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included new stats* workflows in parent pom list of modules, code formatting

This commit is contained in:
Claudio Atzori 2024-03-26 10:42:10 +01:00
parent bfba71a95c
commit ef52128c55
24 changed files with 590 additions and 525 deletions
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8
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java
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@ -1,14 +1,14 @@
package eu.dnetlib.dhp.actionmanager.promote;
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
import java.util.function.BiFunction;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import java.util.function.BiFunction;
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
/** OAF model merging support. */
public class MergeAndGet {

4
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java
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@ -100,7 +100,7 @@ public class MergeAndGetTest {
assertTrue(Relation.class.isAssignableFrom(x.getClass()));
// TODO should be reimplemented
//verify(a).mergeFrom(b);
// verify(a).mergeFrom(b);
assertEquals(a, x);
}
@ -163,7 +163,7 @@ public class MergeAndGetTest {
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
// TODO should be reimplemented
//verify(a).mergeFrom(b);
// verify(a).mergeFrom(b);
assertEquals(a, x);
}
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java
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@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
return projectScores.map((MapFunction<BipProjectModel, Project>) bipProjectScores -> {
Project project = new Project();
//project.setId(bipProjectScores.getProjectId());
// project.setId(bipProjectScores.getProjectId());
project.setMeasures(bipProjectScores.toMeasures());
return project;
}, Encoders.bean(Project.class))

1
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/score/deserializers/BipProjectModel.java
View File

@ -38,7 +38,6 @@ public class BipProjectModel {
return projectId;
}
// each project bip measure has exactly one value, hence one key-value pair
private Measure createMeasure(String measureId, String measureValue) {

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java
View File

@ -166,6 +166,6 @@ public class MapOCIdsInPids implements Serializable {
.option("compression", "gzip")
.json(outputPath);
}
}
}

36
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java
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@ -1,7 +1,26 @@
package eu.dnetlib.dhp.actionmanager.project;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Arrays;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject;
import eu.dnetlib.dhp.actionmanager.project.utils.model.JsonTopic;
@ -15,25 +34,8 @@ import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.dhp.utils.DHPUtils;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2;
import java.util.Arrays;
import java.util.Objects;
import java.util.Optional;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
/**
* Class that makes the ActionSet. To prepare the AS two joins are needed
*

56
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java
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@ -79,35 +79,35 @@ public class CreateActionSetSparkJob implements Serializable {
private static void createActionSet(SparkSession spark, String inputPath, String outputPath) {
JavaRDD<AtomicAction> relations = spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, TransformativeAgreementModel>) value -> OBJECT_MAPPER
.readValue(value, TransformativeAgreementModel.class),
Encoders.bean(TransformativeAgreementModel.class))
.flatMap(
(FlatMapFunction<TransformativeAgreementModel, Relation>) value -> createRelation(
value)
.iterator(),
Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) Objects::nonNull)
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p));
.read()
.textFile(inputPath)
.map(
(MapFunction<String, TransformativeAgreementModel>) value -> OBJECT_MAPPER
.readValue(value, TransformativeAgreementModel.class),
Encoders.bean(TransformativeAgreementModel.class))
.flatMap(
(FlatMapFunction<TransformativeAgreementModel, Relation>) value -> createRelation(
value)
.iterator(),
Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) Objects::nonNull)
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p));
//TODO relations in stand-by waiting to know if we need to create them or not In case we need just make a union before saving the sequence file
spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, TransformativeAgreementModel>) value -> OBJECT_MAPPER
.readValue(value, TransformativeAgreementModel.class),
Encoders.bean(TransformativeAgreementModel.class))
.map(
(MapFunction<TransformativeAgreementModel, Result>) value -> createResult(
value),
Encoders.bean(Result.class))
.filter((FilterFunction<Result>) r -> r != null)
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p))
spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, TransformativeAgreementModel>) value -> OBJECT_MAPPER
.readValue(value, TransformativeAgreementModel.class),
Encoders.bean(TransformativeAgreementModel.class))
.map(
(MapFunction<TransformativeAgreementModel, Result>) value -> createResult(
value),
Encoders.bean(Result.class))
.filter((FilterFunction<Result>) r -> r != null)
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))

42
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/XSLTTransformationFunction.java
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@ -49,29 +49,29 @@ public class XSLTTransformationFunction implements MapFunction<MetadataRecord, M
public MetadataRecord call(MetadataRecord value) {
aggregationCounter.getTotalItems().add(1);
Processor processor = new Processor(false);
Processor processor = new Processor(false);
processor.registerExtensionFunction(cleanFunction);
processor.registerExtensionFunction(new DateCleaner());
processor.registerExtensionFunction(new PersonCleaner());
processor.registerExtensionFunction(cleanFunction);
processor.registerExtensionFunction(new DateCleaner());
processor.registerExtensionFunction(new PersonCleaner());
final XsltCompiler comp = processor.newXsltCompiler();
QName datasourceIDParam = new QName(DATASOURCE_ID_PARAM);
comp.setParameter(datasourceIDParam, new XdmAtomicValue(value.getProvenance().getDatasourceId()));
QName datasourceNameParam = new QName(DATASOURCE_NAME_PARAM);
comp.setParameter(datasourceNameParam, new XdmAtomicValue(value.getProvenance().getDatasourceName()));
XsltExecutable xslt;
XdmNode source;
try {
xslt = comp
.compile(new StreamSource(IOUtils.toInputStream(transformationRule, StandardCharsets.UTF_8)));
source = processor
.newDocumentBuilder()
.build(new StreamSource(IOUtils.toInputStream(value.getBody(), StandardCharsets.UTF_8)));
} catch (Throwable e) {
throw new RuntimeException("Error on parsing xslt", e);
}
try {
final XsltCompiler comp = processor.newXsltCompiler();
QName datasourceIDParam = new QName(DATASOURCE_ID_PARAM);
comp.setParameter(datasourceIDParam, new XdmAtomicValue(value.getProvenance().getDatasourceId()));
QName datasourceNameParam = new QName(DATASOURCE_NAME_PARAM);
comp.setParameter(datasourceNameParam, new XdmAtomicValue(value.getProvenance().getDatasourceName()));
XsltExecutable xslt;
XdmNode source;
try {
xslt = comp
.compile(new StreamSource(IOUtils.toInputStream(transformationRule, StandardCharsets.UTF_8)));
source = processor
.newDocumentBuilder()
.build(new StreamSource(IOUtils.toInputStream(value.getBody(), StandardCharsets.UTF_8)));
} catch (Throwable e) {
throw new RuntimeException("Error on parsing xslt", e);
}
try {
XsltTransformer trans = xslt.load();
trans.setInitialContextNode(source);
final StringWriter output = new StringWriter();

6
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java
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@ -82,9 +82,9 @@ public class BaseTransfomationTest extends AbstractVocabularyTest {
private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception {
final String xslt = new SAXReader()
.read(this.getClass().getResourceAsStream(path))
.selectSingleNode("//CODE/*")
.asXML();
.read(this.getClass().getResourceAsStream(path))
.selectSingleNode("//CODE/*")
.asXML();
final LongAccumulator la = new LongAccumulator();

4
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java
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@ -281,7 +281,7 @@ class TransformationJobTest extends AbstractVocabularyTest {
}
@Test
public void testInvalidXSLT() throws Exception{
public void testInvalidXSLT() throws Exception {
final MetadataRecord mr = new MetadataRecord();
mr.setProvenance(new Provenance("openaire____::cnr_explora", "CNR ExploRA", "cnr_________"));
@ -289,7 +289,7 @@ class TransformationJobTest extends AbstractVocabularyTest {
// We Load the XSLT transformation Rule from the classpath
final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/invalid.xslt");
assertThrows(RuntimeException.class,()->tr.call(mr));
assertThrows(RuntimeException.class, () -> tr.call(mr));
}

313
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
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@ -4,7 +4,6 @@ package eu.dnetlib.dhp.oa.dedup;
import java.util.*;
import java.util.stream.Stream;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import org.apache.commons.beanutils.BeanUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.api.java.function.FlatMapFunction;
@ -15,200 +14,200 @@ import org.apache.spark.sql.*;
import eu.dnetlib.dhp.oa.dedup.model.Identifier;
import eu.dnetlib.dhp.oa.merge.AuthorMerger;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import scala.Tuple2;
import scala.Tuple3;
import scala.collection.JavaConversions;
public class DedupRecordFactory {
public static final class DedupRecordReduceState {
public final String dedupId;
public static final class DedupRecordReduceState {
public final String dedupId;
public final ArrayList<String> aliases = new ArrayList<>();
public final ArrayList<String> aliases = new ArrayList<>();
public final HashSet<String> acceptanceDate = new HashSet<>();
public final HashSet<String> acceptanceDate = new HashSet<>();
public OafEntity entity;
public OafEntity entity;
public DedupRecordReduceState(String dedupId, String id, OafEntity entity) {
this.dedupId = dedupId;
this.entity = entity;
if (entity == null) {
aliases.add(id);
} else {
if (Result.class.isAssignableFrom(entity.getClass())) {
Result result = (Result) entity;
if (result.getDateofacceptance() != null
&& StringUtils.isNotBlank(result.getDateofacceptance().getValue())) {
acceptanceDate.add(result.getDateofacceptance().getValue());
}
}
}
}
public DedupRecordReduceState(String dedupId, String id, OafEntity entity) {
this.dedupId = dedupId;
this.entity = entity;
if (entity == null) {
aliases.add(id);
} else {
if (Result.class.isAssignableFrom(entity.getClass())) {
Result result = (Result) entity;
if (result.getDateofacceptance() != null
&& StringUtils.isNotBlank(result.getDateofacceptance().getValue())) {
acceptanceDate.add(result.getDateofacceptance().getValue());
}
}
}
}
public String getDedupId() {
return dedupId;
}
}
public String getDedupId() {
return dedupId;
}
}
private static final int MAX_ACCEPTANCE_DATE = 20;
private static final int MAX_ACCEPTANCE_DATE = 20;
private DedupRecordFactory() {
}
private DedupRecordFactory() {
}
public static Dataset<OafEntity> createDedupRecord(
final SparkSession spark,
final DataInfo dataInfo,
final String mergeRelsInputPath,
final String entitiesInputPath,
final Class<OafEntity> clazz) {
public static Dataset<OafEntity> createDedupRecord(
final SparkSession spark,
final DataInfo dataInfo,
final String mergeRelsInputPath,
final String entitiesInputPath,
final Class<OafEntity> clazz) {
final long ts = System.currentTimeMillis();
final Encoder<OafEntity> beanEncoder = Encoders.bean(clazz);
final Encoder<OafEntity> kryoEncoder = Encoders.kryo(clazz);
final long ts = System.currentTimeMillis();
final Encoder<OafEntity> beanEncoder = Encoders.bean(clazz);
final Encoder<OafEntity> kryoEncoder = Encoders.kryo(clazz);
// <id, json_entity>
Dataset<Row> entities = spark
.read()
.schema(Encoders.bean(clazz).schema())
.json(entitiesInputPath)
.as(beanEncoder)
.map(
(MapFunction<OafEntity, Tuple2<String, OafEntity>>) entity -> {
return new Tuple2<>(entity.getId(), entity);
},
Encoders.tuple(Encoders.STRING(), kryoEncoder))
.selectExpr("_1 AS id", "_2 AS kryoObject");
// <id, json_entity>
Dataset<Row> entities = spark
.read()
.schema(Encoders.bean(clazz).schema())
.json(entitiesInputPath)
.as(beanEncoder)
.map(
(MapFunction<OafEntity, Tuple2<String, OafEntity>>) entity -> {
return new Tuple2<>(entity.getId(), entity);
},
Encoders.tuple(Encoders.STRING(), kryoEncoder))
.selectExpr("_1 AS id", "_2 AS kryoObject");
// <source, target>: source is the dedup_id, target is the id of the mergedIn
Dataset<Row> mergeRels = spark
.read()
.load(mergeRelsInputPath)
.where("relClass == 'merges'")
.selectExpr("source as dedupId", "target as id");
// <source, target>: source is the dedup_id, target is the id of the mergedIn
Dataset<Row> mergeRels = spark
.read()
.load(mergeRelsInputPath)
.where("relClass == 'merges'")
.selectExpr("source as dedupId", "target as id");
return mergeRels
.join(entities, JavaConversions.asScalaBuffer(Collections.singletonList("id")), "left")
.select("dedupId", "id", "kryoObject")
.as(Encoders.tuple(Encoders.STRING(), Encoders.STRING(), kryoEncoder))
.map(
(MapFunction<Tuple3<String, String, OafEntity>, DedupRecordReduceState>) t -> new DedupRecordReduceState(
t._1(), t._2(), t._3()),
Encoders.kryo(DedupRecordReduceState.class))
.groupByKey(
(MapFunction<DedupRecordReduceState, String>) DedupRecordReduceState::getDedupId, Encoders.STRING())
.reduceGroups(
(ReduceFunction<DedupRecordReduceState>) (t1, t2) -> {
if (t1.entity == null) {
t2.aliases.addAll(t1.aliases);
return t2;
}
if (t1.acceptanceDate.size() < MAX_ACCEPTANCE_DATE) {
t1.acceptanceDate.addAll(t2.acceptanceDate);
}
t1.aliases.addAll(t2.aliases);
t1.entity = reduceEntity(t1.entity, t2.entity);
return mergeRels
.join(entities, JavaConversions.asScalaBuffer(Collections.singletonList("id")), "left")
.select("dedupId", "id", "kryoObject")
.as(Encoders.tuple(Encoders.STRING(), Encoders.STRING(), kryoEncoder))
.map(
(MapFunction<Tuple3<String, String, OafEntity>, DedupRecordReduceState>) t -> new DedupRecordReduceState(
t._1(), t._2(), t._3()),
Encoders.kryo(DedupRecordReduceState.class))
.groupByKey(
(MapFunction<DedupRecordReduceState, String>) DedupRecordReduceState::getDedupId, Encoders.STRING())
.reduceGroups(
(ReduceFunction<DedupRecordReduceState>) (t1, t2) -> {
if (t1.entity == null) {
t2.aliases.addAll(t1.aliases);
return t2;
}
if (t1.acceptanceDate.size() < MAX_ACCEPTANCE_DATE) {
t1.acceptanceDate.addAll(t2.acceptanceDate);
}
t1.aliases.addAll(t2.aliases);
t1.entity = reduceEntity(t1.entity, t2.entity);
return t1;
})
.flatMap((FlatMapFunction<Tuple2<String, DedupRecordReduceState>, OafEntity>) t -> {
String dedupId = t._1();
DedupRecordReduceState agg = t._2();
return t1;
})
.flatMap((FlatMapFunction<Tuple2<String, DedupRecordReduceState>, OafEntity>) t -> {
String dedupId = t._1();
DedupRecordReduceState agg = t._2();
if (agg.acceptanceDate.size() >= MAX_ACCEPTANCE_DATE) {
return Collections.emptyIterator();
}
if (agg.acceptanceDate.size() >= MAX_ACCEPTANCE_DATE) {
return Collections.emptyIterator();
}
return Stream
.concat(
Stream
.of(agg.getDedupId())
.map(id -> createDedupOafEntity(id, agg.entity, dataInfo, ts)),
agg.aliases
.stream()
.map(id -> createMergedDedupAliasOafEntity(id, agg.entity, dataInfo, ts)))
.iterator();
}, beanEncoder);
}
return Stream
.concat(
Stream
.of(agg.getDedupId())
.map(id -> createDedupOafEntity(id, agg.entity, dataInfo, ts)),
agg.aliases
.stream()
.map(id -> createMergedDedupAliasOafEntity(id, agg.entity, dataInfo, ts)))
.iterator();
}, beanEncoder);
}
private static OafEntity createDedupOafEntity(String id, OafEntity base, DataInfo dataInfo, long ts) {
try {
OafEntity res = (OafEntity) BeanUtils.cloneBean(base);
res.setId(id);
res.setDataInfo(dataInfo);
res.setLastupdatetimestamp(ts);
return res;
} catch (Exception e) {
throw new RuntimeException(e);
}
}
private static OafEntity createDedupOafEntity(String id, OafEntity base, DataInfo dataInfo, long ts) {
try {
OafEntity res = (OafEntity) BeanUtils.cloneBean(base);
res.setId(id);
res.setDataInfo(dataInfo);
res.setLastupdatetimestamp(ts);
return res;
} catch (Exception e) {
throw new RuntimeException(e);
}
}
private static OafEntity createMergedDedupAliasOafEntity(String id, OafEntity base, DataInfo dataInfo, long ts) {
try {
OafEntity res = createDedupOafEntity(id, base, dataInfo, ts);
DataInfo ds = (DataInfo) BeanUtils.cloneBean(dataInfo);
ds.setDeletedbyinference(true);
res.setDataInfo(ds);
return res;
} catch (Exception e) {
throw new RuntimeException(e);
}
}
private static OafEntity createMergedDedupAliasOafEntity(String id, OafEntity base, DataInfo dataInfo, long ts) {
try {
OafEntity res = createDedupOafEntity(id, base, dataInfo, ts);
DataInfo ds = (DataInfo) BeanUtils.cloneBean(dataInfo);
ds.setDeletedbyinference(true);
res.setDataInfo(ds);
return res;
} catch (Exception e) {
throw new RuntimeException(e);
}
}
private static OafEntity reduceEntity(OafEntity entity, OafEntity duplicate) {
private static OafEntity reduceEntity(OafEntity entity, OafEntity duplicate) {
if (duplicate == null) {
return entity;
}
if (duplicate == null) {
return entity;
}
int compare = new IdentifierComparator<>()
.compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate));
int compare = new IdentifierComparator<>()
.compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate));
if (compare > 0) {
OafEntity swap = duplicate;
duplicate = entity;
entity = swap;
}
if (compare > 0) {
OafEntity swap = duplicate;
duplicate = entity;
entity = swap;
}
entity = MergeUtils.checkedMerge(entity, duplicate);
entity = MergeUtils.checkedMerge(entity, duplicate);
if (ModelSupport.isSubClass(duplicate, Result.class)) {
Result re = (Result) entity;
Result rd = (Result) duplicate;
if (ModelSupport.isSubClass(duplicate, Result.class)) {
Result re = (Result) entity;
Result rd = (Result) duplicate;
List<List<Author>> authors = new ArrayList<>();
if (re.getAuthor() != null) {
authors.add(re.getAuthor());
}
if (rd.getAuthor() != null) {
authors.add(rd.getAuthor());
}
List<List<Author>> authors = new ArrayList<>();
if (re.getAuthor() != null) {
authors.add(re.getAuthor());
}
if (rd.getAuthor() != null) {
authors.add(rd.getAuthor());
}
re.setAuthor(AuthorMerger.merge(authors));
}
re.setAuthor(AuthorMerger.merge(authors));
}
return entity;
}
return entity;
}
public static <T extends OafEntity> T entityMerger(
String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz) {
T base = entities.next()._2();
public static <T extends OafEntity> T entityMerger(
String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz) {
T base = entities.next()._2();
while (entities.hasNext()) {
T duplicate = entities.next()._2();
if (duplicate != null)
base = (T) reduceEntity(base, duplicate);
}
while (entities.hasNext()) {
T duplicate = entities.next()._2();
if (duplicate != null)
base = (T) reduceEntity(base, duplicate);
}
base.setId(id);
base.setDataInfo(dataInfo);
base.setLastupdatetimestamp(ts);
base.setId(id);
base.setDataInfo(dataInfo);
base.setLastupdatetimestamp(ts);
return base;
}
return base;
}
}

5
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
View File

@ -3,7 +3,6 @@ package eu.dnetlib.dhp.oa.dedup;
import static org.apache.spark.sql.functions.col;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
@ -21,6 +20,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
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.utils.MergeUtils;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import scala.Tuple2;
@ -128,8 +128,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
(MapFunction<Relation, String>) r -> String
.join(" ", r.getSource(), r.getTarget(), r.getRelType(), r.getSubRelType(), r.getRelClass()),
Encoders.STRING())
.reduceGroups((ReduceFunction<Relation>) MergeUtils::mergeRelation
)
.reduceGroups((ReduceFunction<Relation>) MergeUtils::mergeRelation)
.map((MapFunction<Tuple2<String, Relation>, Relation>) Tuple2::_2, REL_BEAN_ENC);
final String outputRelationPath = graphOutputPath + "/relation";

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java
View File

@ -13,7 +13,6 @@ import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
@ -29,6 +28,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import scala.Tuple2;
/**

184
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java
View File

@ -25,118 +25,118 @@ import scala.Tuple2;
public class SparkResultToCommunityThroughSemRelJob {
private static final Logger log = LoggerFactory.getLogger(SparkResultToCommunityThroughSemRelJob.class);
private static final Logger log = LoggerFactory.getLogger(SparkResultToCommunityThroughSemRelJob.class);
public static void main(String[] args) throws Exception {
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkResultToCommunityThroughSemRelJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromsemrel/input_communitytoresult_parameters.json"));
String jsonConfiguration = IOUtils
.toString(
SparkResultToCommunityThroughSemRelJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromsemrel/input_communitytoresult_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String preparedInfoPath = parser.get("preparedInfoPath");
log.info("preparedInfoPath: {}", preparedInfoPath);
final String preparedInfoPath = parser.get("preparedInfoPath");
log.info("preparedInfoPath: {}", preparedInfoPath);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final Boolean saveGraph = Optional
.ofNullable(parser.get("saveGraph"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("saveGraph: {}", saveGraph);
final Boolean saveGraph = Optional
.ofNullable(parser.get("saveGraph"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("saveGraph: {}", saveGraph);
@SuppressWarnings("unchecked")
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
@SuppressWarnings("unchecked")
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
if (saveGraph) {
execPropagation(
spark, inputPath, outputPath, preparedInfoPath, resultClazz);
}
});
}
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
if (saveGraph) {
execPropagation(
spark, inputPath, outputPath, preparedInfoPath, resultClazz);
}
});
}
private static <R extends Result> void execPropagation(
SparkSession spark,
String inputPath,
String outputPath,
String preparedInfoPath,
Class<R> resultClazz) {
private static <R extends Result> void execPropagation(
SparkSession spark,
String inputPath,
String outputPath,
String preparedInfoPath,
Class<R> resultClazz) {
Dataset<ResultCommunityList> possibleUpdates = readPath(spark, preparedInfoPath, ResultCommunityList.class);
Dataset<R> result = readPath(spark, inputPath, resultClazz);
Dataset<ResultCommunityList> possibleUpdates = readPath(spark, preparedInfoPath, ResultCommunityList.class);
Dataset<R> result = readPath(spark, inputPath, resultClazz);
result
.joinWith(
possibleUpdates,
result.col("id").equalTo(possibleUpdates.col("resultId")),
"left_outer")
.map(contextUpdaterFn(), Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
result
.joinWith(
possibleUpdates,
result.col("id").equalTo(possibleUpdates.col("resultId")),
"left_outer")
.map(contextUpdaterFn(), Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
}
private static <R extends Result> MapFunction<Tuple2<R, ResultCommunityList>, R> contextUpdaterFn() {
return value -> {
R ret = value._1();
Optional<ResultCommunityList> rcl = Optional.ofNullable(value._2());
if (rcl.isPresent()) {
Set<String> contexts = new HashSet<>();
ret.getContext().forEach(c -> contexts.add(c.getId()));
rcl
.get()
.getCommunityList()
.stream()
.forEach(
c -> {
if (!contexts.contains(c)) {
Context newContext = new Context();
newContext.setId(c);
newContext
.setDataInfo(
Arrays
.asList(
getDataInfo(
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS)));
ret.getContext().add(newContext);
}
private static <R extends Result> MapFunction<Tuple2<R, ResultCommunityList>, R> contextUpdaterFn() {
return value -> {
R ret = value._1();
Optional<ResultCommunityList> rcl = Optional.ofNullable(value._2());
if (rcl.isPresent()) {
Set<String> contexts = new HashSet<>();
ret.getContext().forEach(c -> contexts.add(c.getId()));
rcl
.get()
.getCommunityList()
.stream()
.forEach(
c -> {
if (!contexts.contains(c)) {
Context newContext = new Context();
newContext.setId(c);
newContext
.setDataInfo(
Arrays
.asList(
getDataInfo(
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS)));
ret.getContext().add(newContext);
}
});
});
}
}
return ret;
};
}
return ret;
};
}
}

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java
View File

@ -7,7 +7,6 @@ import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
@ -25,6 +24,7 @@ import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import scala.Tuple2;
/**
@ -251,7 +251,7 @@ public class MergeGraphTableSparkJob {
return (T) MergeUtils.merge(b, a);
}
if (a instanceof Relation && b instanceof Relation) {
return (T) MergeUtils.mergeRelation((Relation)a, (Relation) b);
return (T) MergeUtils.mergeRelation((Relation) a, (Relation) b);
}
}
return Objects.isNull(a) ? b : a;

363
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -98,8 +98,10 @@ public abstract class AbstractMdRecordToOafMapper {
protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3";
protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/";
protected static final Qualifier ORCID_PID_TYPE = qualifier(ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, DNET_PID_TYPES, DNET_PID_TYPES);
protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
protected static final Qualifier ORCID_PID_TYPE = qualifier(
ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, DNET_PID_TYPES, DNET_PID_TYPES);
protected static final Qualifier MAG_PID_TYPE = qualifier(
"MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
protected static final String DEFAULT_TRUST_FOR_VALIDATED_RELS = "0.999";
@ -122,14 +124,14 @@ public abstract class AbstractMdRecordToOafMapper {
static {
IdentifierFactory.PID_AUTHORITY
.keySet()
.stream()
.forEach(entry -> pidTypeWithAuthority.put(entry.toString().toLowerCase(), entry.toString()));
.keySet()
.stream()
.forEach(entry -> pidTypeWithAuthority.put(entry.toString().toLowerCase(), entry.toString()));
}
protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible,
final boolean shouldHashId, final boolean forceOriginalId) {
final boolean shouldHashId, final boolean forceOriginalId) {
this.vocs = vocs;
this.invisible = invisible;
this.shouldHashId = shouldHashId;
@ -137,7 +139,7 @@ public abstract class AbstractMdRecordToOafMapper {
}
protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible,
final boolean shouldHashId) {
final boolean shouldHashId) {
this.vocs = vocs;
this.invisible = invisible;
this.shouldHashId = shouldHashId;
@ -149,20 +151,26 @@ public abstract class AbstractMdRecordToOafMapper {
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
try {
final Document doc = DocumentHelper
.parseText(xml
.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)
.replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3)
.replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3));
.parseText(
xml
.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)
.replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3)
.replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3));
final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
final KeyValue collectedFrom = getProvenanceDatasource(
doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
if (collectedFrom == null) { return Lists.newArrayList(); }
if (collectedFrom == null) {
return Lists.newArrayList();
}
final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
? collectedFrom
: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
? collectedFrom
: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
if (hostedBy == null) { return Lists.newArrayList(); }
if (hostedBy == null) {
return Lists.newArrayList();
}
final DataInfo entityInfo = prepareDataInfo(doc, this.invisible);
final long lastUpdateTimestamp = new Date().getTime();
@ -183,15 +191,15 @@ public abstract class AbstractMdRecordToOafMapper {
if (StringUtils.isBlank(type) && this.vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
final String instanceType = instances
.stream()
.map(i -> i.getInstancetype().getClassid())
.findFirst()
.filter(s -> !UNKNOWN.equalsIgnoreCase(s))
.orElse("0000"); // Unknown
.stream()
.map(i -> i.getInstancetype().getClassid())
.findFirst()
.filter(s -> !UNKNOWN.equalsIgnoreCase(s))
.orElse("0000"); // Unknown
return Optional
.ofNullable(this.vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType))
.map(Qualifier::getClassid)
.orElse("0000");
.ofNullable(this.vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType))
.map(Qualifier::getClassid)
.orElse("0000");
}
return type;
@ -201,18 +209,20 @@ public abstract class AbstractMdRecordToOafMapper {
final String dsId = doc.valueOf(xpathId);
final String dsName = doc.valueOf(xpathName);
if (StringUtils.isBlank(dsId) || StringUtils.isBlank(dsName)) { return null; }
if (StringUtils.isBlank(dsId) || StringUtils.isBlank(dsName)) {
return null;
}
return keyValue(createOpenaireId(10, dsId, true), dsName);
}
protected List<Oaf> createOafs(
final Document doc,
final String type,
final List<Instance> instances,
final KeyValue collectedFrom,
final DataInfo info,
final long lastUpdateTimestamp) {
final Document doc,
final String type,
final List<Instance> instances,
final KeyValue collectedFrom,
final DataInfo info,
final long lastUpdateTimestamp) {
final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp);
@ -246,52 +256,52 @@ public abstract class AbstractMdRecordToOafMapper {
}
private OafEntity createEntity(final Document doc,
final String type,
final List<Instance> instances,
final KeyValue collectedFrom,
final DataInfo info,
final long lastUpdateTimestamp) {
final String type,
final List<Instance> instances,
final KeyValue collectedFrom,
final DataInfo info,
final long lastUpdateTimestamp) {
switch (type.toLowerCase()) {
case "publication":
final Publication p = new Publication();
populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp);
p.setJournal(prepareJournal(doc, info));
return p;
case "dataset":
final Dataset d = new Dataset();
populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp);
d.setStoragedate(prepareDatasetStorageDate(doc, info));
d.setDevice(prepareDatasetDevice(doc, info));
d.setSize(prepareDatasetSize(doc, info));
d.setVersion(prepareDatasetVersion(doc, info));
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
return d;
case "software":
final Software s = new Software();
populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp);
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
s.setLicense(prepareSoftwareLicenses(doc, info));
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
return s;
case "":
case "otherresearchproducts":
default:
final OtherResearchProduct o = new OtherResearchProduct();
populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp);
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
o.setTool(prepareOtherResearchProductTools(doc, info));
return o;
case "publication":
final Publication p = new Publication();
populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp);
p.setJournal(prepareJournal(doc, info));
return p;
case "dataset":
final Dataset d = new Dataset();
populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp);
d.setStoragedate(prepareDatasetStorageDate(doc, info));
d.setDevice(prepareDatasetDevice(doc, info));
d.setSize(prepareDatasetSize(doc, info));
d.setVersion(prepareDatasetVersion(doc, info));
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
return d;
case "software":
final Software s = new Software();
populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp);
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
s.setLicense(prepareSoftwareLicenses(doc, info));
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
return s;
case "":
case "otherresearchproducts":
default:
final OtherResearchProduct o = new OtherResearchProduct();
populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp);
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
o.setTool(prepareOtherResearchProductTools(doc, info));
return o;
}
}
private List<Oaf> addProjectRels(
final Document doc,
final OafEntity entity,
final DataInfo info) {
final Document doc,
final OafEntity entity,
final DataInfo info) {
final List<Oaf> res = new ArrayList<>();
@ -307,13 +317,21 @@ public abstract class AbstractMdRecordToOafMapper {
final String projectId = createOpenaireId(40, originalId, true);
res
.add(OafMapperUtils
.getRelation(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity.getCollectedfrom(), info, entity
.getLastupdatetimestamp(), validationdDate, null));
.add(
OafMapperUtils
.getRelation(
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity.getCollectedfrom(),
info, entity
.getLastupdatetimestamp(),
validationdDate, null));
res
.add(OafMapperUtils
.getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity.getCollectedfrom(), info, entity
.getLastupdatetimestamp(), validationdDate, null));
.add(
OafMapperUtils
.getRelation(
projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity.getCollectedfrom(), info,
entity
.getLastupdatetimestamp(),
validationdDate, null));
}
}
@ -333,11 +351,11 @@ public abstract class AbstractMdRecordToOafMapper {
final String relClass = element.attributeValue("relClass");
if (StringUtils.isNotBlank(target) && StringUtils.isNotBlank(relType) && StringUtils.isNotBlank(subRelType)
&& StringUtils.isNotBlank(relClass)) {
&& StringUtils.isNotBlank(relClass)) {
final String relClassInverse = ModelSupport
.findInverse(ModelSupport.rel(relType, subRelType, relClass))
.getInverseRelClass();
.findInverse(ModelSupport.rel(relType, subRelType, relClass))
.getInverseRelClass();
final String validationDate = ((Node) o).valueOf("@validationDate");
if (StringUtils.isNotBlank(target)) {
@ -345,13 +363,21 @@ public abstract class AbstractMdRecordToOafMapper {
if (StringUtils.isNotBlank(targetType)) {
final String targetId = createOpenaireId(targetType, target, true);
rels
.add(OafMapperUtils
.getRelation(entity.getId(), targetId, relType, subRelType, relClass, entity.getCollectedfrom(), info, entity
.getLastupdatetimestamp(), validationDate, null));
.add(
OafMapperUtils
.getRelation(
entity.getId(), targetId, relType, subRelType, relClass,
entity.getCollectedfrom(), info, entity
.getLastupdatetimestamp(),
validationDate, null));
rels
.add(OafMapperUtils
.getRelation(targetId, entity.getId(), relType, subRelType, relClassInverse, entity.getCollectedfrom(), info, entity
.getLastupdatetimestamp(), validationDate, null));
.add(
OafMapperUtils
.getRelation(
targetId, entity.getId(), relType, subRelType, relClassInverse,
entity.getCollectedfrom(), info, entity
.getLastupdatetimestamp(),
validationDate, null));
}
}
}
@ -384,30 +410,37 @@ public abstract class AbstractMdRecordToOafMapper {
}
rels
.add(OafMapperUtils
.getRelation(resultId, orgId, RESULT_ORGANIZATION, AFFILIATION, HAS_AUTHOR_INSTITUTION, entity.getCollectedfrom(), info, entity
.getLastupdatetimestamp(), null, properties));
.add(
OafMapperUtils
.getRelation(
resultId, orgId, RESULT_ORGANIZATION, AFFILIATION, HAS_AUTHOR_INSTITUTION,
entity.getCollectedfrom(), info, entity
.getLastupdatetimestamp(),
null, properties));
rels
.add(OafMapperUtils
.getRelation(orgId, resultId, RESULT_ORGANIZATION, AFFILIATION, IS_AUTHOR_INSTITUTION_OF, entity
.getCollectedfrom(), info, entity.getLastupdatetimestamp(), null, properties));
.add(
OafMapperUtils
.getRelation(
orgId, resultId, RESULT_ORGANIZATION, AFFILIATION, IS_AUTHOR_INSTITUTION_OF, entity
.getCollectedfrom(),
info, entity.getLastupdatetimestamp(), null, properties));
}
}
return rels;
}
protected abstract List<Oaf> addOtherResultRels(
final Document doc,
final OafEntity entity,
DataInfo info);
final Document doc,
final OafEntity entity,
DataInfo info);
private void populateResultFields(
final Result r,
final Document doc,
final List<Instance> instances,
final KeyValue collectedFrom,
final DataInfo info,
final long lastUpdateTimestamp) {
final Result r,
final Document doc,
final List<Instance> instances,
final KeyValue collectedFrom,
final DataInfo info,
final long lastUpdateTimestamp) {
r.setDataInfo(info);
r.setLastupdatetimestamp(lastUpdateTimestamp);
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
@ -499,10 +532,10 @@ public abstract class AbstractMdRecordToOafMapper {
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
protected abstract List<Instance> prepareInstances(
Document doc,
DataInfo info,
KeyValue collectedfrom,
KeyValue hostedby);
Document doc,
DataInfo info,
KeyValue collectedfrom,
KeyValue hostedby);
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
@ -527,16 +560,16 @@ public abstract class AbstractMdRecordToOafMapper {
protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductTools(
Document doc,
DataInfo info);
Document doc,
DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
Document doc,
DataInfo info);
Document doc,
DataInfo info);
protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
Document doc,
DataInfo info);
Document doc,
DataInfo info);
protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
@ -545,8 +578,8 @@ public abstract class AbstractMdRecordToOafMapper {
protected abstract List<StructuredProperty> prepareSoftwareLicenses(Document doc, DataInfo info);
protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
Document doc,
DataInfo info);
Document doc,
DataInfo info);
protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
@ -566,13 +599,13 @@ public abstract class AbstractMdRecordToOafMapper {
protected List<InstanceTypeMapping> prepareInstanceTypeMapping(final Document doc) {
return Optional
.ofNullable(findOriginalType(doc))
.map(originalType -> {
final List<InstanceTypeMapping> mappings = Lists.newArrayList();
mappings.add(OafMapperUtils.instanceTypeMapping(originalType, OPENAIRE_COAR_RESOURCE_TYPES_3_1));
return mappings;
})
.orElse(new ArrayList<>());
.ofNullable(findOriginalType(doc))
.map(originalType -> {
final List<InstanceTypeMapping> mappings = Lists.newArrayList();
mappings.add(OafMapperUtils.instanceTypeMapping(originalType, OPENAIRE_COAR_RESOURCE_TYPES_3_1));
return mappings;
})
.orElse(new ArrayList<>());
}
private Journal prepareJournal(final Document doc, final DataInfo info) {
@ -587,7 +620,9 @@ public abstract class AbstractMdRecordToOafMapper {
final String sp = n.valueOf("@sp");
final String vol = n.valueOf("@vol");
final String edition = n.valueOf("@edition");
if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); }
if (StringUtils.isNotBlank(name)) {
return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info);
}
}
return null;
}
@ -596,13 +631,18 @@ public abstract class AbstractMdRecordToOafMapper {
final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
if (n != null) {
final String id = n.valueOf("./*[local-name()='identifier']");
if (StringUtils.isNotBlank(id)) { return Lists.newArrayList(id); }
if (StringUtils.isNotBlank(id)) {
return Lists.newArrayList(id);
}
}
final List<String> idList = doc
.selectNodes("normalize-space(//*[local-name()='header']/*[local-name()='identifier' or local-name()='recordIdentifier']/text())");
.selectNodes(
"normalize-space(//*[local-name()='header']/*[local-name()='identifier' or local-name()='recordIdentifier']/text())");
final Set<String> originalIds = Sets.newHashSet(idList);
if (originalIds.isEmpty()) { throw new IllegalStateException("missing originalID on " + doc.asXML()); }
if (originalIds.isEmpty()) {
throw new IllegalStateException("missing originalID on " + doc.asXML());
}
return Lists.newArrayList(originalIds);
}
@ -628,11 +668,11 @@ public abstract class AbstractMdRecordToOafMapper {
}
protected List<StructuredProperty> prepareListStructPropsWithValidQualifier(
final Node node,
final String xpath,
final String xpathClassId,
final String schemeId,
final DataInfo info) {
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)) {
@ -646,10 +686,10 @@ public abstract class AbstractMdRecordToOafMapper {
}
protected List<StructuredProperty> prepareListStructProps(
final Node node,
final String xpath,
final Qualifier qualifier,
final DataInfo info) {
final Node node,
final String xpath,
final Qualifier qualifier,
final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
@ -659,28 +699,34 @@ public abstract class AbstractMdRecordToOafMapper {
}
protected List<StructuredProperty> prepareListStructProps(
final Node node,
final String xpath,
final DataInfo info) {
final Node node,
final String xpath,
final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
res
.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n
.valueOf("@schemename"), info));
.add(
structuredProperty(
n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n
.valueOf("@schemename"),
info));
}
return res;
}
protected List<Subject> prepareSubjectList(
final Node node,
final String xpath,
final DataInfo info) {
final Node node,
final String xpath,
final DataInfo info) {
final List<Subject> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
res
.add(subject(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info));
.add(
subject(
n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"),
n.valueOf("@schemename"), info));
}
return res;
}
@ -688,7 +734,9 @@ public abstract class AbstractMdRecordToOafMapper {
protected OAIProvenance prepareOAIprovenance(final Document doc) {
final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
if (n == null) { return null; }
if (n == null) {
return null;
}
final String identifier = n.valueOf("./*[local-name()='identifier']");
final String baseURL = n.valueOf("./*[local-name()='baseURL']");
@ -703,7 +751,9 @@ public abstract class AbstractMdRecordToOafMapper {
protected DataInfo prepareDataInfo(final Document doc, final boolean invisible) {
final Node n = doc.selectSingleNode("//oaf:datainfo");
if (n == null) { return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); }
if (n == null) {
return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9");
}
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
@ -715,11 +765,14 @@ public abstract class AbstractMdRecordToOafMapper {
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
final String trust = n.valueOf("./oaf:trust");
return dataInfo(deletedbyinference, inferenceprovenance, inferred, invisible, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
return dataInfo(
deletedbyinference, inferenceprovenance, inferred, invisible,
qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
}
protected List<Field<String>> prepareListURL(final Node node, final String xpath, final DataInfo info) {
return listFields(info, prepareListString(node, xpath)
return listFields(
info, prepareListString(node, xpath)
.stream()
.filter(URL_VALIDATOR::isValid)
.collect(Collectors.toList()));
@ -730,9 +783,9 @@ public abstract class AbstractMdRecordToOafMapper {
}
protected List<Field<String>> prepareListFields(
final Node node,
final String xpath,
final DataInfo info) {
final Node node,
final String xpath,
final DataInfo info) {
return listFields(info, prepareListString(node, xpath));
}
@ -749,11 +802,13 @@ public abstract class AbstractMdRecordToOafMapper {
protected Set<String> validateUrl(final Collection<String> url) {
if (Objects.isNull(url)) { return new HashSet<>(); }
if (Objects.isNull(url)) {
return new HashSet<>();
}
return url
.stream()
.filter(URL_VALIDATOR::isValid)
.collect(Collectors.toCollection(HashSet::new));
.stream()
.filter(URL_VALIDATOR::isValid)
.collect(Collectors.toCollection(HashSet::new));
}
}

36
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
View File

@ -1,16 +1,13 @@
package eu.dnetlib.dhp.oa.graph.raw;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.Text;
@ -21,15 +18,20 @@ import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import scala.Tuple2;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
public class GenerateEntitiesApplication extends AbstractMigrationApplication {
private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.class);

25
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java
View File

@ -1,12 +1,13 @@
package eu.dnetlib.dhp.oa.graph.raw;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.Mockito.lenient;
import java.io.IOException;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.dom4j.DocumentException;
import org.junit.jupiter.api.BeforeEach;
@ -15,12 +16,12 @@ import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import java.io.IOException;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.Mockito.lenient;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class)
class GenerateEntitiesApplicationTest {

9
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
View File

@ -1137,7 +1137,8 @@ public class XmlRecordFactory implements Serializable {
XmlSerializationUtils
.asXmlElement("dateofacceptance", i.getDateofacceptance().getValue()));
}
if (i.getInstancetype() != null && StringUtils.isNotBlank(i.getInstancetype().getClassid())) {
if (i.getInstancetype() != null
&& StringUtils.isNotBlank(i.getInstancetype().getClassid())) {
instanceFields
.add(XmlSerializationUtils.mapQualifier("instancetype", i.getInstancetype()));
}
@ -1178,7 +1179,8 @@ public class XmlRecordFactory implements Serializable {
if (re.getDatasourcetypeui() != null && StringUtils.isNotBlank(re.getDatasourcetypeui().getClassid())) {
metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", re.getDatasourcetypeui()));
}
if (re.getOpenairecompatibility() != null && StringUtils.isNotBlank(re.getOpenairecompatibility().getClassid())) {
if (re.getOpenairecompatibility() != null
&& StringUtils.isNotBlank(re.getOpenairecompatibility().getClassid())) {
metadata
.add(
XmlSerializationUtils
@ -1285,7 +1287,8 @@ public class XmlRecordFactory implements Serializable {
groupInstancesByUrl(((Result) entity).getInstance()).forEach(instance -> {
final List<String> fields = Lists.newArrayList();
if (instance.getAccessright() != null && StringUtils.isNotBlank(instance.getAccessright().getClassid())) {
if (instance.getAccessright() != null
&& StringUtils.isNotBlank(instance.getAccessright().getClassid())) {
fields
.add(XmlSerializationUtils.mapQualifier("accessright", instance.getAccessright()));
}

3
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java
View File

@ -7,10 +7,11 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.lang3.StringUtils;
import scala.Tuple2;
public class XmlSerializationUtils {

2
dhp-workflows/dhp-stats-hist-snaps/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.4-SNAPSHOT</version>
<version>1.2.5-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-stats-hist-snaps</artifactId>

2
dhp-workflows/dhp-stats-monitor-irish/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.4-SNAPSHOT</version>
<version>1.2.5-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-stats-monitor-irish</artifactId>

2
dhp-workflows/dhp-stats-monitor-update/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.4-SNAPSHOT</version>
<version>1.2.5-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-stats-monitor-update</artifactId>

4
dhp-workflows/pom.xml
View File

@ -31,6 +31,10 @@
<module>dhp-enrichment</module>
<module>dhp-graph-provision</module>
<module>dhp-blacklist</module>
<module>dhp-stats-actionsets</module>
<module>dhp-stats-hist-snaps</module>
<module>dhp-stats-monitor-irish</module>
<module>dhp-stats-monitor-update</module>
<module>dhp-stats-update</module>
<module>dhp-stats-promote</module>
<module>dhp-usage-stats-build</module>