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

This commit is contained in:
Sandro La Bruzzo 2020-05-28 09:58:32 +02:00
parent 7d29b61c62 aac1515b58
commit 02f90eeb07
27 changed files with 2047 additions and 185 deletions
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2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java → dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
package eu.dnetlib.dhp.common;
import java.nio.charset.StandardCharsets;
import java.text.Normalizer;

6
dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java
View File

@ -61,12 +61,6 @@ public class BlackListTest {
spark.stop();
}
/*
* String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); final String outputPath =
* parser.get("outputPath"); log.info("outputPath {}: ", outputPath); final String blacklistPath =
* parser.get("hdfsPath"); log.info("blacklistPath {}: ", blacklistPath); final String mergesPath =
* parser.get("mergesPath"); log.info("mergesPath {}: ", mergesPath);
*/
@Test
public void noRemoveTest() throws Exception {
SparkRemoveBlacklistedRelationJob

15
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java
View File

@ -4,6 +4,7 @@ package eu.dnetlib.dhp.bulktag;
import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.ArrayList;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
@ -100,6 +101,7 @@ public class SparkBulkTagJob {
ResultTagger resultTagger = new ResultTagger();
readPath(spark, inputPath, resultClazz)
.map(patchResult(), Encoders.bean(resultClazz))
.map(
(MapFunction<R, R>) value -> resultTagger
.enrichContextCriteria(
@ -119,4 +121,17 @@ public class SparkBulkTagJob {
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
// TODO remove this hack as soon as the values fixed by this method will be provided as NON null
private static <R extends Result> MapFunction<R, R> patchResult() {
return (MapFunction<R, R>) r -> {
if (r.getDataInfo().getDeletedbyinference() == null) {
r.getDataInfo().setDeletedbyinference(false);
}
if (r.getContext() == null) {
r.setContext(new ArrayList<>());
}
return r;
};
}
}

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java
View File

@ -131,7 +131,7 @@ public class CommunityConfiguration implements Serializable {
p -> {
if (p.getSnd() == null)
return p.getFst();
if (((SelectionConstraints) p.getSnd()).verifyCriteria(param))
if (p.getSnd().verifyCriteria(param))
return p.getFst();
else
return null;

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/VerbResolver.java
View File

@ -34,7 +34,7 @@ public class VerbResolver implements Serializable {
.collect(
Collectors
.toMap(
value -> (String) ((ClassInfo) value)
value -> (String) value
.getAnnotationInfo()
.get(0)
.getParameterValues()

65
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java
View File

@ -77,9 +77,15 @@ public class PrepareDatasourceCountryAssociation {
List<String> allowedtypes,
String inputPath,
String outputPath) {
String whitelisted = "";
for (String i : whitelist) {
whitelisted += " OR id = '" + i + "'";
String whitelisted = " d.id = '" + whitelist.get(0) + "'";
for (int i = 1; i < whitelist.size(); i++) {
whitelisted += " OR d.id = '" + whitelist.get(i) + "'";
}
String allowed = "d.datasourcetype.classid = '" + allowedtypes.get(0) + "'";
for (int i = 1; i < allowedtypes.size(); i++) {
allowed += " OR d.datasourcetype.classid = '" + allowedtypes.get(i) + "'";
}
Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class);
@ -90,26 +96,39 @@ public class PrepareDatasourceCountryAssociation {
relation.createOrReplaceTempView("relation");
organization.createOrReplaceTempView("organization");
String query = "SELECT source dataSourceId, named_struct('classid', country.classid, 'classname', country.classname) country "
+ "FROM ( SELECT id "
+ " FROM datasource "
+ " WHERE (datainfo.deletedbyinference = false "
+ whitelisted
+ ") "
+ getConstraintList("datasourcetype.classid = '", allowedtypes)
+ ") d "
+ "JOIN ( SELECT source, target "
+ " FROM relation "
+ " WHERE relclass = '"
+ ModelConstants.IS_PROVIDED_BY
+ "' "
+ " AND datainfo.deletedbyinference = false ) rel "
+ "ON d.id = rel.source "
+ "JOIN (SELECT id, country "
+ " FROM organization "
+ " WHERE datainfo.deletedbyinference = false "
+ " AND length(country.classid) > 0) o "
+ "ON o.id = rel.target";
// String query = "SELECT source dataSourceId, named_struct('classid', country.classid, 'classname', country.classname) country "
// + "FROM ( SELECT id "
// + " FROM datasource "
// + " WHERE (datainfo.deletedbyinference = false "
// + whitelisted
// + ") "
// + getConstraintList("datasourcetype.classid = '", allowedtypes)
// + ") d "
// + "JOIN ( SELECT source, target "
// + " FROM relation "
// + " WHERE relclass = '"
// + ModelConstants.IS_PROVIDED_BY
// + "' "
// + " AND datainfo.deletedbyinference = false ) rel "
// + "ON d.id = rel.source "
// + "JOIN (SELECT id, country "
// + " FROM organization "
// + " WHERE datainfo.deletedbyinference = false "
// + " AND length(country.classid) > 0) o "
// + "ON o.id = rel.target";
String query = "SELECT source dataSourceId, " +
"named_struct('classid', country.classid, 'classname', country.classname) country " +
"FROM datasource d " +
"JOIN relation rel " +
"ON d.id = rel.source " +
"JOIN organization o " +
"ON o.id = rel.target " +
"WHERE rel.datainfo.deletedbyinference = false " +
"and rel.relclass = '" + ModelConstants.IS_PROVIDED_BY + "'" +
"and o.datainfo.deletedbyinference = false " +
"and length(o.country.classid) > 0 " +
"and (" + allowed + " or " + whitelisted + ")";
spark
.sql(query)

38
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java
View File

@ -4,7 +4,12 @@ package eu.dnetlib.dhp.countrypropagation;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.ArrayList;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset;
@ -13,6 +18,7 @@ import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;
public class PrepareResultCountrySet {
private static final Logger log = LoggerFactory.getLogger(PrepareResultCountrySet.class);
@ -60,6 +66,7 @@ public class PrepareResultCountrySet {
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
getPotentialResultToUpdate(
spark,
inputPath,
@ -89,10 +96,33 @@ public class PrepareResultCountrySet {
spark
.sql(RESULT_COUNTRYSET_QUERY)
.as(Encoders.bean(ResultCountrySet.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Append)
.json(outputPath);
.toJavaRDD()
.mapToPair(value -> new Tuple2<>(value.getResultId(), value))
.reduceByKey((a, b) -> {
ArrayList<CountrySbs> countryList = a.getCountrySet();
Set<String> countryCodes = countryList
.stream()
.map(country -> country.getClassid())
.collect(Collectors.toSet());
b
.getCountrySet()
.stream()
.forEach(c -> {
if (!countryCodes.contains(c.getClassid())) {
countryList.add(c);
countryCodes.add(c.getClassid());
}
});
a.setCountrySet(countryList);
return a;
})
.map(couple -> OBJECT_MAPPER.writeValueAsString(couple._2()))
.saveAsTextFile(outputPath, GzipCodec.class);
// .write()
// .option("compression", "gzip")
// .mode(SaveMode.Append)
// .json(outputPath);
}
}

20
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java
View File

@ -22,6 +22,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.PacePerson;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
@ -121,30 +122,39 @@ public class SparkOrcidToResultFromSemRelJob {
}
private static void enrichAuthor(Author a, List<AutoritativeAuthor> au) {
PacePerson pp = new PacePerson(a.getFullname(), false);
for (AutoritativeAuthor aa : au) {
if (enrichAuthor(aa, a)) {
if (enrichAuthor(aa, a, pp.getNormalisedFirstName(), pp.getNormalisedSurname())) {
return;
}
}
}
private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author) {
private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author,
String author_name,
String author_surname) {
boolean toaddpid = false;
if (StringUtils.isNotEmpty(autoritative_author.getSurname())) {
if (StringUtils.isNotEmpty(author.getSurname())) {
author_surname = author.getSurname();
}
if (StringUtils.isNotEmpty(author_surname)) {
if (autoritative_author
.getSurname()
.trim()
.equalsIgnoreCase(author.getSurname().trim())) {
.equalsIgnoreCase(author_surname.trim())) {
// have the same surname. Check the name
if (StringUtils.isNotEmpty(autoritative_author.getName())) {
if (StringUtils.isNotEmpty(author.getName())) {
author_name = author.getName();
}
if (StringUtils.isNotEmpty(author_name)) {
if (autoritative_author
.getName()
.trim()
.equalsIgnoreCase(author.getName().trim())) {
.equalsIgnoreCase(author_name.trim())) {
toaddpid = true;
}
// they could be differently written (i.e. only the initials of the name
@ -154,7 +164,7 @@ public class SparkOrcidToResultFromSemRelJob {
.getName()
.trim()
.substring(0, 0)
.equalsIgnoreCase(author.getName().trim().substring(0, 0))) {
.equalsIgnoreCase(author_name.trim().substring(0, 0))) {
toaddpid = true;
}
}

6
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java
View File

@ -105,11 +105,7 @@ public class SparkResultToProjectThroughSemRelJob {
.stream()
.forEach(
(p -> {
if (potential_update
.getProjectSet()
.contains(p)) {
potential_update.getProjectSet().remove(p);
}
potential_update.getProjectSet().remove(p);
}));
}
String resId = potential_update.getResultId();

24
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java
View File

@ -7,6 +7,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
@ -19,6 +20,7 @@ import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Relation;
import scala.Tuple2;
public class PrepareResultCommunitySet {
@ -93,10 +95,24 @@ public class PrepareResultCommunitySet {
result_organizationset
.map(mapResultCommunityFn(organizationMap), Encoders.bean(ResultCommunityList.class))
.filter(Objects::nonNull)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
.toJavaRDD()
.mapToPair(value -> new Tuple2<>(value.getResultId(), value))
.reduceByKey((a, b) -> {
ArrayList<String> cl = a.getCommunityList();
b.getCommunityList().stream().forEach(s -> {
if (!cl.contains(s)) {
cl.add(s);
}
});
a.setCommunityList(cl);
return a;
})
.map(value -> OBJECT_MAPPER.writeValueAsString(value._2()))
.saveAsTextFile(outputPath, GzipCodec.class);
// .write()
// .mode(SaveMode.Overwrite)
// .option("compression", "gzip")
// .json(outputPath);
}
private static MapFunction<ResultOrganizations, ResultCommunityList> mapResultCommunityFn(

4
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java
View File

@ -136,9 +136,7 @@ public class SparkResultToOrganizationFromIstRepoJob {
.stream()
.forEach(
rId -> {
if (organization_list.contains(rId)) {
organization_list.remove(rId);
}
organization_list.remove(rId);
});
}
String resultId = potential_update.getResultId();

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.qualifier;
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_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.dom4j.Document;
@ -21,6 +38,7 @@ import org.dom4j.DocumentFactory;
import org.dom4j.DocumentHelper;
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.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Context;
@ -43,7 +61,7 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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_3 = "http://datacite.org/schema/kernel-3";
@ -67,8 +85,8 @@ public abstract class AbstractMdRecordToOafMapper {
protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
"main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
this.code2name = code2name;
protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs) {
this.vocs = vocs;
}
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.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
r.setCollectedfrom(Arrays.asList(collectedFrom));
r
.setPid(
prepareListStructProps(
doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
r.setPid(prepareResultPids(doc, info));
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
@ -278,6 +293,8 @@ public abstract class AbstractMdRecordToOafMapper {
r.setBestaccessright(getBestAccessRights(instances));
}
protected abstract List<StructuredProperty> prepareResultPids(Document doc, DataInfo info);
private List<Context> prepareContexts(final Document doc, final DataInfo info) {
final List<Context> list = new ArrayList<>();
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 static Qualifier getBestAccessRights(List<Instance> instanceList) {
protected static Qualifier getBestAccessRights(final List<Instance> instanceList) {
if (instanceList != null) {
final Optional<Qualifier> min = instanceList
.stream()
@ -405,14 +422,12 @@ public abstract class AbstractMdRecordToOafMapper {
return null;
}
protected Qualifier prepareQualifier(
final Node node,
final String xpath,
final String schemeId,
final String schemeName) {
final String classId = node.valueOf(xpath);
final String className = code2name.get(classId);
return qualifier(classId, className, schemeId, schemeName);
protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId) {
return prepareQualifier(node.valueOf(xpath).trim(), schemeId);
}
protected Qualifier prepareQualifier(final String classId, final String schemeId) {
return vocs.getTermAsQualifier(schemeId, classId);
}
protected List<StructuredProperty> prepareListStructProps(
@ -420,14 +435,31 @@ public abstract class AbstractMdRecordToOafMapper {
final String xpath,
final String xpathClassId,
final String schemeId,
final String schemeName,
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);
final String className = code2name.get(classId);
res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info));
final String classId = n.valueOf(xpathClassId).trim();
res.add(structuredProperty(n.getText(), prepareQualifier(classId, schemeId), 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;
}

110
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
View File

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

22
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.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_PID_TYPES;
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.PUBLICATION_DATASET;
@ -13,7 +14,6 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
@ -23,7 +23,8 @@ import org.dom4j.Node;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.oa.graph.raw.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.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Field;
@ -36,8 +37,8 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class OafToOafMapper extends AbstractMdRecordToOafMapper {
public OafToOafMapper(final Map<String, String> code2name) {
super(code2name);
public OafToOafMapper(final VocabularyGroup vocs) {
super(vocs);
}
@Override
@ -83,7 +84,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
@Override
protected Qualifier prepareLanguages(final Document doc) {
return prepareQualifier(doc, "//dc:language", DNET_LANGUAGES, DNET_LANGUAGES);
return prepareQualifier(doc, "//dc:language", DNET_LANGUAGES);
}
@Override
@ -130,14 +131,13 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
final Instance instance = new Instance();
instance
.setInstancetype(
prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE));
instance.setCollectedfrom(collectedfrom);
instance.setHostedby(hostedby);
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
instance
.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES));
.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
instance
@ -297,4 +297,10 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
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);
}
}

41
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_RESOURCE;
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.HAS_PARTS;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PART_OF;
@ -21,14 +22,14 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document;
import org.dom4j.Node;
import eu.dnetlib.dhp.oa.graph.raw.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.DataInfo;
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 OdfToOafMapper(final Map<String, String> code2name) {
super(code2name);
public OdfToOafMapper(final VocabularyGroup vocs) {
super(vocs);
}
@Override
@ -120,14 +121,13 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
final Instance instance = new Instance();
instance
.setInstancetype(
prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE));
instance.setCollectedfrom(collectedfrom);
instance.setHostedby(hostedby);
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
instance
.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES));
.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
@ -211,7 +211,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@Override
protected Qualifier prepareLanguages(final Document doc) {
return prepareQualifier(doc, "//datacite:language", DNET_LANGUAGES, DNET_LANGUAGES);
return prepareQualifier(doc, "//datacite:language", DNET_LANGUAGES);
}
@Override
@ -239,7 +239,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@Override
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
@ -366,7 +366,26 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@Override
protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
return prepareQualifier(
doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE,
DNET_DATA_CITE_RESOURCE);
doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", 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
View File

@ -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
View File

@ -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
View File

@ -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
},
{
"paramName": "pgurl",
"paramLongName": "postgresUrl",
"paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb",
"paramName": "islookup",
"paramLongName": "islookup",
"paramDescription": "the url of the ISLookupService",
"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>
<description>mongo database</description>
</property>
<property>
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>sparkDriverMemory</name>
@ -233,9 +237,7 @@
</spark-opts>
<arg>--sourcePaths</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims</arg>
<arg>--targetPath</arg><arg>${workingDir}/entities_claim</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
<arg>--islookup</arg><arg>${isLookupUrl}</arg>
</spark>
<ok to="GenerateGraph_claims"/>
<error to="Kill"/>
@ -282,9 +284,7 @@
</spark-opts>
<arg>--sourcePaths</arg><arg>${contentPath}/db_records,${contentPath}/oaf_records,${contentPath}/odf_records</arg>
<arg>--targetPath</arg><arg>${workingDir}/entities</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
<arg>--islookup</arg><arg>${isLookupUrl}</arg>
</spark>
<ok to="GenerateGraph"/>
<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>
</property>
<property>
<name>postgresURL</name>
<description>the postgres URL to access to the database</description>
</property>
<property>
<name>postgresUser</name>
<description>the user postgres</description>
</property>
<property>
<name>postgresPassword</name>
<description>the password postgres</description>
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -62,9 +55,7 @@
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>-s</arg><arg>${migrationPathStep1}/db_records,${migrationPathStep1}/oaf_records,${migrationPathStep1}/odf_records</arg>
<arg>-t</arg><arg>${migrationPathStep2}/all_entities</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
<arg>--islookup</arg><arg>${isLookupUrl}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

5
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery Normal file
View File

@ -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
View File

@ -9,7 +9,6 @@ import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
@ -20,6 +19,8 @@ import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
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.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Dataset;
@ -34,18 +35,27 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class MappersTest {
@Mock
private Map<String, String> code2name;
private VocabularyGroup vocs;
@BeforeEach
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
void testPublication() throws IOException {
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());
assertTrue(list.get(0) instanceof Publication);
@ -86,6 +96,10 @@ public class MappersTest {
assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline()));
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());
assertTrue(p.getInstance().size() > 0);
p
@ -115,6 +129,7 @@ public class MappersTest {
assertTrue(StringUtils.isNotBlank(r1.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(r2));
}
@ -123,7 +138,7 @@ public class MappersTest {
void testDataset() throws IOException {
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());
assertTrue(list.get(0) instanceof Dataset);
@ -205,7 +220,7 @@ public class MappersTest {
void testSoftware() throws IOException {
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());
assertTrue(list.get(0) instanceof Software);

6
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
View File

@ -769,7 +769,7 @@ public class XmlRecordFactory implements Serializable {
XmlSerializationUtils.asXmlElement("websiteurl", o.getWebsiteurl().getValue()));
}
if (o.getLogourl() != null) {
metadata.add(XmlSerializationUtils.asXmlElement("websiteurl", o.getLogourl().getValue()));
metadata.add(XmlSerializationUtils.asXmlElement("logourl", o.getLogourl().getValue()));
}
if (o.getEclegalbody() != null) {
@ -801,13 +801,13 @@ public class XmlRecordFactory implements Serializable {
.asXmlElement(
"echighereducation", o.getEchighereducation().getValue()));
}
if (o.getEcinternationalorganization() != null) {
if (o.getEcinternationalorganizationeurinterests() != null) {
metadata
.add(
XmlSerializationUtils
.asXmlElement(
"ecinternationalorganizationeurinterests",
o.getEcinternationalorganization().getValue()));
o.getEcinternationalorganizationeurinterests().getValue()));
}
if (o.getEcinternationalorganization() != null) {
metadata

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$>
$metadata:{$it$}$
$metadata:{ it | $it$ }$
</$name$>

47
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java Normal file
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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());
}
}

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