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dnet-hadoop
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code formatting

This commit is contained in:
Claudio Atzori 2020-05-22 12:34:00 +02:00
parent dc4621b3cb
commit 3cf2796ac6
6 changed files with 315 additions and 244 deletions
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21
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java
View File

@ -1,16 +1,19 @@
package eu.dnetlib.dhp.oa.dedup;
import com.wcohen.ss.JaroWinkler;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.pace.model.Person;
import org.apache.commons.lang3.StringUtils;
import scala.Tuple2;
package eu.dnetlib.dhp.oa.dedup;
import java.text.Normalizer;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import com.wcohen.ss.JaroWinkler;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.pace.model.Person;
import scala.Tuple2;
public class AuthorMerger {
private static final Double THRESHOLD = 0.95;
@ -94,7 +97,9 @@ public class AuthorMerger {
}
public static String pidToComparableString(StructuredProperty pid) {
return (pid.getQualifier()!=null? pid.getQualifier().getClassid()!=null?pid.getQualifier().getClassid().toLowerCase():"":"") + (pid.getValue()!=null? pid.getValue().toLowerCase():"");
return (pid.getQualifier() != null
? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""
: "") + (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
}
public static int countAuthorsPids(List<Author> authors) {

4
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.oa.dedup;
import java.io.Serializable;
@ -73,7 +74,8 @@ public class DedupRecordFactory {
}
public static <T extends OafEntity> T entityMerger(
String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz) throws IllegalAccessException, InstantiationException {
String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz)
throws IllegalAccessException, InstantiationException {
T entity = clazz.newInstance();

21
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java
View File

@ -1,5 +1,8 @@
package eu.dnetlib.dhp.oa.dedup;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
@ -7,15 +10,13 @@ import java.io.Serializable;
import java.nio.file.Paths;
import java.util.*;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.pace.util.MapDocumentUtil;
import org.codehaus.jackson.map.ObjectMapper;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import scala.Tuple2;
import static org.junit.jupiter.api.Assertions.assertEquals;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
public class EntityMergerTest implements Serializable {
@ -45,7 +46,8 @@ public class EntityMergerTest implements Serializable {
@Test
public void publicationMergerTest() throws InstantiationException, IllegalAccessException {
Publication pub_merged = DedupRecordFactory.entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class);
Publication pub_merged = DedupRecordFactory
.entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class);
assertEquals(dedupId, pub_merged.getId());
@ -118,11 +120,11 @@ public class EntityMergerTest implements Serializable {
reader = new BufferedReader(new FileReader(path));
String line = reader.readLine();
while (line != null) {
res.add(
res
.add(
new Tuple2<>(
MapDocumentUtil.getJPathString("$.id", line),
new ObjectMapper().readValue(line, clazz))
);
new ObjectMapper().readValue(line, clazz)));
// read next line
line = reader.readLine();
}
@ -134,5 +136,4 @@ public class EntityMergerTest implements Serializable {
return res;
}
}

59
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -59,8 +59,10 @@ public abstract class AbstractMdRecordToOafMapper {
protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4";
protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3";
protected static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES);
protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
protected static final Qualifier ORCID_PID_TYPE = qualifier(
"ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES);
protected static final Qualifier MAG_PID_TYPE = qualifier(
"MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
protected static final Map<String, String> nsContext = new HashMap<>();
@ -74,7 +76,8 @@ public abstract class AbstractMdRecordToOafMapper {
nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3);
}
protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
"main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
this.code2name = code2name;
@ -88,15 +91,20 @@ public abstract class AbstractMdRecordToOafMapper {
.parseText(xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3));
final String type = doc.valueOf("//dr:CobjCategory/@type");
final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
final KeyValue collectedFrom = getProvenanceDatasource(
doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
if (collectedFrom == null) { return null; }
if (collectedFrom == null) {
return null;
}
final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
? collectedFrom
: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
if (hostedBy == null) { return null; }
if (hostedBy == null) {
return null;
}
final DataInfo info = prepareDataInfo(doc);
final long lastUpdateTimestamp = new Date().getTime();
@ -111,7 +119,9 @@ public abstract class AbstractMdRecordToOafMapper {
final String dsId = doc.valueOf(xpathId);
final String dsName = doc.valueOf(xpathName);
if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { return null; }
if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) {
return null;
}
return keyValue(createOpenaireId(10, dsId, true), dsName);
}
@ -196,9 +206,15 @@ public abstract class AbstractMdRecordToOafMapper {
final String projectId = createOpenaireId(40, originalId, true);
res
.add(getRelation(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, lastUpdateTimestamp));
.add(
getRelation(
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info,
lastUpdateTimestamp));
res
.add(getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, lastUpdateTimestamp));
.add(
getRelation(
projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info,
lastUpdateTimestamp));
}
}
@ -244,7 +260,9 @@ public abstract class AbstractMdRecordToOafMapper {
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
r.setCollectedfrom(Arrays.asList(collectedFrom));
r
.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
.setPid(
prepareListStructProps(
doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
@ -362,7 +380,9 @@ public abstract class AbstractMdRecordToOafMapper {
final String sp = n.valueOf("@sp");
final String vol = n.valueOf("@vol");
final String edition = n.valueOf("@edition");
if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); }
if (StringUtils.isNotBlank(name)) {
return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info);
}
}
return null;
}
@ -415,7 +435,10 @@ public abstract class AbstractMdRecordToOafMapper {
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
res
.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info));
.add(
structuredProperty(
n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"),
n.valueOf("@schemename"), info));
}
return res;
}
@ -423,7 +446,9 @@ public abstract class AbstractMdRecordToOafMapper {
protected OAIProvenance prepareOAIprovenance(final Document doc) {
final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
if (n == null) { return null; }
if (n == null) {
return null;
}
final String identifier = n.valueOf("./*[local-name()='identifier']");
final String baseURL = n.valueOf("./*[local-name()='baseURL']");
@ -438,7 +463,9 @@ public abstract class AbstractMdRecordToOafMapper {
protected DataInfo prepareDataInfo(final Document doc) {
final Node n = doc.selectSingleNode("//oaf:datainfo");
if (n == null) { return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); }
if (n == null) {
return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9");
}
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
@ -450,7 +477,9 @@ public abstract class AbstractMdRecordToOafMapper {
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
final String trust = n.valueOf("./oaf:trust");
return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
return dataInfo(
deletedbyinference, inferenceprovenance, inferred, false,
qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
}
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {

23
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
View File

@ -56,7 +56,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
}
final String pid = e.valueOf("./@nameIdentifier");
final String type = e.valueOf("./@nameIdentifierScheme")
final String type = e
.valueOf("./@nameIdentifierScheme")
.trim()
.toUpperCase()
.replaceAll(" ", "")
@ -66,7 +67,9 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
if (StringUtils.isNotBlank(pid)) {
if (type.startsWith("ORCID")) {
final String cleanedId = pid.replaceAll("http://orcid.org/", "").replaceAll("https://orcid.org/", "");
final String cleanedId = pid
.replaceAll("http://orcid.org/", "")
.replaceAll("https://orcid.org/", "");
author.getPid().add(structuredProperty(cleanedId, ORCID_PID_TYPE, info));
} else if (type.startsWith("MAGID")) {
author.getPid().add(structuredProperty(pid, MAG_PID_TYPE, info));
@ -127,7 +130,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
final Instance instance = new Instance();
instance
.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
.setInstancetype(
prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
instance.setCollectedfrom(collectedfrom);
instance.setHostedby(hostedby);
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
@ -143,7 +147,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
final List<Node> nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier"));
instance
.setUrl(nodes
.setUrl(
nodes
.stream()
.filter(n -> StringUtils.isNotBlank(n.getText()))
.map(n -> n.getText().trim())
@ -274,9 +279,15 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
final String otherId = createOpenaireId(50, originalId, false);
res
.add(getRelation(docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp));
.add(
getRelation(
docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
lastUpdateTimestamp));
res
.add(getRelation(otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp));
.add(
getRelation(
otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
lastUpdateTimestamp));
}
}
return res;

47
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
View File

@ -94,7 +94,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
for (final Object o : n.selectNodes("./datacite:nameIdentifier")) {
final String id = ((Node) o).getText();
final String type = ((Node) o).valueOf("./@nameIdentifierScheme")
final String type = ((Node) o)
.valueOf("./@nameIdentifierScheme")
.trim()
.toUpperCase()
.replaceAll(" ", "")
@ -119,7 +120,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
final Instance instance = new Instance();
instance
.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
.setInstancetype(
prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
instance.setCollectedfrom(collectedfrom);
instance.setHostedby(hostedby);
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
@ -168,7 +170,10 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
&& !dateType.equalsIgnoreCase("Updated")
&& !dateType.equalsIgnoreCase("Available")) {
res
.add(structuredProperty(((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE, info));
.add(
structuredProperty(
((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE,
info));
}
}
return res;
@ -220,14 +225,16 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
protected List<Field<String>> prepareOtherResearchProductContactGroups(
final Document doc,
final DataInfo info) {
return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info);
return prepareListFields(
doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info);
}
@Override
protected List<Field<String>> prepareOtherResearchProductContactPersons(
final Document doc,
final DataInfo info) {
return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info);
return prepareListFields(
doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info);
}
@Override
@ -253,7 +260,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
protected List<Field<String>> prepareSoftwareDocumentationUrls(
final Document doc,
final DataInfo info) {
return prepareListFields(doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
return prepareListFields(
doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
}
// DATASETS
@ -327,16 +335,29 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
if (type.equalsIgnoreCase("IsSupplementTo")) {
res
.add(getRelation(docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info, lastUpdateTimestamp));
.add(
getRelation(
docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info,
lastUpdateTimestamp));
res
.add(getRelation(otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info, lastUpdateTimestamp));
.add(
getRelation(
otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info,
lastUpdateTimestamp));
} else if (type.equals("IsPartOf")) {
res
.add(getRelation(docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info, lastUpdateTimestamp));
.add(
getRelation(
docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info,
lastUpdateTimestamp));
res
.add(getRelation(otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info, lastUpdateTimestamp));
} else {}
.add(
getRelation(
otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info,
lastUpdateTimestamp));
} else {
}
}
}
return res;
@ -344,6 +365,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@Override
protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
return prepareQualifier(doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE, DNET_DATA_CITE_RESOURCE);
return prepareQualifier(
doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE,
DNET_DATA_CITE_RESOURCE);
}
}