${contentPath}/db_records,${contentPath}/oaf_records,${contentPath}/odf_records</arg>
<arg>--targetPath</arg><arg>${workingDir}/entities</arg> <arg>--targetPath</arg><arg>${workingDir}/entities</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg> <arg>--islookup</arg><arg>${isLookupUrl}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
</spark> </spark>
<ok to="GenerateGraph"/> <ok to="GenerateGraph"/>
<error to="Kill"/> <error to="Kill"/>

17
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step2/oozie_app/workflow.xml
View File

@ -9,17 +9,10 @@
<description>the temporary path to store entities before dispatching</description> <description>the temporary path to store entities before dispatching</description>
</property> </property>
<property> <property>
<name>postgresURL</name> <name>isLookupUrl</name>
<description>the postgres URL to access to the database</description> <description>the address of the lookUp service</description>
</property>
<property>
<name>postgresUser</name>
<description>the user postgres</description>
</property>
<property>
<name>postgresPassword</name>
<description>the password postgres</description>
</property> </property>
<property> <property>
<name>sparkDriverMemory</name> <name>sparkDriverMemory</name>
<description>memory for driver process</description> <description>memory for driver process</description>
@ -62,9 +55,7 @@
<arg>-mt</arg> <arg>yarn-cluster</arg> <arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>-s</arg><arg>${migrationPathStep1}/db_records,${migrationPathStep1}/oaf_records,${migrationPathStep1}/odf_records</arg> <arg>-s</arg><arg>${migrationPathStep1}/db_records,${migrationPathStep1}/oaf_records,${migrationPathStep1}/odf_records</arg>
<arg>-t</arg><arg>${migrationPathStep2}/all_entities</arg> <arg>-t</arg><arg>${migrationPathStep2}/all_entities</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg> <arg>--islookup</arg><arg>${isLookupUrl}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
</spark> </spark>
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>

5
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery Normal file
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@ -0,0 +1,5 @@
for $x in collection(' /db/DRIVER/VocabularyDSResources/VocabularyDSResourceType')
let $vocid := $x//VOCABULARY_NAME/@code
let $vocname := $x//VOCABULARY_NAME/text()
for $term in ($x//TERM)
return concat($vocid,' @=@ ',$vocname,' @=@ ',$term/@code,' @=@ ',$term/@english_name)

27
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
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@ -9,7 +9,6 @@ import static org.mockito.Mockito.when;
import java.io.IOException; import java.io.IOException;
import java.util.List; import java.util.List;
import java.util.Map;
import java.util.Optional; import java.util.Optional;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
@ -20,6 +19,8 @@ import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock; import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.Dataset;
@ -34,18 +35,27 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class MappersTest { public class MappersTest {
@Mock @Mock
private Map<String, String> code2name; private VocabularyGroup vocs;
@BeforeEach @BeforeEach
public void setUp() throws Exception { public void setUp() throws Exception {
when(code2name.get(anyString())).thenAnswer(invocation -> invocation.getArgument(0)); when(vocs.getTermAsQualifier(anyString(), anyString()))
.thenAnswer(
invocation -> OafMapperUtils
.qualifier(
invocation.getArgument(1), invocation.getArgument(1), invocation.getArgument(0),
invocation.getArgument(0)));
when(vocs.termExists(anyString(), anyString())).thenReturn(true);
} }
@Test @Test
void testPublication() throws IOException { void testPublication() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml")); final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml"));
final List<Oaf> list = new OafToOafMapper(code2name).processMdRecord(xml); final List<Oaf> list = new OafToOafMapper(vocs).processMdRecord(xml);
assertEquals(3, list.size()); assertEquals(3, list.size());
assertTrue(list.get(0) instanceof Publication); assertTrue(list.get(0) instanceof Publication);
@ -86,6 +96,10 @@ public class MappersTest {
assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline()));
assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); assertTrue(StringUtils.isNotBlank(p.getJournal().getName()));
assertTrue(p.getPid().size() > 0);
assertEquals(p.getPid().get(0).getValue(), "10.3897/oneeco.2.e13718");
assertEquals(p.getPid().get(0).getQualifier().getClassid(), "doi");
assertNotNull(p.getInstance()); assertNotNull(p.getInstance());
assertTrue(p.getInstance().size() > 0); assertTrue(p.getInstance().size() > 0);
p p
@ -115,6 +129,7 @@ public class MappersTest {
assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.getRelType())); assertTrue(StringUtils.isNotBlank(r2.getRelType()));
// System.out.println(new ObjectMapper().writeValueAsString(p));
// System.out.println(new ObjectMapper().writeValueAsString(r1)); // System.out.println(new ObjectMapper().writeValueAsString(r1));
// System.out.println(new ObjectMapper().writeValueAsString(r2)); // System.out.println(new ObjectMapper().writeValueAsString(r2));
} }
@ -123,7 +138,7 @@ public class MappersTest {
void testDataset() throws IOException { void testDataset() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml")); final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml"));
final List<Oaf> list = new OdfToOafMapper(code2name).processMdRecord(xml); final List<Oaf> list = new OdfToOafMapper(vocs).processMdRecord(xml);
assertEquals(3, list.size()); assertEquals(3, list.size());
assertTrue(list.get(0) instanceof Dataset); assertTrue(list.get(0) instanceof Dataset);
@ -205,7 +220,7 @@ public class MappersTest {
void testSoftware() throws IOException { void testSoftware() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml")); final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml"));
final List<Oaf> list = new OdfToOafMapper(code2name).processMdRecord(xml); final List<Oaf> list = new OdfToOafMapper(vocs).processMdRecord(xml);
assertEquals(1, list.size()); assertEquals(1, list.size());
assertTrue(list.get(0) instanceof Software); assertTrue(list.get(0) instanceof Software);

2
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st
View File

@ -1,3 +1,3 @@
<$name$$if(hasId)$ objidentifier="$id$"$else$$endif$> <$name$$if(hasId)$ objidentifier="$id$"$else$$endif$>
$metadata:{$it$}$ $metadata:{ it | $it$ }$
</$name$> </$name$>

47
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java Normal file
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@ -0,0 +1,47 @@
package eu.dnetlib.dhp.oa.provision;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
import org.apache.commons.io.IOUtils;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.io.SAXReader;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.io.StringReader;
import static org.junit.jupiter.api.Assertions.*;
public class XmlRecordFactoryTest {
private static final String otherDsTypeId = "scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource";
@Test
public void testXMLRecordFactory() throws IOException, DocumentException {
String json = IOUtils.toString(getClass().getResourceAsStream("joined_entity.json"));
assertNotNull(json);
JoinedEntity je = new ObjectMapper().readValue(json, JoinedEntity.class);
assertNotNull(je);
ContextMapper contextMapper = new ContextMapper();
XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, otherDsTypeId);
String xml = xmlRecordFactory.build(je);
assertNotNull(xml);
Document doc = new SAXReader().read(new StringReader(xml));
assertNotNull(doc);
System.out.println(doc.asXML());
}
}

1551
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/joined_entity.json Normal file
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