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Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta

This commit is contained in:
Miriam Baglioni 2022-12-16 13:18:32 +01:00
parent d791840b82 7b80b24f82
commit dc0ec88a58
11 changed files with 151 additions and 50 deletions
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27
dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java
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@ -4,6 +4,7 @@ package eu.dnetlib.dhp.common.vocabulary;
import java.io.Serializable;
import java.util.HashMap;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.lang3.StringUtils;
@ -66,27 +67,39 @@ public class Vocabulary implements Serializable {
}
public Qualifier getTermAsQualifier(final String termId) {
if (StringUtils.isBlank(termId)) {
return getTermAsQualifier(termId, false);
}
public Qualifier getTermAsQualifier(final String termId, boolean strict) {
final VocabularyTerm term = getTerm(termId);
if (Objects.nonNull(term)) {
return OafMapperUtils.qualifier(term.getId(), term.getName(), getId(), getName());
} else if (Objects.isNull(term) && strict) {
return OafMapperUtils.unknown(getId(), getName());
} else if (termExists(termId)) {
final VocabularyTerm t = getTerm(termId);
return OafMapperUtils.qualifier(t.getId(), t.getName(), getId(), getName());
} else {
return OafMapperUtils.qualifier(termId, termId, getId(), getName());
}
}
public Qualifier getSynonymAsQualifier(final String syn) {
return getSynonymAsQualifier(syn, false);
}
public Qualifier getSynonymAsQualifier(final String syn, boolean strict) {
return Optional
.ofNullable(getTermBySynonym(syn))
.map(term -> getTermAsQualifier(term.getId()))
.map(term -> getTermAsQualifier(term.getId(), strict))
.orElse(null);
}
public Qualifier lookup(String id) {
return lookup(id, false);
}
public Qualifier lookup(String id, boolean strict) {
return Optional
.ofNullable(getSynonymAsQualifier(id))
.orElse(getTermAsQualifier(id));
.ofNullable(getSynonymAsQualifier(id, strict))
.orElse(getTermAsQualifier(id, strict));
}
}

2
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
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@ -333,7 +333,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) {
i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY);
}
if (Objects.isNull(i.getRefereed())) {
if (Objects.isNull(i.getRefereed()) || StringUtils.isBlank(i.getRefereed().getClassid())) {
i.setRefereed(qualifier("0000", "Unknown", ModelConstants.DNET_REVIEW_LEVELS));
}
if (Objects.nonNull(i.getDateofacceptance())) {

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java
View File

@ -42,7 +42,7 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
vocabularies.find(vocabularyId).ifPresent(vocabulary -> {
if (ModelConstants.DNET_SUBJECT_KEYWORD.equalsIgnoreCase(subject.getQualifier().getClassid())) {
Qualifier newValue = vocabulary.lookup(subject.getValue());
Qualifier newValue = vocabulary.lookup(subject.getValue(), true);
if (!ModelConstants.UNKNOWN.equals(newValue.getClassid())) {
subject.setValue(newValue.getClassid());
subject.getQualifier().setClassid(vocabularyId);

44
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java
View File

@ -13,6 +13,7 @@ import java.util.stream.Stream;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
@ -105,6 +106,7 @@ public class CleanCfHbSparkJob {
resolved
.joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId")))
.map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class))
.filter((FilterFunction<IdCfHbMapping>) m -> Objects.nonNull(m.getMasterId()))
.write()
.mode(SaveMode.Overwrite)
.json(resolvedPath);
@ -134,22 +136,50 @@ public class CleanCfHbSparkJob {
private static MapFunction<Tuple2<IdCfHbMapping, MasterDuplicate>, IdCfHbMapping> asIdCfHbMapping() {
return t -> {
t._1().setMasterId(t._2().getMasterId());
t._1().setMasterName(t._2().getMasterName());
return t._1();
final IdCfHbMapping mapping = t._1();
Optional
.ofNullable(t._2())
.ifPresent(t2 -> {
mapping.setMasterId(t2.getMasterId());
mapping.setMasterName(t2.getMasterName());
});
return mapping;
};
}
private static <T extends Result> FlatMapFunction<T, IdCfHbMapping> flattenCfHbFn() {
return r -> Stream
.concat(
r.getCollectedfrom().stream().map(KeyValue::getKey),
Optional
.ofNullable(r.getCollectedfrom())
.map(cf -> cf.stream().map(KeyValue::getKey))
.orElse(Stream.empty()),
Stream
.concat(
r.getInstance().stream().map(Instance::getHostedby).map(KeyValue::getKey),
r.getInstance().stream().map(Instance::getCollectedfrom).map(KeyValue::getKey)))
Optional
.ofNullable(r.getInstance())
.map(
instances -> instances
.stream()
.map(i -> Optional.ofNullable(i.getHostedby()).map(KeyValue::getKey).orElse("")))
.orElse(Stream.empty())
.filter(StringUtils::isNotBlank),
Optional
.ofNullable(r.getInstance())
.map(
instances -> instances
.stream()
.map(
i -> Optional
.ofNullable(i.getCollectedfrom())
.map(KeyValue::getKey)
.orElse("")))
.orElse(Stream.empty())
.filter(StringUtils::isNotBlank)))
.distinct()
.map(s -> asIdCfHbMapping(r.getId(), s))
.filter(StringUtils::isNotBlank)
.map(cfHb -> asIdCfHbMapping(r.getId(), cfHb))
.iterator();
}

44
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java
View File

@ -4,9 +4,12 @@ package eu.dnetlib.dhp.oa.graph.clean.country;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import javax.swing.text.html.Option;
@ -30,6 +33,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob;
import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
@ -110,8 +114,8 @@ public class CleanCountrySparkJob implements Serializable {
return r;
}
if (r
.getPid()
List<StructuredProperty> ids = getPidsAndAltIds(r).collect(Collectors.toList());
if (ids
.stream()
.anyMatch(
p -> p
@ -148,6 +152,42 @@ public class CleanCountrySparkJob implements Serializable {
.json(inputPath);
}
private static <T extends Result> Stream<StructuredProperty> getPidsAndAltIds(T r) {
final Stream<StructuredProperty> resultPids = Optional
.ofNullable(r.getPid())
.map(Collection::stream)
.orElse(Stream.empty());
final Stream<StructuredProperty> instancePids = Optional
.ofNullable(r.getInstance())
.map(
instance -> instance
.stream()
.flatMap(
i -> Optional
.ofNullable(i.getPid())
.map(Collection::stream)
.orElse(Stream.empty())))
.orElse(Stream.empty());
final Stream<StructuredProperty> instanceAltIds = Optional
.ofNullable(r.getInstance())
.map(
instance -> instance
.stream()
.flatMap(
i -> Optional
.ofNullable(i.getAlternateIdentifier())
.map(Collection::stream)
.orElse(Stream.empty())))
.orElse(Stream.empty());
return Stream
.concat(
Stream.concat(resultPids, instancePids),
instanceAltIds);
}
private static boolean pidInParam(String value, String[] verifyParam) {
for (String s : verifyParam)
if (value.startsWith(s))

8
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java
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@ -82,10 +82,10 @@ public class CleanContextTest {
CleanContextSparkJob.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--inputPath", workingDir.toString() + "/publication",
"-graphTableClassName", Publication.class.getCanonicalName(),
"-workingPath", workingDir.toString() + "/working",
"-contextId", "sobigdata",
"-verifyParam", "gCube "
"--graphTableClassName", Publication.class.getCanonicalName(),
"--workingDir", workingDir.toString() + "/working",
"--contextId", "sobigdata",
"--verifyParam", "gCube "
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());

12
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java
View File

@ -84,12 +84,12 @@ public class CleanCountryTest {
CleanCountrySparkJob.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--inputPath", workingDir.toString() + "/publication",
"-graphTableClassName", Publication.class.getCanonicalName(),
"-workingPath", workingDir.toString() + "/working",
"-country", "NL",
"-verifyParam", "10.17632",
"-collectedfrom", "NARCIS",
"-hostedBy", getClass()
"--graphTableClassName", Publication.class.getCanonicalName(),
"--workingDir", workingDir.toString() + "/working",
"--country", "NL",
"--verifyParam", "10.17632",
"--collectedfrom", "NARCIS",
"--hostedBy", getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")
.getPath()
});

24
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java
View File

@ -7,6 +7,7 @@ import static org.mockito.Mockito.lenient;
import java.io.IOException;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream;
@ -278,20 +279,25 @@ public class GraphCleaningFunctionsTest {
s -> "0102 computer and information sciences".equals(s.getValue()) &
ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid())));
List<Subject> s1 = p_cleaned
.getSubject()
.stream()
.filter(s -> s.getValue().equals("In Situ Hybridization"))
.collect(Collectors.toList());
assertNotNull(s1);
assertEquals(1, s1.size());
assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get(0).getQualifier().getClassid());
assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get(0).getQualifier().getClassname());
verify_keyword(p_cleaned, "In Situ Hybridization");
verify_keyword(p_cleaned, "Avicennia");
// TODO add more assertions to verity the cleaned values
System.out.println(MAPPER.writeValueAsString(p_cleaned));
}
private static void verify_keyword(Publication p_cleaned, String subject) {
Optional<Subject> s1 = p_cleaned
.getSubject()
.stream()
.filter(s -> s.getValue().equals(subject))
.findFirst();
assertTrue(s1.isPresent());
assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassid());
assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassname());
}
private Stream<Qualifier> getAuthorPidTypes(Result pub) {
return pub
.getAuthor()

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java
View File

@ -143,7 +143,7 @@ public class CleanCfHbSparkJobTest {
"--outputPath", outputPath,
"--resolvedPath", resolvedPath + "/dataset",
"--graphTableClassName", Dataset.class.getCanonicalName(),
"--datasourceMasterDuplicate", dsMasterDuplicatePath
"--masterDuplicatePath", dsMasterDuplicatePath
});
assertTrue(Files.exists(Paths.get(graphOutputPath, "dataset")));

21
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -26,6 +26,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
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.GraphCleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -238,7 +239,11 @@ class MappersTest {
assertNotNull(i.getAccessright());
assertEquals("OPEN", i.getAccessright().getClassid());
});
assertEquals("UNKNOWN", p.getInstance().get(0).getRefereed().getClassid());
Publication p_cleaned = cleanup(p, vocs);
assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid());
assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname());
assertNotNull(p.getInstance().get(0).getPid());
assertEquals(2, p.getInstance().get(0).getPid().size());
@ -453,7 +458,10 @@ class MappersTest {
assertNotNull(i.getAccessright());
assertEquals("OPEN", i.getAccessright().getClassid());
});
assertEquals("UNKNOWN", p.getInstance().get(0).getRefereed().getClassid());
Publication p_cleaned = cleanup(p, vocs);
assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid());
assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname());
}
@Test
@ -570,7 +578,9 @@ class MappersTest {
assertTrue(i.getUrl().contains("http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT02321059"));
assertTrue(i.getUrl().contains("https://clinicaltrials.gov/ct2/show/NCT02321059"));
assertEquals("UNKNOWN", i.getRefereed().getClassid());
Dataset d_cleaned = cleanup(d, vocs);
assertEquals("0000", d_cleaned.getInstance().get(0).getRefereed().getClassid());
assertEquals("Unknown", d_cleaned.getInstance().get(0).getRefereed().getClassname());
}
@Test
@ -871,7 +881,10 @@ class MappersTest {
assertNotNull(i.getAccessright());
assertEquals("UNKNOWN", i.getAccessright().getClassid());
});
assertEquals("UNKNOWN", p.getInstance().get(0).getRefereed().getClassid());
Dataset p_cleaned = cleanup(p, vocs);
assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid());
assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname());
}
@Test

15
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json
View File

@ -907,24 +907,23 @@
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"classid": "sysimport:actionset",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
"classid": "FOS",
"classname": "Fields of Science and Technology classification",
"schemeid": "dnet:subject_classification_typologies",
"schemename": "dnet:subject_classification_typologies"
},
"value": "doped silicon"
"value": "Avicennia"
},
{
"dataInfo": {