dimitris.pierrakos
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dnet-hadoop
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Merge branch 'beta' into hierarchical_orgs_relations

This commit is contained in:
Claudio Atzori 2022-02-17 10:30:04 +01:00
parent 3a4d925386 3aa2020b24
commit 89c7313fc5
326 changed files with 20960 additions and 13199 deletions
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4
.gitignore vendored
View File

@ -3,8 +3,6 @@
*.iws
*.ipr
*.iml
*.ipr
*.iws
*~
.vscode
.metals
@ -27,4 +25,4 @@ spark-warehouse
/**/job-override.properties
/**/*.log
/**/.factorypath
/**/.scalafmt.conf

14
dhp-build/dhp-code-style/pom.xml
View File

@ -22,9 +22,20 @@
<id>dnet45-releases</id>
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
</repository>
<site>
<id>DHPSite</id>
<url>${dhp.site.stage.path}/dhp-build/dhp-code-style</url>
</site>
</distributionManagement>
<build>
<extensions>
<extension>
<groupId>org.apache.maven.wagon</groupId>
<artifactId>wagon-ssh</artifactId>
<version>2.10</version>
</extension>
</extensions>
<pluginManagement>
<plugins>
<plugin>
@ -35,7 +46,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.7.1</version>
<version>3.9.1</version>
</plugin>
</plugins>
</pluginManagement>
@ -43,6 +54,7 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<dhp.site.stage.path>sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop</dhp.site.stage.path>
</properties>
</project>

21
dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf Normal file
View File

@ -0,0 +1,21 @@
style = defaultWithAlign
align.openParenCallSite = false
align.openParenDefnSite = false
align.tokens = [{code = "->"}, {code = "<-"}, {code = "=>", owner = "Case"}]
continuationIndent.callSite = 2
continuationIndent.defnSite = 2
danglingParentheses = true
indentOperator = spray
maxColumn = 120
newlines.alwaysBeforeTopLevelStatements = true
project.excludeFilters = [".*\\.sbt"]
rewrite.rules = [AvoidInfix]
rewrite.rules = [ExpandImportSelectors]
rewrite.rules = [RedundantBraces]
rewrite.rules = [RedundantParens]
rewrite.rules = [SortImports]
rewrite.rules = [SortModifiers]
rewrite.rules = [PreferCurlyFors]
spaces.inImportCurlyBraces = false
unindentTopLevelOperators = true

21
dhp-build/dhp-code-style/src/site/site.xml Normal file
View File

@ -0,0 +1,21 @@
<?xml version="1.0" encoding="ISO-8859-1"?>
<project xmlns="http://maven.apache.org/DECORATION/1.8.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/DECORATION/1.8.0 https://maven.apache.org/xsd/decoration-1.8.0.xsd"
name="DHP-Aggregation">
<skin>
<groupId>org.apache.maven.skins</groupId>
<artifactId>maven-fluido-skin</artifactId>
<version>1.8</version>
</skin>
<poweredBy>
<logo name="OpenAIRE Research Graph" href="https://graph.openaire.eu/"
img="https://graph.openaire.eu/assets/common-assets/logo-large-graph.png"/>
</poweredBy>
<body>
<links>
<item name="Code" href="https://code-repo.d4science.org/" />
</links>
<menu ref="modules" />
<menu ref="reports"/>
</body>
</project>

11
dhp-build/pom.xml
View File

@ -10,6 +10,9 @@
<packaging>pom</packaging>
<description>This module is a container for the build tools used in dnet-hadoop</description>
<properties>
<maven.javadoc.skip>true</maven.javadoc.skip>
</properties>
<modules>
<module>dhp-code-style</module>
@ -17,4 +20,12 @@
<module>dhp-build-properties-maven-plugin</module>
</modules>
<distributionManagement>
<site>
<id>DHPSite</id>
<url>${dhp.site.stage.path}/dhp-build/</url>
</site>
</distributionManagement>
</project>

22
dhp-build/src/site/site.xml Normal file
View File

@ -0,0 +1,22 @@
<?xml version="1.0" encoding="ISO-8859-1"?>
<project xmlns="http://maven.apache.org/DECORATION/1.8.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/DECORATION/1.8.0 https://maven.apache.org/xsd/decoration-1.8.0.xsd"
name="DHP-Aggregation">
<skin>
<groupId>org.apache.maven.skins</groupId>
<artifactId>maven-fluido-skin</artifactId>
<version>1.8</version>
</skin>
<poweredBy>
<logo name="OpenAIRE Research Graph" href="https://graph.openaire.eu/"
img="https://graph.openaire.eu/assets/common-assets/logo-large-graph.png"/>
</poweredBy>
<body>
<links>
<item name="Code" href="https://code-repo.d4science.org/" />
</links>
<menu ref="modules" />
<menu ref="reports"/>
</body>
</project>

44
dhp-common/pom.xml
View File

@ -13,7 +13,51 @@
<artifactId>dhp-common</artifactId>
<packaging>jar</packaging>
<distributionManagement>
<site>
<id>DHPSite</id>
<url>${dhp.site.stage.path}/dhp-common</url>
</site>
</distributionManagement>
<description>This module contains common utilities meant to be used across the dnet-hadoop submodules</description>
<build>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>${net.alchim31.maven.version}</version>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>initialize</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
<execution>
<id>scala-doc</id>
<phase>process-resources</phase> <!-- or wherever -->
<goals>
<goal>doc</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>

413
dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java
View File

@ -1,413 +0,0 @@
package eu.dnetlib.dhp.common;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.*;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class GraphResultMapper implements Serializable {
public static <E extends eu.dnetlib.dhp.schema.oaf.OafEntity> Result map(
E in) {
CommunityResult out = new CommunityResult();
eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in;
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> ort = Optional.ofNullable(input.getResulttype());
if (ort.isPresent()) {
switch (ort.get().getClassid()) {
case "publication":
Optional<Journal> journal = Optional
.ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal());
if (journal.isPresent()) {
Journal j = journal.get();
Container c = new Container();
c.setConferencedate(j.getConferencedate());
c.setConferenceplace(j.getConferenceplace());
c.setEdition(j.getEdition());
c.setEp(j.getEp());
c.setIss(j.getIss());
c.setIssnLinking(j.getIssnLinking());
c.setIssnOnline(j.getIssnOnline());
c.setIssnPrinted(j.getIssnPrinted());
c.setName(j.getName());
c.setSp(j.getSp());
c.setVol(j.getVol());
out.setContainer(c);
out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname());
}
break;
case "dataset":
eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input;
Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue()));
Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue()));
out
.setGeolocation(
Optional
.ofNullable(id.getGeolocation())
.map(
igl -> igl
.stream()
.filter(Objects::nonNull)
.map(gli -> {
GeoLocation gl = new GeoLocation();
gl.setBox(gli.getBox());
gl.setPlace(gli.getPlace());
gl.setPoint(gli.getPoint());
return gl;
})
.collect(Collectors.toList()))
.orElse(null));
out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname());
break;
case "software":
eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input;
Optional
.ofNullable(is.getCodeRepositoryUrl())
.ifPresent(value -> out.setCodeRepositoryUrl(value.getValue()));
Optional
.ofNullable(is.getDocumentationUrl())
.ifPresent(
value -> out
.setDocumentationUrl(
value
.stream()
.map(Field::getValue)
.collect(Collectors.toList())));
Optional
.ofNullable(is.getProgrammingLanguage())
.ifPresent(value -> out.setProgrammingLanguage(value.getClassid()));
out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname());
break;
case "other":
eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input;
out
.setContactgroup(
Optional
.ofNullable(ir.getContactgroup())
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out
.setContactperson(
Optional
.ofNullable(ir.getContactperson())
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out
.setTool(
Optional
.ofNullable(ir.getTool())
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname());
break;
}
Optional
.ofNullable(input.getAuthor())
.ifPresent(
ats -> out.setAuthor(ats.stream().map(GraphResultMapper::getAuthor).collect(Collectors.toList())));
// I do not map Access Right UNKNOWN or OTHER
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oar = Optional.ofNullable(input.getBestaccessright());
if (oar.isPresent()) {
if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) {
String code = Constants.accessRightsCoarMap.get(oar.get().getClassid());
out
.setBestaccessright(
AccessRight
.newInstance(
code,
Constants.coarCodeLabelMap.get(code),
Constants.COAR_ACCESS_RIGHT_SCHEMA));
}
}
final List<String> contributorList = new ArrayList<>();
Optional
.ofNullable(input.getContributor())
.ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue())));
out.setContributor(contributorList);
Optional
.ofNullable(input.getCountry())
.ifPresent(
value -> out
.setCountry(
value
.stream()
.map(
c -> {
if (c.getClassid().equals((ModelConstants.UNKNOWN))) {
return null;
}
Country country = new Country();
country.setCode(c.getClassid());
country.setLabel(c.getClassname());
Optional
.ofNullable(c.getDataInfo())
.ifPresent(
provenance -> country
.setProvenance(
Provenance
.newInstance(
provenance
.getProvenanceaction()
.getClassname(),
c.getDataInfo().getTrust())));
return country;
})
.filter(Objects::nonNull)
.collect(Collectors.toList())));
final List<String> coverageList = new ArrayList<>();
Optional
.ofNullable(input.getCoverage())
.ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue())));
out.setCoverage(coverageList);
out.setDateofcollection(input.getDateofcollection());
final List<String> descriptionList = new ArrayList<>();
Optional
.ofNullable(input.getDescription())
.ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue())));
out.setDescription(descriptionList);
Optional<Field<String>> oStr = Optional.ofNullable(input.getEmbargoenddate());
if (oStr.isPresent()) {
out.setEmbargoenddate(oStr.get().getValue());
}
final List<String> formatList = new ArrayList<>();
Optional
.ofNullable(input.getFormat())
.ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue())));
out.setFormat(formatList);
out.setId(input.getId());
out.setOriginalId(input.getOriginalId());
Optional<List<eu.dnetlib.dhp.schema.oaf.Instance>> oInst = Optional
.ofNullable(input.getInstance());
if (oInst.isPresent()) {
out
.setInstance(
oInst.get().stream().map(GraphResultMapper::getInstance).collect(Collectors.toList()));
}
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oL = Optional.ofNullable(input.getLanguage());
if (oL.isPresent()) {
eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get();
out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname()));
}
Optional<Long> oLong = Optional.ofNullable(input.getLastupdatetimestamp());
if (oLong.isPresent()) {
out.setLastupdatetimestamp(oLong.get());
}
Optional<List<StructuredProperty>> otitle = Optional.ofNullable(input.getTitle());
if (otitle.isPresent()) {
List<StructuredProperty> iTitle = otitle
.get()
.stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title"))
.collect(Collectors.toList());
if (!iTitle.isEmpty()) {
out.setMaintitle(iTitle.get(0).getValue());
}
iTitle = otitle
.get()
.stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
.collect(Collectors.toList());
if (!iTitle.isEmpty()) {
out.setSubtitle(iTitle.get(0).getValue());
}
}
List<ControlledField> pids = new ArrayList<>();
Optional
.ofNullable(input.getPid())
.ifPresent(
value -> value
.stream()
.forEach(
p -> pids
.add(
ControlledField
.newInstance(p.getQualifier().getClassid(), p.getValue()))));
out.setPid(pids);
oStr = Optional.ofNullable(input.getDateofacceptance());
if (oStr.isPresent()) {
out.setPublicationdate(oStr.get().getValue());
}
oStr = Optional.ofNullable(input.getPublisher());
if (oStr.isPresent()) {
out.setPublisher(oStr.get().getValue());
}
List<String> sourceList = new ArrayList<>();
Optional
.ofNullable(input.getSource())
.ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue())));
// out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList()));
List<Subject> subjectList = new ArrayList<>();
Optional
.ofNullable(input.getSubject())
.ifPresent(
value -> value
.forEach(s -> subjectList.add(getSubject(s))));
out.setSubjects(subjectList);
out.setType(input.getResulttype().getClassid());
}
out
.setCollectedfrom(
input
.getCollectedfrom()
.stream()
.map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue()))
.collect(Collectors.toList()));
return out;
}
private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) {
CommunityInstance instance = new CommunityInstance();
setCommonValue(i, instance);
instance
.setCollectedfrom(
KeyValue
.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
instance
.setHostedby(
KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue()));
return instance;
}
private static <I extends Instance> void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) {
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> opAr = Optional
.ofNullable(i.getAccessright());
if (opAr.isPresent()) {
if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) {
String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid());
instance
.setAccessright(
AccessRight
.newInstance(
code,
Constants.coarCodeLabelMap.get(code),
Constants.COAR_ACCESS_RIGHT_SCHEMA));
}
}
Optional
.ofNullable(i.getLicense())
.ifPresent(value -> instance.setLicense(value.getValue()));
Optional
.ofNullable(i.getDateofacceptance())
.ifPresent(value -> instance.setPublicationdate(value.getValue()));
Optional
.ofNullable(i.getRefereed())
.ifPresent(value -> instance.setRefereed(value.getClassname()));
Optional
.ofNullable(i.getInstancetype())
.ifPresent(value -> instance.setType(value.getClassname()));
Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value));
}
private static Subject getSubject(StructuredProperty s) {
Subject subject = new Subject();
subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue()));
Optional<DataInfo> di = Optional.ofNullable(s.getDataInfo());
if (di.isPresent()) {
Provenance p = new Provenance();
p.setProvenance(di.get().getProvenanceaction().getClassname());
p.setTrust(di.get().getTrust());
subject.setProvenance(p);
}
return subject;
}
private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) {
Author a = new Author();
a.setFullname(oa.getFullname());
a.setName(oa.getName());
a.setSurname(oa.getSurname());
a.setRank(oa.getRank());
Optional<List<StructuredProperty>> oPids = Optional
.ofNullable(oa.getPid());
if (oPids.isPresent()) {
Pid pid = getOrcid(oPids.get());
if (pid != null) {
a.setPid(pid);
}
}
return a;
}
private static Pid getOrcid(List<StructuredProperty> p) {
for (StructuredProperty pid : p) {
if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) {
Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo());
if (di.isPresent()) {
return Pid
.newInstance(
ControlledField
.newInstance(
pid.getQualifier().getClassid(),
pid.getValue()),
Provenance
.newInstance(
di.get().getProvenanceaction().getClassname(),
di.get().getTrust()));
} else {
return Pid
.newInstance(
ControlledField
.newInstance(
pid.getQualifier().getClassid(),
pid.getValue())
);
}
}
}
return null;
}
}

8
dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java
View File

@ -57,9 +57,17 @@ public class VocabularyGroup implements Serializable {
final String syn = arr[2].trim();
vocs.addSynonyms(vocId, termId, syn);
}
}
// add the term names as synonyms
vocs.vocs.values().forEach(voc -> {
voc.getTerms().values().forEach(term -> {
voc.addSynonym(term.getName().toLowerCase(), term.getId());
});
});
return vocs;
}

4
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DispatchEntitiesSparkJob.java → dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/DispatchEntitiesSparkJob.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.dedup;
package eu.dnetlib.dhp.oa.merge;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
@ -38,7 +38,7 @@ public class DispatchEntitiesSparkJob {
.requireNonNull(
DispatchEntitiesSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/dispatch_entities_parameters.json")));
"/eu/dnetlib/dhp/oa/merge/dispatch_entities_parameters.json")));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);

4
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/GroupEntitiesSparkJob.java → dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.dedup;
package eu.dnetlib.dhp.oa.merge;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;
@ -53,7 +53,7 @@ public class GroupEntitiesSparkJob {
.toString(
GroupEntitiesSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/group_graph_entities_parameters.json"));
"/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);

61
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
View File

@ -16,6 +16,8 @@ import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.common.vocabulary.Vocabulary;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
@ -86,6 +88,22 @@ public class GraphCleaningFunctions extends CleaningFunctions {
}
public static <T extends Oaf> boolean filter(T value) {
if (Boolean.TRUE
.equals(
Optional
.ofNullable(value)
.map(
o -> Optional
.ofNullable(o.getDataInfo())
.map(
d -> Optional
.ofNullable(d.getInvisible())
.orElse(true))
.orElse(true))
.orElse(true))) {
return true;
}
if (value instanceof Datasource) {
// nothing to evaluate here
} else if (value instanceof Project) {
@ -115,7 +133,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
return true;
}
public static <T extends Oaf> T cleanup(T value) {
public static <T extends Oaf> T cleanup(T value, VocabularyGroup vocs) {
if (value instanceof Datasource) {
// nothing to clean here
} else if (value instanceof Project) {
@ -212,6 +230,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList()));
}
if (Objects.nonNull(r.getFormat())) {
r
.setFormat(
r
.getFormat()
.stream()
.map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList()));
}
if (Objects.nonNull(r.getDescription())) {
r
.setDescription(
@ -234,6 +261,38 @@ public class GraphCleaningFunctions extends CleaningFunctions {
if (Objects.nonNull(r.getInstance())) {
for (Instance i : r.getInstance()) {
if (!vocs.termExists(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getClassid())) {
if (r instanceof Publication) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0038", "Other literature type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
} else if (r instanceof Dataset) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0039", "Other dataset type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
} else if (r instanceof Software) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0040", "Other software type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
} else if (r instanceof OtherResearchProduct) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0020", "Other ORP type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
}
}
if (Objects.nonNull(i.getPid())) {
i.setPid(processPidCleaning(i.getPid()));
}

23
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
View File

@ -47,6 +47,17 @@ public class OafMapperUtils {
}
public static Result mergeResults(Result left, Result right) {
final boolean leftFromDelegatedAuthority = isFromDelegatedAuthority(left);
final boolean rightFromDelegatedAuthority = isFromDelegatedAuthority(right);
if (leftFromDelegatedAuthority && !rightFromDelegatedAuthority) {
return left;
}
if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
return right;
}
if (new ResultTypeComparator().compare(left, right) < 0) {
left.mergeFrom(right);
return left;
@ -56,6 +67,18 @@ public class OafMapperUtils {
}
}
private static boolean isFromDelegatedAuthority(Result r) {
return Optional
.ofNullable(r.getInstance())
.map(
instance -> instance
.stream()
.filter(i -> Objects.nonNull(i.getCollectedfrom()))
.map(i -> i.getCollectedfrom().getKey())
.anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId)))
.orElse(false);
}
public static KeyValue keyValue(final String k, final String v) {
final KeyValue kv = new KeyValue();
kv.setKey(k);

0
dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/dispatch_entities_parameters.json → dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/dispatch_entities_parameters.json
View File

0
dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/group_graph_entities_parameters.json → dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json
View File

73
dhp-common/src/main/scala/eu/dnetlib/dhp/application/SparkScalaApplication.scala Normal file
View File

@ -0,0 +1,73 @@
package eu.dnetlib.dhp.application
import scala.io.Source
/** This is the main Interface SparkApplication
* where all the Spark Scala class should inherit
*/
trait SparkScalaApplication {
/** This is the path in the classpath of the json
* describes all the argument needed to run
*/
val propertyPath: String
/** Utility to parse the arguments using the
* property json in the classpath identified from
* the variable propertyPath
*
* @param args the list of arguments
*/
def parseArguments(args: Array[String]): ArgumentApplicationParser = {
val parser = new ArgumentApplicationParser(
Source.fromInputStream(getClass.getResourceAsStream(propertyPath)).mkString
)
parser.parseArgument(args)
parser
}
/** Here all the spark applications runs this method
* where the whole logic of the spark node is defined
*/
def run(): Unit
}
import org.apache.spark.SparkConf
import org.apache.spark.sql.SparkSession
import org.slf4j.Logger
abstract class AbstractScalaApplication(
val propertyPath: String,
val args: Array[String],
log: Logger
) extends SparkScalaApplication {
var parser: ArgumentApplicationParser = null
var spark: SparkSession = null
def initialize(): SparkScalaApplication = {
parser = parseArguments(args)
spark = createSparkSession()
this
}
/** Utility for creating a spark session starting from parser
*
* @return a spark Session
*/
private def createSparkSession(): SparkSession = {
require(parser != null)
val conf: SparkConf = new SparkConf()
val master = parser.get("master")
log.info(s"Creating Spark session: Master: $master")
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(master)
.getOrCreate()
}
}

442
dhp-common/src/main/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala Normal file
View File

@ -0,0 +1,442 @@
package eu.dnetlib.dhp.sx.graph.scholix
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.sx.scholix._
import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, Typology}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql.{Encoder, Encoders}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import scala.collection.JavaConverters._
import scala.io.Source
object ScholixUtils extends Serializable {
val DNET_IDENTIFIER_SCHEMA: String = "DNET Identifier"
val DATE_RELATION_KEY: String = "RelationDate"
case class RelationVocabulary(original: String, inverse: String) {}
case class RelatedEntities(id: String, relatedDataset: Long, relatedPublication: Long) {}
val relations: Map[String, RelationVocabulary] = {
val input = Source
.fromInputStream(
getClass.getResourceAsStream("/eu/dnetlib/scholexplorer/relation/relations.json")
)
.mkString
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
json.extract[Map[String, RelationVocabulary]]
}
def extractRelationDate(relation: Relation): String = {
if (relation.getProperties == null || !relation.getProperties.isEmpty)
null
else {
val date = relation.getProperties.asScala
.find(p => DATE_RELATION_KEY.equalsIgnoreCase(p.getKey))
.map(p => p.getValue)
if (date.isDefined)
date.get
else
null
}
}
def extractRelationDate(summary: ScholixSummary): String = {
if (summary.getDate == null || summary.getDate.isEmpty)
null
else {
summary.getDate.get(0)
}
}
def inverseRelationShip(rel: ScholixRelationship): ScholixRelationship = {
new ScholixRelationship(rel.getInverse, rel.getSchema, rel.getName)
}
def generateScholixResourceFromResult(r: Result): ScholixResource = {
generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
}
val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] =
new Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] with Serializable {
override def zero: RelatedEntities = null
override def reduce(b: RelatedEntities, a: (String, String, Long)): RelatedEntities = {
val relatedDataset = if ("dataset".equalsIgnoreCase(a._2)) a._3 else 0
val relatedPublication = if ("publication".equalsIgnoreCase(a._2)) a._3 else 0
if (b == null)
RelatedEntities(a._1, relatedDataset, relatedPublication)
else
RelatedEntities(
a._1,
b.relatedDataset + relatedDataset,
b.relatedPublication + relatedPublication
)
}
override def merge(b1: RelatedEntities, b2: RelatedEntities): RelatedEntities = {
if (b1 != null && b2 != null)
RelatedEntities(
b1.id,
b1.relatedDataset + b2.relatedDataset,
b1.relatedPublication + b2.relatedPublication
)
else if (b1 != null)
b1
else
b2
}
override def finish(reduction: RelatedEntities): RelatedEntities = reduction
override def bufferEncoder: Encoder[RelatedEntities] = Encoders.bean(classOf[RelatedEntities])
override def outputEncoder: Encoder[RelatedEntities] = Encoders.bean(classOf[RelatedEntities])
}
val scholixAggregator: Aggregator[(String, Scholix), Scholix, Scholix] =
new Aggregator[(String, Scholix), Scholix, Scholix] with Serializable {
override def zero: Scholix = null
def scholix_complete(s: Scholix): Boolean = {
if (s == null || s.getIdentifier == null) {
false
} else if (s.getSource == null || s.getTarget == null) {
false
} else if (s.getLinkprovider == null || s.getLinkprovider.isEmpty)
false
else
true
}
override def reduce(b: Scholix, a: (String, Scholix)): Scholix = {
if (scholix_complete(b)) b else a._2
}
override def merge(b1: Scholix, b2: Scholix): Scholix = {
if (scholix_complete(b1)) b1 else b2
}
override def finish(reduction: Scholix): Scholix = reduction
override def bufferEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
override def outputEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
}
def createInverseScholixRelation(scholix: Scholix): Scholix = {
val s = new Scholix
s.setPublicationDate(scholix.getPublicationDate)
s.setPublisher(scholix.getPublisher)
s.setLinkprovider(scholix.getLinkprovider)
s.setRelationship(inverseRelationShip(scholix.getRelationship))
s.setSource(scholix.getTarget)
s.setTarget(scholix.getSource)
s.setIdentifier(
DHPUtils.md5(
s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}"
)
)
s
}
def extractCollectedFrom(summary: ScholixResource): List[ScholixEntityId] = {
if (summary.getCollectedFrom != null && !summary.getCollectedFrom.isEmpty) {
val l: List[ScholixEntityId] = summary.getCollectedFrom.asScala.map { d =>
new ScholixEntityId(d.getProvider.getName, d.getProvider.getIdentifiers)
}(collection.breakOut)
l
} else List()
}
def extractCollectedFrom(summary: ScholixSummary): List[ScholixEntityId] = {
if (summary.getDatasources != null && !summary.getDatasources.isEmpty) {
val l: List[ScholixEntityId] = summary.getDatasources.asScala.map { d =>
new ScholixEntityId(
d.getDatasourceName,
List(new ScholixIdentifier(d.getDatasourceId, "DNET Identifier", null)).asJava
)
}(collection.breakOut)
l
} else List()
}
def extractCollectedFrom(relation: Relation): List[ScholixEntityId] = {
if (relation.getCollectedfrom != null && !relation.getCollectedfrom.isEmpty) {
val l: List[ScholixEntityId] = relation.getCollectedfrom.asScala.map { c =>
new ScholixEntityId(
c.getValue,
List(new ScholixIdentifier(c.getKey, DNET_IDENTIFIER_SCHEMA, null)).asJava
)
}.toList
l
} else List()
}
def generateCompleteScholix(scholix: Scholix, target: ScholixSummary): Scholix = {
val s = new Scholix
s.setPublicationDate(scholix.getPublicationDate)
s.setPublisher(scholix.getPublisher)
s.setLinkprovider(scholix.getLinkprovider)
s.setRelationship(scholix.getRelationship)
s.setSource(scholix.getSource)
s.setTarget(generateScholixResourceFromSummary(target))
s.setIdentifier(
DHPUtils.md5(
s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}"
)
)
s
}
def generateCompleteScholix(scholix: Scholix, target: ScholixResource): Scholix = {
val s = new Scholix
s.setPublicationDate(scholix.getPublicationDate)
s.setPublisher(scholix.getPublisher)
s.setLinkprovider(scholix.getLinkprovider)
s.setRelationship(scholix.getRelationship)
s.setSource(scholix.getSource)
s.setTarget(target)
s.setIdentifier(
DHPUtils.md5(
s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}"
)
)
s
}
def generateScholixResourceFromSummary(summaryObject: ScholixSummary): ScholixResource = {
val r = new ScholixResource
r.setIdentifier(summaryObject.getLocalIdentifier)
r.setDnetIdentifier(summaryObject.getId)
r.setObjectType(summaryObject.getTypology.toString)
r.setObjectSubType(summaryObject.getSubType)
if (summaryObject.getTitle != null && !summaryObject.getTitle.isEmpty)
r.setTitle(summaryObject.getTitle.get(0))
if (summaryObject.getAuthor != null && !summaryObject.getAuthor.isEmpty) {
val l: List[ScholixEntityId] =
summaryObject.getAuthor.asScala.map(a => new ScholixEntityId(a, null)).toList
if (l.nonEmpty)
r.setCreator(l.asJava)
}
if (summaryObject.getDate != null && !summaryObject.getDate.isEmpty)
r.setPublicationDate(summaryObject.getDate.get(0))
if (summaryObject.getPublisher != null && !summaryObject.getPublisher.isEmpty) {
val plist: List[ScholixEntityId] =
summaryObject.getPublisher.asScala.map(p => new ScholixEntityId(p, null)).toList
if (plist.nonEmpty)
r.setPublisher(plist.asJava)
}
if (summaryObject.getDatasources != null && !summaryObject.getDatasources.isEmpty) {
val l: List[ScholixCollectedFrom] = summaryObject.getDatasources.asScala
.map(c =>
new ScholixCollectedFrom(
new ScholixEntityId(
c.getDatasourceName,
List(new ScholixIdentifier(c.getDatasourceId, DNET_IDENTIFIER_SCHEMA, null)).asJava
),
"collected",
"complete"
)
)
.toList
if (l.nonEmpty)
r.setCollectedFrom(l.asJava)
}
r
}
def scholixFromSource(relation: Relation, source: ScholixResource): Scholix = {
if (relation == null || source == null)
return null
val s = new Scholix
var l: List[ScholixEntityId] = extractCollectedFrom(relation)
if (l.isEmpty)
l = extractCollectedFrom(source)
if (l.isEmpty)
return null
s.setLinkprovider(l.asJava)
var d = extractRelationDate(relation)
if (d == null)
d = source.getPublicationDate
s.setPublicationDate(d)
if (source.getPublisher != null && !source.getPublisher.isEmpty) {
s.setPublisher(source.getPublisher)
}
val semanticRelation = relations.getOrElse(relation.getRelClass.toLowerCase, null)
if (semanticRelation == null)
return null
s.setRelationship(
new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse)
)
s.setSource(source)
s
}
def scholixFromSource(relation: Relation, source: ScholixSummary): Scholix = {
if (relation == null || source == null)
return null
val s = new Scholix
var l: List[ScholixEntityId] = extractCollectedFrom(relation)
if (l.isEmpty)
l = extractCollectedFrom(source)
if (l.isEmpty)
return null
s.setLinkprovider(l.asJava)
var d = extractRelationDate(relation)
if (d == null)
d = extractRelationDate(source)
s.setPublicationDate(d)
if (source.getPublisher != null && !source.getPublisher.isEmpty) {
val l: List[ScholixEntityId] = source.getPublisher.asScala
.map { p =>
new ScholixEntityId(p, null)
}(collection.breakOut)
if (l.nonEmpty)
s.setPublisher(l.asJava)
}
val semanticRelation = relations.getOrElse(relation.getRelClass.toLowerCase, null)
if (semanticRelation == null)
return null
s.setRelationship(
new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse)
)
s.setSource(generateScholixResourceFromSummary(source))
s
}
def findURLForPID(
pidValue: List[StructuredProperty],
urls: List[String]
): List[(StructuredProperty, String)] = {
pidValue.map { p =>
val pv = p.getValue
val r = urls.find(u => u.toLowerCase.contains(pv.toLowerCase))
(p, r.orNull)
}
}
def extractTypedIdentifierFromInstance(r: Result): List[ScholixIdentifier] = {
if (r.getInstance() == null || r.getInstance().isEmpty)
return List()
r.getInstance()
.asScala
.filter(i => i.getUrl != null && !i.getUrl.isEmpty)
.filter(i => i.getPid != null && i.getUrl != null)
.flatMap(i => findURLForPID(i.getPid.asScala.toList, i.getUrl.asScala.toList))
.map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2))
.distinct
.toList
}
def resultToSummary(r: Result): ScholixSummary = {
val s = new ScholixSummary
s.setId(r.getId)
if (r.getPid == null || r.getPid.isEmpty)
return null
val persistentIdentifiers: List[ScholixIdentifier] = extractTypedIdentifierFromInstance(r)
if (persistentIdentifiers.isEmpty)
return null
s.setLocalIdentifier(persistentIdentifiers.asJava)
if (r.isInstanceOf[Publication])
s.setTypology(Typology.publication)
else
s.setTypology(Typology.dataset)
s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)
if (r.getTitle != null && r.getTitle.asScala.nonEmpty) {
val titles: List[String] = r.getTitle.asScala.map(t => t.getValue).toList
if (titles.nonEmpty)
s.setTitle(titles.asJava)
else
return null
}
if (r.getAuthor != null && !r.getAuthor.isEmpty) {
val authors: List[String] = r.getAuthor.asScala.map(a => a.getFullname).toList
if (authors.nonEmpty)
s.setAuthor(authors.asJava)
}
if (r.getInstance() != null) {
val dt: List[String] = r
.getInstance()
.asScala
.filter(i => i.getDateofacceptance != null)
.map(i => i.getDateofacceptance.getValue)
.toList
if (dt.nonEmpty)
s.setDate(dt.distinct.asJava)
}
if (r.getDescription != null && !r.getDescription.isEmpty) {
val d = r.getDescription.asScala.find(f => f != null && f.getValue != null)
if (d.isDefined)
s.setDescription(d.get.getValue)
}
if (r.getSubject != null && !r.getSubject.isEmpty) {
val subjects: List[SchemeValue] = r.getSubject.asScala
.map(s => new SchemeValue(s.getQualifier.getClassname, s.getValue))
.toList
if (subjects.nonEmpty)
s.setSubject(subjects.asJava)
}
if (r.getPublisher != null)
s.setPublisher(List(r.getPublisher.getValue).asJava)
if (r.getCollectedfrom != null && !r.getCollectedfrom.isEmpty) {
val cf: List[CollectedFromType] = r.getCollectedfrom.asScala
.map(c => new CollectedFromType(c.getValue, c.getKey, "complete"))
.toList
if (cf.nonEmpty)
s.setDatasources(cf.distinct.asJava)
}
s.setRelatedDatasets(0)
s.setRelatedPublications(0)
s.setRelatedUnknown(0)
s
}
}

18
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
View File

@ -107,7 +107,7 @@ class OafMapperUtilsTest {
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("2006-01-02T15:04:05+0000").get());
assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09-07:00").get());
assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09").get());
assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get());
assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get());
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.3186369").get());
assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000").get());
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.123").get());
@ -185,6 +185,22 @@ class OafMapperUtilsTest {
.getClassid());
}
@Test
void testDelegatedAuthority() throws IOException {
Dataset d1 = read("dataset_2.json", Dataset.class);
Dataset d2 = read("dataset_delegated.json", Dataset.class);
assertEquals(1, d2.getCollectedfrom().size());
assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID));
Result res = OafMapperUtils.mergeResults(d1, d2);
assertEquals(d2, res);
System.out.println(OBJECT_MAPPER.writeValueAsString(res));
}
protected HashSet<String> cfId(List<KeyValue> collectedfrom) {
return collectedfrom.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new));
}

141
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/dataset_2.json
View File

@ -1 +1,140 @@
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g", "resuttype" : { "classid" : "dataset" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e3", "value" : "Repository B"} ]}
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g",
"resuttype": {"classid": "dataset"},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2011.03.013"
},
{
"qualifier": {"classid": "urn"},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {"classid": "scp-number"},
"value": "79953761260"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
}
],
"collectedfrom": [
{
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e3",
"value": "Repository B"
}
],
"instance": [
{
"refereed": {
"classid": "0000",
"classname": "UNKNOWN",
"schemeid": "dnet:review_levels",
"schemename": "dnet:review_levels"
},
"hostedby": {
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
},
"accessright": {
"classid": "OPEN",
"classname": "Open Access",
"schemeid": "dnet:access_modes",
"schemename": "dnet:access_modes"
},
"processingchargecurrency": {
"dataInfo": {
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"deletedbyinference": false,
"inferred": false,
"inferenceprovenance": "",
"invisible": true,
"trust": "0.9"
},
"value": "EUR"
},
"pid": [
{
"dataInfo": {
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"deletedbyinference": false,
"inferred": false,
"inferenceprovenance": "",
"invisible": true,
"trust": "0.9"
},
"qualifier": {
"classid": "doi",
"classname": "Digital Object Identifier",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1371/journal.pone.0085605"
}
],
"distributionlocation": "",
"url": ["https://doi.org/10.1371/journal.pone.0085605"],
"alternateIdentifier": [
{
"dataInfo": {
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"deletedbyinference": false,
"inferred": false,
"inferenceprovenance": "",
"invisible": true,
"trust": "0.9"
},
"qualifier": {
"classid": "pmid",
"classname": "PubMed ID",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "24454899.0"
}
],
"collectedfrom": {
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e3",
"value": "Repository B"
},
"processingchargeamount": {
"dataInfo": {
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"deletedbyinference": false,
"inferred": false,
"inferenceprovenance": "",
"invisible": true,
"trust": "0.9"
},
"value": "1022.02"
},
"instancetype": {
"classid": "0004",
"classname": "Conference object",
"schemeid": "dnet:publication_resource",
"schemename": "dnet:publication_resource"
}
}
]
}

140
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/dataset_delegated.json Normal file
View File

@ -0,0 +1,140 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g",
"resuttype": {"classid": "dataset"},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2011.03.013"
},
{
"qualifier": {"classid": "urn"},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {"classid": "scp-number"},
"value": "79953761260"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
}
],
"collectedfrom": [
{
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
}
],
"instance": [
{
"refereed": {
"classid": "0000",
"classname": "UNKNOWN",
"schemeid": "dnet:review_levels",
"schemename": "dnet:review_levels"
},
"hostedby": {
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
},
"accessright": {
"classid": "OPEN",
"classname": "Open Access",
"schemeid": "dnet:access_modes",
"schemename": "dnet:access_modes"
},
"processingchargecurrency": {
"dataInfo": {
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"deletedbyinference": false,
"inferred": false,
"inferenceprovenance": "",
"invisible": true,
"trust": "0.9"
},
"value": "EUR"
},
"pid": [
{
"dataInfo": {
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"deletedbyinference": false,
"inferred": false,
"inferenceprovenance": "",
"invisible": true,
"trust": "0.9"
},
"qualifier": {
"classid": "doi",
"classname": "Digital Object Identifier",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1371/journal.pone.0085605"
}
],
"distributionlocation": "",
"url": ["https://doi.org/10.1371/journal.pone.0085605"],
"alternateIdentifier": [
{
"dataInfo": {
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"deletedbyinference": false,
"inferred": false,
"inferenceprovenance": "",
"invisible": true,
"trust": "0.9"
},
"qualifier": {
"classid": "pmid",
"classname": "PubMed ID",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "24454899.0"
}
],
"collectedfrom": {
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
},
"processingchargeamount": {
"dataInfo": {
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"deletedbyinference": false,
"inferred": false,
"inferenceprovenance": "",
"invisible": true,
"trust": "0.9"
},
"value": "1022.02"
},
"instancetype": {
"classid": "0004",
"classname": "Conference object",
"schemeid": "dnet:publication_resource",
"schemename": "dnet:publication_resource"
}
}
]
}

45
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/Constants.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
package eu.dnetlib.dhp.actionmanager;
import java.util.Optional;
@ -11,19 +11,29 @@ import org.apache.spark.sql.SparkSession;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
public class Constants {
public static final String DOI = "doi";
public static final String DOI_CLASSNAME = "Digital Object Identifier";
public static final String DEFAULT_DELIMITER = ",";
public static final String UPDATE_DATA_INFO_TYPE = "update";
public static final String UPDATE_SUBJECT_FOS_CLASS_ID = "subject:fos";
public static final String UPDATE_CLASS_NAME = "Inferred by OpenAIRE";
public static final String UPDATE_MEASURE_BIP_CLASS_ID = "measure:bip";
public static final String UPDATE_SUBJECT_SDG_CLASS_ID = "subject:sdg";
public static final String FOS_CLASS_ID = "FOS";
public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification";
public static final String SDG_CLASS_ID = "SDG";
public static final String SDG_CLASS_NAME = "Sustainable Development Goals";
public static final String NULL = "NULL";
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
@ -46,4 +56,37 @@ public class Constants {
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
public static StructuredProperty getSubject(String sbj, String classid, String classname,
String diqualifierclassid) {
if (sbj.equals(NULL))
return null;
StructuredProperty sp = new StructuredProperty();
sp.setValue(sbj);
sp
.setQualifier(
OafMapperUtils
.qualifier(
classid,
classname,
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
ModelConstants.DNET_SUBJECT_TYPOLOGIES));
sp
.setDataInfo(
OafMapperUtils
.dataInfo(
false,
UPDATE_DATA_INFO_TYPE,
true,
false,
OafMapperUtils
.qualifier(
diqualifierclassid,
UPDATE_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
""));
return sp;
}
}

86
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java
View File

@ -1,86 +0,0 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
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.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.schema.oaf.Result;
/**
* Just collects all the atomic actions produced for the different results and saves them in
* outputpath for the ActionSet
*/
public class CollectAndSave implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
Objects
.requireNonNull(
CollectAndSave.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json")));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
collectAndSave(spark, inputPath, outputPath);
});
}
private static void collectAndSave(SparkSession spark, String inputPath, String outputPath) {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
sc
.sequenceFile(inputPath + "/publication", Text.class, Text.class)
.union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class))
.union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class))
.union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
}

28
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java
View File

@ -1,28 +0,0 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
/**
* Subset of the information of the generic results that are needed to create the atomic action
*/
public class PreparedResult implements Serializable {
private String id; // openaire id
private String value; // doi
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}

88
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java
View File

@ -1,6 +1,7 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import static eu.dnetlib.dhp.actionmanager.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
@ -15,7 +16,6 @@ import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
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;
@ -24,11 +24,15 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize;
import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import scala.Tuple2;
/**
@ -46,7 +50,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
.toString(
SparkAtomicActionScoreJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json"));
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
@ -65,14 +69,6 @@ public class SparkAtomicActionScoreJob implements Serializable {
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
final String bipScorePath = parser.get("bipScorePath");
log.info("bipScorePath: {}", bipScorePath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
Class<I> inputClazz = (Class<I>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
runWithSparkSession(
@ -80,12 +76,11 @@ public class SparkAtomicActionScoreJob implements Serializable {
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
prepareResults(spark, inputPath, outputPath, bipScorePath, inputClazz);
prepareResults(spark, inputPath, outputPath);
});
}
private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath,
String bipScorePath, Class<I> inputClazz) {
private static <I extends Result> void prepareResults(SparkSession spark, String bipScorePath, String outputPath) {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -101,41 +96,19 @@ public class SparkAtomicActionScoreJob implements Serializable {
return bs;
}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class));
Dataset<I> results = readPath(spark, inputPath, inputClazz);
results.createOrReplaceTempView("result");
Dataset<PreparedResult> preparedResult = spark
.sql(
"select pIde.value value, id " +
"from result " +
"lateral view explode (pid) p as pIde " +
"where dataInfo.deletedbyinference = false and pIde.qualifier.classid = '" + DOI + "'")
.as(Encoders.bean(PreparedResult.class));
bipScores
.joinWith(
preparedResult, bipScores.col("id").equalTo(preparedResult.col("value")),
"inner")
.map((MapFunction<Tuple2<BipScore, PreparedResult>, BipScore>) value -> {
BipScore ret = value._1();
ret.setId(value._2().getId());
return ret;
}, Encoders.bean(BipScore.class))
.groupByKey((MapFunction<BipScore, String>) BipScore::getId, Encoders.STRING())
.mapGroups((MapGroupsFunction<String, BipScore, Result>) (k, it) -> {
Result ret = new Result();
ret.setDataInfo(getDataInfo());
BipScore first = it.next();
ret.setId(first.getId());
ret.setMeasures(getMeasure(first));
it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value)));
.map((MapFunction<BipScore, Result>) bs -> {
Result ret = new Result();
ret.setId(bs.getId());
ret.setMeasures(getMeasure(bs));
return ret;
}, Encoders.bean(Result.class))
.toJavaRDD()
.map(p -> new AtomicAction(inputClazz, p))
.map(p -> new AtomicAction(Result.class, p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
@ -159,7 +132,21 @@ public class SparkAtomicActionScoreJob implements Serializable {
KeyValue kv = new KeyValue();
kv.setValue(unit.getValue());
kv.setKey(unit.getKey());
kv.setDataInfo(getDataInfo());
kv
.setDataInfo(
OafMapperUtils
.dataInfo(
false,
UPDATE_DATA_INFO_TYPE,
true,
false,
OafMapperUtils
.qualifier(
UPDATE_MEASURE_BIP_CLASS_ID,
UPDATE_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
""));
return kv;
})
.collect(Collectors.toList()));
@ -168,21 +155,6 @@ public class SparkAtomicActionScoreJob implements Serializable {
.collect(Collectors.toList());
}
private static DataInfo getDataInfo() {
DataInfo di = new DataInfo();
di.setInferred(false);
di.setInvisible(false);
di.setDeletedbyinference(false);
di.setTrust("");
Qualifier qualifier = new Qualifier();
qualifier.setClassid("sysimport:actionset");
qualifier.setClassname("Harvested");
qualifier.setSchemename("dnet:provenanceActions");
qualifier.setSchemeid("dnet:provenanceActions");
di.setProvenanceaction(qualifier);
return di;
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/BipDeserialize.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
package eu.dnetlib.dhp.actionmanager.bipmodel;
import java.io.Serializable;
import java.util.ArrayList;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/BipScore.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
package eu.dnetlib.dhp.actionmanager.bipmodel;
import java.io.Serializable;
import java.util.List;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/KeyValue.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
package eu.dnetlib.dhp.actionmanager.bipmodel;
import java.io.Serializable;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/Score.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
package eu.dnetlib.dhp.actionmanager.bipmodel;
import java.io.Serializable;
import java.util.List;

77
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSData.java
View File

@ -1,77 +0,0 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.Serializable;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.collection.GetCSV;
public class GetFOSData implements Serializable {
private static final Logger log = LoggerFactory.getLogger(GetFOSData.class);
public static final char DEFAULT_DELIMITER = '\t';
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
GetFOSData.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_fos_parameters.json"))));
parser.parseArgument(args);
// the path where the original fos csv file is stored
final String sourcePath = parser.get("sourcePath");
log.info("sourcePath {}", sourcePath);
// the path where to put the file as json
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final String hdfsNameNode = parser.get("hdfsNameNode");
log.info("hdfsNameNode {}", hdfsNameNode);
final String classForName = parser.get("classForName");
log.info("classForName {}", classForName);
final char delimiter = Optional
.ofNullable(parser.get("delimiter"))
.map(s -> s.charAt(0))
.orElse(DEFAULT_DELIMITER);
log.info("delimiter {}", delimiter);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
new GetFOSData().doRewrite(sourcePath, outputPath, classForName, delimiter, fileSystem);
}
public void doRewrite(String inputPath, String outputFile, String classForName, char delimiter, FileSystem fs)
throws IOException, ClassNotFoundException {
// reads the csv and writes it as its json equivalent
try (InputStreamReader reader = new InputStreamReader(fs.open(new Path(inputPath)))) {
GetCSV.getCsv(fs, reader, outputFile, classForName, delimiter);
}
}
}

91
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java Normal file
View File

@ -0,0 +1,91 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
import static eu.dnetlib.dhp.actionmanager.Constants.isSparkSessionManaged;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class GetFOSSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(GetFOSSparkJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
GetFOSSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
// the path where the original fos csv file is stored
final String sourcePath = parser.get("sourcePath");
log.info("sourcePath {}", sourcePath);
// the path where to put the file as json
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final String delimiter = Optional
.ofNullable(parser.get("delimiter"))
.orElse(DEFAULT_DELIMITER);
SparkConf sconf = new SparkConf();
runWithSparkSession(
sconf,
isSparkSessionManaged,
spark -> {
getFOS(
spark,
sourcePath,
outputPath,
delimiter);
});
}
private static void getFOS(SparkSession spark, String sourcePath, String outputPath, String delimiter) {
Dataset<Row> fosData = spark
.read()
.format("csv")
.option("sep", delimiter)
.option("inferSchema", "true")
.option("header", "true")
.option("quotes", "\"")
.load(sourcePath);
fosData.map((MapFunction<Row, FOSDataModel>) r -> {
FOSDataModel fosDataModel = new FOSDataModel();
fosDataModel.setDoi(r.getString(0).toLowerCase());
fosDataModel.setLevel1(r.getString(1));
fosDataModel.setLevel2(r.getString(2));
fosDataModel.setLevel3(r.getString(3));
return fosDataModel;
}, Encoders.bean(FOSDataModel.class))
.write()
.mode(SaveMode.Overwrite)
.json(outputPath);
}
}

91
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetSDGSparkJob.java Normal file
View File

@ -0,0 +1,91 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
import static eu.dnetlib.dhp.actionmanager.Constants.isSparkSessionManaged;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class GetSDGSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(GetSDGSparkJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
GetSDGSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
// the path where the original fos csv file is stored
final String sourcePath = parser.get("sourcePath");
log.info("sourcePath {}", sourcePath);
// the path where to put the file as json
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final String delimiter = Optional
.ofNullable(parser.get("delimiter"))
.orElse(DEFAULT_DELIMITER);
SparkConf sconf = new SparkConf();
runWithSparkSession(
sconf,
isSparkSessionManaged,
spark -> {
getSDG(
spark,
sourcePath,
outputPath,
delimiter);
});
}
private static void getSDG(SparkSession spark, String sourcePath, String outputPath, String delimiter) {
Dataset<Row> sdgData = spark
.read()
.format("csv")
.option("sep", delimiter)
.option("inferSchema", "true")
.option("header", "true")
.option("quotes", "\"")
.load(sourcePath);
sdgData.map((MapFunction<Row, SDGDataModel>) r -> {
SDGDataModel sdgDataModel = new SDGDataModel();
sdgDataModel.setDoi(r.getString(0).toLowerCase());
sdgDataModel.setSbj(r.getString(1));
return sdgDataModel;
}, Encoders.bean(SDGDataModel.class))
.filter((FilterFunction<SDGDataModel>) sdg -> sdg.getSbj() != null)
.write()
.mode(SaveMode.Overwrite)
.json(outputPath);
}
}

49
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java
View File

@ -1,17 +1,17 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*;
import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.UPDATE_CLASS_NAME;
import static eu.dnetlib.dhp.actionmanager.Constants.*;
import static eu.dnetlib.dhp.actionmanager.Constants.UPDATE_CLASS_NAME;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.hdfs.client.HdfsUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
@ -24,14 +24,16 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.BipDeserialize;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.BipScore;
import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize;
import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Measure;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.utils.DHPUtils;
@ -40,7 +42,7 @@ public class PrepareBipFinder implements Serializable {
private static final Logger log = LoggerFactory.getLogger(PrepareBipFinder.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static <I extends Result> void main(String[] args) throws Exception {
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
@ -76,7 +78,7 @@ public class PrepareBipFinder implements Serializable {
});
}
private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath) {
private static void prepareResults(SparkSession spark, String inputPath, String outputPath) {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -89,13 +91,44 @@ public class PrepareBipFinder implements Serializable {
BipScore bs = new BipScore();
bs.setId(key);
bs.setScoreList(entry.get(key));
return bs;
}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class))
.map((MapFunction<BipScore, Result>) v -> {
Result r = new Result();
final String cleanedPid = CleaningFunctions.normalizePidValue(DOI, v.getId());
r.setId(DHPUtils.generateUnresolvedIdentifier(v.getId(), DOI));
r.setMeasures(getMeasure(v));
Instance inst = new Instance();
inst.setMeasures(getMeasure(v));
inst
.setPid(
Arrays
.asList(
OafMapperUtils
.structuredProperty(
cleanedPid,
OafMapperUtils
.qualifier(
DOI, DOI_CLASSNAME,
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES),
null)));
r.setInstance(Arrays.asList(inst));
r
.setDataInfo(
OafMapperUtils
.dataInfo(
false, null, true,
false,
OafMapperUtils
.qualifier(
ModelConstants.PROVENANCE_ENRICH,
null,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
null));
return r;
}, Encoders.bean(Result.class))
.write()

90
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java
View File

@ -1,7 +1,7 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*;
import static eu.dnetlib.dhp.actionmanager.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
@ -10,8 +10,8 @@ import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FlatMapFunction;
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.SaveMode;
@ -67,20 +67,36 @@ public class PrepareFOSSparkJob implements Serializable {
private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) {
Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
fosDataset.flatMap((FlatMapFunction<FOSDataModel, FOSDataModel>) v -> {
List<FOSDataModel> fosList = new ArrayList<>();
final String level1 = v.getLevel1();
final String level2 = v.getLevel2();
final String level3 = v.getLevel3();
Arrays
.stream(v.getDoi().split("\u0002"))
.forEach(d -> fosList.add(FOSDataModel.newInstance(d, level1, level2, level3)));
return fosList.iterator();
}, Encoders.bean(FOSDataModel.class))
.map((MapFunction<FOSDataModel, Result>) value -> {
fosDataset
.groupByKey((MapFunction<FOSDataModel, String>) v -> v.getDoi().toLowerCase(), Encoders.STRING())
.mapGroups((MapGroupsFunction<String, FOSDataModel, Result>) (k, it) -> {
Result r = new Result();
r.setId(DHPUtils.generateUnresolvedIdentifier(value.getDoi(), DOI));
r.setSubject(getSubjects(value));
FOSDataModel first = it.next();
r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
HashSet<String> level1 = new HashSet<>();
HashSet<String> level2 = new HashSet<>();
HashSet<String> level3 = new HashSet<>();
addLevels(level1, level2, level3, first);
it.forEachRemaining(v -> addLevels(level1, level2, level3, v));
List<StructuredProperty> sbjs = new ArrayList<>();
level1.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
level2.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
level3.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
r.setSubject(sbjs);
r
.setDataInfo(
OafMapperUtils
.dataInfo(
false, null, true,
false,
OafMapperUtils
.qualifier(
ModelConstants.PROVENANCE_ENRICH,
null,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
null));
return r;
}, Encoders.bean(Result.class))
.write()
@ -89,45 +105,11 @@ public class PrepareFOSSparkJob implements Serializable {
.json(outputPath + "/fos");
}
private static List<StructuredProperty> getSubjects(FOSDataModel fos) {
return Arrays
.asList(getSubject(fos.getLevel1()), getSubject(fos.getLevel2()), getSubject(fos.getLevel3()))
.stream()
.filter(Objects::nonNull)
.collect(Collectors.toList());
}
private static StructuredProperty getSubject(String sbj) {
if (sbj.equals(NULL))
return null;
StructuredProperty sp = new StructuredProperty();
sp.setValue(sbj);
sp
.setQualifier(
OafMapperUtils
.qualifier(
FOS_CLASS_ID,
FOS_CLASS_NAME,
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
ModelConstants.DNET_SUBJECT_TYPOLOGIES));
sp
.setDataInfo(
OafMapperUtils
.dataInfo(
false,
UPDATE_DATA_INFO_TYPE,
true,
false,
OafMapperUtils
.qualifier(
UPDATE_SUBJECT_FOS_CLASS_ID,
UPDATE_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
""));
return sp;
private static void addLevels(HashSet<String> level1, HashSet<String> level2, HashSet<String> level3,
FOSDataModel first) {
level1.add(first.getLevel1());
level2.add(first.getLevel2());
level3.add(first.getLevel3());
}
}

104
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java Normal file
View File

@ -0,0 +1,104 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import static eu.dnetlib.dhp.actionmanager.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.io.IOUtils;
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.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.utils.DHPUtils;
public class PrepareSDGSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(PrepareSDGSparkJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareSDGSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String sourcePath = parser.get("sourcePath");
log.info("sourcePath: {}", sourcePath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
doPrepare(
spark,
sourcePath,
outputPath);
});
}
private static void doPrepare(SparkSession spark, String sourcePath, String outputPath) {
Dataset<SDGDataModel> sdgDataset = readPath(spark, sourcePath, SDGDataModel.class);
sdgDataset
.groupByKey((MapFunction<SDGDataModel, String>) r -> r.getDoi().toLowerCase(), Encoders.STRING())
.mapGroups((MapGroupsFunction<String, SDGDataModel, Result>) (k, it) -> {
Result r = new Result();
r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
SDGDataModel first = it.next();
List<StructuredProperty> sbjs = new ArrayList<>();
sbjs.add(getSubject(first.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID));
it
.forEachRemaining(
s -> sbjs
.add(getSubject(s.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
r.setSubject(sbjs);
r
.setDataInfo(
OafMapperUtils
.dataInfo(
false, null, true,
false,
OafMapperUtils
.qualifier(
ModelConstants.PROVENANCE_ENRICH,
null,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
null));
return r;
}, Encoders.bean(Result.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + "/sdg");
}
}

21
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java
View File

@ -1,10 +1,11 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*;
import static eu.dnetlib.dhp.actionmanager.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
@ -20,7 +21,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Result;
public class SparkSaveUnresolved implements Serializable {
private static final Logger log = LoggerFactory.getLogger(PrepareFOSSparkJob.class);
private static final Logger log = LoggerFactory.getLogger(SparkSaveUnresolved.class);
public static void main(String[] args) throws Exception {
@ -64,10 +65,22 @@ public class SparkSaveUnresolved implements Serializable {
.map(
(MapFunction<String, Result>) l -> OBJECT_MAPPER.readValue(l, Result.class),
Encoders.bean(Result.class))
.groupByKey((MapFunction<Result, String>) r -> r.getId(), Encoders.STRING())
.groupByKey((MapFunction<Result, String>) Result::getId, Encoders.STRING())
.mapGroups((MapGroupsFunction<String, Result, Result>) (k, it) -> {
Result ret = it.next();
it.forEachRemaining(r -> ret.mergeFrom(r));
it.forEachRemaining(r -> {
if (r.getInstance() != null) {
ret.setInstance(r.getInstance());
}
if (r.getSubject() != null) {
if (ret.getSubject() != null)
ret.getSubject().addAll(r.getSubject());
else
ret.setSubject(r.getSubject());
}
// ret.mergeFrom(r)
});
return ret;
}, Encoders.bean(Result.class))
.write()

28
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/BipDeserialize.java
View File

@ -1,28 +0,0 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
/**
* Class that maps the model of the bipFinder! input data.
* Only needed for deserialization purposes
*/
public class BipDeserialize extends HashMap<String, List<Score>> implements Serializable {
public BipDeserialize() {
super();
}
public List<Score> get(String key) {
if (super.get(key) == null) {
return new ArrayList<>();
}
return super.get(key);
}
}

30
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/BipScore.java
View File

@ -1,30 +0,0 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
import java.io.Serializable;
import java.util.List;
/**
* Rewriting of the bipFinder input data by extracting the identifier of the result (doi)
*/
public class BipScore implements Serializable {
private String id; // doi
private List<Score> scoreList; // unit as given in the inputfile
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<Score> getScoreList() {
return scoreList;
}
public void setScoreList(List<Score> scoreList) {
this.scoreList = scoreList;
}
}

8
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/FOSDataModel.java
View File

@ -6,19 +6,19 @@ import java.io.Serializable;
import com.opencsv.bean.CsvBindByPosition;
public class FOSDataModel implements Serializable {
@CsvBindByPosition(position = 1)
@CsvBindByPosition(position = 0)
// @CsvBindByName(column = "doi")
private String doi;
@CsvBindByPosition(position = 2)
@CsvBindByPosition(position = 1)
// @CsvBindByName(column = "level1")
private String level1;
@CsvBindByPosition(position = 3)
@CsvBindByPosition(position = 2)
// @CsvBindByName(column = "level2")
private String level2;
@CsvBindByPosition(position = 4)
@CsvBindByPosition(position = 3)
// @CsvBindByName(column = "level3")
private String level3;

26
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/KeyValue.java
View File

@ -1,26 +0,0 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
import java.io.Serializable;
public class KeyValue implements Serializable {
private String key;
private String value;
public String getKey() {
return key;
}
public void setKey(String key) {
this.key = key;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}

47
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/SDGDataModel.java Normal file
View File

@ -0,0 +1,47 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
import java.io.Serializable;
import com.opencsv.bean.CsvBindByPosition;
public class SDGDataModel implements Serializable {
@CsvBindByPosition(position = 0)
// @CsvBindByName(column = "doi")
private String doi;
@CsvBindByPosition(position = 1)
// @CsvBindByName(column = "sdg")
private String sbj;
public SDGDataModel() {
}
public SDGDataModel(String doi, String sbj) {
this.doi = doi;
this.sbj = sbj;
}
public static SDGDataModel newInstance(String d, String sbj) {
return new SDGDataModel(d, sbj);
}
public String getDoi() {
return doi;
}
public void setDoi(String doi) {
this.doi = doi;
}
public String getSbj() {
return sbj;
}
public void setSbj(String sbj) {
this.sbj = sbj;
}
}

30
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/Score.java
View File

@ -1,30 +0,0 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
import java.io.Serializable;
import java.util.List;
/**
* represents the score in the input file
*/
public class Score implements Serializable {
private String id;
private List<KeyValue> unit;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<KeyValue> getUnit() {
return unit;
}
public void setUnit(List<KeyValue> unit) {
this.unit = unit;
}
}

46
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java
View File

@ -14,6 +14,7 @@ import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
@ -21,6 +22,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelConstants;
@ -83,10 +85,13 @@ public class CreateActionSetSparkJob implements Serializable {
private static void extractContent(SparkSession spark, String inputPath, String outputPath,
boolean shouldDuplicateRels) {
spark
.sqlContext()
.createDataset(spark.sparkContext().textFile(inputPath + "/*", 6000), Encoders.STRING())
.read()
.textFile(inputPath + "/*")
.map(
(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
Encoders.bean(COCI.class))
.flatMap(
(FlatMapFunction<String, Relation>) value -> createRelation(value, shouldDuplicateRels).iterator(),
(FlatMapFunction<COCI, Relation>) value -> createRelation(value, shouldDuplicateRels).iterator(),
Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) value -> value != null)
.toJavaRDD()
@ -98,26 +103,29 @@ public class CreateActionSetSparkJob implements Serializable {
}
private static List<Relation> createRelation(String value, boolean duplicate) {
String[] line = value.split(",");
if (!line[1].startsWith("10.")) {
return new ArrayList<>();
}
private static List<Relation> createRelation(COCI value, boolean duplicate) {
List<Relation> relationList = new ArrayList<>();
String citing = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[1]));
final String cited = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[2]));
String citing = ID_PREFIX
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCiting()));
final String cited = ID_PREFIX
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCited()));
relationList
.addAll(
getRelations(
citing,
cited));
if(!citing.equals(cited)){
relationList
.addAll(
getRelations(
citing,
cited));
if (duplicate && line[1].endsWith(".refs")) {
citing = ID_PREFIX + IdentifierFactory
.md5(CleaningFunctions.normalizePidValue("doi", line[1].substring(0, line[1].indexOf(".refs"))));
relationList.addAll(getRelations(citing, cited));
if (duplicate && value.getCiting().endsWith(".refs")) {
citing = ID_PREFIX + IdentifierFactory
.md5(
CleaningFunctions
.normalizePidValue("doi", value.getCiting().substring(0, value.getCiting().indexOf(".refs"))));
relationList.addAll(getRelations(citing, cited));
}
}
return relationList;

103
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java Normal file
View File

@ -0,0 +1,103 @@
package eu.dnetlib.dhp.actionmanager.opencitations;
import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
import static eu.dnetlib.dhp.actionmanager.Constants.isSparkSessionManaged;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.LocatedFileStatus;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.fs.RemoteIterator;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class ReadCOCI implements Serializable {
private static final Logger log = LoggerFactory.getLogger(ReadCOCI.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
ReadCOCI.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String[] inputFile = parser.get("inputFile").split(";");
log.info("inputFile {}", inputFile.toString());
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath {}", workingPath);
SparkConf sconf = new SparkConf();
final String delimiter = Optional
.ofNullable(parser.get("delimiter"))
.orElse(DEFAULT_DELIMITER);
runWithSparkSession(
sconf,
isSparkSessionManaged,
spark -> {
doRead(
spark,
workingPath,
inputFile,
outputPath,
delimiter);
});
}
private static void doRead(SparkSession spark, String workingPath, String[] inputFiles,
String outputPath,
String delimiter) throws IOException {
for(String inputFile : inputFiles){
String p_string = workingPath + "/" + inputFile + ".gz";
Dataset<Row> cociData = spark
.read()
.format("csv")
.option("sep", delimiter)
.option("inferSchema", "true")
.option("header", "true")
.option("quotes", "\"")
.load(p_string)
.repartition(100);
cociData.map((MapFunction<Row, COCI>) row -> {
COCI coci = new COCI();
coci.setOci(row.getString(0));
coci.setCiting(row.getString(1));
coci.setCited(row.getString(2));
return coci;
}, Encoders.bean(COCI.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + inputFile);
}
}
}

41
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/model/COCI.java Normal file
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package eu.dnetlib.dhp.actionmanager.opencitations.model;
import java.io.Serializable;
import com.opencsv.bean.CsvBindByPosition;
public class COCI implements Serializable {
private String oci;
private String citing;
private String cited;
public String getOci() {
return oci;
}
public void setOci(String oci) {
this.oci = oci;
}
public String getCiting() {
return citing;
}
public void setCiting(String citing) {
this.citing = citing;
}
public String getCited() {
return cited;
}
public void setCited(String cited) {
this.cited = cited;
}
}

69
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkCreateActionset.scala
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package eu.dnetlib.dhp.actionmanager.scholix
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
import org.apache.spark.SparkConf
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object SparkCreateActionset {
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/generate_actionset.json")).mkString)
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
val workingDirFolder = parser.get("workingDirFolder")
log.info(s"workingDirFolder -> $workingDirFolder")
implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val resultEncoders: Encoder[Result] = Encoders.kryo[Result]
implicit val relationEncoders: Encoder[Relation] = Encoders.kryo[Relation]
import spark.implicits._
val relation = spark.read.load(s"$sourcePath/relation").as[Relation]
relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
.flatMap(r => List(r.getSource, r.getTarget)).distinct().write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/id_relation")
val idRelation = spark.read.load(s"$workingDirFolder/id_relation").as[String]
log.info("extract source and target Identifier involved in relations")
log.info("save relation filtered")
relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
.write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/actionSetOaf")
log.info("saving entities")
val entities: Dataset[(String, Result)] = spark.read.load(s"$sourcePath/entities/*").as[Result].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING, resultEncoders))
entities
.joinWith(idRelation, entities("_1").equalTo(idRelation("value")))
.map(p => p._1._2)
.write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
}
}

86
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkSaveActionSet.scala
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package eu.dnetlib.dhp.actionmanager.scholix
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{Oaf, Dataset => OafDataset,Publication, Software, OtherResearchProduct, Relation}
import org.apache.hadoop.io.Text
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.hadoop.mapred.SequenceFileOutputFormat
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object SparkSaveActionSet {
def toActionSet(item: Oaf): (String, String) = {
val mapper = new ObjectMapper()
item match {
case dataset: OafDataset =>
val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset]
a.setClazz(classOf[OafDataset])
a.setPayload(dataset)
(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
case publication: Publication =>
val a: AtomicAction[Publication] = new AtomicAction[Publication]
a.setClazz(classOf[Publication])
a.setPayload(publication)
(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
case software: Software =>
val a: AtomicAction[Software] = new AtomicAction[Software]
a.setClazz(classOf[Software])
a.setPayload(software)
(software.getClass.getCanonicalName, mapper.writeValueAsString(a))
case orp: OtherResearchProduct =>
val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct]
a.setClazz(classOf[OtherResearchProduct])
a.setPayload(orp)
(orp.getClass.getCanonicalName, mapper.writeValueAsString(a))
case relation: Relation =>
val a: AtomicAction[Relation] = new AtomicAction[Relation]
a.setClazz(classOf[Relation])
a.setPayload(relation)
(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
case _ =>
null
}
}
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/save_actionset.json")).mkString)
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val tEncoder: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
spark.read.load(sourcePath).as[Oaf]
.map(o => toActionSet(o))
.filter(o => o != null)
.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text, Text]], classOf[GzipCodec])
}
}

608
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala
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package eu.dnetlib.dhp.datacite
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
import eu.dnetlib.dhp.schema.oaf.{AccessRight, Author, DataInfo, Instance, KeyValue, Oaf, OtherResearchProduct, Publication, Qualifier, Relation, Result, Software, StructuredProperty, Dataset => OafDataset}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
import java.nio.charset.CodingErrorAction
import java.text.SimpleDateFormat
import java.time.LocalDate
import java.time.chrono.ThaiBuddhistDate
import java.time.format.DateTimeFormatter
import java.util.regex.Pattern
import java.util.{Date, Locale}
import scala.collection.JavaConverters._
import scala.io.{Codec, Source}
import scala.language.postfixOps
case class DataciteType(doi: String, timestamp: Long, isActive: Boolean, json: String) {}
case class RelatedIdentifierType(relationType: String, relatedIdentifier: String, relatedIdentifierType: String) {}
case class NameIdentifiersType(nameIdentifierScheme: Option[String], schemeUri: Option[String], nameIdentifier: Option[String]) {}
case class CreatorType(nameType: Option[String], nameIdentifiers: Option[List[NameIdentifiersType]], name: Option[String], familyName: Option[String], givenName: Option[String], affiliation: Option[List[String]]) {}
case class TitleType(title: Option[String], titleType: Option[String], lang: Option[String]) {}
case class SubjectType(subject: Option[String], subjectScheme: Option[String]) {}
case class DescriptionType(descriptionType: Option[String], description: Option[String]) {}
case class FundingReferenceType(funderIdentifierType: Option[String], awardTitle: Option[String], awardUri: Option[String], funderName: Option[String], funderIdentifier: Option[String], awardNumber: Option[String]) {}
case class DateType(date: Option[String], dateType: Option[String]) {}
case class HostedByMapType(openaire_id: String, datacite_name: String, official_name: String, similarity: Option[Float]) {}
object DataciteToOAFTransformation {
val REL_TYPE_VALUE:String = "resultResult"
val DATE_RELATION_KEY = "RelationDate"
val subRelTypeMapping: Map[String,(String,String)] = Map(
"References" ->("IsReferencedBy","relationship"),
"IsSupplementTo" ->("IsSupplementedBy","supplement"),
"IsPartOf" ->("HasPart","part"),
"HasPart" ->("IsPartOf","part"),
"IsVersionOf" ->("HasVersion","version"),
"HasVersion" ->("IsVersionOf","version"),
"IsIdenticalTo" ->("IsIdenticalTo","relationship"),
"IsPreviousVersionOf" ->("IsNewVersionOf","version"),
"IsContinuedBy" ->("Continues","relationship"),
"Continues" ->("IsContinuedBy","relationship"),
"IsNewVersionOf" ->("IsPreviousVersionOf","version"),
"IsSupplementedBy" ->("IsSupplementTo","supplement"),
"IsDocumentedBy" ->("Documents","relationship"),
"IsSourceOf" ->("IsDerivedFrom","relationship"),
"Cites" ->("IsCitedBy","citation"),
"IsCitedBy" ->("Cites","citation"),
"IsDerivedFrom" ->("IsSourceOf","relationship"),
"IsVariantFormOf" ->("IsDerivedFrom","version"),
"IsReferencedBy" ->("References","relationship"),
"IsObsoletedBy" ->("IsNewVersionOf","version"),
"Reviews" ->("IsReviewedBy","review"),
"Documents" ->("IsDocumentedBy","relationship"),
"IsCompiledBy" ->("Compiles","relationship"),
"Compiles" ->("IsCompiledBy","relationship"),
"IsReviewedBy" ->("Reviews","review")
)
implicit val codec: Codec = Codec("UTF-8")
codec.onMalformedInput(CodingErrorAction.REPLACE)
codec.onUnmappableCharacter(CodingErrorAction.REPLACE)
val DOI_CLASS = "doi"
val SUBJ_CLASS = "keywords"
val j_filter: List[String] = {
val s = Source.fromInputStream(getClass.getResourceAsStream("datacite_filter")).mkString
s.lines.toList
}
val mapper = new ObjectMapper()
val unknown_repository: HostedByMapType = HostedByMapType(ModelConstants.UNKNOWN_REPOSITORY_ORIGINALID, ModelConstants.UNKNOWN_REPOSITORY.getValue, ModelConstants.UNKNOWN_REPOSITORY.getValue, Some(1.0F))
val dataInfo: DataInfo = generateDataInfo("0.9")
val DATACITE_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue(ModelConstants.DATACITE_ID, "Datacite")
val hostedByMap: Map[String, HostedByMapType] = {
val s = Source.fromInputStream(getClass.getResourceAsStream("hostedBy_map.json")).mkString
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(s)
json.extract[Map[String, HostedByMapType]]
}
val df_en: DateTimeFormatter = DateTimeFormatter.ofPattern("[MM-dd-yyyy][MM/dd/yyyy][dd-MM-yy][dd-MMM-yyyy][dd/MMM/yyyy][dd-MMM-yy][dd/MMM/yy][dd-MM-yy][dd/MM/yy][dd-MM-yyyy][dd/MM/yyyy][yyyy-MM-dd][yyyy/MM/dd]", Locale.ENGLISH)
val df_it: DateTimeFormatter = DateTimeFormatter.ofPattern("[dd-MM-yyyy][dd/MM/yyyy]", Locale.ITALIAN)
val funder_regex: List[(Pattern, String)] = List(
(Pattern.compile("(info:eu-repo/grantagreement/ec/h2020/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda__h2020::"),
(Pattern.compile("(info:eu-repo/grantagreement/ec/fp7/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda_______::")
)
val Date_regex: List[Pattern] = List(
//Y-M-D
Pattern.compile("(18|19|20)\\d\\d([- /.])(0[1-9]|1[012])\\2(0[1-9]|[12][0-9]|3[01])", Pattern.MULTILINE),
//M-D-Y
Pattern.compile("((0[1-9]|1[012])|([1-9]))([- /.])(0[1-9]|[12][0-9]|3[01])([- /.])(18|19|20)?\\d\\d", Pattern.MULTILINE),
//D-M-Y
Pattern.compile("(?:(?:31(/|-|\\.)(?:0?[13578]|1[02]|(?:Jan|Mar|May|Jul|Aug|Oct|Dec)))\\1|(?:(?:29|30)(/|-|\\.)(?:0?[1,3-9]|1[0-2]|(?:Jan|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec))\\2))(?:(?:1[6-9]|[2-9]\\d)?\\d{2})|(?:29(/|-|\\.)(?:0?2|(?:Feb))\\3(?:(?:(?:1[6-9]|[2-9]\\d)?(?:0[48]|[2468][048]|[13579][26])|(?:(?:16|[2468][048]|[3579][26])00))))|(?:0?[1-9]|1\\d|2[0-8])(/|-|\\.)(?:(?:0?[1-9]|(?:Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep))|(?:1[0-2]|(?:Oct|Nov|Dec)))\\4(?:(?:1[6-9]|[2-9]\\d)?\\d{2})", Pattern.MULTILINE),
//Y
Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE)
)
def filter_json(json: String): Boolean = {
j_filter.exists(f => json.contains(f))
}
def toActionSet(item: Oaf): (String, String) = {
val mapper = new ObjectMapper()
item match {
case dataset: OafDataset =>
val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset]
a.setClazz(classOf[OafDataset])
a.setPayload(dataset)
(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
case publication: Publication =>
val a: AtomicAction[Publication] = new AtomicAction[Publication]
a.setClazz(classOf[Publication])
a.setPayload(publication)
(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
case software: Software =>
val a: AtomicAction[Software] = new AtomicAction[Software]
a.setClazz(classOf[Software])
a.setPayload(software)
(software.getClass.getCanonicalName, mapper.writeValueAsString(a))
case orp: OtherResearchProduct =>
val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct]
a.setClazz(classOf[OtherResearchProduct])
a.setPayload(orp)
(orp.getClass.getCanonicalName, mapper.writeValueAsString(a))
case relation: Relation =>
val a: AtomicAction[Relation] = new AtomicAction[Relation]
a.setClazz(classOf[Relation])
a.setPayload(relation)
(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
case _ =>
null
}
}
def embargo_end(embargo_end_date: String): Boolean = {
val dt = LocalDate.parse(embargo_end_date, DateTimeFormatter.ofPattern("[yyyy-MM-dd]"))
val td = LocalDate.now()
td.isAfter(dt)
}
def extract_date(input: String): Option[String] = {
val d = Date_regex.map(pattern => {
val matcher = pattern.matcher(input)
if (matcher.find())
matcher.group(0)
else
null
}
).find(s => s != null)
if (d.isDefined) {
val a_date = if (d.get.length == 4) s"01-01-${d.get}" else d.get
try {
return Some(LocalDate.parse(a_date, df_en).toString)
} catch {
case _: Throwable => try {
return Some(LocalDate.parse(a_date, df_it).toString)
} catch {
case _: Throwable =>
return None
}
}
}
d
}
def fix_thai_date(input:String, format:String) :String = {
try {
val a_date = LocalDate.parse(input,DateTimeFormatter.ofPattern(format))
val d = ThaiBuddhistDate.of(a_date.getYear, a_date.getMonth.getValue, a_date.getDayOfMonth)
LocalDate.from(d).toString
} catch {
case _: Throwable => ""
}
}
def getTypeQualifier(resourceType: String, resourceTypeGeneral: String, schemaOrg: String, vocabularies: VocabularyGroup): (Qualifier, Qualifier) = {
if (resourceType != null && resourceType.nonEmpty) {
val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceType)
if (typeQualifier != null)
return (typeQualifier, vocabularies.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid))
}
if (schemaOrg != null && schemaOrg.nonEmpty) {
val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, schemaOrg)
if (typeQualifier != null)
return (typeQualifier, vocabularies.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid))
}
if (resourceTypeGeneral != null && resourceTypeGeneral.nonEmpty) {
val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceTypeGeneral)
if (typeQualifier != null)
return (typeQualifier, vocabularies.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid))
}
null
}
def getResult(resourceType: String, resourceTypeGeneral: String, schemaOrg: String, vocabularies: VocabularyGroup): Result = {
val typeQualifiers: (Qualifier, Qualifier) = getTypeQualifier(resourceType, resourceTypeGeneral, schemaOrg, vocabularies)
if (typeQualifiers == null)
return null
val i = new Instance
i.setInstancetype(typeQualifiers._1)
typeQualifiers._2.getClassname match {
case "dataset" =>
val r = new OafDataset
r.setInstance(List(i).asJava)
return r
case "publication" =>
val r = new Publication
r.setInstance(List(i).asJava)
return r
case "software" =>
val r = new Software
r.setInstance(List(i).asJava)
return r
case "other" =>
val r = new OtherResearchProduct
r.setInstance(List(i).asJava)
return r
}
null
}
def available_date(input: String): Boolean = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(input)
val l: List[String] = for {
JObject(dates) <- json \\ "dates"
JField("dateType", JString(dateTypes)) <- dates
} yield dateTypes
l.exists(p => p.equalsIgnoreCase("available"))
}
/**
* As describe in ticket #6377
* when the result come from figshare we need to remove subject
* and set Access rights OPEN.
*
* @param r
*/
def fix_figshare(r: Result): Unit = {
if (r.getInstance() != null) {
val hosted_by_figshare = r.getInstance().asScala.exists(i => i.getHostedby != null && "figshare".equalsIgnoreCase(i.getHostedby.getValue))
if (hosted_by_figshare) {
r.getInstance().asScala.foreach(i => i.setAccessright(ModelConstants.OPEN_ACCESS_RIGHT()))
val l: List[StructuredProperty] = List()
r.setSubject(l.asJava)
}
}
}
def createDNetTargetIdentifier(pid: String, pidType: String, idPrefix: String): String = {
val f_part = s"$idPrefix|${pidType.toLowerCase}".padTo(15, '_')
s"$f_part::${IdentifierFactory.md5(pid.toLowerCase)}"
}
def generateOAFDate(dt: String, q: Qualifier): StructuredProperty = {
OafMapperUtils.structuredProperty(dt, q, null)
}
def generateRelation(sourceId: String, targetId: String, relClass: String, cf: KeyValue, di: DataInfo): Relation = {
val r = new Relation
r.setSource(sourceId)
r.setTarget(targetId)
r.setRelType(ModelConstants.RESULT_PROJECT)
r.setRelClass(relClass)
r.setSubRelType(ModelConstants.OUTCOME)
r.setCollectedfrom(List(cf).asJava)
r.setDataInfo(di)
r
}
def get_projectRelation(awardUri: String, sourceId: String): List[Relation] = {
val match_pattern = funder_regex.find(s => s._1.matcher(awardUri).find())
if (match_pattern.isDefined) {
val m = match_pattern.get._1
val p = match_pattern.get._2
val grantId = m.matcher(awardUri).replaceAll("$2")
val targetId = s"$p${DHPUtils.md5(grantId)}"
List(
generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo)
// REMOVED INVERSE RELATION since there is a specific method that should generate later
// generateRelation(targetId, sourceId, "produces", DATACITE_COLLECTED_FROM, dataInfo)
)
}
else
List()
}
def generateOAF(input: String, ts: Long, dateOfCollection: Long, vocabularies: VocabularyGroup, exportLinks: Boolean): List[Oaf] = {
if (filter_json(input))
return List()
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val resourceType = (json \ "attributes" \ "types" \ "resourceType").extractOrElse[String](null)
val resourceTypeGeneral = (json \ "attributes" \ "types" \ "resourceTypeGeneral").extractOrElse[String](null)
val schemaOrg = (json \ "attributes" \ "types" \ "schemaOrg").extractOrElse[String](null)
val doi = (json \ "attributes" \ "doi").extract[String]
if (doi.isEmpty)
return List()
//Mapping type based on vocabularies dnet:publication_resource and dnet:result_typologies
val result = getResult(resourceType, resourceTypeGeneral, schemaOrg, vocabularies)
if (result == null)
return List()
val doi_q = OafMapperUtils.qualifier("doi", "doi", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES)
val pid = OafMapperUtils.structuredProperty(doi, doi_q, dataInfo)
result.setPid(List(pid).asJava)
result.setId(OafMapperUtils.createOpenaireId(50, s"datacite____::$doi", true))
result.setOriginalId(List(doi).asJava)
val d = new Date(dateOfCollection * 1000)
val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US)
result.setDateofcollection(ISO8601FORMAT.format(d))
result.setDateoftransformation(ISO8601FORMAT.format(d))
result.setDataInfo(dataInfo)
val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List())
val authors = creators.zipWithIndex.map { case (c, idx) =>
val a = new Author
a.setFullname(c.name.orNull)
a.setName(c.givenName.orNull)
a.setSurname(c.familyName.orNull)
if (c.nameIdentifiers != null && c.nameIdentifiers.isDefined && c.nameIdentifiers.get != null) {
a.setPid(c.nameIdentifiers.get.map(ni => {
val q = if (ni.nameIdentifierScheme.isDefined) vocabularies.getTermAsQualifier(ModelConstants.DNET_PID_TYPES, ni.nameIdentifierScheme.get.toLowerCase()) else null
if (ni.nameIdentifier != null && ni.nameIdentifier.isDefined) {
OafMapperUtils.structuredProperty(ni.nameIdentifier.get, q, dataInfo)
}
else
null
}
)
.asJava)
}
if (c.affiliation.isDefined)
a.setAffiliation(c.affiliation.get.filter(af => af.nonEmpty).map(af => OafMapperUtils.field(af, dataInfo)).asJava)
a.setRank(idx + 1)
a
}
val titles: List[TitleType] = (json \\ "titles").extractOrElse[List[TitleType]](List())
result.setTitle(titles.filter(t => t.title.nonEmpty).map(t => {
if (t.titleType.isEmpty) {
OafMapperUtils.structuredProperty(t.title.get, ModelConstants.MAIN_TITLE_QUALIFIER, null)
} else {
OafMapperUtils.structuredProperty(t.title.get, t.titleType.get, t.titleType.get, ModelConstants.DNET_DATACITE_TITLE, ModelConstants.DNET_DATACITE_TITLE, null)
}
}).asJava)
if (authors == null || authors.isEmpty || !authors.exists(a => a != null))
return List()
result.setAuthor(authors.asJava)
val dates = (json \\ "dates").extract[List[DateType]]
val publication_year = (json \\ "publicationYear").extractOrElse[String](null)
val i_date = dates
.filter(d => d.date.isDefined && d.dateType.isDefined)
.find(d => d.dateType.get.equalsIgnoreCase("issued"))
.map(d => extract_date(d.date.get))
val a_date: Option[String] = dates
.filter(d => d.date.isDefined && d.dateType.isDefined && d.dateType.get.equalsIgnoreCase("available"))
.map(d => extract_date(d.date.get))
.find(d => d != null && d.isDefined)
.map(d => d.get)
if (a_date.isDefined) {
if(doi.startsWith("10.14457"))
result.setEmbargoenddate(OafMapperUtils.field(fix_thai_date(a_date.get,"[yyyy-MM-dd]"), null))
else
result.setEmbargoenddate(OafMapperUtils.field(a_date.get, null))
}
if (i_date.isDefined && i_date.get.isDefined) {
if(doi.startsWith("10.14457")) {
result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get,"[yyyy-MM-dd]"), null))
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get,"[yyyy-MM-dd]"), null))
}
else {
result.setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
}
}
else if (publication_year != null) {
if(doi.startsWith("10.14457")) {
result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year","[dd-MM-yyyy]"), null))
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year","[dd-MM-yyyy]"), null))
} else {
result.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
}
}
result.setRelevantdate(dates.filter(d => d.date.isDefined && d.dateType.isDefined)
.map(d => (extract_date(d.date.get), d.dateType.get))
.filter(d => d._1.isDefined)
.map(d => (d._1.get, vocabularies.getTermAsQualifier(ModelConstants.DNET_DATACITE_DATE, d._2.toLowerCase())))
.filter(d => d._2 != null)
.map(d => generateOAFDate(d._1, d._2)).asJava)
val subjects = (json \\ "subjects").extract[List[SubjectType]]
result.setSubject(subjects.filter(s => s.subject.nonEmpty)
.map(s =>
OafMapperUtils.structuredProperty(s.subject.get, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, null)
).asJava)
result.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
val descriptions = (json \\ "descriptions").extract[List[DescriptionType]]
result.setDescription(
descriptions
.filter(d => d.description.isDefined).
map(d =>
OafMapperUtils.field(d.description.get, null)
).filter(s => s != null).asJava)
val publisher = (json \\ "publisher").extractOrElse[String](null)
if (publisher != null)
result.setPublisher(OafMapperUtils.field(publisher, null))
val language: String = (json \\ "language").extractOrElse[String](null)
if (language != null)
result.setLanguage(vocabularies.getSynonymAsQualifier(ModelConstants.DNET_LANGUAGES, language))
val instance = result.getInstance().get(0)
val client = (json \ "relationships" \ "client" \\ "id").extractOpt[String]
val accessRights: List[String] = for {
JObject(rightsList) <- json \\ "rightsList"
JField("rightsUri", JString(rightsUri)) <- rightsList
} yield rightsUri
val aRights: Option[AccessRight] = accessRights.map(r => {
vocabularies.getSynonymAsQualifier(ModelConstants.DNET_ACCESS_MODES, r)
}).find(q => q != null).map(q => {
val a = new AccessRight
a.setClassid(q.getClassid)
a.setClassname(q.getClassname)
a.setSchemeid(q.getSchemeid)
a.setSchemename(q.getSchemename)
a
})
val access_rights_qualifier = if (aRights.isDefined) aRights.get else OafMapperUtils.accessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE, ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
if (client.isDefined) {
val hb = hostedByMap.getOrElse(client.get.toUpperCase(), unknown_repository)
instance.setHostedby(OafMapperUtils.keyValue(generateDSId(hb.openaire_id), hb.official_name))
instance.setCollectedfrom(DATACITE_COLLECTED_FROM)
instance.setUrl(List(s"https://dx.doi.org/$doi").asJava)
instance.setAccessright(access_rights_qualifier)
instance.setPid(result.getPid)
val license = accessRights
.find(r => r.startsWith("http") && r.matches(".*(/licenses|/publicdomain|unlicense\\.org/|/legal-and-data-protection-notices|/download/license|/open-government-licence).*"))
if (license.isDefined)
instance.setLicense(OafMapperUtils.field(license.get, null))
}
val awardUris: List[String] = for {
JObject(fundingReferences) <- json \\ "fundingReferences"
JField("awardUri", JString(awardUri)) <- fundingReferences
} yield awardUri
result.setId(IdentifierFactory.createIdentifier(result))
var relations: List[Relation] = awardUris.flatMap(a => get_projectRelation(a, result.getId)).filter(r => r != null)
fix_figshare(result)
if (result.getId == null)
return List()
if (exportLinks) {
val rels: List[RelatedIdentifierType] = for {
JObject(relIdentifier) <- json \\ "relatedIdentifiers"
JField("relationType", JString(relationType)) <- relIdentifier
JField("relatedIdentifierType", JString(relatedIdentifierType)) <- relIdentifier
JField("relatedIdentifier", JString(relatedIdentifier)) <- relIdentifier
} yield RelatedIdentifierType(relationType, relatedIdentifier, relatedIdentifierType)
relations = relations ::: generateRelations(rels,result.getId, if (i_date.isDefined && i_date.get.isDefined) i_date.get.get else null)
}
if (relations != null && relations.nonEmpty) {
List(result) ::: relations
}
else
List(result)
}
private def generateRelations(rels: List[RelatedIdentifierType], id:String, date:String):List[Relation] = {
rels
.filter(r =>
subRelTypeMapping.contains(r.relationType) && (
r.relatedIdentifierType.equalsIgnoreCase("doi") ||
r.relatedIdentifierType.equalsIgnoreCase("pmid") ||
r.relatedIdentifierType.equalsIgnoreCase("arxiv"))
)
.map(r => {
val rel = new Relation
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
rel.setDataInfo(dataInfo)
val subRelType = subRelTypeMapping(r.relationType)._2
rel.setRelType(REL_TYPE_VALUE)
rel.setSubRelType(subRelType)
rel.setRelClass(r.relationType)
val dateProps:KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
rel.setProperties(List(dateProps).asJava)
rel.setSource(id)
rel.setTarget(DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier,r.relatedIdentifierType))
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
rel.getCollectedfrom.asScala.map(c => c.getValue).toList
rel
}).toList
}
def generateDataInfo(trust: String): DataInfo = {
val di = new DataInfo
di.setDeletedbyinference(false)
di.setInferred(false)
di.setInvisible(false)
di.setTrust(trust)
di.setProvenanceaction(ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER)
di
}
def generateDSId(input: String): String = {
val b = StringUtils.substringBefore(input, "::")
val a = StringUtils.substringAfter(input, "::")
s"10|$b::${DHPUtils.md5(a)}"
}
}

64
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala
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@ -1,64 +0,0 @@
package eu.dnetlib.dhp.datacite
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations
import eu.dnetlib.dhp.common.Constants.MDSTORE_DATA_PATH
import eu.dnetlib.dhp.common.Constants.MDSTORE_SIZE_PATH
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord}
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile
import eu.dnetlib.dhp.utils.ISLookupClientFactory
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object GenerateDataciteDatasetSpark {
val log: Logger = LoggerFactory.getLogger(GenerateDataciteDatasetSpark.getClass)
def main(args: Array[String]): Unit = {
val conf = new SparkConf
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/datacite/generate_dataset_params.json")).mkString)
parser.parseArgument(args)
val master = parser.get("master")
val sourcePath = parser.get("sourcePath")
val exportLinks = "true".equalsIgnoreCase(parser.get("exportLinks"))
val isLookupUrl: String = parser.get("isLookupUrl")
log.info("isLookupUrl: {}", isLookupUrl)
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
val spark: SparkSession = SparkSession.builder().config(conf)
.appName(GenerateDataciteDatasetSpark.getClass.getSimpleName)
.master(master)
.getOrCreate()
import spark.implicits._
implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord]
implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
val mapper = new ObjectMapper()
val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
val outputBasePath = cleanedMdStoreVersion.getHdfsPath
log.info("outputBasePath: {}", outputBasePath)
val targetPath = s"$outputBasePath/$MDSTORE_DATA_PATH"
spark.read.load(sourcePath).as[DataciteType]
.filter(d => d.isActive)
.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks))
.filter(d => d != null)
.flatMap(i => fixRelations(i)).filter(i => i != null)
.write.mode(SaveMode.Overwrite).save(targetPath)
val total_items = spark.read.load(targetPath).as[Oaf].count()
writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$total_items", outputBasePath + MDSTORE_SIZE_PATH)
}
}

394
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala
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package eu.dnetlib.dhp.sx.bio
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, OafMapperUtils}
import eu.dnetlib.dhp.schema.oaf._
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.{compact, parse, render}
import collection.JavaConverters._
object BioDBToOAF {
case class EBILinkItem(id: Long, links: String) {}
case class EBILinks(relType: String, date: String, title: String, pmid: String, targetPid: String, targetPidType: String, targetUrl: String) {}
case class UniprotDate(date: String, date_info: String) {}
case class ScholixResolved(pid: String, pidType: String, typology: String, tilte: List[String], datasource: List[String], date: List[String], authors: List[String]) {}
val DATA_INFO: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9")
val SUBJ_CLASS = "Keywords"
val DATE_RELATION_KEY = "RelationDate"
val resolvedURL: Map[String, String] = Map(
"genbank" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
"ncbi-n" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
"ncbi-wgs" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
"ncbi-p" -> "https://www.ncbi.nlm.nih.gov/protein/",
"ena" -> "https://www.ebi.ac.uk/ena/browser/view/",
"clinicaltrials.gov" -> "https://clinicaltrials.gov/ct2/show/",
"onim" -> "https://omim.org/entry/",
"refseq" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
"geo" -> "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="
)
val collectedFromMap: Map[String, KeyValue] = {
val PDBCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|opendoar____::d1c373ab1570cfb9a7dbb53c186b37a2", "Protein Data Bank")
val enaCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|re3data_____::c2a591f440598b63d854556beaf01591", "European Nucleotide Archive")
val ncbiCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|re3data_____::7d4f90870fe1e493232c9e86c43ae6f6", "NCBI Nucleotide")
val UNIPROTCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|re3data_____::296e1abaf1302897a6838d3588cd0310", "UniProtKB/Swiss-Prot")
val ElsevierCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|openaire____::8f87e10869299a5fe80b315695296b88", "Elsevier")
val springerNatureCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|openaire____::6e380d9cf51138baec8480f5a0ce3a2e", "Springer Nature")
val EBICollectedFrom: KeyValue = OafMapperUtils.keyValue("10|opendoar____::83e60e09c222f206c725385f53d7e567c", "EMBL-EBIs Protein Data Bank in Europe (PDBe)")
val pubmedCollectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
UNIPROTCollectedFrom.setDataInfo(DATA_INFO)
PDBCollectedFrom.setDataInfo(DATA_INFO)
ElsevierCollectedFrom.setDataInfo(DATA_INFO)
EBICollectedFrom.setDataInfo(DATA_INFO)
pubmedCollectedFrom.setDataInfo(DATA_INFO)
enaCollectedFrom.setDataInfo(DATA_INFO)
ncbiCollectedFrom.setDataInfo(DATA_INFO)
springerNatureCollectedFrom.setDataInfo(DATA_INFO)
Map(
"uniprot" -> UNIPROTCollectedFrom,
"pdb" -> PDBCollectedFrom,
"elsevier" -> ElsevierCollectedFrom,
"ebi" -> EBICollectedFrom,
"Springer Nature" -> springerNatureCollectedFrom,
"NCBI Nucleotide" -> ncbiCollectedFrom,
"European Nucleotide Archive" -> enaCollectedFrom,
"Europe PMC" -> pubmedCollectedFrom
)
}
def crossrefLinksToOaf(input: String): Oaf = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val source_pid = (json \ "Source" \ "Identifier" \ "ID").extract[String].toLowerCase
val source_pid_type = (json \ "Source" \ "Identifier" \ "IDScheme").extract[String].toLowerCase
val target_pid = (json \ "Target" \ "Identifier" \ "ID").extract[String].toLowerCase
val target_pid_type = (json \ "Target" \ "Identifier" \ "IDScheme").extract[String].toLowerCase
val relation_semantic = (json \ "RelationshipType" \ "Name").extract[String]
val date = GraphCleaningFunctions.cleanDate((json \ "LinkedPublicationDate").extract[String])
createRelation(target_pid, target_pid_type, generate_unresolved_id(source_pid, source_pid_type), collectedFromMap("elsevier"), "relationship", relation_semantic, date)
}
def scholixResolvedToOAF(input: ScholixResolved): Oaf = {
val d = new Dataset
d.setPid(
List(
OafMapperUtils.structuredProperty(input.pid.toLowerCase, input.pidType.toLowerCase, input.pidType.toLowerCase, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, DATA_INFO)
).asJava
)
d.setDataInfo(DATA_INFO)
val nsPrefix = input.pidType.toLowerCase.padTo(12, '_')
d.setId(OafMapperUtils.createOpenaireId(50, s"$nsPrefix::${input.pid.toLowerCase}", true))
if (input.tilte != null && input.tilte.nonEmpty)
d.setTitle(List(OafMapperUtils.structuredProperty(input.tilte.head, ModelConstants.MAIN_TITLE_QUALIFIER, DATA_INFO)).asJava)
d.setOriginalId(List(input.pid).asJava)
val i = new Instance
i.setPid(d.getPid)
if (resolvedURL.contains(input.pidType)) {
i.setUrl(List(s"${resolvedURL(input.pidType)}${input.pid}").asJava)
}
if (input.pidType.equalsIgnoreCase("clinicaltrials.gov"))
i.setInstancetype(OafMapperUtils.qualifier("0037", "Clinical Trial", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
else
i.setInstancetype(OafMapperUtils.qualifier("0046", "Bioentity", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
if (input.datasource == null || input.datasource.isEmpty)
return null
val ds = input.datasource.head
d.setCollectedfrom(List(collectedFromMap(ds)).asJava)
i.setCollectedfrom(collectedFromMap(ds))
d.setInstance(List(i).asJava)
if (input.authors != null && input.authors.nonEmpty) {
val authors = input.authors.map(a => {
val authorOAF = new Author
authorOAF.setFullname(a)
authorOAF
})
d.setAuthor(authors.asJava)
}
if (input.date != null && input.date.nonEmpty) {
val dt = input.date.head
i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
}
d
}
def uniprotToOAF(input: String): List[Oaf] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val pid = (json \ "pid").extract[String]
val d = new Dataset
d.setPid(
List(
OafMapperUtils.structuredProperty(pid, "uniprot", "uniprot", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, DATA_INFO)
).asJava
)
d.setDataInfo(DATA_INFO)
d.setId(OafMapperUtils.createOpenaireId(50, s"uniprot_____::$pid", true))
d.setCollectedfrom(List(collectedFromMap("uniprot")).asJava)
val title: String = (json \ "title").extractOrElse[String](null)
if (title != null)
d.setTitle(List(OafMapperUtils.structuredProperty(title, ModelConstants.MAIN_TITLE_QUALIFIER, DATA_INFO)).asJava)
d.setOriginalId(List(pid).asJava)
val i = new Instance
i.setPid(d.getPid)
i.setUrl(List(s"https://www.uniprot.org/uniprot/$pid").asJava)
i.setInstancetype(OafMapperUtils.qualifier("0046", "Bioentity", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
i.setCollectedfrom(collectedFromMap("uniprot"))
d.setInstance(List(i).asJava)
val dates: List[UniprotDate] = for {
JObject(dateOBJ) <- json \ "dates"
JField("date", JString(date)) <- dateOBJ
JField("date_info", JString(date_info)) <- dateOBJ
} yield UniprotDate(GraphCleaningFunctions.cleanDate(date), date_info)
val subjects: List[String] = (json \\ "subjects").extractOrElse[List[String]](null)
if (subjects != null) {
d.setSubject(
subjects.map(s =>
OafMapperUtils.structuredProperty(s, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, null)
).asJava)
}
var i_date: Option[UniprotDate] = None
if (dates.nonEmpty) {
i_date = dates.find(d => d.date_info.contains("entry version"))
if (i_date.isDefined) {
i.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
}
val relevant_dates: List[StructuredProperty] = dates.filter(d => !d.date_info.contains("entry version"))
.map(date => OafMapperUtils.structuredProperty(date.date, ModelConstants.UNKNOWN, ModelConstants.UNKNOWN, ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO))
if (relevant_dates != null && relevant_dates.nonEmpty)
d.setRelevantdate(relevant_dates.asJava)
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
}
val references_pmid: List[String] = for {
JObject(reference) <- json \ "references"
JField("PubMed", JString(pid)) <- reference
} yield pid
val references_doi: List[String] = for {
JObject(reference) <- json \ "references"
JField(" DOI", JString(pid)) <- reference
} yield pid
if (references_pmid != null && references_pmid.nonEmpty) {
val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null)
rel.getCollectedfrom
List(d, rel)
}
else if (references_doi != null && references_doi.nonEmpty) {
val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null)
List(d, rel)
}
else
List(d)
}
def generate_unresolved_id(pid: String, pidType: String): String = {
s"unresolved::$pid::$pidType"
}
def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType: String, relClass: String, date: String): Relation = {
val rel = new Relation
rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava)
rel.setDataInfo(DATA_INFO)
rel.setRelType(ModelConstants.RESULT_RESULT)
rel.setSubRelType(subRelType)
rel.setRelClass(relClass)
rel.setSource(sourceId)
rel.setTarget(s"unresolved::$pid::$pidType")
val dateProps: KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
rel.setProperties(List(dateProps).asJava)
rel.getTarget.startsWith("unresolved")
rel.setCollectedfrom(List(collectedFrom).asJava)
rel
}
def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date: String): Relation = {
createRelation(pid, pidType, sourceId, collectedFrom, ModelConstants.SUPPLEMENT, ModelConstants.IS_SUPPLEMENT_TO, date)
}
def pdbTOOaf(input: String): List[Oaf] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val pdb = (json \ "pdb").extract[String].toLowerCase
if (pdb.isEmpty)
return List()
val d = new Dataset
d.setPid(
List(
OafMapperUtils.structuredProperty(pdb, "pdb", "Protein Data Bank Identifier", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, DATA_INFO)
).asJava
)
d.setCollectedfrom(List(collectedFromMap("pdb")).asJava)
d.setDataInfo(DATA_INFO)
d.setId(OafMapperUtils.createOpenaireId(50, s"pdb_________::$pdb", true))
d.setOriginalId(List(pdb).asJava)
val title = (json \ "title").extractOrElse[String](null)
if (title == null)
return List()
d.setTitle(List(OafMapperUtils.structuredProperty(title, ModelConstants.MAIN_TITLE_QUALIFIER, DATA_INFO)).asJava)
val authors: List[String] = (json \ "authors").extractOrElse[List[String]](null)
if (authors != null) {
val convertedAuthors = authors.zipWithIndex.map { a =>
val res = new Author
res.setFullname(a._1)
res.setRank(a._2 + 1)
res
}
d.setAuthor(convertedAuthors.asJava)
}
val i = new Instance
i.setPid(d.getPid)
i.setUrl(List(s"https://www.rcsb.org/structure/$pdb").asJava)
i.setInstancetype(OafMapperUtils.qualifier("0046", "Bioentity", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
i.setCollectedfrom(collectedFromMap("pdb"))
d.setInstance(List(i).asJava)
val pmid = (json \ "pmid").extractOrElse[String](null)
if (pmid != null)
List(d, createSupplementaryRelation(pmid, "pmid", d.getId, collectedFromMap("pdb"), null))
else
List(d)
}
def extractEBILinksFromDump(input: String): EBILinkItem = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val pmid = (json \ "publication" \ "pmid").extract[String]
val links = (json \ "links").extract[JObject]
EBILinkItem(pmid.toLong, compact(render(links)))
}
def EBITargetLinksFilter(input: EBILinks): Boolean = {
input.targetPidType.equalsIgnoreCase("ena") || input.targetPidType.equalsIgnoreCase("pdb") || input.targetPidType.equalsIgnoreCase("uniprot")
}
def parse_ebi_links(input: String): List[EBILinks] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val pmid = (json \ "request" \ "id").extract[String]
for {
JObject(link) <- json \\ "Link"
JField("Target", JObject(target)) <- link
JField("RelationshipType", JObject(relType)) <- link
JField("Name", JString(relation)) <- relType
JField("PublicationDate", JString(publicationDate)) <- link
JField("Title", JString(title)) <- target
JField("Identifier", JObject(identifier)) <- target
JField("IDScheme", JString(idScheme)) <- identifier
JField("IDURL", JString(idUrl)) <- identifier
JField("ID", JString(id)) <- identifier
} yield EBILinks(relation, GraphCleaningFunctions.cleanDate(publicationDate), title, pmid, id, idScheme, idUrl)
}
def convertEBILinksToOaf(input: EBILinks): List[Oaf] = {
val d = new Dataset
d.setCollectedfrom(List(collectedFromMap("ebi")).asJava)
d.setDataInfo(DATA_INFO)
d.setTitle(List(OafMapperUtils.structuredProperty(input.title, ModelConstants.MAIN_TITLE_QUALIFIER, DATA_INFO)).asJava)
val nsPrefix = input.targetPidType.toLowerCase.padTo(12, '_')
d.setId(OafMapperUtils.createOpenaireId(50, s"$nsPrefix::${input.targetPid.toLowerCase}", true))
d.setOriginalId(List(input.targetPid.toLowerCase).asJava)
d.setPid(
List(
OafMapperUtils.structuredProperty(input.targetPid.toLowerCase, input.targetPidType.toLowerCase, "Protein Data Bank Identifier", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, DATA_INFO)
).asJava
)
val i = new Instance
i.setPid(d.getPid)
i.setUrl(List(input.targetUrl).asJava)
i.setInstancetype(OafMapperUtils.qualifier("0046", "Bioentity", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
i.setCollectedfrom(collectedFromMap("ebi"))
d.setInstance(List(i).asJava)
i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO))
d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO))
List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, GraphCleaningFunctions.cleanDate(input.date)))
}
}

146
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala
View File

@ -1,146 +0,0 @@
package eu.dnetlib.dhp.sx.bio.pubmed
import scala.xml.MetaData
import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
/**
*
* @param xml
*/
class PMParser(xml:XMLEventReader) extends Iterator[PMArticle] {
var currentArticle:PMArticle = generateNextArticle()
override def hasNext: Boolean = currentArticle!= null
override def next(): PMArticle = {
val tmp = currentArticle
currentArticle = generateNextArticle()
tmp
}
def extractAttributes(attrs:MetaData, key:String):String = {
val res = attrs.get(key)
if (res.isDefined) {
val s =res.get
if (s != null && s.nonEmpty)
s.head.text
else
null
}
else null
}
def validate_Date(year:String, month:String, day:String):String = {
try {
f"${year.toInt}-${month.toInt}%02d-${day.toInt}%02d"
} catch {
case _: Throwable =>null
}
}
def generateNextArticle():PMArticle = {
var currentSubject:PMSubject = null
var currentAuthor: PMAuthor = null
var currentJournal: PMJournal = null
var currentGrant: PMGrant = null
var currNode: String = null
var currentYear = "0"
var currentMonth = "01"
var currentDay = "01"
var currentArticleType:String = null
while (xml.hasNext) {
xml.next match {
case EvElemStart(_, label, attrs, _) =>
currNode = label
label match {
case "PubmedArticle" => currentArticle = new PMArticle
case "Author" => currentAuthor = new PMAuthor
case "Journal" => currentJournal = new PMJournal
case "Grant" => currentGrant = new PMGrant
case "PublicationType" | "DescriptorName" =>
currentSubject = new PMSubject
currentSubject.setMeshId(extractAttributes(attrs, "UI"))
case "ArticleId" => currentArticleType = extractAttributes(attrs,"IdType")
case _ =>
}
case EvElemEnd(_, label) =>
label match {
case "PubmedArticle" => return currentArticle
case "Author" => currentArticle.getAuthors.add(currentAuthor)
case "Journal" => currentArticle.setJournal(currentJournal)
case "Grant" => currentArticle.getGrants.add(currentGrant)
case "PubMedPubDate" => if (currentArticle.getDate== null)
currentArticle.setDate(validate_Date(currentYear,currentMonth,currentDay))
case "PubDate" => currentJournal.setDate(s"$currentYear-$currentMonth-$currentDay")
case "DescriptorName" => currentArticle.getSubjects.add(currentSubject)
case "PublicationType" =>currentArticle.getPublicationTypes.add(currentSubject)
case _ =>
}
case EvText(text) =>
if (currNode!= null && text.trim.nonEmpty)
currNode match {
case "ArticleTitle" => {
if (currentArticle.getTitle==null)
currentArticle.setTitle(text.trim)
else
currentArticle.setTitle(currentArticle.getTitle + text.trim)
}
case "AbstractText" => {
if (currentArticle.getDescription==null)
currentArticle.setDescription(text.trim)
else
currentArticle.setDescription(currentArticle.getDescription + text.trim)
}
case "PMID" => currentArticle.setPmid(text.trim)
case "ArticleId" => if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim)
case "Language" => currentArticle.setLanguage(text.trim)
case "ISSN" => currentJournal.setIssn(text.trim)
case "GrantID" => currentGrant.setGrantID(text.trim)
case "Agency" => currentGrant.setAgency(text.trim)
case "Country" => if (currentGrant != null) currentGrant.setCountry(text.trim)
case "Year" => currentYear = text.trim
case "Month" => currentMonth = text.trim
case "Day" => currentDay = text.trim
case "Volume" => currentJournal.setVolume( text.trim)
case "Issue" => currentJournal.setIssue (text.trim)
case "PublicationType" | "DescriptorName" => currentSubject.setValue(text.trim)
case "LastName" => {
if (currentAuthor != null)
currentAuthor.setLastName(text.trim)
}
case "ForeName" => if (currentAuthor != null)
currentAuthor.setForeName(text.trim)
case "Title" =>
if (currentJournal.getTitle==null)
currentJournal.setTitle(text.trim)
else
currentJournal.setTitle(currentJournal.getTitle + text.trim)
case _ =>
}
case _ =>
}
}
null
}
}

32
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json
View File

@ -1,32 +0,0 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "rtn",
"paramLongName": "resultTableName",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "bsp",
"paramLongName": "bipScorePath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
}
]

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/config-default.xml → dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/config-default.xml
View File

@ -27,4 +27,4 @@
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>
</configuration>

173
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml
View File

@ -1,9 +1,5 @@
<workflow-app name="BipFinderScore" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>inputPath</name>
<description>the input path of the resources to be extended</description>
</property>
<property>
<name>bipScorePath</name>
@ -13,8 +9,61 @@
<name>outputPath</name>
<description>the path where to store the actionset</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="deleteoutputpath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
@ -30,14 +79,8 @@
<error to="Kill"/>
</action>
<fork name="atomicactions">
<path start="atomicactions_publication"/>
<path start="atomicactions_dataset"/>
<path start="atomicactions_orp"/>
<path start="atomicactions_software"/>
</fork>
<action name="atomicactions_publication">
<action name="atomicactions">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
@ -54,113 +97,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/publication</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<action name="atomicactions_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for datasets</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/dataset</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<action name="atomicactions_orp">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for orp</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<action name="atomicactions_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for software</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/software</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<join name="join_aa" to="collectandsave"/>
<action name="collectandsave">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>saves all the aa produced for the several types of results in the as output path</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.CollectAndSave</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${workingDir}</arg>
<arg>--inputPath</arg><arg>${bipScorePath}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>

14
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_fos_parameters.json → dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_parameters.json
View File

@ -19,15 +19,9 @@
"paramRequired": false
},
{
"paramName": "hnn",
"paramLongName": "hdfsNameNode",
"paramDescription": "the path used to store the HostedByMap",
"paramRequired": true
},
{
"paramName": "cfn",
"paramLongName": "classForName",
"paramDescription": "the path used to store the HostedByMap",
"paramRequired": true
"paramName": "d",
"paramLongName": "delimiter",
"paramDescription": "the delimiter if different from the default one (,)",
"paramRequired": false
}
]

73
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml
View File

@ -79,6 +79,7 @@
<fork name="prepareInfo">
<path start="prepareBip"/>
<path start="getFOS"/>
<path start="getSDG"/>
</fork>
<action name="prepareBip">
@ -106,17 +107,30 @@
</action>
<action name="getFOS">
<java>
<main-class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSData</main-class>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Gets Data from FOS csv file</name>
<class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSSparkJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${fosPath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/input/fos</arg>
<arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel</arg>
</java>
</spark>
<ok to="prepareFos"/>
<error to="Kill"/>
</action>
<action name="prepareFos">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -142,6 +156,55 @@
<error to="Kill"/>
</action>
<action name="getSDG">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Gets Data from SDG csv file</name>
<class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetSDGSparkJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sdgPath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/input/sdg</arg>
</spark>
<ok to="prepareSDG"/>
<error to="Kill"/>
</action>
<action name="prepareSDG">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the unresolved from FOS!</name>
<class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareSDGSparkJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/input/sdg</arg>
<arg>--outputPath</arg><arg>${workingDir}/prepared</arg>
</spark>
<ok to="join"/>
<error to="Kill"/>
</action>
<join name="join" to="produceUnresolved"/>

37
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json Normal file
View File

@ -0,0 +1,37 @@
[
{
"paramName": "wp",
"paramLongName": "workingPath",
"paramDescription": "the zipped opencitations file",
"paramRequired": true
},
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "the hdfs name node",
"paramRequired": false
},
{
"paramName": "d",
"paramLongName": "delimiter",
"paramDescription": "the hdfs name node",
"paramRequired": false
},
{
"paramName": "op",
"paramLongName": "outputPath",
"paramDescription": "the hdfs name node",
"paramRequired": true
},
{
"paramName": "if",
"paramLongName": "inputFile",
"paramDescription": "the hdfs name node",
"paramRequired": true
}
]

29
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml
View File

@ -26,6 +26,7 @@
<switch>
<case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
<case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</case>
<case to="read">${wf:conf('resumeFrom') eq 'ReadContent'}</case>
<default to="create_actionset"/> <!-- first action to be done when downloadDump is to be performed -->
</switch>
</decision>
@ -60,6 +61,32 @@
<arg>--inputFile</arg><arg>${inputFile}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</java>
<ok to="read"/>
<error to="Kill"/>
</action>
<action name="read">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the AS for OC</name>
<class>eu.dnetlib.dhp.actionmanager.opencitations.ReadCOCI</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}/COCI</arg>
<arg>--outputPath</arg><arg>${workingPath}/COCI_JSON</arg>
<arg>--delimiter</arg><arg>${delimiter}</arg>
<arg>--inputFile</arg><arg>${inputFileCoci}</arg>
</spark>
<ok to="create_actionset"/>
<error to="Kill"/>
</action>
@ -81,7 +108,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${workingPath}/COCI</arg>
<arg>--inputPath</arg><arg>${workingPath}/COCI_JSON</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>

63
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/create_updated_hb_map.py Normal file
View File

@ -0,0 +1,63 @@
from urllib.request import urlopen
import json
def retrieve_datacite_clients(base_url):
datacite_clients = {}
while base_url is not None:
with urlopen(base_url) as response:
print(f"requesting {base_url}")
response_content = response.read()
data = json.loads(response_content)
if 'data' in data and len(data['data'])>0:
for item in data['data']:
datacite_clients[item['id'].lower()]= item['attributes']['re3data'].lower().replace("https://doi.org/","")
base_url = data['links']['next']
else:
base_url = None
return datacite_clients
def retrieve_r3data(start_url):
r3data_clients = {}
page_number = 1
base_url = start_url
while base_url is not None:
with urlopen(base_url) as response:
print(f"requesting {base_url}")
response_content = response.read()
data = json.loads(response_content)
if 'data' in data and len(data['data'])>0:
for item in data['data']:
r3data_clients[item['id'].lower()]= dict(
openaire_id= "re3data_____::"+item['attributes']['re3dataId'].lower(),
official_name=item['attributes']['repositoryName']
)
page_number +=1
base_url = f"{start_url}&page[number]={page_number}"
else:
base_url = None
return r3data_clients
base_url ="https://api.datacite.org/clients?query=re3data_id:*&page[size]=250"
dc = retrieve_datacite_clients(base_url)
r3 = retrieve_r3data("https://api.datacite.org/re3data?page[size]=250")
result = {}
for item in dc:
res = dc[item].lower()
if res not in r3:
print(f"missing {res} for {item} in dictionary")
else:
result[item.upper()]= dict(openaire_id=r3[res]["openaire_id"],datacite_name=r3[res]["official_name"], official_name=r3[res]["official_name"] )
with open('hostedBy_map.json', 'w', encoding='utf8') as json_file:
json.dump(result, json_file, ensure_ascii=False, indent=1)

2070
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json
View File

File diff suppressed because it is too large Load Diff

19
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/graph/datacite/oozie_app/config-default.xml Normal file
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@ -0,0 +1,19 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

62
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/graph/datacite/oozie_app/workflow.xml Normal file
View File

@ -0,0 +1,62 @@
<workflow-app name="Retrieve Scholix Update" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path of scholix graph</description>
</property>
<property>
<name>datacitePath</name>
<description>the datacite native path</description>
</property>
<property>
<name>workingSupportPath</name>
<description>the working Support path</description>
</property>
<property>
<name>isLookupUrl</name>
<description>The IS lookUp service endopoint</description>
</property>
<property>
<name>updateDS</name>
<value>false</value>
<description>The transformation Rule to apply</description>
</property>
</parameters>
<start to="RetrieveDeltaDatacite"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="RetrieveDeltaDatacite">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>New Update from Datacite to Scholix</name>
<class>eu.dnetlib.dhp.sx.graph.SparkRetrieveDataciteDelta</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=6000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--datacitePath</arg><arg>${datacitePath}</arg>
<arg>--master</arg><arg>yarn</arg>
<arg>--workingSupportPath</arg><arg>${workingSupportPath}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--updateDS</arg><arg>${updateDS}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

41
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/graph/retrieve_datacite_delta_params.json Normal file
View File

@ -0,0 +1,41 @@
[
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the source mdstore path",
"paramRequired": true
},
{
"paramName": "d",
"paramLongName": "datacitePath",
"paramDescription": "the datacite native path",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingSupportPath",
"paramDescription": "the working Support path",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "isLookupUrl",
"paramDescription": "the isLookup URL",
"paramRequired": true
},
{
"paramName": "m",
"paramLongName": "master",
"paramDescription": "the master name",
"paramRequired": true
},
{
"paramName": "u",
"paramLongName": "updateDS",
"paramDescription": "Need to regenerate all support Dataset",
"paramRequired": false
}
]

3
dhp-workflows/dhp-aggregation/src/main/resources/log4j.properties
View File

@ -7,3 +7,6 @@ log4j.appender.A1=org.apache.log4j.ConsoleAppender
# A1 uses PatternLayout.
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
log4j.logger.org.apache.spark=FATAL
log4j.logger.org.spark_project=FATAL

34
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/CollectionUtils.scala
View File

@ -1,20 +1,20 @@
package eu.dnetlib.dhp.collection
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.common.ModelSupport
import eu.dnetlib.dhp.schema.oaf.{Oaf, OafEntity, Relation}
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode}
object CollectionUtils {
/**
* This method in pipeline to the transformation phase,
* generates relations in both verse, typically it should be a phase of flatMap
*
* @param i input OAF
* @return
* If the input OAF is an entity -> List(i)
* If the input OAF is a relation -> List(relation, inverseRelation)
*
*/
/** This method in pipeline to the transformation phase,
* generates relations in both verse, typically it should be a phase of flatMap
*
* @param i input OAF
* @return
* If the input OAF is an entity -> List(i)
* If the input OAF is a relation -> List(relation, inverseRelation)
*/
def fixRelations(i: Oaf): List[Oaf] = {
if (i.isInstanceOf[OafEntity])
@ -46,4 +46,18 @@ object CollectionUtils {
List()
}
def saveDataset(dataset: Dataset[Oaf], targetPath: String): Unit = {
implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
val mapper = new ObjectMapper
dataset
.flatMap(i => CollectionUtils.fixRelations(i))
.filter(i => i != null)
.map(r => mapper.writeValueAsString(r))(Encoders.STRING)
.write
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.text(targetPath)
}
}

16
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/AbstractRestClient.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/AbstractRestClient.scala
View File

@ -6,7 +6,6 @@ import org.apache.http.client.methods.{HttpGet, HttpPost, HttpUriRequest}
import org.apache.http.entity.StringEntity
import org.apache.http.impl.client.HttpClientBuilder
abstract class AbstractRestClient extends Iterator[String] {
var buffer: List[String] = List()
@ -16,12 +15,10 @@ abstract class AbstractRestClient extends Iterator[String] {
var complete: Boolean = false
def extractInfo(input: String): Unit
protected def getBufferData(): Unit
def doHTTPGETRequest(url: String): String = {
val httpGet = new HttpGet(url)
doHTTPRequest(httpGet)
@ -43,7 +40,6 @@ abstract class AbstractRestClient extends Iterator[String] {
buffer.nonEmpty && current_index < buffer.size
}
override def next(): String = {
val next_item: String = buffer(current_index)
current_index = current_index + 1
@ -52,13 +48,14 @@ abstract class AbstractRestClient extends Iterator[String] {
next_item
}
private def doHTTPRequest[A <: HttpUriRequest](r: A): String = {
val timeout = 60; // seconds
val config = RequestConfig.custom()
val config = RequestConfig
.custom()
.setConnectTimeout(timeout * 1000)
.setConnectionRequestTimeout(timeout * 1000)
.setSocketTimeout(timeout * 1000).build()
.setSocketTimeout(timeout * 1000)
.build()
val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
try {
var tries = 4
@ -69,8 +66,7 @@ abstract class AbstractRestClient extends Iterator[String] {
println(s"get response with status${response.getStatusLine.getStatusCode}")
if (response.getStatusLine.getStatusCode > 400) {
tries -= 1
}
else
} else
return IOUtils.toString(response.getEntity.getContent)
} catch {
case e: Throwable =>
@ -87,4 +83,4 @@ abstract class AbstractRestClient extends Iterator[String] {
}
getBufferData()
}
}

12
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteAPIImporter.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteAPIImporter.scala
View File

@ -3,7 +3,7 @@ package eu.dnetlib.dhp.datacite
import org.json4s.jackson.JsonMethods.{compact, parse, render}
import org.json4s.{DefaultFormats, JValue}
class DataciteAPIImporter(timestamp: Long = 0, blocks: Long = 10, until:Long = -1) extends AbstractRestClient {
class DataciteAPIImporter(timestamp: Long = 0, blocks: Long = 10, until: Long = -1) extends AbstractRestClient {
override def extractInfo(input: String): Unit = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
@ -16,16 +16,18 @@ class DataciteAPIImporter(timestamp: Long = 0, blocks: Long = 10, until:Long = -
current_index = 0
}
def get_url():String ={
val to = if (until> 0) s"$until" else "*"
def get_url(): String = {
val to = if (until > 0) s"$until" else "*"
s"https://api.datacite.org/dois?page[cursor]=1&page[size]=$blocks&query=updated:[$timestamp%20TO%20$to]"
}
override def getBufferData(): Unit = {
if (!complete) {
val response = if (scroll_value.isDefined) doHTTPGETRequest(scroll_value.get) else doHTTPGETRequest(get_url())
val response =
if (scroll_value.isDefined) doHTTPGETRequest(scroll_value.get)
else doHTTPGETRequest(get_url())
extractInfo(response)
}
}
}
}

278
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteModelConstants.scala Normal file
View File

@ -0,0 +1,278 @@
package eu.dnetlib.dhp.datacite
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
import java.io.InputStream
import java.time.format.DateTimeFormatter
import java.util.Locale
import java.util.regex.Pattern
import scala.io.Source
/** This class represent the dataModel of the input Dataset of Datacite
* @param doi THE DOI
* @param timestamp timestamp of last update date
* @param isActive the record is active or deleted
* @param json the json native records
*/
case class DataciteType(doi: String, timestamp: Long, isActive: Boolean, json: String) {}
/*
The following class are utility class used for the mapping from
json datacite to OAF Shema
*/
case class RelatedIdentifierType(
relationType: String,
relatedIdentifier: String,
relatedIdentifierType: String
) {}
case class NameIdentifiersType(
nameIdentifierScheme: Option[String],
schemeUri: Option[String],
nameIdentifier: Option[String]
) {}
case class CreatorType(
nameType: Option[String],
nameIdentifiers: Option[List[NameIdentifiersType]],
name: Option[String],
familyName: Option[String],
givenName: Option[String],
affiliation: Option[List[String]]
) {}
case class TitleType(title: Option[String], titleType: Option[String], lang: Option[String]) {}
case class SubjectType(subject: Option[String], subjectScheme: Option[String]) {}
case class DescriptionType(descriptionType: Option[String], description: Option[String]) {}
case class FundingReferenceType(
funderIdentifierType: Option[String],
awardTitle: Option[String],
awardUri: Option[String],
funderName: Option[String],
funderIdentifier: Option[String],
awardNumber: Option[String]
) {}
case class DateType(date: Option[String], dateType: Option[String]) {}
case class OAFRelations(relation: String, inverse: String, relType: String)
class DataciteModelConstants extends Serializable {}
object DataciteModelConstants {
val REL_TYPE_VALUE: String = "resultResult"
val DATE_RELATION_KEY = "RelationDate"
val DATACITE_FILTER_PATH = "/eu/dnetlib/dhp/datacite/datacite_filter"
val DOI_CLASS = "doi"
val SUBJ_CLASS = "keywords"
val DATACITE_NAME = "Datacite"
val dataInfo: DataInfo = dataciteDataInfo("0.9")
val DATACITE_COLLECTED_FROM: KeyValue =
OafMapperUtils.keyValue(ModelConstants.DATACITE_ID, DATACITE_NAME)
val subRelTypeMapping: Map[String, OAFRelations] = Map(
ModelConstants.REFERENCES -> OAFRelations(
ModelConstants.REFERENCES,
ModelConstants.IS_REFERENCED_BY,
ModelConstants.RELATIONSHIP
),
ModelConstants.IS_REFERENCED_BY -> OAFRelations(
ModelConstants.IS_REFERENCED_BY,
ModelConstants.REFERENCES,
ModelConstants.RELATIONSHIP
),
ModelConstants.IS_SUPPLEMENTED_BY -> OAFRelations(
ModelConstants.IS_SUPPLEMENTED_BY,
ModelConstants.IS_SUPPLEMENT_TO,
ModelConstants.SUPPLEMENT
),
ModelConstants.IS_SUPPLEMENT_TO -> OAFRelations(
ModelConstants.IS_SUPPLEMENT_TO,
ModelConstants.IS_SUPPLEMENTED_BY,
ModelConstants.SUPPLEMENT
),
ModelConstants.HAS_PART -> OAFRelations(
ModelConstants.HAS_PART,
ModelConstants.IS_PART_OF,
ModelConstants.PART
),
ModelConstants.IS_PART_OF -> OAFRelations(
ModelConstants.IS_PART_OF,
ModelConstants.HAS_PART,
ModelConstants.PART
),
ModelConstants.IS_VERSION_OF -> OAFRelations(
ModelConstants.IS_VERSION_OF,
ModelConstants.HAS_VERSION,
ModelConstants.VERSION
),
ModelConstants.HAS_VERSION -> OAFRelations(
ModelConstants.HAS_VERSION,
ModelConstants.IS_VERSION_OF,
ModelConstants.VERSION
),
ModelConstants.IS_IDENTICAL_TO -> OAFRelations(
ModelConstants.IS_IDENTICAL_TO,
ModelConstants.IS_IDENTICAL_TO,
ModelConstants.RELATIONSHIP
),
ModelConstants.IS_CONTINUED_BY -> OAFRelations(
ModelConstants.IS_CONTINUED_BY,
ModelConstants.CONTINUES,
ModelConstants.RELATIONSHIP
),
ModelConstants.CONTINUES -> OAFRelations(
ModelConstants.CONTINUES,
ModelConstants.IS_CONTINUED_BY,
ModelConstants.RELATIONSHIP
),
ModelConstants.IS_NEW_VERSION_OF -> OAFRelations(
ModelConstants.IS_NEW_VERSION_OF,
ModelConstants.IS_PREVIOUS_VERSION_OF,
ModelConstants.VERSION
),
ModelConstants.IS_PREVIOUS_VERSION_OF -> OAFRelations(
ModelConstants.IS_PREVIOUS_VERSION_OF,
ModelConstants.IS_NEW_VERSION_OF,
ModelConstants.VERSION
),
ModelConstants.IS_DOCUMENTED_BY -> OAFRelations(
ModelConstants.IS_DOCUMENTED_BY,
ModelConstants.DOCUMENTS,
ModelConstants.RELATIONSHIP
),
ModelConstants.DOCUMENTS -> OAFRelations(
ModelConstants.DOCUMENTS,
ModelConstants.IS_DOCUMENTED_BY,
ModelConstants.RELATIONSHIP
),
ModelConstants.IS_SOURCE_OF -> OAFRelations(
ModelConstants.IS_SOURCE_OF,
ModelConstants.IS_DERIVED_FROM,
ModelConstants.VERSION
),
ModelConstants.IS_DERIVED_FROM -> OAFRelations(
ModelConstants.IS_DERIVED_FROM,
ModelConstants.IS_SOURCE_OF,
ModelConstants.VERSION
),
ModelConstants.CITES -> OAFRelations(
ModelConstants.CITES,
ModelConstants.IS_CITED_BY,
ModelConstants.CITATION
),
ModelConstants.IS_CITED_BY -> OAFRelations(
ModelConstants.IS_CITED_BY,
ModelConstants.CITES,
ModelConstants.CITATION
),
ModelConstants.IS_VARIANT_FORM_OF -> OAFRelations(
ModelConstants.IS_VARIANT_FORM_OF,
ModelConstants.IS_DERIVED_FROM,
ModelConstants.VERSION
),
ModelConstants.IS_OBSOLETED_BY -> OAFRelations(
ModelConstants.IS_OBSOLETED_BY,
ModelConstants.IS_NEW_VERSION_OF,
ModelConstants.VERSION
),
ModelConstants.REVIEWS -> OAFRelations(
ModelConstants.REVIEWS,
ModelConstants.IS_REVIEWED_BY,
ModelConstants.REVIEW
),
ModelConstants.IS_REVIEWED_BY -> OAFRelations(
ModelConstants.IS_REVIEWED_BY,
ModelConstants.REVIEWS,
ModelConstants.REVIEW
),
ModelConstants.DOCUMENTS -> OAFRelations(
ModelConstants.DOCUMENTS,
ModelConstants.IS_DOCUMENTED_BY,
ModelConstants.RELATIONSHIP
),
ModelConstants.IS_DOCUMENTED_BY -> OAFRelations(
ModelConstants.IS_DOCUMENTED_BY,
ModelConstants.DOCUMENTS,
ModelConstants.RELATIONSHIP
),
ModelConstants.COMPILES -> OAFRelations(
ModelConstants.COMPILES,
ModelConstants.IS_COMPILED_BY,
ModelConstants.RELATIONSHIP
),
ModelConstants.IS_COMPILED_BY -> OAFRelations(
ModelConstants.IS_COMPILED_BY,
ModelConstants.COMPILES,
ModelConstants.RELATIONSHIP
)
)
val datacite_filter: List[String] = {
val stream: InputStream = getClass.getResourceAsStream(DATACITE_FILTER_PATH)
require(stream != null)
Source.fromInputStream(stream).getLines().toList
}
def dataciteDataInfo(trust: String): DataInfo = OafMapperUtils.dataInfo(
false,
null,
false,
false,
ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER,
trust
)
val df_en: DateTimeFormatter = DateTimeFormatter.ofPattern(
"[MM-dd-yyyy][MM/dd/yyyy][dd-MM-yy][dd-MMM-yyyy][dd/MMM/yyyy][dd-MMM-yy][dd/MMM/yy][dd-MM-yy][dd/MM/yy][dd-MM-yyyy][dd/MM/yyyy][yyyy-MM-dd][yyyy/MM/dd]",
Locale.ENGLISH
)
val df_it: DateTimeFormatter =
DateTimeFormatter.ofPattern("[dd-MM-yyyy][dd/MM/yyyy]", Locale.ITALIAN)
val funder_regex: List[(Pattern, String)] = List(
(
Pattern.compile(
"(info:eu-repo/grantagreement/ec/h2020/)(\\d\\d\\d\\d\\d\\d)(.*)",
Pattern.MULTILINE | Pattern.CASE_INSENSITIVE
),
"40|corda__h2020::"
),
(
Pattern.compile(
"(info:eu-repo/grantagreement/ec/fp7/)(\\d\\d\\d\\d\\d\\d)(.*)",
Pattern.MULTILINE | Pattern.CASE_INSENSITIVE
),
"40|corda_______::"
)
)
val Date_regex: List[Pattern] = List(
//Y-M-D
Pattern.compile(
"(18|19|20)\\d\\d([- /.])(0[1-9]|1[012])\\2(0[1-9]|[12][0-9]|3[01])",
Pattern.MULTILINE
),
//M-D-Y
Pattern.compile(
"((0[1-9]|1[012])|([1-9]))([- /.])(0[1-9]|[12][0-9]|3[01])([- /.])(18|19|20)?\\d\\d",
Pattern.MULTILINE
),
//D-M-Y
Pattern.compile(
"(?:(?:31(/|-|\\.)(?:0?[13578]|1[02]|(?:Jan|Mar|May|Jul|Aug|Oct|Dec)))\\1|(?:(?:29|30)(/|-|\\.)(?:0?[1,3-9]|1[0-2]|(?:Jan|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec))\\2))(?:(?:1[6-9]|[2-9]\\d)?\\d{2})|(?:29(/|-|\\.)(?:0?2|(?:Feb))\\3(?:(?:(?:1[6-9]|[2-9]\\d)?(?:0[48]|[2468][048]|[13579][26])|(?:(?:16|[2468][048]|[3579][26])00))))|(?:0?[1-9]|1\\d|2[0-8])(/|-|\\.)(?:(?:0?[1-9]|(?:Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep))|(?:1[0-2]|(?:Oct|Nov|Dec)))\\4(?:(?:1[6-9]|[2-9]\\d)?\\d{2})",
Pattern.MULTILINE
),
//Y
Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE)
)
}

652
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala Normal file
View File

@ -0,0 +1,652 @@
package eu.dnetlib.dhp.datacite
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.datacite.DataciteModelConstants._
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
import java.text.SimpleDateFormat
import java.time.LocalDate
import java.time.chrono.ThaiBuddhistDate
import java.time.format.DateTimeFormatter
import java.util.{Date, Locale}
import scala.collection.JavaConverters._
import scala.io.{Codec, Source}
object DataciteToOAFTransformation {
case class HostedByMapType(
openaire_id: String,
datacite_name: String,
official_name: String,
similarity: Option[Float]
) {}
val mapper = new ObjectMapper()
val unknown_repository: HostedByMapType = HostedByMapType(
ModelConstants.UNKNOWN_REPOSITORY_ORIGINALID,
ModelConstants.UNKNOWN_REPOSITORY.getValue,
ModelConstants.UNKNOWN_REPOSITORY.getValue,
Some(1.0f)
)
val hostedByMap: Map[String, HostedByMapType] = {
val s = Source.fromInputStream(getClass.getResourceAsStream("hostedBy_map.json")).mkString
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(s)
json.extract[Map[String, HostedByMapType]]
}
/** This method should skip record if json contains invalid text
* defined in gile datacite_filter
*
* @param json
* @return True if the record should be skipped
*/
def skip_record(json: String): Boolean = {
datacite_filter.exists(f => json.contains(f))
}
@deprecated("this method will be removed", "dhp")
def toActionSet(item: Oaf): (String, String) = {
val mapper = new ObjectMapper()
item match {
case dataset: OafDataset =>
val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset]
a.setClazz(classOf[OafDataset])
a.setPayload(dataset)
(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
case publication: Publication =>
val a: AtomicAction[Publication] = new AtomicAction[Publication]
a.setClazz(classOf[Publication])
a.setPayload(publication)
(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
case software: Software =>
val a: AtomicAction[Software] = new AtomicAction[Software]
a.setClazz(classOf[Software])
a.setPayload(software)
(software.getClass.getCanonicalName, mapper.writeValueAsString(a))
case orp: OtherResearchProduct =>
val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct]
a.setClazz(classOf[OtherResearchProduct])
a.setPayload(orp)
(orp.getClass.getCanonicalName, mapper.writeValueAsString(a))
case relation: Relation =>
val a: AtomicAction[Relation] = new AtomicAction[Relation]
a.setClazz(classOf[Relation])
a.setPayload(relation)
(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
case _ =>
null
}
}
def embargo_end(embargo_end_date: String): Boolean = {
val dt = LocalDate.parse(embargo_end_date, DateTimeFormatter.ofPattern("[yyyy-MM-dd]"))
val td = LocalDate.now()
td.isAfter(dt)
}
def extract_date(input: String): Option[String] = {
val d = Date_regex
.map(pattern => {
val matcher = pattern.matcher(input)
if (matcher.find())
matcher.group(0)
else
null
})
.find(s => s != null)
if (d.isDefined) {
val a_date = if (d.get.length == 4) s"01-01-${d.get}" else d.get
try {
return Some(LocalDate.parse(a_date, df_en).toString)
} catch {
case _: Throwable =>
try {
return Some(LocalDate.parse(a_date, df_it).toString)
} catch {
case _: Throwable =>
return None
}
}
}
d
}
def fix_thai_date(input: String, format: String): String = {
try {
val a_date = LocalDate.parse(input, DateTimeFormatter.ofPattern(format))
val d = ThaiBuddhistDate.of(a_date.getYear, a_date.getMonth.getValue, a_date.getDayOfMonth)
LocalDate.from(d).toString
} catch {
case _: Throwable => ""
}
}
def getTypeQualifier(
resourceType: String,
resourceTypeGeneral: String,
schemaOrg: String,
vocabularies: VocabularyGroup
): (Qualifier, Qualifier) = {
if (resourceType != null && resourceType.nonEmpty) {
val typeQualifier =
vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceType)
if (typeQualifier != null)
return (
typeQualifier,
vocabularies.getSynonymAsQualifier(
ModelConstants.DNET_RESULT_TYPOLOGIES,
typeQualifier.getClassid
)
)
}
if (schemaOrg != null && schemaOrg.nonEmpty) {
val typeQualifier =
vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, schemaOrg)
if (typeQualifier != null)
return (
typeQualifier,
vocabularies.getSynonymAsQualifier(
ModelConstants.DNET_RESULT_TYPOLOGIES,
typeQualifier.getClassid
)
)
}
if (resourceTypeGeneral != null && resourceTypeGeneral.nonEmpty) {
val typeQualifier = vocabularies.getSynonymAsQualifier(
ModelConstants.DNET_PUBLICATION_RESOURCE,
resourceTypeGeneral
)
if (typeQualifier != null)
return (
typeQualifier,
vocabularies.getSynonymAsQualifier(
ModelConstants.DNET_RESULT_TYPOLOGIES,
typeQualifier.getClassid
)
)
}
null
}
def getResult(
resourceType: String,
resourceTypeGeneral: String,
schemaOrg: String,
vocabularies: VocabularyGroup
): Result = {
val typeQualifiers: (Qualifier, Qualifier) =
getTypeQualifier(resourceType, resourceTypeGeneral, schemaOrg, vocabularies)
if (typeQualifiers == null)
return null
val i = new Instance
i.setInstancetype(typeQualifiers._1)
typeQualifiers._2.getClassname match {
case "dataset" =>
val r = new OafDataset
r.setInstance(List(i).asJava)
return r
case "publication" =>
val r = new Publication
r.setInstance(List(i).asJava)
return r
case "software" =>
val r = new Software
r.setInstance(List(i).asJava)
return r
case "other" =>
val r = new OtherResearchProduct
r.setInstance(List(i).asJava)
return r
}
null
}
def available_date(input: String): Boolean = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(input)
val l: List[String] = for {
JObject(dates) <- json \\ "dates"
JField("dateType", JString(dateTypes)) <- dates
} yield dateTypes
l.exists(p => p.equalsIgnoreCase("available"))
}
/** As describe in ticket #6377
* when the result come from figshare we need to remove subject
* and set Access rights OPEN.
*
* @param r
*/
def fix_figshare(r: Result): Unit = {
if (r.getInstance() != null) {
val hosted_by_figshare = r
.getInstance()
.asScala
.exists(i => i.getHostedby != null && "figshare".equalsIgnoreCase(i.getHostedby.getValue))
if (hosted_by_figshare) {
r.getInstance().asScala.foreach(i => i.setAccessright(ModelConstants.OPEN_ACCESS_RIGHT()))
val l: List[StructuredProperty] = List()
r.setSubject(l.asJava)
}
}
}
def createDNetTargetIdentifier(pid: String, pidType: String, idPrefix: String): String = {
val f_part = s"$idPrefix|${pidType.toLowerCase}".padTo(15, '_')
s"$f_part::${IdentifierFactory.md5(pid.toLowerCase)}"
}
def generateOAFDate(dt: String, q: Qualifier): StructuredProperty = {
OafMapperUtils.structuredProperty(dt, q, null)
}
def generateRelation(
sourceId: String,
targetId: String,
relClass: String,
cf: KeyValue,
di: DataInfo
): Relation = {
val r = new Relation
r.setSource(sourceId)
r.setTarget(targetId)
r.setRelType(ModelConstants.RESULT_PROJECT)
r.setRelClass(relClass)
r.setSubRelType(ModelConstants.OUTCOME)
r.setCollectedfrom(List(cf).asJava)
r.setDataInfo(di)
r
}
def get_projectRelation(awardUri: String, sourceId: String): List[Relation] = {
val match_pattern = funder_regex.find(s => s._1.matcher(awardUri).find())
if (match_pattern.isDefined) {
val m = match_pattern.get._1
val p = match_pattern.get._2
val grantId = m.matcher(awardUri).replaceAll("$2")
val targetId = s"$p${DHPUtils.md5(grantId)}"
List(generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo))
} else
List()
}
def generateOAF(
input: String,
ts: Long,
dateOfCollection: Long,
vocabularies: VocabularyGroup,
exportLinks: Boolean
): List[Oaf] = {
if (skip_record(input))
return List()
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val resourceType = (json \ "attributes" \ "types" \ "resourceType").extractOrElse[String](null)
val resourceTypeGeneral =
(json \ "attributes" \ "types" \ "resourceTypeGeneral").extractOrElse[String](null)
val schemaOrg = (json \ "attributes" \ "types" \ "schemaOrg").extractOrElse[String](null)
val doi = (json \ "attributes" \ "doi").extract[String]
if (doi.isEmpty)
return List()
//Mapping type based on vocabularies dnet:publication_resource and dnet:result_typologies
val result = getResult(resourceType, resourceTypeGeneral, schemaOrg, vocabularies)
if (result == null)
return List()
val doi_q = OafMapperUtils.qualifier(
"doi",
"doi",
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES
)
val pid = OafMapperUtils.structuredProperty(doi, doi_q, dataInfo)
result.setPid(List(pid).asJava)
result.setId(OafMapperUtils.createOpenaireId(50, s"datacite____::$doi", true))
result.setOriginalId(List(doi).asJava)
val d = new Date(dateOfCollection * 1000)
val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US)
result.setDateofcollection(ISO8601FORMAT.format(d))
result.setDateoftransformation(ISO8601FORMAT.format(d))
result.setDataInfo(dataInfo)
val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List())
val authors = creators.zipWithIndex.map { case (c, idx) =>
val a = new Author
a.setFullname(c.name.orNull)
a.setName(c.givenName.orNull)
a.setSurname(c.familyName.orNull)
if (c.nameIdentifiers != null && c.nameIdentifiers.isDefined && c.nameIdentifiers.get != null) {
a.setPid(
c.nameIdentifiers.get
.map(ni => {
val q =
if (ni.nameIdentifierScheme.isDefined)
vocabularies.getTermAsQualifier(
ModelConstants.DNET_PID_TYPES,
ni.nameIdentifierScheme.get.toLowerCase()
)
else null
if (ni.nameIdentifier != null && ni.nameIdentifier.isDefined) {
OafMapperUtils.structuredProperty(ni.nameIdentifier.get, q, dataInfo)
} else
null
})
.asJava
)
}
if (c.affiliation.isDefined)
a.setAffiliation(
c.affiliation.get
.filter(af => af.nonEmpty)
.map(af => OafMapperUtils.field(af, dataInfo))
.asJava
)
a.setRank(idx + 1)
a
}
val titles: List[TitleType] = (json \\ "titles").extractOrElse[List[TitleType]](List())
result.setTitle(
titles
.filter(t => t.title.nonEmpty)
.map(t => {
if (t.titleType.isEmpty) {
OafMapperUtils
.structuredProperty(t.title.get, ModelConstants.MAIN_TITLE_QUALIFIER, null)
} else {
OafMapperUtils.structuredProperty(
t.title.get,
t.titleType.get,
t.titleType.get,
ModelConstants.DNET_DATACITE_TITLE,
ModelConstants.DNET_DATACITE_TITLE,
null
)
}
})
.asJava
)
if (authors == null || authors.isEmpty || !authors.exists(a => a != null))
return List()
result.setAuthor(authors.asJava)
val dates = (json \\ "dates").extract[List[DateType]]
val publication_year = (json \\ "publicationYear").extractOrElse[String](null)
val i_date = dates
.filter(d => d.date.isDefined && d.dateType.isDefined)
.find(d => d.dateType.get.equalsIgnoreCase("issued"))
.map(d => extract_date(d.date.get))
val a_date: Option[String] = dates
.filter(d => d.date.isDefined && d.dateType.isDefined && d.dateType.get.equalsIgnoreCase("available"))
.map(d => extract_date(d.date.get))
.find(d => d != null && d.isDefined)
.map(d => d.get)
if (a_date.isDefined) {
if (doi.startsWith("10.14457"))
result.setEmbargoenddate(
OafMapperUtils.field(fix_thai_date(a_date.get, "[yyyy-MM-dd]"), null)
)
else
result.setEmbargoenddate(OafMapperUtils.field(a_date.get, null))
}
if (i_date.isDefined && i_date.get.isDefined) {
if (doi.startsWith("10.14457")) {
result.setDateofacceptance(
OafMapperUtils.field(fix_thai_date(i_date.get.get, "[yyyy-MM-dd]"), null)
)
result
.getInstance()
.get(0)
.setDateofacceptance(
OafMapperUtils.field(fix_thai_date(i_date.get.get, "[yyyy-MM-dd]"), null)
)
} else {
result.setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
}
} else if (publication_year != null) {
if (doi.startsWith("10.14457")) {
result.setDateofacceptance(
OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year", "[dd-MM-yyyy]"), null)
)
result
.getInstance()
.get(0)
.setDateofacceptance(
OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year", "[dd-MM-yyyy]"), null)
)
} else {
result.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
result
.getInstance()
.get(0)
.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
}
}
result.setRelevantdate(
dates
.filter(d => d.date.isDefined && d.dateType.isDefined)
.map(d => (extract_date(d.date.get), d.dateType.get))
.filter(d => d._1.isDefined)
.map(d =>
(
d._1.get,
vocabularies.getTermAsQualifier(ModelConstants.DNET_DATACITE_DATE, d._2.toLowerCase())
)
)
.filter(d => d._2 != null)
.map(d => generateOAFDate(d._1, d._2))
.asJava
)
val subjects = (json \\ "subjects").extract[List[SubjectType]]
result.setSubject(
subjects
.filter(s => s.subject.nonEmpty)
.map(s =>
OafMapperUtils.structuredProperty(
s.subject.get,
SUBJ_CLASS,
SUBJ_CLASS,
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
null
)
)
.asJava
)
result.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
val descriptions = (json \\ "descriptions").extract[List[DescriptionType]]
result.setDescription(
descriptions
.filter(d => d.description.isDefined)
.map(d => OafMapperUtils.field(d.description.get, null))
.filter(s => s != null)
.asJava
)
val publisher = (json \\ "publisher").extractOrElse[String](null)
if (publisher != null)
result.setPublisher(OafMapperUtils.field(publisher, null))
val language: String = (json \\ "language").extractOrElse[String](null)
if (language != null)
result.setLanguage(
vocabularies.getSynonymAsQualifier(ModelConstants.DNET_LANGUAGES, language)
)
val instance = result.getInstance().get(0)
val client = (json \ "relationships" \ "client" \\ "id").extractOpt[String]
val accessRights: List[String] = for {
JObject(rightsList) <- json \\ "rightsList"
JField("rightsUri", JString(rightsUri)) <- rightsList
} yield rightsUri
val aRights: Option[AccessRight] = accessRights
.map(r => {
vocabularies.getSynonymAsQualifier(ModelConstants.DNET_ACCESS_MODES, r)
})
.find(q => q != null)
.map(q => {
val a = new AccessRight
a.setClassid(q.getClassid)
a.setClassname(q.getClassname)
a.setSchemeid(q.getSchemeid)
a.setSchemename(q.getSchemename)
a
})
val access_rights_qualifier =
if (aRights.isDefined) aRights.get
else
OafMapperUtils.accessRight(
ModelConstants.UNKNOWN,
ModelConstants.NOT_AVAILABLE,
ModelConstants.DNET_ACCESS_MODES,
ModelConstants.DNET_ACCESS_MODES
)
if (client.isDefined) {
val hb = hostedByMap.getOrElse(client.get.toUpperCase(), unknown_repository)
instance.setHostedby(OafMapperUtils.keyValue(generateDSId(hb.openaire_id), hb.official_name))
instance.setCollectedfrom(DATACITE_COLLECTED_FROM)
instance.setUrl(List(s"https://dx.doi.org/$doi").asJava)
instance.setAccessright(access_rights_qualifier)
instance.setPid(result.getPid)
val license = accessRights
.find(r =>
r.startsWith("http") && r.matches(
".*(/licenses|/publicdomain|unlicense\\.org/|/legal-and-data-protection-notices|/download/license|/open-government-licence).*"
)
)
if (license.isDefined)
instance.setLicense(OafMapperUtils.field(license.get, null))
}
val awardUris: List[String] = for {
JObject(fundingReferences) <- json \\ "fundingReferences"
JField("awardUri", JString(awardUri)) <- fundingReferences
} yield awardUri
result.setId(IdentifierFactory.createIdentifier(result))
var relations: List[Relation] =
awardUris.flatMap(a => get_projectRelation(a, result.getId)).filter(r => r != null)
fix_figshare(result)
if (result.getId == null)
return List()
if (exportLinks) {
val rels: List[RelatedIdentifierType] = for {
JObject(relIdentifier) <- json \\ "relatedIdentifiers"
JField("relationType", JString(relationType)) <- relIdentifier
JField("relatedIdentifierType", JString(relatedIdentifierType)) <- relIdentifier
JField("relatedIdentifier", JString(relatedIdentifier)) <- relIdentifier
} yield RelatedIdentifierType(relationType, relatedIdentifier, relatedIdentifierType)
relations = relations ::: generateRelations(
rels,
result.getId,
if (i_date.isDefined && i_date.get.isDefined) i_date.get.get else null
)
}
if (relations != null && relations.nonEmpty) {
List(result) ::: relations
} else
List(result)
}
private def generateRelations(
rels: List[RelatedIdentifierType],
id: String,
date: String
): List[Relation] = {
rels
.filter(r =>
subRelTypeMapping
.contains(r.relationType) && (r.relatedIdentifierType.equalsIgnoreCase("doi") ||
r.relatedIdentifierType.equalsIgnoreCase("pmid") ||
r.relatedIdentifierType.equalsIgnoreCase("arxiv"))
)
.map(r => {
val rel = new Relation
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
rel.setDataInfo(dataInfo)
val subRelType = subRelTypeMapping(r.relationType).relType
rel.setRelType(REL_TYPE_VALUE)
rel.setSubRelType(subRelType)
rel.setRelClass(r.relationType)
val dateProps: KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
rel.setProperties(List(dateProps).asJava)
rel.setSource(id)
rel.setTarget(
DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier, r.relatedIdentifierType)
)
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
rel.getCollectedfrom.asScala.map(c => c.getValue).toList
rel
})
}
def generateDSId(input: String): String = {
val b = StringUtils.substringBefore(input, "::")
val a = StringUtils.substringAfter(input, "::")
s"10|$b::${DHPUtils.md5(a)}"
}
}

110
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala Normal file
View File

@ -0,0 +1,110 @@
package eu.dnetlib.dhp.datacite
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.AbstractScalaApplication
import eu.dnetlib.dhp.collection.CollectionUtils
import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord}
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile
import eu.dnetlib.dhp.utils.ISLookupClientFactory
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
class GenerateDataciteDatasetSpark(propertyPath: String, args: Array[String], log: Logger)
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
/** Here all the spark applications runs this method
* where the whole logic of the spark node is defined
*/
override def run(): Unit = {
val sourcePath = parser.get("sourcePath")
log.info(s"SourcePath is '$sourcePath'")
val exportLinks = "true".equalsIgnoreCase(parser.get("exportLinks"))
log.info(s"exportLinks is '$exportLinks'")
val isLookupUrl: String = parser.get("isLookupUrl")
log.info("isLookupUrl: {}", isLookupUrl)
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
require(vocabularies != null)
val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
log.info(s"mdstoreOutputVersion is '$mdstoreOutputVersion'")
val mapper = new ObjectMapper()
val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
val outputBasePath = cleanedMdStoreVersion.getHdfsPath
log.info(s"outputBasePath is '$outputBasePath'")
val targetPath = s"$outputBasePath$MDSTORE_DATA_PATH"
log.info(s"targetPath is '$targetPath'")
generateDataciteDataset(sourcePath, exportLinks, vocabularies, targetPath, spark)
reportTotalSize(targetPath, outputBasePath)
}
/** For working with MDStore we need to store in a file on hdfs the size of
* the current dataset
* @param targetPath
* @param outputBasePath
*/
def reportTotalSize(targetPath: String, outputBasePath: String): Unit = {
val total_items = spark.read.text(targetPath).count()
writeHdfsFile(
spark.sparkContext.hadoopConfiguration,
s"$total_items",
outputBasePath + MDSTORE_SIZE_PATH
)
}
/** Generate the transformed and cleaned OAF Dataset from the native one
*
* @param sourcePath sourcePath of the native Dataset in format JSON/Datacite
* @param exportLinks If true it generates unresolved links
* @param vocabularies vocabularies for cleaning
* @param targetPath the targetPath of the result Dataset
*/
def generateDataciteDataset(
sourcePath: String,
exportLinks: Boolean,
vocabularies: VocabularyGroup,
targetPath: String,
spark: SparkSession
): Unit = {
require(spark != null)
import spark.implicits._
implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord]
implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
CollectionUtils.saveDataset(
spark.read
.load(sourcePath)
.as[DataciteType]
.filter(d => d.isActive)
.flatMap(d =>
DataciteToOAFTransformation
.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks)
)
.filter(d => d != null),
targetPath
)
}
}
object GenerateDataciteDatasetSpark {
val log: Logger = LoggerFactory.getLogger(GenerateDataciteDatasetSpark.getClass)
def main(args: Array[String]): Unit = {
new GenerateDataciteDatasetSpark(
"/eu/dnetlib/dhp/datacite/generate_dataset_params.json",
args,
log
).initialize().run()
}
}

100
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/ImportDatacite.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/ImportDatacite.scala
View File

@ -22,7 +22,6 @@ object ImportDatacite {
val log: Logger = LoggerFactory.getLogger(ImportDatacite.getClass)
def convertAPIStringToDataciteItem(input: String): DataciteType = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(input)
@ -32,14 +31,26 @@ object ImportDatacite {
val timestamp_string = (json \ "attributes" \ "updated").extract[String]
val dt = LocalDateTime.parse(timestamp_string, ISO_DATE_TIME)
DataciteType(doi = doi, timestamp = dt.toInstant(ZoneOffset.UTC).toEpochMilli / 1000, isActive = isActive, json = input)
DataciteType(
doi = doi,
timestamp = dt.toInstant(ZoneOffset.UTC).toEpochMilli / 1000,
isActive = isActive,
json = input
)
}
def main(args: Array[String]): Unit = {
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/import_from_api.json")).mkString)
val parser = new ArgumentApplicationParser(
Source
.fromInputStream(
getClass.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/datacite/import_from_api.json"
)
)
.mkString
)
parser.parseArgument(args)
val master = parser.get("master")
@ -60,7 +71,8 @@ object ImportDatacite {
val spkipImport = parser.get("skipImport")
log.info(s"skipImport is $spkipImport")
val spark: SparkSession = SparkSession.builder()
val spark: SparkSession = SparkSession
.builder()
.appName(ImportDatacite.getClass.getSimpleName)
.master(master)
.getOrCreate()
@ -78,45 +90,48 @@ object ImportDatacite {
import spark.implicits._
val dataciteAggregator: Aggregator[DataciteType, DataciteType, DataciteType] =
new Aggregator[DataciteType, DataciteType, DataciteType] with Serializable {
val dataciteAggregator: Aggregator[DataciteType, DataciteType, DataciteType] = new Aggregator[DataciteType, DataciteType, DataciteType] with Serializable {
override def zero: DataciteType = null
override def zero: DataciteType = null
override def reduce(a: DataciteType, b: DataciteType): DataciteType = {
if (b == null)
return a
if (a == null)
return b
if (a.timestamp > b.timestamp) {
return a
override def reduce(a: DataciteType, b: DataciteType): DataciteType = {
if (b == null)
return a
if (a == null)
return b
if (a.timestamp > b.timestamp) {
return a
}
b
}
b
override def merge(a: DataciteType, b: DataciteType): DataciteType = {
reduce(a, b)
}
override def bufferEncoder: Encoder[DataciteType] = implicitly[Encoder[DataciteType]]
override def outputEncoder: Encoder[DataciteType] = implicitly[Encoder[DataciteType]]
override def finish(reduction: DataciteType): DataciteType = reduction
}
override def merge(a: DataciteType, b: DataciteType): DataciteType = {
reduce(a, b)
}
override def bufferEncoder: Encoder[DataciteType] = implicitly[Encoder[DataciteType]]
override def outputEncoder: Encoder[DataciteType] = implicitly[Encoder[DataciteType]]
override def finish(reduction: DataciteType): DataciteType = reduction
}
val dump: Dataset[DataciteType] = spark.read.load(dataciteDump).as[DataciteType]
val ts = dump.select(max("timestamp")).first().getLong(0)
println(s"last Timestamp is $ts")
val cnt = if ("true".equalsIgnoreCase(spkipImport)) 1 else writeSequenceFile(hdfsTargetPath, ts, conf, bs)
val cnt =
if ("true".equalsIgnoreCase(spkipImport)) 1
else writeSequenceFile(hdfsTargetPath, ts, conf, bs)
println(s"Imported from Datacite API $cnt documents")
if (cnt > 0) {
val inputRdd: RDD[DataciteType] = sc.sequenceFile(targetPath, classOf[Int], classOf[Text])
val inputRdd: RDD[DataciteType] = sc
.sequenceFile(targetPath, classOf[Int], classOf[Text])
.map(s => s._2.toString)
.map(s => convertAPIStringToDataciteItem(s))
spark.createDataset(inputRdd).write.mode(SaveMode.Overwrite).save(s"${targetPath}_dataset")
@ -129,7 +144,9 @@ object ImportDatacite {
.agg(dataciteAggregator.toColumn)
.map(s => s._2)
.repartition(4000)
.write.mode(SaveMode.Overwrite).save(s"${dataciteDump}_updated")
.write
.mode(SaveMode.Overwrite)
.save(s"${dataciteDump}_updated")
val fs = FileSystem.get(sc.hadoopConfiguration)
fs.delete(new Path(s"$dataciteDump"), true)
@ -137,14 +154,24 @@ object ImportDatacite {
}
}
private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs: Int): Long = {
private def writeSequenceFile(
hdfsTargetPath: Path,
timestamp: Long,
conf: Configuration,
bs: Int
): Long = {
var from: Long = timestamp * 1000
val delta: Long = 100000000L
var client: DataciteAPIImporter = null
val now: Long = System.currentTimeMillis()
var i = 0
try {
val writer = SequenceFile.createWriter(conf, SequenceFile.Writer.file(hdfsTargetPath), SequenceFile.Writer.keyClass(classOf[IntWritable]), SequenceFile.Writer.valueClass(classOf[Text]))
val writer = SequenceFile.createWriter(
conf,
SequenceFile.Writer.file(hdfsTargetPath),
SequenceFile.Writer.keyClass(classOf[IntWritable]),
SequenceFile.Writer.valueClass(classOf[Text])
)
try {
var start: Long = System.currentTimeMillis
while (from < now) {
@ -153,16 +180,16 @@ object ImportDatacite {
val key: IntWritable = new IntWritable(i)
val value: Text = new Text
while (client.hasNext) {
key.set({
key.set {
i += 1;
i - 1
})
}
value.set(client.next())
writer.append(key, value)
writer.hflush()
if (i % 1000 == 0) {
end = System.currentTimeMillis
val time = (end - start) / 1000.0F
val time = (end - start) / 1000.0f
println(s"Imported $i in $time seconds")
start = System.currentTimeMillis
}
@ -174,8 +201,7 @@ object ImportDatacite {
case e: Throwable =>
println("Error", e)
} finally if (writer != null) writer.close()
}
catch {
} catch {
case e: Throwable =>
log.error("Error", e)
}

24
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/SparkDownloadUpdateDatacite.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/SparkDownloadUpdateDatacite.scala
View File

@ -17,7 +17,13 @@ object SparkDownloadUpdateDatacite {
def main(args: Array[String]): Unit = {
val conf = new SparkConf
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/datacite/generate_dataset_params.json")).mkString)
val parser = new ArgumentApplicationParser(
Source
.fromInputStream(
getClass.getResourceAsStream("/eu/dnetlib/dhp/datacite/generate_dataset_params.json")
)
.mkString
)
parser.parseArgument(args)
val master = parser.get("master")
val sourcePath = parser.get("sourcePath")
@ -26,8 +32,9 @@ object SparkDownloadUpdateDatacite {
val hdfsuri = parser.get("namenode")
log.info(s"namenode is $hdfsuri")
val spark: SparkSession = SparkSession.builder().config(conf)
val spark: SparkSession = SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(master)
.getOrCreate()
@ -37,13 +44,18 @@ object SparkDownloadUpdateDatacite {
import spark.implicits._
val maxDate: String = spark.read.load(workingPath).as[Oaf].filter(s => s.isInstanceOf[Result]).map(r => r.asInstanceOf[Result].getDateofcollection).select(max("value")).first().getString(0)
val maxDate: String = spark.read
.load(workingPath)
.as[Oaf]
.filter(s => s.isInstanceOf[Result])
.map(r => r.asInstanceOf[Result].getDateofcollection)
.select(max("value"))
.first()
.getString(0)
val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US)
val string_to_date = ISO8601FORMAT.parse(maxDate)
val ts = string_to_date.getTime
}
}

597
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala Normal file
View File

@ -0,0 +1,597 @@
package eu.dnetlib.dhp.sx.bio
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, OafMapperUtils}
import eu.dnetlib.dhp.schema.oaf._
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.{compact, parse, render}
import collection.JavaConverters._
object BioDBToOAF {
case class EBILinkItem(id: Long, links: String) {}
case class EBILinks(
relType: String,
date: String,
title: String,
pmid: String,
targetPid: String,
targetPidType: String,
targetUrl: String
) {}
case class UniprotDate(date: String, date_info: String) {}
case class ScholixResolved(
pid: String,
pidType: String,
typology: String,
tilte: List[String],
datasource: List[String],
date: List[String],
authors: List[String]
) {}
val DATA_INFO: DataInfo = OafMapperUtils.dataInfo(
false,
null,
false,
false,
ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER,
"0.9"
)
val SUBJ_CLASS = "Keywords"
val DATE_RELATION_KEY = "RelationDate"
val resolvedURL: Map[String, String] = Map(
"genbank" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
"ncbi-n" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
"ncbi-wgs" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
"ncbi-p" -> "https://www.ncbi.nlm.nih.gov/protein/",
"ena" -> "https://www.ebi.ac.uk/ena/browser/view/",
"clinicaltrials.gov" -> "https://clinicaltrials.gov/ct2/show/",
"onim" -> "https://omim.org/entry/",
"refseq" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
"geo" -> "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="
)
val collectedFromMap: Map[String, KeyValue] = {
val PDBCollectedFrom: KeyValue = OafMapperUtils.keyValue(
"10|opendoar____::d1c373ab1570cfb9a7dbb53c186b37a2",
"Protein Data Bank"
)
val enaCollectedFrom: KeyValue = OafMapperUtils.keyValue(
"10|re3data_____::c2a591f440598b63d854556beaf01591",
"European Nucleotide Archive"
)
val ncbiCollectedFrom: KeyValue = OafMapperUtils.keyValue(
"10|re3data_____::7d4f90870fe1e493232c9e86c43ae6f6",
"NCBI Nucleotide"
)
val UNIPROTCollectedFrom: KeyValue = OafMapperUtils.keyValue(
"10|re3data_____::296e1abaf1302897a6838d3588cd0310",
"UniProtKB/Swiss-Prot"
)
val ElsevierCollectedFrom: KeyValue =
OafMapperUtils.keyValue("10|openaire____::8f87e10869299a5fe80b315695296b88", "Elsevier")
val springerNatureCollectedFrom: KeyValue = OafMapperUtils.keyValue(
"10|openaire____::6e380d9cf51138baec8480f5a0ce3a2e",
"Springer Nature"
)
val EBICollectedFrom: KeyValue = OafMapperUtils.keyValue(
"10|opendoar____::83e60e09c222f206c725385f53d7e567c",
"EMBL-EBIs Protein Data Bank in Europe (PDBe)"
)
val pubmedCollectedFrom: KeyValue =
OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
UNIPROTCollectedFrom.setDataInfo(DATA_INFO)
PDBCollectedFrom.setDataInfo(DATA_INFO)
ElsevierCollectedFrom.setDataInfo(DATA_INFO)
EBICollectedFrom.setDataInfo(DATA_INFO)
pubmedCollectedFrom.setDataInfo(DATA_INFO)
enaCollectedFrom.setDataInfo(DATA_INFO)
ncbiCollectedFrom.setDataInfo(DATA_INFO)
springerNatureCollectedFrom.setDataInfo(DATA_INFO)
Map(
"uniprot" -> UNIPROTCollectedFrom,
"pdb" -> PDBCollectedFrom,
"elsevier" -> ElsevierCollectedFrom,
"ebi" -> EBICollectedFrom,
"Springer Nature" -> springerNatureCollectedFrom,
"NCBI Nucleotide" -> ncbiCollectedFrom,
"European Nucleotide Archive" -> enaCollectedFrom,
"Europe PMC" -> pubmedCollectedFrom
)
}
def crossrefLinksToOaf(input: String): Oaf = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val source_pid = (json \ "Source" \ "Identifier" \ "ID").extract[String].toLowerCase
val source_pid_type = (json \ "Source" \ "Identifier" \ "IDScheme").extract[String].toLowerCase
val target_pid = (json \ "Target" \ "Identifier" \ "ID").extract[String].toLowerCase
val target_pid_type = (json \ "Target" \ "Identifier" \ "IDScheme").extract[String].toLowerCase
val relation_semantic = (json \ "RelationshipType" \ "Name").extract[String]
val date = GraphCleaningFunctions.cleanDate((json \ "LinkedPublicationDate").extract[String])
createRelation(
target_pid,
target_pid_type,
generate_unresolved_id(source_pid, source_pid_type),
collectedFromMap("elsevier"),
"relationship",
relation_semantic,
date
)
}
def scholixResolvedToOAF(input: ScholixResolved): Oaf = {
val d = new Dataset
d.setPid(
List(
OafMapperUtils.structuredProperty(
input.pid.toLowerCase,
input.pidType.toLowerCase,
input.pidType.toLowerCase,
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES,
DATA_INFO
)
).asJava
)
d.setDataInfo(DATA_INFO)
val nsPrefix = input.pidType.toLowerCase.padTo(12, '_')
d.setId(OafMapperUtils.createOpenaireId(50, s"$nsPrefix::${input.pid.toLowerCase}", true))
if (input.tilte != null && input.tilte.nonEmpty)
d.setTitle(
List(
OafMapperUtils.structuredProperty(
input.tilte.head,
ModelConstants.MAIN_TITLE_QUALIFIER,
DATA_INFO
)
).asJava
)
d.setOriginalId(List(input.pid).asJava)
val i = new Instance
i.setPid(d.getPid)
if (resolvedURL.contains(input.pidType)) {
i.setUrl(List(s"${resolvedURL(input.pidType)}${input.pid}").asJava)
}
if (input.pidType.equalsIgnoreCase("clinicaltrials.gov"))
i.setInstancetype(
OafMapperUtils.qualifier(
"0037",
"Clinical Trial",
ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE
)
)
else
i.setInstancetype(
OafMapperUtils.qualifier(
"0046",
"Bioentity",
ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE
)
)
if (input.datasource == null || input.datasource.isEmpty)
return null
val ds = input.datasource.head
d.setCollectedfrom(List(collectedFromMap(ds)).asJava)
i.setCollectedfrom(collectedFromMap(ds))
d.setInstance(List(i).asJava)
if (input.authors != null && input.authors.nonEmpty) {
val authors = input.authors.map(a => {
val authorOAF = new Author
authorOAF.setFullname(a)
authorOAF
})
d.setAuthor(authors.asJava)
}
if (input.date != null && input.date.nonEmpty) {
val dt = input.date.head
i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
}
d
}
def uniprotToOAF(input: String): List[Oaf] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val pid = (json \ "pid").extract[String]
val d = new Dataset
d.setPid(
List(
OafMapperUtils.structuredProperty(
pid,
"uniprot",
"uniprot",
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES,
DATA_INFO
)
).asJava
)
d.setDataInfo(DATA_INFO)
d.setId(OafMapperUtils.createOpenaireId(50, s"uniprot_____::$pid", true))
d.setCollectedfrom(List(collectedFromMap("uniprot")).asJava)
val title: String = (json \ "title").extractOrElse[String](null)
if (title != null)
d.setTitle(
List(
OafMapperUtils.structuredProperty(title, ModelConstants.MAIN_TITLE_QUALIFIER, DATA_INFO)
).asJava
)
d.setOriginalId(List(pid).asJava)
val i = new Instance
i.setPid(d.getPid)
i.setUrl(List(s"https://www.uniprot.org/uniprot/$pid").asJava)
i.setInstancetype(
OafMapperUtils.qualifier(
"0046",
"Bioentity",
ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE
)
)
i.setCollectedfrom(collectedFromMap("uniprot"))
d.setInstance(List(i).asJava)
val dates: List[UniprotDate] = for {
JObject(dateOBJ) <- json \ "dates"
JField("date", JString(date)) <- dateOBJ
JField("date_info", JString(date_info)) <- dateOBJ
} yield UniprotDate(GraphCleaningFunctions.cleanDate(date), date_info)
val subjects: List[String] = (json \\ "subjects").extractOrElse[List[String]](null)
if (subjects != null) {
d.setSubject(
subjects
.map(s =>
OafMapperUtils.structuredProperty(
s,
SUBJ_CLASS,
SUBJ_CLASS,
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
null
)
)
.asJava
)
}
var i_date: Option[UniprotDate] = None
if (dates.nonEmpty) {
i_date = dates.find(d => d.date_info.contains("entry version"))
if (i_date.isDefined) {
i.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
}
val relevant_dates: List[StructuredProperty] = dates
.filter(d => !d.date_info.contains("entry version"))
.map(date =>
OafMapperUtils.structuredProperty(
date.date,
ModelConstants.UNKNOWN,
ModelConstants.UNKNOWN,
ModelConstants.DNET_DATACITE_DATE,
ModelConstants.DNET_DATACITE_DATE,
DATA_INFO
)
)
if (relevant_dates != null && relevant_dates.nonEmpty)
d.setRelevantdate(relevant_dates.asJava)
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
}
val references_pmid: List[String] = for {
JObject(reference) <- json \ "references"
JField("PubMed", JString(pid)) <- reference
} yield pid
val references_doi: List[String] = for {
JObject(reference) <- json \ "references"
JField(" DOI", JString(pid)) <- reference
} yield pid
if (references_pmid != null && references_pmid.nonEmpty) {
val rel = createRelation(
references_pmid.head,
"pmid",
d.getId,
collectedFromMap("uniprot"),
ModelConstants.RELATIONSHIP,
ModelConstants.IS_RELATED_TO,
if (i_date.isDefined) i_date.get.date else null
)
rel.getCollectedfrom
List(d, rel)
} else if (references_doi != null && references_doi.nonEmpty) {
val rel = createRelation(
references_doi.head,
"doi",
d.getId,
collectedFromMap("uniprot"),
ModelConstants.RELATIONSHIP,
ModelConstants.IS_RELATED_TO,
if (i_date.isDefined) i_date.get.date else null
)
List(d, rel)
} else
List(d)
}
def generate_unresolved_id(pid: String, pidType: String): String = {
s"unresolved::$pid::$pidType"
}
def createRelation(
pid: String,
pidType: String,
sourceId: String,
collectedFrom: KeyValue,
subRelType: String,
relClass: String,
date: String
): Relation = {
val rel = new Relation
rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava)
rel.setDataInfo(DATA_INFO)
rel.setRelType(ModelConstants.RESULT_RESULT)
rel.setSubRelType(subRelType)
rel.setRelClass(relClass)
rel.setSource(sourceId)
rel.setTarget(s"unresolved::$pid::$pidType")
val dateProps: KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
rel.setProperties(List(dateProps).asJava)
rel.getTarget.startsWith("unresolved")
rel.setCollectedfrom(List(collectedFrom).asJava)
rel
}
def createSupplementaryRelation(
pid: String,
pidType: String,
sourceId: String,
collectedFrom: KeyValue,
date: String
): Relation = {
createRelation(
pid,
pidType,
sourceId,
collectedFrom,
ModelConstants.SUPPLEMENT,
ModelConstants.IS_SUPPLEMENT_TO,
date
)
}
def pdbTOOaf(input: String): List[Oaf] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val pdb = (json \ "pdb").extract[String].toLowerCase
if (pdb.isEmpty)
return List()
val d = new Dataset
d.setPid(
List(
OafMapperUtils.structuredProperty(
pdb,
"pdb",
"Protein Data Bank Identifier",
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES,
DATA_INFO
)
).asJava
)
d.setCollectedfrom(List(collectedFromMap("pdb")).asJava)
d.setDataInfo(DATA_INFO)
d.setId(OafMapperUtils.createOpenaireId(50, s"pdb_________::$pdb", true))
d.setOriginalId(List(pdb).asJava)
val title = (json \ "title").extractOrElse[String](null)
if (title == null)
return List()
d.setTitle(
List(
OafMapperUtils.structuredProperty(title, ModelConstants.MAIN_TITLE_QUALIFIER, DATA_INFO)
).asJava
)
val authors: List[String] = (json \ "authors").extractOrElse[List[String]](null)
if (authors != null) {
val convertedAuthors = authors.zipWithIndex.map { a =>
val res = new Author
res.setFullname(a._1)
res.setRank(a._2 + 1)
res
}
d.setAuthor(convertedAuthors.asJava)
}
val i = new Instance
i.setPid(d.getPid)
i.setUrl(List(s"https://www.rcsb.org/structure/$pdb").asJava)
i.setInstancetype(
OafMapperUtils.qualifier(
"0046",
"Bioentity",
ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE
)
)
i.setCollectedfrom(collectedFromMap("pdb"))
d.setInstance(List(i).asJava)
val pmid = (json \ "pmid").extractOrElse[String](null)
if (pmid != null)
List(d, createSupplementaryRelation(pmid, "pmid", d.getId, collectedFromMap("pdb"), null))
else
List(d)
}
def extractEBILinksFromDump(input: String): EBILinkItem = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val pmid = (json \ "publication" \ "pmid").extract[String]
val links = (json \ "links").extract[JObject]
EBILinkItem(pmid.toLong, compact(render(links)))
}
def EBITargetLinksFilter(input: EBILinks): Boolean = {
input.targetPidType.equalsIgnoreCase("ena") || input.targetPidType.equalsIgnoreCase(
"pdb"
) || input.targetPidType.equalsIgnoreCase("uniprot")
}
def parse_ebi_links(input: String): List[EBILinks] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val pmid = (json \ "request" \ "id").extract[String]
for {
JObject(link) <- json \\ "Link"
JField("Target", JObject(target)) <- link
JField("RelationshipType", JObject(relType)) <- link
JField("Name", JString(relation)) <- relType
JField("PublicationDate", JString(publicationDate)) <- link
JField("Title", JString(title)) <- target
JField("Identifier", JObject(identifier)) <- target
JField("IDScheme", JString(idScheme)) <- identifier
JField("IDURL", JString(idUrl)) <- identifier
JField("ID", JString(id)) <- identifier
} yield EBILinks(
relation,
GraphCleaningFunctions.cleanDate(publicationDate),
title,
pmid,
id,
idScheme,
idUrl
)
}
def convertEBILinksToOaf(input: EBILinks): List[Oaf] = {
val d = new Dataset
d.setCollectedfrom(List(collectedFromMap("ebi")).asJava)
d.setDataInfo(DATA_INFO)
d.setTitle(
List(
OafMapperUtils.structuredProperty(
input.title,
ModelConstants.MAIN_TITLE_QUALIFIER,
DATA_INFO
)
).asJava
)
val nsPrefix = input.targetPidType.toLowerCase.padTo(12, '_')
d.setId(OafMapperUtils.createOpenaireId(50, s"$nsPrefix::${input.targetPid.toLowerCase}", true))
d.setOriginalId(List(input.targetPid.toLowerCase).asJava)
d.setPid(
List(
OafMapperUtils.structuredProperty(
input.targetPid.toLowerCase,
input.targetPidType.toLowerCase,
"Protein Data Bank Identifier",
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES,
DATA_INFO
)
).asJava
)
val i = new Instance
i.setPid(d.getPid)
i.setUrl(List(input.targetUrl).asJava)
i.setInstancetype(
OafMapperUtils.qualifier(
"0046",
"Bioentity",
ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE
)
)
i.setCollectedfrom(collectedFromMap("ebi"))
d.setInstance(List(i).asJava)
i.setDateofacceptance(
OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO)
)
d.setDateofacceptance(
OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO)
)
List(
d,
createRelation(
input.pmid,
"pmid",
d.getId,
collectedFromMap("ebi"),
ModelConstants.RELATIONSHIP,
ModelConstants.IS_RELATED_TO,
GraphCleaningFunctions.cleanDate(input.date)
)
)
}
}

35
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala
View File

@ -1,12 +1,12 @@
package eu.dnetlib.dhp.sx.bio
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Oaf
import BioDBToOAF.ScholixResolved
import eu.dnetlib.dhp.collection.CollectionUtils
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkTransformBioDatabaseToOAF {
@ -14,7 +14,11 @@ object SparkTransformBioDatabaseToOAF {
def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf()
val log: Logger = LoggerFactory.getLogger(getClass)
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json")))
val parser = new ArgumentApplicationParser(
IOUtils.toString(
getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json")
)
)
parser.parseArgument(args)
val database: String = parser.get("database")
log.info("database: {}", database)
@ -29,20 +33,33 @@ object SparkTransformBioDatabaseToOAF {
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
.master(parser.get("master"))
.getOrCreate()
val sc = spark.sparkContext
implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
import spark.implicits._
database.toUpperCase() match {
case "UNIPROT" =>
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
CollectionUtils.saveDataset(
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))),
targetPath
)
case "PDB" =>
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
CollectionUtils.saveDataset(
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))),
targetPath
)
case "SCHOLIX" =>
spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
CollectionUtils.saveDataset(
spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)),
targetPath
)
case "CROSSREF_LINKS" =>
spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
CollectionUtils.saveDataset(
spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))),
targetPath
)
}
}

124
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala
View File

@ -1,9 +1,10 @@
package eu.dnetlib.dhp.sx.bio.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.collection.CollectionUtils
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.oaf.Result
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
import eu.dnetlib.dhp.sx.bio.pubmed._
import eu.dnetlib.dhp.utils.ISLookupClientFactory
import org.apache.commons.io.IOUtils
import org.apache.hadoop.conf.Configuration
@ -23,31 +24,37 @@ import scala.xml.pull.XMLEventReader
object SparkCreateBaselineDataFrame {
def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = {
val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
val result = data.lines.filter(l => l.startsWith("<a href=")).map { l =>
val end = l.lastIndexOf("\">")
val start = l.indexOf("<a href=\"")
val result = data.lines
.filter(l => l.startsWith("<a href="))
.map { l =>
val end = l.lastIndexOf("\">")
val start = l.indexOf("<a href=\"")
if (start >= 0 && end > start)
l.substring(start + 9, end - start)
else
""
}.filter(s => s.endsWith(".gz")).filter(s => s > maxFile).map(s => (s, s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s")).toList
if (start >= 0 && end > start)
l.substring(start + 9, end - start)
else
""
}
.filter(s => s.endsWith(".gz"))
.filter(s => s > maxFile)
.map(s => (s, s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s"))
.toList
result
}
def downloadBaselinePart(url: String): InputStream = {
val r = new HttpGet(url)
val timeout = 60; // seconds
val config = RequestConfig.custom()
val config = RequestConfig
.custom()
.setConnectTimeout(timeout * 1000)
.setConnectionRequestTimeout(timeout * 1000)
.setSocketTimeout(timeout * 1000).build()
.setSocketTimeout(timeout * 1000)
.build()
val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
val response = client.execute(r)
println(s"get response with status${response.getStatusLine.getStatusCode}")
@ -58,10 +65,12 @@ object SparkCreateBaselineDataFrame {
def requestPage(url: String): String = {
val r = new HttpGet(url)
val timeout = 60; // seconds
val config = RequestConfig.custom()
val config = RequestConfig
.custom()
.setConnectTimeout(timeout * 1000)
.setConnectionRequestTimeout(timeout * 1000)
.setSocketTimeout(timeout * 1000).build()
.setSocketTimeout(timeout * 1000)
.build()
val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
try {
var tries = 4
@ -72,8 +81,7 @@ object SparkCreateBaselineDataFrame {
println(s"get response with status${response.getStatusLine.getStatusCode}")
if (response.getStatusLine.getStatusCode > 400) {
tries -= 1
}
else
} else
return IOUtils.toString(response.getEntity.getContent)
} catch {
case e: Throwable =>
@ -89,10 +97,8 @@ object SparkCreateBaselineDataFrame {
}
}
def downloadBaseLineUpdate(baselinePath: String, hdfsServerUri: String): Unit = {
val conf = new Configuration
conf.set("fs.defaultFS", hdfsServerUri)
val fs = FileSystem.get(conf)
@ -121,31 +127,36 @@ object SparkCreateBaselineDataFrame {
}
val pmArticleAggregator: Aggregator[(String, PMArticle), PMArticle, PMArticle] =
new Aggregator[(String, PMArticle), PMArticle, PMArticle] with Serializable {
override def zero: PMArticle = new PMArticle
val pmArticleAggregator: Aggregator[(String, PMArticle), PMArticle, PMArticle] = new Aggregator[(String, PMArticle), PMArticle, PMArticle] with Serializable {
override def zero: PMArticle = new PMArticle
override def reduce(b: PMArticle, a: (String, PMArticle)): PMArticle = {
if (b != null && b.getPmid != null) b else a._2
}
override def reduce(b: PMArticle, a: (String, PMArticle)): PMArticle = {
if (b != null && b.getPmid != null) b else a._2
override def merge(b1: PMArticle, b2: PMArticle): PMArticle = {
if (b1 != null && b1.getPmid != null) b1 else b2
}
override def finish(reduction: PMArticle): PMArticle = reduction
override def bufferEncoder: Encoder[PMArticle] = Encoders.kryo[PMArticle]
override def outputEncoder: Encoder[PMArticle] = Encoders.kryo[PMArticle]
}
override def merge(b1: PMArticle, b2: PMArticle): PMArticle = {
if (b1 != null && b1.getPmid != null) b1 else b2
}
override def finish(reduction: PMArticle): PMArticle = reduction
override def bufferEncoder: Encoder[PMArticle] = Encoders.kryo[PMArticle]
override def outputEncoder: Encoder[PMArticle] = Encoders.kryo[PMArticle]
}
def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf()
val log: Logger = LoggerFactory.getLogger(getClass)
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json")))
val parser = new ArgumentApplicationParser(
IOUtils.toString(
SparkEBILinksToOaf.getClass.getResourceAsStream(
"/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json"
)
)
)
parser.parseArgument(args)
val isLookupUrl: String = parser.get("isLookupUrl")
log.info("isLookupUrl: {}", isLookupUrl)
@ -161,7 +172,6 @@ object SparkCreateBaselineDataFrame {
val skipUpdate = parser.get("skipUpdate")
log.info("skipUpdate: {}", skipUpdate)
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
val spark: SparkSession =
@ -169,7 +179,8 @@ object SparkCreateBaselineDataFrame {
.builder()
.config(conf)
.appName(SparkEBILinksToOaf.getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
.master(parser.get("master"))
.getOrCreate()
val sc = spark.sparkContext
import spark.implicits._
@ -177,24 +188,35 @@ object SparkCreateBaselineDataFrame {
implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor])
implicit val resultEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
if (!"true".equalsIgnoreCase(skipUpdate)) {
downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri)
val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline", 2000)
val ds: Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i => {
val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
new PMParser(xml)
}))
ds.map(p => (p.getPmid, p))(Encoders.tuple(Encoders.STRING, PMEncoder)).groupByKey(_._1)
val ds: Dataset[PMArticle] = spark.createDataset(
k.filter(i => i._1.endsWith(".gz"))
.flatMap(i => {
val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
new PMParser(xml)
})
)
ds.map(p => (p.getPmid, p))(Encoders.tuple(Encoders.STRING, PMEncoder))
.groupByKey(_._1)
.agg(pmArticleAggregator.toColumn)
.map(p => p._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_dataset")
.map(p => p._2)
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/baseline_dataset")
}
val exported_dataset = spark.read.load(s"$workingPath/baseline_dataset").as[PMArticle]
exported_dataset
.map(a => PubMedToOaf.convert(a, vocabularies)).as[Result]
.filter(p => p != null)
.write.mode(SaveMode.Overwrite).save(targetPath)
CollectionUtils.saveDataset(
exported_dataset
.map(a => PubMedToOaf.convert(a, vocabularies))
.as[Oaf]
.filter(p => p != null),
targetPath
)
}
}

55
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala
View File

@ -1,9 +1,8 @@
package eu.dnetlib.dhp.sx.bio.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
import eu.dnetlib.dhp.sx.bio.pubmed.PMJournal
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
import org.apache.commons.io.IOUtils
import org.apache.http.client.config.RequestConfig
import org.apache.http.client.methods.HttpGet
@ -26,10 +25,12 @@ object SparkDownloadEBILinks {
def requestPage(url: String): String = {
val r = new HttpGet(url)
val timeout = 60; // seconds
val config = RequestConfig.custom()
val config = RequestConfig
.custom()
.setConnectTimeout(timeout * 1000)
.setConnectionRequestTimeout(timeout * 1000)
.setSocketTimeout(timeout * 1000).build()
.setSocketTimeout(timeout * 1000)
.build()
val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
try {
var tries = 4
@ -40,8 +41,7 @@ object SparkDownloadEBILinks {
println(s"get response with status${response.getStatusLine.getStatusCode}")
if (response.getStatusLine.getStatusCode > 400) {
tries -= 1
}
else
} else
return IOUtils.toString(response.getEntity.getContent)
} catch {
case e: Throwable =>
@ -67,14 +67,19 @@ object SparkDownloadEBILinks {
val log: Logger = LoggerFactory.getLogger(getClass)
val MAX_ITEM_PER_PARTITION = 20000
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/ebi_download_update.json")))
val parser = new ArgumentApplicationParser(
IOUtils.toString(
getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/ebi_download_update.json")
)
)
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(SparkEBILinksToOaf.getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
.master(parser.get("master"))
.getOrCreate()
import spark.implicits._
@ -88,22 +93,40 @@ object SparkDownloadEBILinks {
log.info(s"workingPath -> $workingPath")
log.info("Getting max pubmedId where the links have already requested")
val links: Dataset[EBILinkItem] = spark.read.load(s"$sourcePath/ebi_links_dataset").as[EBILinkItem]
val links: Dataset[EBILinkItem] =
spark.read.load(s"$sourcePath/ebi_links_dataset").as[EBILinkItem]
val lastPMIDRequested = links.map(l => l.id).select(max("value")).first.getLong(0)
log.info("Retrieving PMID to request links")
val pubmed = spark.read.load(s"$sourcePath/baseline_dataset").as[PMArticle]
pubmed.map(p => p.getPmid.toLong).where(s"value > $lastPMIDRequested").write.mode(SaveMode.Overwrite).save(s"$workingPath/id_to_request")
pubmed
.map(p => p.getPmid.toLong)
.where(s"value > $lastPMIDRequested")
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/id_to_request")
val pmidToReq: Dataset[Long] = spark.read.load(s"$workingPath/id_to_request").as[Long]
val total = pmidToReq.count()
spark.createDataset(pmidToReq.rdd.repartition((total / MAX_ITEM_PER_PARTITION).toInt).map(pmid => createEBILinks(pmid)).filter(l => l != null)).write.mode(SaveMode.Overwrite).save(s"$workingPath/links_update")
spark
.createDataset(
pmidToReq.rdd
.repartition((total / MAX_ITEM_PER_PARTITION).toInt)
.map(pmid => createEBILinks(pmid))
.filter(l => l != null)
)
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/links_update")
val updates: Dataset[EBILinkItem] = spark.read.load(s"$workingPath/links_update").as[EBILinkItem]
val updates: Dataset[EBILinkItem] =
spark.read.load(s"$workingPath/links_update").as[EBILinkItem]
links.union(updates).groupByKey(_.id)
links
.union(updates)
.groupByKey(_.id)
.reduceGroups { (x, y) =>
if (x == null || x.links == null)
y
@ -113,6 +136,10 @@ object SparkDownloadEBILinks {
x
else
y
}.map(_._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/links_final")
}
.map(_._2)
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/links_final")
}
}

30
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala
View File

@ -1,11 +1,10 @@
package eu.dnetlib.dhp.sx.bio.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.collection.CollectionUtils
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.sx.bio.BioDBToOAF
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
import BioDBToOAF.EBILinkItem
import eu.dnetlib.dhp.collection.CollectionUtils
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql._
@ -16,15 +15,19 @@ object SparkEBILinksToOaf {
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json")))
val parser = new ArgumentApplicationParser(
IOUtils.toString(
getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json")
)
)
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(SparkEBILinksToOaf.getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
.master(parser.get("master"))
.getOrCreate()
import spark.implicits._
val sourcePath = parser.get("sourcePath")
@ -33,12 +36,17 @@ object SparkEBILinksToOaf {
log.info(s"targetPath -> $targetPath")
implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
val ebLinks: Dataset[EBILinkItem] = spark.read.load(sourcePath).as[EBILinkItem].filter(l => l.links != null && l.links.startsWith("{"))
val ebLinks: Dataset[EBILinkItem] = spark.read
.load(sourcePath)
.as[EBILinkItem]
.filter(l => l.links != null && l.links.startsWith("{"))
ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
.filter(p => BioDBToOAF.EBITargetLinksFilter(p))
.flatMap(p => BioDBToOAF.convertEBILinksToOaf(p))
.flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null)
.write.mode(SaveMode.Overwrite).save(targetPath)
CollectionUtils.saveDataset(
ebLinks
.flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
.filter(p => BioDBToOAF.EBITargetLinksFilter(p))
.flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)),
targetPath
)
}
}

133
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala Normal file
View File

@ -0,0 +1,133 @@
package eu.dnetlib.dhp.sx.bio.pubmed
import scala.xml.MetaData
import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
/** @param xml
*/
class PMParser(xml: XMLEventReader) extends Iterator[PMArticle] {
var currentArticle: PMArticle = generateNextArticle()
override def hasNext: Boolean = currentArticle != null
override def next(): PMArticle = {
val tmp = currentArticle
currentArticle = generateNextArticle()
tmp
}
def extractAttributes(attrs: MetaData, key: String): String = {
val res = attrs.get(key)
if (res.isDefined) {
val s = res.get
if (s != null && s.nonEmpty)
s.head.text
else
null
} else null
}
def validate_Date(year: String, month: String, day: String): String = {
try {
f"${year.toInt}-${month.toInt}%02d-${day.toInt}%02d"
} catch {
case _: Throwable => null
}
}
def generateNextArticle(): PMArticle = {
var currentSubject: PMSubject = null
var currentAuthor: PMAuthor = null
var currentJournal: PMJournal = null
var currentGrant: PMGrant = null
var currNode: String = null
var currentYear = "0"
var currentMonth = "01"
var currentDay = "01"
var currentArticleType: String = null
while (xml.hasNext) {
xml.next match {
case EvElemStart(_, label, attrs, _) =>
currNode = label
label match {
case "PubmedArticle" => currentArticle = new PMArticle
case "Author" => currentAuthor = new PMAuthor
case "Journal" => currentJournal = new PMJournal
case "Grant" => currentGrant = new PMGrant
case "PublicationType" | "DescriptorName" =>
currentSubject = new PMSubject
currentSubject.setMeshId(extractAttributes(attrs, "UI"))
case "ArticleId" => currentArticleType = extractAttributes(attrs, "IdType")
case _ =>
}
case EvElemEnd(_, label) =>
label match {
case "PubmedArticle" => return currentArticle
case "Author" => currentArticle.getAuthors.add(currentAuthor)
case "Journal" => currentArticle.setJournal(currentJournal)
case "Grant" => currentArticle.getGrants.add(currentGrant)
case "PubMedPubDate" =>
if (currentArticle.getDate == null)
currentArticle.setDate(validate_Date(currentYear, currentMonth, currentDay))
case "PubDate" => currentJournal.setDate(s"$currentYear-$currentMonth-$currentDay")
case "DescriptorName" => currentArticle.getSubjects.add(currentSubject)
case "PublicationType" => currentArticle.getPublicationTypes.add(currentSubject)
case _ =>
}
case EvText(text) =>
if (currNode != null && text.trim.nonEmpty)
currNode match {
case "ArticleTitle" => {
if (currentArticle.getTitle == null)
currentArticle.setTitle(text.trim)
else
currentArticle.setTitle(currentArticle.getTitle + text.trim)
}
case "AbstractText" => {
if (currentArticle.getDescription == null)
currentArticle.setDescription(text.trim)
else
currentArticle.setDescription(currentArticle.getDescription + text.trim)
}
case "PMID" => currentArticle.setPmid(text.trim)
case "ArticleId" =>
if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim)
case "Language" => currentArticle.setLanguage(text.trim)
case "ISSN" => currentJournal.setIssn(text.trim)
case "GrantID" => currentGrant.setGrantID(text.trim)
case "Agency" => currentGrant.setAgency(text.trim)
case "Country" => if (currentGrant != null) currentGrant.setCountry(text.trim)
case "Year" => currentYear = text.trim
case "Month" => currentMonth = text.trim
case "Day" => currentDay = text.trim
case "Volume" => currentJournal.setVolume(text.trim)
case "Issue" => currentJournal.setIssue(text.trim)
case "PublicationType" | "DescriptorName" => currentSubject.setValue(text.trim)
case "LastName" => {
if (currentAuthor != null)
currentAuthor.setLastName(text.trim)
}
case "ForeName" =>
if (currentAuthor != null)
currentAuthor.setForeName(text.trim)
case "Title" =>
if (currentJournal.getTitle == null)
currentJournal.setTitle(text.trim)
else
currentJournal.setTitle(currentJournal.getTitle + text.trim)
case _ =>
}
case _ =>
}
}
null
}
}

187
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
View File

@ -4,36 +4,43 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType}
import eu.dnetlib.dhp.schema.oaf._
import scala.collection.JavaConverters._
import collection.JavaConverters._
import java.util.regex.Pattern
/**
*
*/
*/
object PubMedToOaf {
val SUBJ_CLASS = "keywords"
val urlMap = Map(
"pmid" -> "https://pubmed.ncbi.nlm.nih.gov/",
"doi" -> "https://dx.doi.org/"
"doi" -> "https://dx.doi.org/"
)
val dataInfo: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9")
val collectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
val dataInfo: DataInfo = OafMapperUtils.dataInfo(
false,
null,
false,
false,
ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER,
"0.9"
)
val collectedFrom: KeyValue =
OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
/**
* Cleaning the DOI Applying regex in order to
* remove doi starting with URL
* @param doi input DOI
* @return cleaned DOI
*/
/** Cleaning the DOI Applying regex in order to
* remove doi starting with URL
*
* @param doi input DOI
* @return cleaned DOI
*/
def cleanDoi(doi: String): String = {
val regex = "^10.\\d{4,9}\\/[\\[\\]\\-\\<\\>._;()\\/:A-Z0-9]+$"
val pattern = Pattern.compile(regex, Pattern.CASE_INSENSITIVE)
val matcher = pattern.matcher(doi)
@ -43,33 +50,34 @@ object PubMedToOaf {
null
}
/**
*
* Create an instance of class extends Result
* starting from OAF instanceType value
*
* @param cobjQualifier OAF instance type
* @param vocabularies All dnet vocabularies
* @return the correct instance
*/
/** Create an instance of class extends Result
* starting from OAF instanceType value
*
* @param cobjQualifier OAF instance type
* @param vocabularies All dnet vocabularies
* @return the correct instance
*/
def createResult(cobjQualifier: Qualifier, vocabularies: VocabularyGroup): Result = {
val result_typologies = getVocabularyTerm(ModelConstants.DNET_RESULT_TYPOLOGIES, vocabularies, cobjQualifier.getClassid)
val result_typologies = getVocabularyTerm(
ModelConstants.DNET_RESULT_TYPOLOGIES,
vocabularies,
cobjQualifier.getClassid
)
result_typologies.getClassid match {
case "dataset" => new Dataset
case "dataset" => new Dataset
case "publication" => new Publication
case "other" => new OtherResearchProduct
case "software" => new Software
case _ => null
case "other" => new OtherResearchProduct
case "software" => new Software
case _ => null
}
}
/**
* Mapping the Pubmedjournal info into the OAF Journale
*
* @param j the pubmedJournal
* @return the OAF Journal
*/
/** Mapping the Pubmedjournal info into the OAF Journale
*
* @param j the pubmedJournal
* @return the OAF Journal
*/
def mapJournal(j: PMJournal): Journal = {
if (j == null)
return null
@ -83,42 +91,47 @@ object PubMedToOaf {
journal.setIss(j.getIssue)
journal
}
/**
*
* Find vocabulary term into synonyms and term in the vocabulary
*
* @param vocabularyName the input vocabulary name
* @param vocabularies all the vocabularies
* @param term the term to find
*
* @return the cleaned term value
*/
def getVocabularyTerm(vocabularyName: String, vocabularies: VocabularyGroup, term: String): Qualifier = {
/** Find vocabulary term into synonyms and term in the vocabulary
*
* @param vocabularyName the input vocabulary name
* @param vocabularies all the vocabularies
* @param term the term to find
* @return the cleaned term value
*/
def getVocabularyTerm(
vocabularyName: String,
vocabularies: VocabularyGroup,
term: String
): Qualifier = {
val a = vocabularies.getSynonymAsQualifier(vocabularyName, term)
val b = vocabularies.getTermAsQualifier(vocabularyName, term)
if (a == null) b else a
}
/**
* Map the Pubmed Article into the OAF instance
*
*
* @param article the pubmed articles
* @param vocabularies the vocabularies
* @return The OAF instance if the mapping did not fail
*/
def convert(article: PMArticle, vocabularies: VocabularyGroup): Result = {
/** Map the Pubmed Article into the OAF instance
*
* @param article the pubmed articles
* @param vocabularies the vocabularies
* @return The OAF instance if the mapping did not fail
*/
def convert(article: PMArticle, vocabularies: VocabularyGroup): Oaf = {
if (article.getPublicationTypes == null)
return null
// MAP PMID into pid with classid = classname = pmid
val pidList: List[StructuredProperty] = List(OafMapperUtils.structuredProperty(article.getPmid, PidType.pmid.toString, PidType.pmid.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo))
val pidList: List[StructuredProperty] = List(
OafMapperUtils.structuredProperty(
article.getPmid,
PidType.pmid.toString,
PidType.pmid.toString,
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES,
dataInfo
)
)
if (pidList == null)
return null
@ -127,7 +140,14 @@ object PubMedToOaf {
if (article.getDoi != null) {
val normalizedPid = cleanDoi(article.getDoi)
if (normalizedPid != null)
alternateIdentifier = OafMapperUtils.structuredProperty(normalizedPid, PidType.doi.toString, PidType.doi.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo)
alternateIdentifier = OafMapperUtils.structuredProperty(
normalizedPid,
PidType.doi.toString,
PidType.doi.toString,
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES,
dataInfo
)
}
// INSTANCE MAPPING
@ -135,10 +155,12 @@ object PubMedToOaf {
// If the article contains the typology Journal Article then we apply this type
//else We have to find a terms that match the vocabulary otherwise we discard it
val ja = article.getPublicationTypes.asScala.find(s => "Journal Article".equalsIgnoreCase(s.getValue))
val ja =
article.getPublicationTypes.asScala.find(s => "Journal Article".equalsIgnoreCase(s.getValue))
val pubmedInstance = new Instance
if (ja.isDefined) {
val cojbCategory = getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, ja.get.getValue)
val cojbCategory =
getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, ja.get.getValue)
pubmedInstance.setInstancetype(cojbCategory)
} else {
val i_type = article.getPublicationTypes.asScala
@ -157,7 +179,9 @@ object PubMedToOaf {
if (alternateIdentifier != null)
pubmedInstance.setAlternateIdentifier(List(alternateIdentifier).asJava)
result.setInstance(List(pubmedInstance).asJava)
pubmedInstance.getPid.asScala.filter(p => "pmid".equalsIgnoreCase(p.getQualifier.getClassid)).map(p => p.getValue)(collection.breakOut)
pubmedInstance.getPid.asScala
.filter(p => "pmid".equalsIgnoreCase(p.getQualifier.getClassid))
.map(p => p.getValue)(collection.breakOut)
//CREATE URL From pmid
val urlLists: List[String] = pidList
.map(s => (urlMap.getOrElse(s.getQualifier.getClassid, ""), s.getValue))
@ -167,7 +191,9 @@ object PubMedToOaf {
pubmedInstance.setUrl(urlLists.asJava)
//ASSIGN DateofAcceptance
pubmedInstance.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo))
pubmedInstance.setDateofacceptance(
OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo)
)
//ASSIGN COLLECTEDFROM
pubmedInstance.setCollectedfrom(collectedFrom)
result.setPid(pidList.asJava)
@ -175,7 +201,6 @@ object PubMedToOaf {
//END INSTANCE MAPPING
//--------------------------------------------------------------------------------------
// JOURNAL MAPPING
//--------------------------------------------------------------------------------------
if (article.getJournal != null && result.isInstanceOf[Publication])
@ -184,32 +209,48 @@ object PubMedToOaf {
//END JOURNAL MAPPING
//--------------------------------------------------------------------------------------
// RESULT MAPPING
//--------------------------------------------------------------------------------------
result.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo))
result.setDateofacceptance(
OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo)
)
if (article.getTitle == null || article.getTitle.isEmpty)
return null
result.setTitle(List(OafMapperUtils.structuredProperty(article.getTitle, ModelConstants.MAIN_TITLE_QUALIFIER, dataInfo)).asJava)
result.setTitle(
List(
OafMapperUtils.structuredProperty(
article.getTitle,
ModelConstants.MAIN_TITLE_QUALIFIER,
dataInfo
)
).asJava
)
if (article.getDescription != null && article.getDescription.nonEmpty)
result.setDescription(List(OafMapperUtils.field(article.getDescription, dataInfo)).asJava)
if (article.getLanguage != null) {
val term = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_LANGUAGES, article.getLanguage)
val term =
vocabularies.getSynonymAsQualifier(ModelConstants.DNET_LANGUAGES, article.getLanguage)
if (term != null)
result.setLanguage(term)
}
val subjects: List[StructuredProperty] = article.getSubjects.asScala.map(s => OafMapperUtils.structuredProperty(s.getValue, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, dataInfo))(collection.breakOut)
val subjects: List[StructuredProperty] = article.getSubjects.asScala.map(s =>
OafMapperUtils.structuredProperty(
s.getValue,
SUBJ_CLASS,
SUBJ_CLASS,
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
dataInfo
)
)(collection.breakOut)
if (subjects != null)
result.setSubject(subjects.asJava)
val authors: List[Author] = article.getAuthors.asScala.zipWithIndex.map { case (a, index) =>
val author = new Author()
author.setName(a.getForeName)
@ -219,15 +260,12 @@ object PubMedToOaf {
author
}(collection.breakOut)
if (authors != null && authors.nonEmpty)
result.setAuthor(authors.asJava)
result.setOriginalId(pidList.map(s => s.getValue).asJava)
result.setId(article.getPmid)
// END RESULT MAPPING
//--------------------------------------------------------------------------------------
val id = IdentifierFactory.createIdentifier(result)
@ -237,5 +275,4 @@ object PubMedToOaf {
result
}
}

345
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkRetrieveDataciteDelta.scala Normal file
View File

@ -0,0 +1,345 @@
package eu.dnetlib.dhp.sx.graph
import eu.dnetlib.dhp.application.AbstractScalaApplication
import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.datacite.{DataciteToOAFTransformation, DataciteType}
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixResource}
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
import eu.dnetlib.dhp.utils.{DHPUtils, ISLookupClientFactory}
import org.apache.hadoop.fs.{FileSystem, Path}
import org.apache.spark.sql.functions.max
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import java.text.SimpleDateFormat
class SparkRetrieveDataciteDelta(propertyPath: String, args: Array[String], log: Logger)
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
val ISO_DATE_PATTERN = "yyyy-MM-dd'T'HH:mm:ssZ"
val simpleFormatter = new SimpleDateFormat(ISO_DATE_PATTERN)
val SCHOLIX_RESOURCE_PATH_NAME = "scholixResource"
val DATACITE_OAF_PATH_NAME = "dataciteOAFUpdate"
val PID_MAP_PATH_NAME = "pidMap"
val RESOLVED_REL_PATH_NAME = "resolvedRelation"
val SCHOLIX_PATH_NAME = "scholix"
def scholixResourcePath(workingPath: String) = s"$workingPath/$SCHOLIX_RESOURCE_PATH_NAME"
def dataciteOAFPath(workingPath: String) = s"$workingPath/$DATACITE_OAF_PATH_NAME"
def pidMapPath(workingPath: String) = s"$workingPath/$PID_MAP_PATH_NAME"
def resolvedRelationPath(workingPath: String) = s"$workingPath/$RESOLVED_REL_PATH_NAME"
def scholixPath(workingPath: String) = s"$workingPath/$SCHOLIX_PATH_NAME"
/** Utility to parse Date in ISO8601 to epochMillis
* @param inputDate The String represents an input date in ISO8601
* @return The relative epochMillis of parsed date
*/
def ISO8601toEpochMillis(inputDate: String): Long = {
simpleFormatter.parse(inputDate).getTime
}
/** This method tries to retrieve the last collection date from all datacite
* records in HDFS.
* This method should be called before indexing scholexplorer to retrieve
* the delta of Datacite record to download, since from the generation of
* raw graph to the generation of Scholexplorer sometimes it takes 20 days
* @param spark
* @param entitiesPath
* @return the last collection date from the current scholexplorer Graph of the datacite records
*/
def retrieveLastCollectedFrom(spark: SparkSession, entitiesPath: String): Long = {
log.info("Retrieve last entities collected From")
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val resultEncoder: Encoder[Result] = Encoders.kryo[Result]
import spark.implicits._
val entitiesDS = spark.read
.load(s"$entitiesPath/*")
.as[Oaf]
.filter(o => o.isInstanceOf[Result])
.map(r => r.asInstanceOf[Result])
val date = entitiesDS
.filter(r => r.getDateofcollection != null)
.map(_.getDateofcollection)
.select(max("value"))
.first
.getString(0)
ISO8601toEpochMillis(date) / 1000
}
/** The method of update Datacite relationships on Scholexplorer
* needs some utilities data structures
* One is the scholixResource DS that stores all the nodes in the Scholix Graph
* in format ScholixResource
* @param summaryPath the path of the summary in Scholix
* @param workingPath the working path
* @param spark the spark session
*/
def generateScholixResource(
summaryPath: String,
workingPath: String,
spark: SparkSession
): Unit = {
implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
implicit val scholixResourceEncoder: Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
log.info("Convert All summary to ScholixResource")
spark.read
.load(summaryPath)
.as[ScholixSummary]
.map(ScholixUtils.generateScholixResourceFromSummary)(scholixResourceEncoder)
.filter(r => r.getIdentifier != null && r.getIdentifier.size > 0)
.write
.mode(SaveMode.Overwrite)
.save(s"${scholixResourcePath(workingPath)}_native")
}
/** This method convert the new Datacite Resource into Scholix Resource
* Needed to fill the source and the type of Scholix Relationships
* @param workingPath the Working Path
* @param spark The spark Session
*/
def addMissingScholixResource(workingPath: String, spark: SparkSession): Unit = {
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val scholixResourceEncoder: Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
implicit val resultEncoder: Encoder[Result] = Encoders.kryo[Result]
import spark.implicits._
spark.read
.load(dataciteOAFPath(workingPath))
.as[Oaf]
.filter(_.isInstanceOf[Result])
.map(_.asInstanceOf[Result])
.map(ScholixUtils.generateScholixResourceFromResult)
.filter(r => r.getIdentifier != null && r.getIdentifier.size > 0)
.write
.mode(SaveMode.Overwrite)
.save(s"${scholixResourcePath(workingPath)}_update")
val update = spark.read.load(s"${scholixResourcePath(workingPath)}_update").as[ScholixResource]
val native = spark.read.load(s"${scholixResourcePath(workingPath)}_native").as[ScholixResource]
val graph = update
.union(native)
.groupByKey(_.getDnetIdentifier)
.reduceGroups((a, b) => if (a != null && a.getDnetIdentifier != null) a else b)
.map(_._2)
graph.write.mode(SaveMode.Overwrite).save(s"${scholixResourcePath(workingPath)}_graph")
}
/** This method get and Transform only datacite records with
* timestamp greater than timestamp
* @param datacitePath the datacite input Path
* @param timestamp the timestamp
* @param workingPath the working path where save the generated Dataset
* @param spark SparkSession
* @param vocabularies Vocabularies needed for transformation
*/
def getDataciteUpdate(
datacitePath: String,
timestamp: Long,
workingPath: String,
spark: SparkSession,
vocabularies: VocabularyGroup
): Long = {
import spark.implicits._
val ds = spark.read.load(datacitePath).as[DataciteType]
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
val total = ds.filter(_.timestamp >= timestamp).count()
if (total > 0) {
ds.filter(_.timestamp >= timestamp)
.flatMap(d =>
DataciteToOAFTransformation
.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks = true)
)
.flatMap(i => fixRelations(i))
.filter(i => i != null)
.write
.mode(SaveMode.Overwrite)
.save(dataciteOAFPath(workingPath))
}
total
}
/** After added the new ScholixResource, we need to update the scholix Pid Map
* to intersected with the new Datacite Relations
*
* @param workingPath The working Path starting from save the new Map
* @param spark the spark session
*/
def generatePidMap(workingPath: String, spark: SparkSession): Unit = {
implicit val scholixResourceEncoder: Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
import spark.implicits._
spark.read
.load(s"${scholixResourcePath(workingPath)}_graph")
.as[ScholixResource]
.flatMap(r =>
r.getIdentifier.asScala
.map(i => DHPUtils.generateUnresolvedIdentifier(i.getIdentifier, i.getSchema))
.map(t => (t, r.getDnetIdentifier))
)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.groupByKey(_._1)
.reduceGroups((a, b) => if (a != null && a._2 != null) a else b)
.map(_._2)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write
.mode(SaveMode.Overwrite)
.save(pidMapPath(workingPath))
}
/** This method resolve the datacite relation and filter the resolved
* relation
* @param workingPath the working path
* @param spark the spark session
*/
def resolveUpdateRelation(workingPath: String, spark: SparkSession): Unit = {
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val relationEncoder: Encoder[Relation] = Encoders.kryo[Relation]
import spark.implicits._
val pidMap = spark.read.load(pidMapPath(workingPath)).as[(String, String)]
val unresolvedRelations: Dataset[(String, Relation)] = spark.read
.load(dataciteOAFPath(workingPath))
.as[Oaf]
.filter(_.isInstanceOf[Relation])
.map(_.asInstanceOf[Relation])
.map { r =>
if (r.getSource.startsWith("unresolved"))
(r.getSource, r)
else
(r.getTarget, r)
}(Encoders.tuple(Encoders.STRING, relationEncoder))
unresolvedRelations
.joinWith(pidMap, unresolvedRelations("_1").equalTo(pidMap("_1")))
.map(t => {
val r = t._1._2
val resolvedIdentifier = t._2._2
if (r.getSource.startsWith("unresolved"))
r.setSource(resolvedIdentifier)
else
r.setTarget(resolvedIdentifier)
r
})(relationEncoder)
.filter(r => !(r.getSource.startsWith("unresolved") || r.getTarget.startsWith("unresolved")))
.write
.mode(SaveMode.Overwrite)
.save(resolvedRelationPath(workingPath))
}
/** This method generate scholix starting from resolved relation
*
* @param workingPath
* @param spark
*/
def generateScholixUpdate(workingPath: String, spark: SparkSession): Unit = {
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
implicit val scholixResourceEncoder: Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
implicit val relationEncoder: Encoder[Relation] = Encoders.kryo[Relation]
implicit val intermediateEncoder: Encoder[(String, Scholix)] =
Encoders.tuple(Encoders.STRING, scholixEncoder)
val relations: Dataset[(String, Relation)] = spark.read
.load(resolvedRelationPath(workingPath))
.as[Relation]
.map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relationEncoder))
val id_summary: Dataset[(String, ScholixResource)] = spark.read
.load(s"${scholixResourcePath(workingPath)}_graph")
.as[ScholixResource]
.map(r => (r.getDnetIdentifier, r))(Encoders.tuple(Encoders.STRING, scholixResourceEncoder))
id_summary.cache()
relations
.joinWith(id_summary, relations("_1").equalTo(id_summary("_1")), "inner")
.map(t => (t._1._2.getTarget, ScholixUtils.scholixFromSource(t._1._2, t._2._2)))
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/scholix_one_verse")
val source_scholix: Dataset[(String, Scholix)] =
spark.read.load(s"$workingPath/scholix_one_verse").as[(String, Scholix)]
source_scholix
.joinWith(id_summary, source_scholix("_1").equalTo(id_summary("_1")), "inner")
.map(t => {
val target: ScholixResource = t._2._2
val scholix: Scholix = t._1._2
ScholixUtils.generateCompleteScholix(scholix, target)
})(scholixEncoder)
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/scholix")
}
/** Here all the spark applications runs this method
* where the whole logic of the spark node is defined
*/
override def run(): Unit = {
val sourcePath = parser.get("sourcePath")
log.info(s"SourcePath is '$sourcePath'")
val datacitePath = parser.get("datacitePath")
log.info(s"DatacitePath is '$datacitePath'")
val workingPath = parser.get("workingSupportPath")
log.info(s"workingPath is '$workingPath'")
val isLookupUrl: String = parser.get("isLookupUrl")
log.info("isLookupUrl: {}", isLookupUrl)
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
require(vocabularies != null)
val updateDS: Boolean = "true".equalsIgnoreCase(parser.get("updateDS"))
log.info(s"updateDS is '$updateDS'")
var lastCollectionDate = 0L
if (updateDS) {
generateScholixResource(s"$sourcePath/provision/summaries", workingPath, spark)
log.info("Retrieve last entities collected From starting from scholix Graph")
lastCollectionDate = retrieveLastCollectedFrom(spark, s"$sourcePath/entities")
} else {
val fs = FileSystem.get(spark.sparkContext.hadoopConfiguration)
fs.delete(new Path(s"${scholixResourcePath(workingPath)}_native"), true)
fs.rename(
new Path(s"${scholixResourcePath(workingPath)}_graph"),
new Path(s"${scholixResourcePath(workingPath)}_native")
)
lastCollectionDate = retrieveLastCollectedFrom(spark, dataciteOAFPath(workingPath))
}
val numRecords =
getDataciteUpdate(datacitePath, lastCollectionDate, workingPath, spark, vocabularies)
if (numRecords > 0) {
addMissingScholixResource(workingPath, spark)
generatePidMap(workingPath, spark)
resolveUpdateRelation(workingPath, spark)
generateScholixUpdate(workingPath, spark)
}
}
}
object SparkRetrieveDataciteDelta {
val log: Logger = LoggerFactory.getLogger(SparkRetrieveDataciteDelta.getClass)
def main(args: Array[String]): Unit = {
new SparkRetrieveDataciteDelta(
"/eu/dnetlib/dhp/sx/graph/retrieve_datacite_delta_params.json",
args,
log
).initialize().run()
}
}

17
dhp-workflows/dhp-aggregation/src/site/markdown/index.md
View File

@ -1,9 +1,20 @@
##DHP-Aggregation
This module defines a set of oozie workflows for the **collection** and **transformation** of metadata records.
This module defines a set of oozie workflows for
Both workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure
1. the **collection** and **transformation** of metadata records.
2. the **integration** of new external information in the result
### Collection and Transformation
The workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure
the consistency of the read/write operations on the data as the MdSM in fact keeps track of the logical-physical mapping
of each MDStore.
It defines [mappings](mappings.md) for transformation of different datasource (See mapping section).
It defines [mappings](mappings.md) for transformation of different datasource (See mapping section).
### Integration of external information in the result
The workflows create new entity in the OpenAIRE format (OAF) whose aim is to enrich the result already contained in the graph.
See integration section for more insight

36
dhp-workflows/dhp-aggregation/src/site/markdown/integration.md Normal file
View File

@ -0,0 +1,36 @@
DHP Aggregation - Integration method
=====================================
The integration method can be applied every time new information, which is not aggregated from the repositories
nor computed directly by OpenAIRE, should be added to the results of the graph.
The information integrated so far is:
1. Article impact measures
1. [Bip!Finder](https://dl.acm.org/doi/10.1145/3357384.3357850) scores
2. Result Subjects
1. Integration of Fields of Science and Techonology ([FOS](https://www.qnrf.org/en-us/FOS)) classification in
results subjects.
The method always consists in the creation of a new entity in the OpenAIRE format (OAF entity) containing only the id
and the element in the OAF model that should be used to map the information we want to integrate.
The id is set by using a particular encoding of the given PID
*unresolved::[pid]::[pidtype]*
where
1. *unresolved* is a constant value
2. *pid* is the persistent id value, e.g. 10.5281/zenodo.4707307
3. *pidtype* is the persistent id type, e.g. doi
Such entities are matched against those available in the graph using the result.instance.pid values.
This mechanism can be used to integrate enrichments produced as associated by a given PID.
If a match will be found with one of the results already in the graph that said result will be enriched with the information
present in the new OAF.
All the entities for which a match is not found are discarded.

10
dhp-workflows/dhp-aggregation/src/site/markdown/pubmed.md
View File

@ -4,13 +4,13 @@ This section describes the mapping implemented for [MEDLINE/PubMed](https://pubm
Collection
---------
The native data is collected from [ftp baseline](https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/) containing XML with
the following [shcema](https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html)
the following [schema](https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html)
Parsing
-------
The resposible class of parsing is [PMParser](./scaladocs/#eu.dnetlib.dhp.sx.bio.pubmed.PMParser) that generates
an intermediate mapping of PubMed Article defined [here](/apidocs/eu/dnetlib/dhp/sx/bio/pubmed/package-summary.html)
The resposible class of parsing is [PMParser](/dnet-hadoop/scaladocs/#eu.dnetlib.dhp.sx.bio.pubmed.PMParser) that generates
an intermediate mapping of PubMed Article defined [here](/dnet-hadoop/apidocs/eu/dnetlib/dhp/sx/bio/pubmed/package-summary.html)
Mapping
@ -50,6 +50,10 @@ The table below describes the mapping from the XML Native to the OAF mapping
|//Author/FullName| author.Forename| Concatenation of forname + lastName if exist |
|FOR ALL AUTHOR | author.rank| sequential number starting from 1|
#TODO
Missing item mapped

4
dhp-workflows/dhp-aggregation/src/site/site.xml
View File

@ -20,7 +20,9 @@
<item name="Pubmed" href="pubmed.html"/>
<item name="Datacite" href="datacite.html"/>
</item>
<item name="Release Notes" href="release-notes.html" />
<item name="Integration" href="integration.html" collapse="true">
</item>
<item name="General Information" href="about.html"/>
<item name="JavaDoc" href="apidocs/" />

218
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java
View File

@ -28,6 +28,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Result;
public class SparkAtomicActionScoreJobTest {
@ -69,13 +70,9 @@ public class SparkAtomicActionScoreJobTest {
}
@Test
void matchOne() throws Exception {
void testMatch() throws Exception {
String bipScoresPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
.getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json")
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores_oid.json")
.getPath();
SparkAtomicActionScoreJob
@ -84,234 +81,57 @@ public class SparkAtomicActionScoreJobTest {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
JavaRDD<Result> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
.map(aa -> ((Result) aa.getPayload()));
assertEquals(1, tmp.count());
assertEquals(4, tmp.count());
Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
Dataset<Result> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Result.class));
verificationDataset.createOrReplaceTempView("result");
Dataset<Row> execVerification = spark
.sql(
"Select p.id oaid, mes.id, mUnit.value from publication p " +
"Select p.id oaid, mes.id, mUnit.value from result p " +
"lateral view explode(measures) m as mes " +
"lateral view explode(mes.unit) u as mUnit ");
Assertions.assertEquals(2, execVerification.count());
Assertions.assertEquals(12, execVerification.count());
Assertions
.assertEquals(
"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb",
execVerification.select("oaid").collectAsList().get(0).getString(0));
Assertions
.assertEquals(
"1.47565045883e-08",
execVerification.filter("id = 'influence'").select("value").collectAsList().get(0).getString(0));
Assertions
.assertEquals(
"0.227515392",
execVerification.filter("id = 'popularity'").select("value").collectAsList().get(0).getString(0));
}
@Test
void matchOneWithTwo() throws Exception {
String bipScoresPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
.getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json")
.getPath();
SparkAtomicActionScoreJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
assertEquals(1, tmp.count());
Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
Dataset<Row> execVerification = spark
.sql(
"Select p.id oaid, mes.id, mUnit.value from publication p " +
"lateral view explode(measures) m as mes " +
"lateral view explode(mes.unit) u as mUnit ");
Assertions.assertEquals(4, execVerification.count());
Assertions
.assertEquals(
"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb",
execVerification.select("oaid").collectAsList().get(0).getString(0));
Assertions
.assertEquals(
2,
execVerification.filter("id = 'influence'").count());
Assertions
.assertEquals(
2,
execVerification.filter("id = 'popularity'").count());
List<Row> tmp_ds = execVerification.filter("id = 'influence'").select("value").collectAsList();
String tmp_influence = tmp_ds.get(0).getString(0);
assertTrue(
"1.47565045883e-08".equals(tmp_influence) ||
"1.98956540239e-08".equals(tmp_influence));
tmp_influence = tmp_ds.get(1).getString(0);
assertTrue(
"1.47565045883e-08".equals(tmp_influence) ||
"1.98956540239e-08".equals(tmp_influence));
assertNotEquals(tmp_ds.get(1).getString(0), tmp_ds.get(0).getString(0));
}
@Test
void matchTwo() throws Exception {
String bipScoresPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
.getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json")
.getPath();
SparkAtomicActionScoreJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
assertEquals(2, tmp.count());
Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
Dataset<Row> execVerification = spark
.sql(
"Select p.id oaid, mes.id, mUnit.value from publication p " +
"lateral view explode(measures) m as mes " +
"lateral view explode(mes.unit) u as mUnit ");
Assertions.assertEquals(4, execVerification.count());
Assertions
.assertEquals(
2,
execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb'").count());
Assertions
.assertEquals(
2,
execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09'").count());
Assertions
.assertEquals(
2,
execVerification.filter("id = 'influence'").count());
Assertions
.assertEquals(
2,
execVerification.filter("id = 'popularity'").count());
Assertions
.assertEquals(
"1.47565045883e-08",
execVerification
"6.63451994567e-09", execVerification
.filter(
"oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " +
"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
"and id = 'influence'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
Assertions
.assertEquals(
"1.98956540239e-08",
execVerification
"0.348694533145", execVerification
.filter(
"oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " +
"and id = 'influence'")
"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
"and id = 'popularity_alt'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
Assertions
.assertEquals(
"0.282046161584",
execVerification
"2.16094680115e-09", execVerification
.filter(
"oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " +
"and id = 'popularity'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
Assertions
.assertEquals(
"0.227515392",
execVerification
.filter(
"oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " +
"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
"and id = 'popularity'")
.select("value")
.collectAsList()

170
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java
View File

@ -18,17 +18,14 @@ import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
import eu.dnetlib.dhp.schema.oaf.Result;
public class PrepareTest {
@ -96,13 +93,18 @@ public class PrepareTest {
String doi1 = "unresolved::10.0000/096020199389707::doi";
Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).count());
Assertions.assertEquals(3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getMeasures().size());
Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().size());
Assertions
.assertEquals(
3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().get(0).getMeasures().size());
Assertions
.assertEquals(
"6.34596412687e-09", tmp
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getInstance()
.get(0)
.getMeasures()
.stream()
.filter(sl -> sl.getId().equals("influence"))
@ -117,6 +119,8 @@ public class PrepareTest {
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getInstance()
.get(0)
.getMeasures()
.stream()
.filter(sl -> sl.getId().equals("popularity_alt"))
@ -131,6 +135,8 @@ public class PrepareTest {
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getInstance()
.get(0)
.getMeasures()
.stream()
.filter(sl -> sl.getId().equals("popularity"))
@ -140,34 +146,10 @@ public class PrepareTest {
.get(0)
.getValue());
}
final String doi2 = "unresolved::10.3390/s18072310::doi";
@Test
void getFOSFileTest() throws IOException, ClassNotFoundException {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/h2020_fos_sbs.csv")
.getPath();
final String outputPath = workingDir.toString() + "/fos.json";
new GetFOSData()
.doRewrite(
sourcePath, outputPath, "eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel",
'\t', fs);
BufferedReader in = new BufferedReader(
new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
String line;
int count = 0;
while ((line = in.readLine()) != null) {
FOSDataModel fos = new ObjectMapper().readValue(line, FOSDataModel.class);
System.out.println(new ObjectMapper().writeValueAsString(fos));
count += 1;
}
assertEquals(38, count);
Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).count());
Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).collect().get(0).getInstance().size());
}
@ -195,15 +177,8 @@ public class PrepareTest {
String doi1 = "unresolved::10.3390/s18072310::doi";
assertEquals(50, tmp.count());
assertEquals(20, tmp.count());
assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count());
assertTrue(
tmp
.filter(r -> r.getId().equals(doi1))
.flatMap(r -> r.getSubject().iterator())
.map(sbj -> sbj.getValue())
.collect()
.contains("engineering and technology"));
assertTrue(
tmp
@ -211,16 +186,16 @@ public class PrepareTest {
.flatMap(r -> r.getSubject().iterator())
.map(sbj -> sbj.getValue())
.collect()
.contains("nano-technology"));
.contains("04 agricultural and veterinary sciences"));
assertTrue(
tmp
.filter(r -> r.getId().equals(doi1))
.flatMap(r -> r.getSubject().iterator())
.map(sbj -> sbj.getValue())
.collect()
.contains("nanoscience & nanotechnology"));
.contains("0404 agricultural biotechnology"));
String doi = "unresolved::10.1111/1365-2656.12831::doi";
String doi = "unresolved::10.1007/s11164-020-04383-6::doi";
assertEquals(1, tmp.filter(row -> row.getId().equals(doi)).count());
assertTrue(
tmp
@ -228,7 +203,7 @@ public class PrepareTest {
.flatMap(r -> r.getSubject().iterator())
.map(sbj -> sbj.getValue())
.collect()
.contains("psychology and cognitive sciences"));
.contains("01 natural sciences"));
assertTrue(
tmp
@ -236,15 +211,114 @@ public class PrepareTest {
.flatMap(r -> r.getSubject().iterator())
.map(sbj -> sbj.getValue())
.collect()
.contains("social sciences"));
assertFalse(
.contains("0104 chemical sciences"));
assertTrue(
tmp
.filter(r -> r.getId().equals(doi))
.flatMap(r -> r.getSubject().iterator())
.map(sbj -> sbj.getValue())
.collect()
.contains("NULL"));
.contains("010402 general chemistry"));
}
@Test
void sdgPrepareTest() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/sdg/sdg.json")
.getPath();
PrepareSDGSparkJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath,
"-outputPath", workingDir.toString() + "/work"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Result> tmp = sc
.textFile(workingDir.toString() + "/work/sdg")
.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
String doi1 = "unresolved::10.1001/amaguidesnewsletters.2019.sepoct02::doi";
assertEquals(32, tmp.count());
assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count());
assertTrue(
tmp
.filter(r -> r.getId().equals(doi1))
.flatMap(r -> r.getSubject().iterator())
.map(sbj -> sbj.getValue())
.collect()
.contains("3. Good health"));
assertTrue(
tmp
.filter(r -> r.getId().equals(doi1))
.flatMap(r -> r.getSubject().iterator())
.map(sbj -> sbj.getValue())
.collect()
.contains("8. Economic growth"));
Assertions.assertEquals(32, tmp.filter(row -> row.getDataInfo() != null).count());
}
// @Test
// void test3() throws Exception {
// final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_fos_results_20_12_2021.csv.gz";
//
// final String outputPath = workingDir.toString() + "/fos.json";
// GetFOSSparkJob
// .main(
// new String[] {
// "--isSparkSessionManaged", Boolean.FALSE.toString(),
// "--sourcePath", sourcePath,
//
// "-outputPath", outputPath
//
// });
//
// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
//
// JavaRDD<FOSDataModel> tmp = sc
// .textFile(outputPath)
// .map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
//
// tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
// tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
// tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
// tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
//
// }
//
// @Test
// void test4() throws Exception {
// final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_sdg_results_20_12_21.csv.gz";
//
// final String outputPath = workingDir.toString() + "/sdg.json";
// GetSDGSparkJob
// .main(
// new String[] {
// "--isSparkSessionManaged", Boolean.FALSE.toString(),
// "--sourcePath", sourcePath,
//
// "-outputPath", outputPath
//
// });
//
// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
//
// JavaRDD<SDGDataModel> tmp = sc
// .textFile(outputPath)
// .map(item -> OBJECT_MAPPER.readValue(item, SDGDataModel.class));
//
// tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
// tmp.foreach(t -> Assertions.assertTrue(t.getSbj() != null));
//
// }
}

492
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java
View File

@ -24,6 +24,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.Constants;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
@ -67,70 +68,12 @@ public class ProduceTest {
}
@Test
void produceTest() throws Exception {
void produceTestSubjects() throws Exception {
final String bipPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
.getPath();
PrepareBipFinder
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", bipPath,
"--outputPath", workingDir.toString() + "/work"
});
final String fosPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
.getPath();
PrepareFOSSparkJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", fosPath,
"-outputPath", workingDir.toString() + "/work"
});
SparkSaveUnresolved.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", workingDir.toString() + "/work",
"-outputPath", workingDir.toString() + "/unresolved"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Result> tmp = sc
.textFile(workingDir.toString() + "/unresolved")
.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
Assertions.assertEquals(135, tmp.count());
Assertions.assertEquals(1, tmp.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi")).count());
Assertions
.assertEquals(
3, tmp
.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertEquals(
3, tmp
.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
.collect()
.get(0)
.getMeasures()
.size());
JavaRDD<Result> tmp = getResultJavaRDD();
List<StructuredProperty> sbjs = tmp
.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
.filter(row -> row.getSubject() != null && row.getSubject().size() > 0)
.flatMap(row -> row.getSubject().iterator())
.collect();
@ -172,14 +115,105 @@ public class ProduceTest {
.assertEquals(
ModelConstants.DNET_PROVENANCE_ACTIONS,
sbj.getDataInfo().getProvenanceaction().getSchemename()));
}
sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("engineering and technology"));
sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("nano-technology"));
sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("nanoscience & nanotechnology"));
@Test
void produceTestMeasuress() throws Exception {
JavaRDD<Result> tmp = getResultJavaRDD();
List<KeyValue> mes = tmp
.filter(row -> row.getInstance() != null && row.getInstance().size() > 0)
.flatMap(row -> row.getInstance().iterator())
.flatMap(i -> i.getMeasures().iterator())
.flatMap(m -> m.getUnit().iterator())
.collect();
mes.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getDeletedbyinference()));
mes.forEach(sbj -> Assertions.assertEquals(true, sbj.getDataInfo().getInferred()));
mes.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getInvisible()));
mes.forEach(sbj -> Assertions.assertEquals("", sbj.getDataInfo().getTrust()));
mes.forEach(sbj -> Assertions.assertEquals("update", sbj.getDataInfo().getInferenceprovenance()));
mes
.forEach(
sbj -> Assertions.assertEquals("measure:bip", sbj.getDataInfo().getProvenanceaction().getClassid()));
mes
.forEach(
sbj -> Assertions
.assertEquals("Inferred by OpenAIRE", sbj.getDataInfo().getProvenanceaction().getClassname()));
mes
.forEach(
sbj -> Assertions
.assertEquals(
ModelConstants.DNET_PROVENANCE_ACTIONS, sbj.getDataInfo().getProvenanceaction().getSchemeid()));
mes
.forEach(
sbj -> Assertions
.assertEquals(
ModelConstants.DNET_PROVENANCE_ACTIONS,
sbj.getDataInfo().getProvenanceaction().getSchemename()));
}
@Test
void produceTest6Subjects() throws Exception {
final String doi = "unresolved::10.3390/s18072310::doi";
JavaRDD<Result> tmp = getResultJavaRDD();
Assertions
.assertEquals(
6, tmp
.filter(row -> row.getId().equals(doi))
.collect()
.get(0)
.getSubject()
.size());
List<StructuredProperty> sbjs = tmp
.filter(row -> row.getId().equals(doi))
.flatMap(row -> row.getSubject().iterator())
.collect();
Assertions
.assertEquals(
true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("04 agricultural and veterinary sciences")));
Assertions
.assertEquals(
true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0404 agricultural biotechnology")));
Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("040502 food science")));
Assertions
.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("03 medical and health sciences")));
Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0303 health sciences")));
Assertions
.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("030309 nutrition & dietetics")));
}
@Test
void produceTest3Measures() throws Exception {
final String doi = "unresolved::10.3390/s18072310::doi";
JavaRDD<Result> tmp = getResultJavaRDD();
tmp
.filter(row -> row.getId().equals(doi))
.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
Assertions
.assertEquals(
3, tmp
.filter(row -> row.getId().equals(doi))
.collect()
.get(0)
.getInstance()
.get(0)
.getMeasures()
.size());
List<Measure> measures = tmp
.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
.flatMap(row -> row.getMeasures().iterator())
.filter(row -> row.getId().equals(doi))
.flatMap(row -> row.getInstance().iterator())
.flatMap(inst -> inst.getMeasures().iterator())
.collect();
Assertions
.assertEquals(
@ -216,8 +250,82 @@ public class ProduceTest {
Assertions
.assertEquals(
49, tmp
.filter(row -> !row.getId().equals("unresolved::10.3390/s18072310::doi"))
"10.3390/s18072310",
tmp
.filter(row -> row.getId().equals(doi))
.collect()
.get(0)
.getInstance()
.get(0)
.getPid()
.get(0)
.getValue()
.toLowerCase());
Assertions
.assertEquals(
"doi",
tmp
.filter(row -> row.getId().equals(doi))
.collect()
.get(0)
.getInstance()
.get(0)
.getPid()
.get(0)
.getQualifier()
.getClassid());
Assertions
.assertEquals(
"Digital Object Identifier",
tmp
.filter(row -> row.getId().equals(doi))
.collect()
.get(0)
.getInstance()
.get(0)
.getPid()
.get(0)
.getQualifier()
.getClassname());
}
@Test
void produceTestMeasures() throws Exception {
final String doi = "unresolved::10.3390/s18072310::doi";
JavaRDD<Result> tmp = getResultJavaRDD();
List<StructuredProperty> mes = tmp
.filter(row -> row.getInstance() != null && row.getInstance().size() > 0)
.flatMap(row -> row.getInstance().iterator())
.flatMap(i -> i.getPid().iterator())
.collect();
Assertions.assertEquals(86, mes.size());
tmp
.filter(row -> row.getInstance() != null && row.getInstance().size() > 0)
.foreach(
e -> Assertions.assertEquals("sysimport:enrich", e.getDataInfo().getProvenanceaction().getClassid()));
}
@Test
void produceTestSomeNumbers() throws Exception {
final String doi = "unresolved::10.3390/s18072310::doi";
JavaRDD<Result> tmp = getResultJavaRDD();
Assertions.assertEquals(105, tmp.count());
Assertions.assertEquals(1, tmp.filter(row -> row.getId().equals(doi)).count());
Assertions
.assertEquals(
19, tmp
.filter(row -> !row.getId().equals(doi))
.filter(row -> row.getSubject() != null)
.count());
@ -225,10 +333,254 @@ public class ProduceTest {
.assertEquals(
85,
tmp
.filter(row -> !row.getId().equals("unresolved::10.3390/s18072310::doi"))
.filter(r -> r.getMeasures() != null)
.filter(row -> !row.getId().equals(doi))
.filter(r -> r.getInstance() != null && r.getInstance().size() > 0)
.count());
}
private JavaRDD<Result> getResultJavaRDD() throws Exception {
final String bipPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
.getPath();
PrepareBipFinder
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", bipPath,
"--outputPath", workingDir.toString() + "/work"
});
final String fosPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
.getPath();
PrepareFOSSparkJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", fosPath,
"-outputPath", workingDir.toString() + "/work"
});
SparkSaveUnresolved.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", workingDir.toString() + "/work",
"-outputPath", workingDir.toString() + "/unresolved"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
return sc
.textFile(workingDir.toString() + "/unresolved")
.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
}
@Test
void prepareTest5Subjects() throws Exception {
final String doi = "unresolved::10.1063/5.0032658::doi";
JavaRDD<Result> tmp = getResultJavaRDD();
Assertions.assertEquals(1, tmp.filter(row -> row.getId().equals(doi)).count());
Assertions
.assertEquals(
5, tmp
.filter(row -> row.getId().equals(doi))
.collect()
.get(0)
.getSubject()
.size());
List<StructuredProperty> sbjs = tmp
.filter(row -> row.getId().equals(doi))
.flatMap(row -> row.getSubject().iterator())
.collect();
Assertions
.assertEquals(
true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("01 natural sciences")));
Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0103 physical sciences")));
Assertions
.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("010304 chemical physics")));
Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0104 chemical sciences")));
Assertions
.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("010402 general chemistry")));
}
private JavaRDD<Result> getResultJavaRDDPlusSDG() throws Exception {
final String bipPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
.getPath();
PrepareBipFinder
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", bipPath,
"--outputPath", workingDir.toString() + "/work"
});
final String fosPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
.getPath();
PrepareFOSSparkJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", fosPath,
"-outputPath", workingDir.toString() + "/work"
});
final String sdgPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/sdg/sdg.json")
.getPath();
PrepareSDGSparkJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sdgPath,
"-outputPath", workingDir.toString() + "/work"
});
SparkSaveUnresolved.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", workingDir.toString() + "/work",
"-outputPath", workingDir.toString() + "/unresolved"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
return sc
.textFile(workingDir.toString() + "/unresolved")
.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
}
@Test
void produceTestSomeNumbersWithSDG() throws Exception {
final String doi = "unresolved::10.3390/s18072310::doi";
JavaRDD<Result> tmp = getResultJavaRDDPlusSDG();
Assertions.assertEquals(136, tmp.count());
Assertions.assertEquals(1, tmp.filter(row -> row.getId().equals(doi)).count());
Assertions
.assertEquals(
50, tmp
.filter(row -> !row.getId().equals(doi))
.filter(row -> row.getSubject() != null)
.count());
Assertions
.assertEquals(
85,
tmp
.filter(row -> !row.getId().equals(doi))
.filter(r -> r.getInstance() != null && r.getInstance().size() > 0)
.count());
}
@Test
void produceTest7Subjects() throws Exception {
final String doi = "unresolved::10.3390/s18072310::doi";
JavaRDD<Result> tmp = getResultJavaRDDPlusSDG();
Assertions
.assertEquals(
7, tmp
.filter(row -> row.getId().equals(doi))
.collect()
.get(0)
.getSubject()
.size());
List<StructuredProperty> sbjs = tmp
.filter(row -> row.getId().equals(doi))
.flatMap(row -> row.getSubject().iterator())
.collect();
Assertions
.assertEquals(
true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("04 agricultural and veterinary sciences")));
Assertions
.assertEquals(
true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0404 agricultural biotechnology")));
Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("040502 food science")));
Assertions
.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("03 medical and health sciences")));
Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0303 health sciences")));
Assertions
.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("030309 nutrition & dietetics")));
Assertions
.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("1. No poverty")));
}
@Test
void produceTestSubjectsWithSDG() throws Exception {
JavaRDD<Result> tmp = getResultJavaRDDPlusSDG();
List<StructuredProperty> sbjs_sdg = tmp
.filter(row -> row.getSubject() != null && row.getSubject().size() > 0)
.flatMap(row -> row.getSubject().iterator())
.filter(sbj -> sbj.getQualifier().getClassid().equals(Constants.SDG_CLASS_ID))
.collect();
sbjs_sdg.forEach(sbj -> Assertions.assertEquals("SDG", sbj.getQualifier().getClassid()));
sbjs_sdg
.forEach(
sbj -> Assertions
.assertEquals(
"Sustainable Development Goals", sbj.getQualifier().getClassname()));
sbjs_sdg
.forEach(
sbj -> Assertions
.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemeid()));
sbjs_sdg
.forEach(
sbj -> Assertions
.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemename()));
sbjs_sdg.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getDeletedbyinference()));
sbjs_sdg.forEach(sbj -> Assertions.assertEquals(true, sbj.getDataInfo().getInferred()));
sbjs_sdg.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getInvisible()));
sbjs_sdg.forEach(sbj -> Assertions.assertEquals("", sbj.getDataInfo().getTrust()));
sbjs_sdg.forEach(sbj -> Assertions.assertEquals("update", sbj.getDataInfo().getInferenceprovenance()));
sbjs_sdg
.forEach(
sbj -> Assertions.assertEquals("subject:sdg", sbj.getDataInfo().getProvenanceaction().getClassid()));
sbjs_sdg
.forEach(
sbj -> Assertions
.assertEquals("Inferred by OpenAIRE", sbj.getDataInfo().getProvenanceaction().getClassname()));
sbjs_sdg
.forEach(
sbj -> Assertions
.assertEquals(
ModelConstants.DNET_PROVENANCE_ACTIONS, sbj.getDataInfo().getProvenanceaction().getSchemeid()));
sbjs_sdg
.forEach(
sbj -> Assertions
.assertEquals(
ModelConstants.DNET_PROVENANCE_ACTIONS,
sbj.getDataInfo().getProvenanceaction().getSchemename()));
}
}

50
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java
View File

@ -76,7 +76,7 @@ public class CreateOpenCitationsASTest {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
CreateActionSetSparkJob
@ -89,17 +89,17 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet1"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
assertEquals(60, tmp.count());
assertEquals(62, tmp.count());
// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
@ -110,7 +110,7 @@ public class CreateOpenCitationsASTest {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
CreateActionSetSparkJob
@ -121,17 +121,17 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet2"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet2", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
assertEquals(44, tmp.count());
assertEquals(46, tmp.count());
// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
@ -142,7 +142,7 @@ public class CreateOpenCitationsASTest {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
CreateActionSetSparkJob
@ -153,13 +153,13 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet3"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet3", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
@ -175,7 +175,7 @@ public class CreateOpenCitationsASTest {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
CreateActionSetSparkJob
@ -186,13 +186,13 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet4"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet4", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
@ -215,7 +215,7 @@ public class CreateOpenCitationsASTest {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
CreateActionSetSparkJob
@ -226,13 +226,13 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet5"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet5", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
@ -240,8 +240,8 @@ public class CreateOpenCitationsASTest {
assertEquals("citation", r.getSubRelType());
assertEquals("resultResult", r.getRelType());
});
assertEquals(22, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
assertEquals(22, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
assertEquals(23, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
assertEquals(23, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
}
@ -250,7 +250,7 @@ public class CreateOpenCitationsASTest {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
CreateActionSetSparkJob
@ -261,13 +261,13 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet6"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet6", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
@ -295,7 +295,7 @@ public class CreateOpenCitationsASTest {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
CreateActionSetSparkJob
@ -306,13 +306,13 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet7"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet7", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));

140
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCITest.java Normal file
View File

@ -0,0 +1,140 @@
package eu.dnetlib.dhp.actionmanager.opencitations;
import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.LocalFileSystem;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
import eu.dnetlib.dhp.schema.oaf.Dataset;
public class ReadCOCITest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(ReadCOCITest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(ReadCOCITest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(ReadCOCITest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(ReadCOCITest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void testReadCOCI() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
.getPath();
LocalFileSystem fs = FileSystem.getLocal(new Configuration());
fs
.copyFromLocalFile(
false, new org.apache.hadoop.fs.Path(getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input1.gz")
.getPath()),
new org.apache.hadoop.fs.Path(workingDir + "/COCI/input1.gz"));
fs
.copyFromLocalFile(
false, new org.apache.hadoop.fs.Path(getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input2.gz")
.getPath()),
new org.apache.hadoop.fs.Path(workingDir + "/COCI/input2.gz"));
fs
.copyFromLocalFile(
false, new org.apache.hadoop.fs.Path(getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input3.gz")
.getPath()),
new org.apache.hadoop.fs.Path(workingDir + "/COCI/input3.gz"));
fs
.copyFromLocalFile(
false, new org.apache.hadoop.fs.Path(getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input4.gz")
.getPath()),
new org.apache.hadoop.fs.Path(workingDir + "/COCI/input4.gz"));
fs
.copyFromLocalFile(
false, new org.apache.hadoop.fs.Path(getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input5.gz")
.getPath()),
new org.apache.hadoop.fs.Path(workingDir + "/COCI/input5.gz"));
ReadCOCI
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-workingPath",
workingDir.toString() + "/COCI",
"-outputPath",
workingDir.toString() + "/COCI_json/",
"-inputFile", "input1;input2;input3;input4;input5"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<COCI> tmp = sc
.textFile(workingDir.toString() + "/COCI_json/*/")
.map(item -> OBJECT_MAPPER.readValue(item, COCI.class));
Assertions.assertEquals(24, tmp.count());
Assertions.assertEquals(1, tmp.filter(c -> c.getCiting().equals("10.1207/s15327647jcd3,4-01")).count());
Assertions.assertEquals(8, tmp.filter(c -> c.getCiting().indexOf(".refs") > -1).count());
}
}

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dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala
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package eu.dnetlib.dhp.datacite
import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature}
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
import eu.dnetlib.dhp.schema.oaf.Oaf
import org.junit.jupiter.api.extension.ExtendWith
import org.junit.jupiter.api.{BeforeEach, Test}
import org.mockito.junit.jupiter.MockitoExtension
import java.text.SimpleDateFormat
import java.util.Locale
import scala.io.Source
@ExtendWith(Array(classOf[MockitoExtension]))
class DataciteToOAFTest extends AbstractVocabularyTest{
@BeforeEach
def setUp() :Unit = {
super.setUpVocabulary()
}
@Test
def testDateMapping:Unit = {
val inputDate = "2021-07-14T11:52:54+0000"
val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US)
val dt = ISO8601FORMAT.parse(inputDate)
println(dt.getTime)
}
@Test
def testMapping() :Unit = {
val record =Source.fromInputStream(getClass.getResourceAsStream("record.json")).mkString
val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
val res:List[Oaf] =DataciteToOAFTransformation.generateOAF(record, 0L,0L, vocabularies, true )
res.foreach(r => {
println (mapper.writeValueAsString(r))
println("----------------------------")
})
}
}

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package eu.dnetlib.dhp.sx.bio
import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature}
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf}
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.extension.ExtendWith
import org.junit.jupiter.api.{BeforeEach, Test}
import org.mockito.junit.jupiter.MockitoExtension
import java.io.{BufferedReader, InputStream, InputStreamReader}
import java.util.zip.GZIPInputStream
import scala.collection.JavaConverters._
import scala.io.Source
import scala.xml.pull.XMLEventReader
@ExtendWith(Array(classOf[MockitoExtension]))
class BioScholixTest extends AbstractVocabularyTest{
val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false)
@BeforeEach
def setUp() :Unit = {
super.setUpVocabulary()
}
class BufferedReaderIterator(reader: BufferedReader) extends Iterator[String] {
override def hasNext() = reader.ready
override def next() = reader.readLine()
}
object GzFileIterator {
def apply(is: InputStream, encoding: String) = {
new BufferedReaderIterator(
new BufferedReader(
new InputStreamReader(
new GZIPInputStream(
is), encoding)))
}
}
@Test
def testEBIData() = {
val inputXML = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml")).mkString
val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes()))
new PMParser(xml).foreach(s =>println(mapper.writeValueAsString(s)))
}
@Test
def testPubmedToOaf(): Unit = {
assertNotNull(vocabularies)
assertTrue(vocabularies.vocabularyExists("dnet:publication_resource"))
val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump")).mkString
val r:List[Oaf] = records.lines.toList.map(s=>mapper.readValue(s, classOf[PMArticle])).map(a => PubMedToOaf.convert(a, vocabularies))
assertEquals(10, r.size)
assertTrue(r.map(p => p.asInstanceOf[Result]).flatMap(p => p.getInstance().asScala.map(i => i.getInstancetype.getClassid)).exists(p => "0037".equalsIgnoreCase(p)))
println(mapper.writeValueAsString(r.head))
}
@Test
def testPDBToOAF():Unit = {
assertNotNull(vocabularies)
assertTrue(vocabularies.vocabularyExists("dnet:publication_resource"))
val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pdb_dump")).mkString
records.lines.foreach(s => assertTrue(s.nonEmpty))
val result:List[Oaf]= records.lines.toList.flatMap(o => BioDBToOAF.pdbTOOaf(o))
assertTrue(result.nonEmpty)
result.foreach(r => assertNotNull(r))
println(result.count(o => o.isInstanceOf[Relation]))
println(mapper.writeValueAsString(result.head))
}
@Test
def testUNIprotToOAF():Unit = {
assertNotNull(vocabularies)
assertTrue(vocabularies.vocabularyExists("dnet:publication_resource"))
val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump")).mkString
records.lines.foreach(s => assertTrue(s.nonEmpty))
val result:List[Oaf]= records.lines.toList.flatMap(o => BioDBToOAF.uniprotToOAF(o))
assertTrue(result.nonEmpty)
result.foreach(r => assertNotNull(r))
println(result.count(o => o.isInstanceOf[Relation]))
println(mapper.writeValueAsString(result.head))
}
case class EBILinks(relType:String, date:String, title:String, pmid:String, targetPid:String, targetPidType:String) {}
def parse_ebi_links(input:String):List[EBILinks] ={
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val pmid = (json \ "publication" \"pmid").extract[String]
for {
JObject(link) <- json \\ "Link"
JField("Target",JObject(target)) <- link
JField("RelationshipType",JObject(relType)) <- link
JField("Name", JString(relation)) <- relType
JField("PublicationDate",JString(publicationDate)) <- link
JField("Title", JString(title)) <- target
JField("Identifier",JObject(identifier)) <- target
JField("IDScheme", JString(idScheme)) <- identifier
JField("ID", JString(id)) <- identifier
} yield EBILinks(relation, publicationDate, title, pmid, id, idScheme)
}
@Test
def testCrossrefLinksToOAF():Unit = {
val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/crossref_links")).mkString
records.lines.foreach(s => assertTrue(s.nonEmpty))
val result:List[Oaf] =records.lines.map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList
assertNotNull(result)
assertTrue(result.nonEmpty)
println(mapper.writeValueAsString(result.head))
}
@Test
def testEBILinksToOAF():Unit = {
val iterator = GzFileIterator(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/ebi_links.gz"), "UTF-8")
val data = iterator.next()
val res = BioDBToOAF.parse_ebi_links(BioDBToOAF.extractEBILinksFromDump(data).links).filter(BioDBToOAF.EBITargetLinksFilter).flatMap(BioDBToOAF.convertEBILinksToOaf)
print(res.length)
println(mapper.writeValueAsString(res.head))
}
@Test
def scholixResolvedToOAF():Unit ={
val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved")).mkString
records.lines.foreach(s => assertTrue(s.nonEmpty))
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
val l:List[ScholixResolved] = records.lines.map{input =>
lazy val json = parse(input)
json.extract[ScholixResolved]
}.toList
val result:List[Oaf] = l.map(s => BioDBToOAF.scholixResolvedToOAF(s))
assertTrue(result.nonEmpty)
}
}

1101
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json
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{"50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1": [{"id": "influence", "unit": [{"value": "6.63451994567e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.348694533145", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "2.16094680115e-09", "key": "score"}]}]}
{"50|dedup_wf_001::05b1f8ce98702f69d07aa5f0429de1e3": [{"id": "influence", "unit": [{"value": "6.25057357279e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "7.0208", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "2.40234462244e-08", "key": "score"}]}]}
{"50|dedup_wf_001::08823c8f5c3ca2eae523817036cdda67": [{"id": "influence", "unit": [{"value": "5.54921449123e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "3.53012887452e-10", "key": "score"}]}]}
{"50|dedup_wf_001::0e72b399325d6efcbe3271891a1dfe4c": [{"id": "influence", "unit": [{"value": "1.63466096315e-08", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "20.9870879741", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "5.49501495323e-08", "key": "score"}]}]}

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dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json
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{"doi":"10.3390/s18072310","level1":"engineering and technology","level2":"nano-technology","level3":"nanoscience & nanotechnology"}
{"doi":"10.1111/1365-2656.12831\u000210.17863/cam.24369","level1":"social sciences","level2":"psychology and cognitive sciences","level3":"NULL"}
{"doi":"10.3929/ethz-b-000187584\u000210.1002/chem.201701644","level1":"natural sciences","level2":"NULL","level3":"NULL"}
{"doi":"10.1080/01913123.2017.1367361","level1":"medical and health sciences","level2":"clinical medicine","level3":"oncology & carcinogenesis"}
{"doi":"10.1051/e3sconf/20199207011","level1":"natural sciences","level2":"earth and related environmental sciences","level3":"environmental sciences"}
{"doi":"10.1038/onc.2015.333","level1":"medical and health sciences","level2":"clinical medicine","level3":"oncology & carcinogenesis"}
{"doi":"10.1093/mnras/staa256","level1":"natural sciences","level2":"physical sciences","level3":"NULL"}
{"doi":"10.1016/j.jclepro.2018.07.166","level1":"engineering and technology","level2":"other engineering and technologies","level3":"building & construction"}
{"doi":"10.1103/physrevlett.125.037403","level1":"natural sciences","level2":"physical sciences","level3":"nuclear & particles physics"}
{"doi":"10.1080/03602532.2017.1316285","level1":"natural sciences","level2":"NULL","level3":"NULL"}
{"doi":"10.1001/jamanetworkopen.2019.1868","level1":"medical and health sciences","level2":"other medical science","level3":"health policy & services"}
{"doi":"10.1128/mra.00874-18","level1":"natural sciences","level2":"biological sciences","level3":"plant biology & botany"}
{"doi":"10.1016/j.nancom.2018.03.001","level1":"engineering and technology","level2":"NULL","level3":"NULL"}
{"doi":"10.1112/topo.12174","level1":"natural sciences","level2":"NULL","level3":"NULL"}
{"doi":"10.12688/wellcomeopenres.15846.1","level1":"medical and health sciences","level2":"health sciences","level3":"NULL"}
{"doi":"10.21468/scipostphys.3.1.001","level1":"natural sciences","level2":"physical sciences","level3":"NULL"}
{"doi":"10.1088/1741-4326/ab6c77","level1":"natural sciences","level2":"physical sciences","level3":"nuclear & particles physics"}
{"doi":"10.1109/tpwrs.2019.2944747","level1":"engineering and technology","level2":"electrical engineering, electronic engineering, information engineering","level3":"electrical & electronic engineering"}
{"doi":"10.1016/j.expthermflusci.2019.109994\u000210.17863/cam.46212","level1":"engineering and technology","level2":"mechanical engineering","level3":"mechanical engineering & transports"}
{"doi":"10.1109/tc.2018.2860012","level1":"engineering and technology","level2":"electrical engineering, electronic engineering, information engineering","level3":"computer hardware & architecture"}
{"doi":"10.1002/mma.6622","level1":"natural sciences","level2":"mathematics","level3":"numerical & computational mathematics"}
{"doi":"10.1051/radiopro/2020020","level1":"natural sciences","level2":"chemical sciences","level3":"NULL"}
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{"doi":"10.3390/cancers12010236","level1":"medical and health sciences","level2":"health sciences","level3":"biochemistry & molecular biology"}
{"doi":"10.6084/m9.figshare.9912614\u000210.6084/m9.figshare.9912614.v1\u000210.1080/00268976.2019.1665199","level1":"natural sciences","level2":"chemical sciences","level3":"physical chemistry"}
{"doi":"10.1175/jpo-d-17-0239.1","level1":"natural sciences","level2":"biological sciences","level3":"marine biology & hydrobiology"}
{"doi":"10.1007/s13218-020-00674-7","level1":"engineering and technology","level2":"industrial biotechnology","level3":"industrial engineering & automation"}
{"doi":"10.1016/j.psyneuen.2016.02.003\u000210.1016/j.psyneuen.2016.02.00310.7892/boris.78886\u000210.7892/boris.78886","level1":"medical and health sciences","level2":"basic medicine","level3":"NULL"}
{"doi":"10.1109/ted.2018.2813542","level1":"engineering and technology","level2":"electrical engineering, electronic engineering, information engineering","level3":"electrical & electronic engineering"}
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{"doi":"10.3390/su12187503","level1":"natural sciences","level2":"earth and related environmental sciences","level3":"NULL"}
{"doi":"10.1016/j.ccell.2018.08.017","level1":"medical and health sciences","level2":"basic medicine","level3":"biochemistry & molecular biology"}
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{"doi":"10.1039/c8cp03234c","level1":"natural sciences","level2":"NULL","level3":"NULL"}
{"doi":"10.5281/zenodo.3696557\u000210.5281/zenodo.3696556\u000210.1109/jsac.2016.2545384","level1":"engineering and technology","level2":"electrical engineering, electronic engineering, information engineering","level3":"networking & telecommunications"}
{"doi":"10.1038/ng.3667\u000210.1038/ng.3667.\u000210.17615/tct6-4m26\u000210.17863/cam.15649","level1":"medical and health sciences","level2":"health sciences","level3":"genetics & heredity"}
{"doi":"10.1016/j.jclepro.2019.119065","level1":"engineering and technology","level2":"other engineering and technologies","level3":"building & construction"}
{"doi":"10.1111/pce.13392","level1":"agricultural and veterinary sciences","level2":"agriculture, forestry, and fisheries","level3":"agronomy & agriculture"}
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{"doi":"10.1186/s40425-019-0732-8","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030220 oncology & carcinogenesis"}
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{"doi":"10.1155/2021/6643273","level1":"01 natural sciences","level2":"0103 physical sciences","level3":"010301 acoustics"}
{"doi":"10.1155/2021/6643273","level1":"02 engineering and technology","level2":"0209 industrial biotechnology","level3":"020901 industrial engineering & automation"}
{"doi":"10.12737/article_5d6613dbf2ad51.82646096","level1":"02 engineering and technology","level2":"0210 nano-technology","level3":"021001 nanoscience & nanotechnology"}
{"doi":"10.12737/article_5d6613dbf2ad51.82646096","level1":"01 natural sciences","level2":"0103 physical sciences","level3":"010302 applied physics"}
{"doi":"10.1216/jie.2020.32.457","level1":"01 natural sciences","level2":"0101 mathematics","level3":"010101 applied mathematics"}
{"doi":"10.1216/jie.2020.32.457","level1":"01 natural sciences","level2":"0101 mathematics","level3":"010102 general mathematics"}
{"doi":"10.3934/naco.2021021","level1":"02 engineering and technology","level2":"0211 other engineering and technologies","level3":"021103 operations research"}
{"doi":"10.3934/naco.2021021","level1":"02 engineering and technology","level2":"0209 industrial biotechnology","level3":"020901 industrial engineering & automation"}
{"doi":"10.1080/1034912x.2021.1910933","level1":"05 social sciences","level2":"050301 education","level3":"050301 education"}
{"doi":"10.1080/1034912x.2021.1910933","level1":"05 social sciences","level2":"0501 psychology and cognitive sciences","level3":"050104 developmental & child psychology"}
{"doi":"10.1016/j.rtbm.2020.100596","level1":"05 social sciences","level2":"0502 economics and business","level3":"050211 marketing"}
{"doi":"10.1016/j.rtbm.2020.100596","level1":"05 social sciences","level2":"0502 economics and business","level3":"050212 sport, leisure & tourism"}
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{"doi":"10.1063/5.0032658","level1":"01 natural sciences","level2":"0104 chemical sciences","level3":"010402 general chemistry"}
{"doi":"10.1145/3411174.3411195","level1":"02 engineering and technology","level2":"0202 electrical engineering, electronic engineering, information engineering","level3":"020201 artificial intelligence & image processing"}
{"doi":"10.1145/3411174.3411195","level1":"02 engineering and technology","level2":"0202 electrical engineering, electronic engineering, information engineering","level3":"020206 networking & telecommunications"}
{"doi":"10.1021/acs.joc.0c02755","level1":"01 natural sciences","level2":"0104 chemical sciences","level3":"010405 organic chemistry"}
{"doi":"10.1021/acs.joc.0c02755","level1":"01 natural sciences","level2":"0104 chemical sciences","level3":"010402 general chemistry"}
{"doi":"10.1002/jcp.28608","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030220 oncology & carcinogenesis"}
{"doi":"10.1002/jcp.28608","level1":"03 medical and health sciences","level2":"0301 basic medicine","level3":"030304 developmental biology"}
{"doi":"10.1097/cmr.0000000000000579","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030220 oncology & carcinogenesis"}
{"doi":"10.1097/cmr.0000000000000579","level1":"03 medical and health sciences","level2":"0301 basic medicine","level3":"030304 developmental biology"}
{"doi":"10.1007/s11164-020-04383-6","level1":"01 natural sciences","level2":"0104 chemical sciences","level3":"010405 organic chemistry"}
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{"doi":"10.1016/j.actpsy.2020.103155","level1":"05 social sciences","level2":"0501 psychology and cognitive sciences","level3":"050105 experimental psychology"}
{"doi":"10.1016/j.actpsy.2020.103155","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030217 neurology & neurosurgery"}
{"doi":"10.1109/memea49120.2020.9137187","level1":"02 engineering and technology","level2":"0202 electrical engineering, electronic engineering, information engineering","level3":"020208 electrical & electronic engineering"}

39
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs.csv Normal file
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10.1080/1536383x.2020.1868997,02 engineering and technology,0210 nano-technology,021001 nanoscience & nanotechnology
10.1080/1536383x.2020.1868997,01 natural sciences,0104 chemical sciences,010402 general chemistry
10.1186/s40425-019-0732-8,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis
10.1186/s40425-019-0732-8,03 medical and health sciences,0301 basic medicine,030304 developmental biology
10.1007/s10482-021-01529-3,03 medical and health sciences,0301 basic medicine,030304 developmental biology
10.1007/s10482-021-01529-3,03 medical and health sciences,0301 basic medicine,030306 microbiology
10.1155/2021/6643273,01 natural sciences,0103 physical sciences,010301 acoustics
10.1155/2021/6643273,02 engineering and technology,0209 industrial biotechnology,020901 industrial engineering & automation
10.12737/article_5d6613dbf2ad51.82646096,02 engineering and technology,0210 nano-technology,021001 nanoscience & nanotechnology
10.12737/article_5d6613dbf2ad51.82646096,01 natural sciences,0103 physical sciences,010302 applied physics
10.1216/jie.2020.32.457,01 natural sciences,0101 mathematics,010101 applied mathematics
10.1216/jie.2020.32.457,01 natural sciences,0101 mathematics,010102 general mathematics
10.3934/naco.2021021,02 engineering and technology,0211 other engineering and technologies,021103 operations research
10.3934/naco.2021021,02 engineering and technology,0209 industrial biotechnology,020901 industrial engineering & automation
10.1080/1034912x.2021.1910933,05 social sciences,050301 education,050301 education
10.1080/1034912x.2021.1910933,05 social sciences,0501 psychology and cognitive sciences,050104 developmental & child psychology
10.1016/j.rtbm.2020.100596,05 social sciences,0502 economics and business,050211 marketing
10.1016/j.rtbm.2020.100596,05 social sciences,0502 economics and business,"050212 sport, leisure & tourism"
10.14807/ijmp.v11i8.1220,05 social sciences,0502 economics and business,050211 marketing
10.14807/ijmp.v11i8.1220,05 social sciences,0502 economics and business,050203 business & management
10.1007/s13205-020-02415-x,03 medical and health sciences,0303 health sciences,030304 developmental biology
10.1007/s13205-020-02415-x,03 medical and health sciences,0303 health sciences,030302 biochemistry & molecular biology
10.3390/foods10040865,04 agricultural and veterinary sciences,0404 agricultural biotechnology,040502 food science
10.3390/foods10040865,03 medical and health sciences,0303 health sciences,030309 nutrition & dietetics
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15 10.1001/amaguidesnewsletters.2021.mayjune02 10. No inequality
16 10.4336/2021.pfb.41e201902078 15. Life on land
17 10.4337/ejeep.2019.00045 16. Peace & justice
18 10.4337/ejeep.2019.00050 1. No poverty
19 10.4337/ejeep.2019.0045 16. Peace & justice
20 10.4337/ejeep.2019.0050 1. No poverty
21 10.4337/ejeep.2019.0051 16. Peace & justice
22 10.4337/ejeep.2019.0052 16. Peace & justice
23 10.4337/ejeep.2020.0058 1. No poverty
24 10.4337/ejeep.2020.0058 10. No inequality
25 10.4337/ejeep.2020.0060 10. No inequality
26 10.4337/ejeep.2020.0065 16. Peace & justice
27 10.4337/ejeep.2020.02.03 16. Peace & justice
28 10.4337/ejeep.2020.02.05 8. Economic growth
29 10.4337/ejeep.2020.02.06 16. Peace & justice
30 10.4337/ejeep.2020.02.09 16. Peace & justice
31 10.4337/roke.2020.01.01 16. Peace & justice
32 10.4337/roke.2020.01.03 16. Peace & justice
33 10.4337/roke.2020.01.05 1. No poverty
34 10.4337/roke.2020.01.05 8. Economic growth
35 10.4337/roke.2020.01.07 8. Economic growth
36 10.4337/roke.2020.02.03 8. Economic growth
37 10.4337/roke.2020.02.04 1. No poverty

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