From c6af36496a6b03b497043b735070afaff939ca7d Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 26 May 2020 13:11:09 +0200 Subject: [PATCH] result pids (new xpaths + IS vocabularies) --- .../eu/dnetlib/dhp/schema/oaf/Result.java | 13 +- .../dhp/oa/dedup/EntityMergerTest.java | 4 +- .../raw/AbstractMdRecordToOafMapper.java | 137 +++++++++++------- .../raw/GenerateEntitiesApplication.java | 75 +++++----- .../dhp/oa/graph/raw/OafToOafMapper.java | 31 ++-- .../dhp/oa/graph/raw/OdfToOafMapper.java | 61 ++++++-- 6 files changed, 198 insertions(+), 123 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index 213a585a8c..11fdaa4f92 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java @@ -244,20 +244,20 @@ public class Result extends OafEntity implements Serializable { subject = mergeLists(subject, r.getSubject()); - //merge title lists: main title with higher trust and distinct between the others + // merge title lists: main title with higher trust and distinct between the others StructuredProperty baseMainTitle = null; - if(title != null) { + if (title != null) { baseMainTitle = getMainTitle(title); title.remove(baseMainTitle); } StructuredProperty newMainTitle = null; - if(r.getTitle() != null) { + if (r.getTitle() != null) { newMainTitle = getMainTitle(r.getTitle()); r.getTitle().remove(newMainTitle); } - if (newMainTitle != null && compareTrust(this, r) < 0 ) + if (newMainTitle != null && compareTrust(this, r) < 0) baseMainTitle = newMainTitle; title = mergeLists(title, r.getTitle()); @@ -314,8 +314,9 @@ public class Result extends OafEntity implements Serializable { } private StructuredProperty getMainTitle(List titles) { - //need to check if the list of titles contains more than 1 main title? (in that case, we should chose which main title select in the list) - for (StructuredProperty title: titles) { + // need to check if the list of titles contains more than 1 main title? (in that case, we should chose which + // main title select in the list) + for (StructuredProperty title : titles) { if (title.getQualifier() != null && title.getQualifier().getClassid() != null) if (title.getQualifier().getClassid().equals("main title")) return title; diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index f4b2c22522..b8ccb038d7 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -91,9 +91,9 @@ public class EntityMergerTest implements Serializable { assertEquals(pub_merged.getAuthor().size(), 9); assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4); - //verify title + // verify title int count = 0; - for (StructuredProperty title: pub_merged.getTitle()){ + for (StructuredProperty title : pub_merged.getTitle()) { if (title.getQualifier().getClassid().equals("main title")) count++; } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 278544e0b0..99334dd7f9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -64,8 +64,10 @@ 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 nsContext = new HashMap<>(); @@ -79,7 +81,8 @@ 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 code2name) { this.code2name = code2name; @@ -93,15 +96,20 @@ 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(); @@ -116,7 +124,9 @@ 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); } @@ -132,47 +142,47 @@ public abstract class AbstractMdRecordToOafMapper { final List oafs = new ArrayList<>(); switch (type.toLowerCase()) { - case "publication": - final Publication p = new Publication(); - populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); - p.setJournal(prepareJournal(doc, info)); - oafs.add(p); - break; - case "dataset": - final Dataset d = new Dataset(); - populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - d.setResulttype(DATASET_DEFAULT_RESULTTYPE); - d.setStoragedate(prepareDatasetStorageDate(doc, info)); - d.setDevice(prepareDatasetDevice(doc, info)); - d.setSize(prepareDatasetSize(doc, info)); - d.setVersion(prepareDatasetVersion(doc, info)); - d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); - d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); - d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - oafs.add(d); - break; - case "software": - final Software s = new Software(); - populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); - s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); - s.setLicense(prepareSoftwareLicenses(doc, info)); - s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); - s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - oafs.add(s); - break; - case "": - case "otherresearchproducts": - default: - final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - o.setResulttype(ORP_DEFAULT_RESULTTYPE); - o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); - o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); - o.setTool(prepareOtherResearchProductTools(doc, info)); - oafs.add(o); - break; + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); + p.setJournal(prepareJournal(doc, info)); + oafs.add(p); + break; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + d.setResulttype(DATASET_DEFAULT_RESULTTYPE); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + oafs.add(d); + break; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + oafs.add(s); + break; + case "": + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + o.setResulttype(ORP_DEFAULT_RESULTTYPE); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + oafs.add(o); + break; } if (!oafs.isEmpty()) { @@ -201,9 +211,15 @@ 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)); } } @@ -398,7 +414,9 @@ 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; } @@ -451,7 +469,10 @@ 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; } @@ -459,7 +480,9 @@ 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']"); @@ -474,7 +497,9 @@ 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"); @@ -486,7 +511,9 @@ 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 prepareField(final Node node, final String xpath, final DataInfo info) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index d184364174..0d140e9adc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -56,8 +56,9 @@ public class GenerateEntitiesApplication { public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(GenerateEntitiesApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json"))); + .toString( + GenerateEntitiesApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json"))); parser.parseArgument(args); @@ -105,21 +106,23 @@ public class GenerateEntitiesApplication { for (final String sp : existingSourcePaths) { inputRdd = inputRdd - .union(sc - .sequenceFile(sp, Text.class, Text.class) - .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) - .map(k -> convertToListOaf(k._1(), k._2(), code2name)) - .filter(Objects::nonNull) - .flatMap(list -> list.iterator())); + .union( + sc + .sequenceFile(sp, Text.class, Text.class) + .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) + .map(k -> convertToListOaf(k._1(), k._2(), code2name)) + .filter(Objects::nonNull) + .flatMap(list -> list.iterator())); } inputRdd .mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf)) .reduceByKey((o1, o2) -> merge(o1, o2)) .map(Tuple2::_2) - .map(oaf -> oaf.getClass().getSimpleName().toLowerCase() - + "|" - + OBJECT_MAPPER.writeValueAsString(oaf)) + .map( + oaf -> oaf.getClass().getSimpleName().toLowerCase() + + "|" + + OBJECT_MAPPER.writeValueAsString(oaf)) .saveAsTextFile(targetPath, GzipCodec.class); } @@ -141,28 +144,28 @@ public class GenerateEntitiesApplication { final String type = StringUtils.substringAfter(id, ":"); switch (type.toLowerCase()) { - case "native_oaf": - return new OafToOafMapper(code2name).processMdRecord(s); - case "native_odf": - return new OdfToOafMapper(code2name).processMdRecord(s); - case "datasource": - return Arrays.asList(convertFromJson(s, Datasource.class)); - case "organization": - return Arrays.asList(convertFromJson(s, Organization.class)); - case "project": - return Arrays.asList(convertFromJson(s, Project.class)); - case "relation": - return Arrays.asList(convertFromJson(s, Relation.class)); - case "publication": - return Arrays.asList(convertFromJson(s, Publication.class)); - case "dataset": - return Arrays.asList(convertFromJson(s, Dataset.class)); - case "software": - return Arrays.asList(convertFromJson(s, Software.class)); - case "otherresearchproduct": - return Arrays.asList(convertFromJson(s, OtherResearchProduct.class)); - default: - throw new RuntimeException("type not managed: " + type.toLowerCase()); + case "native_oaf": + return new OafToOafMapper(code2name).processMdRecord(s); + case "native_odf": + return new OdfToOafMapper(code2name).processMdRecord(s); + case "datasource": + return Arrays.asList(convertFromJson(s, Datasource.class)); + case "organization": + return Arrays.asList(convertFromJson(s, Organization.class)); + case "project": + return Arrays.asList(convertFromJson(s, Project.class)); + case "relation": + return Arrays.asList(convertFromJson(s, Relation.class)); + case "publication": + return Arrays.asList(convertFromJson(s, Publication.class)); + case "dataset": + return Arrays.asList(convertFromJson(s, Dataset.class)); + case "software": + return Arrays.asList(convertFromJson(s, Software.class)); + case "otherresearchproduct": + return Arrays.asList(convertFromJson(s, OtherResearchProduct.class)); + default: + throw new RuntimeException("type not managed: " + type.toLowerCase()); } } @@ -194,8 +197,10 @@ public class GenerateEntitiesApplication { private static Map loadVocsFromIS(final String isLookupUrl) throws IOException, ISLookUpException { final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl); - final String xquery = - IOUtils.toString(GenerateEntitiesApplication.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery")); + final String xquery = IOUtils + .toString( + GenerateEntitiesApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery")); final Map map = new HashMap<>(); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 61fe08722e..3b8f1170f7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -130,7 +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)); @@ -146,13 +147,14 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final List nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier")); instance - .setUrl(nodes - .stream() - .filter(n -> StringUtils.isNotBlank(n.getText())) - .map(n -> n.getText().trim()) - .filter(u -> u.startsWith("http")) - .distinct() - .collect(Collectors.toCollection(ArrayList::new))); + .setUrl( + nodes + .stream() + .filter(n -> StringUtils.isNotBlank(n.getText())) + .map(n -> n.getText().trim()) + .filter(u -> u.startsWith("http")) + .distinct() + .collect(Collectors.toCollection(ArrayList::new))); return Lists.newArrayList(instance); } @@ -277,9 +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; @@ -292,6 +300,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { @Override protected List prepareResultPids(final Document doc, final DataInfo info) { - return prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info); + return prepareListStructProps( + doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 9026874366..f8d9b3cd92 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -120,7 +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)); @@ -169,7 +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; @@ -221,14 +225,16 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { protected List> 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> 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 @@ -254,7 +260,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { protected List> 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 @@ -328,16 +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; @@ -345,15 +365,28 @@ 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); } @Override protected List prepareResultPids(final Document doc, final DataInfo info) { final List res = new ArrayList<>(); - res.addAll(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); - res.addAll(prepareListStructProps(doc, "//datacite:identifier[@identifierType != 'URL']", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); - res.addAll(prepareListStructProps(doc, "//datacite:alternateIdentifier[@alternateIdentifierType != 'URL']", "@alternateIdentifierType", "dnet:pid_types", "dnet:pid_types", info)); + res + .addAll( + prepareListStructProps( + doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); + res + .addAll( + prepareListStructProps( + doc, "//datacite:identifier[@identifierType != 'URL']", "@identifierType", "dnet:pid_types", + "dnet:pid_types", info)); + res + .addAll( + prepareListStructProps( + doc, "//datacite:alternateIdentifier[@alternateIdentifierType != 'URL']", + "@alternateIdentifierType", "dnet:pid_types", "dnet:pid_types", info)); return res; }