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dhp-schemas
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Graph model footprint optimisation #23

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claudio.atzori wants to merge 16 commits from ticket_8369 into master
pull from: ticket_8369
merge into: D-Net:master
Conversation 0 Commits 16 Files Changed 79 +1080 -4240
79 changed files with 1080 additions and 4240 deletions
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3
README.md
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@ -4,9 +4,8 @@ This project defines **object schemas** of the OpenAIRE main entities and the re
Namely it defines the model for Namely it defines the model for
- the graph internal representation, defined under the package `eu.dnetlib.dhp.schema.oaf` - the graph internal representation, defined under the package `eu.dnetlib.dhp.schema.oaf`
- the public graph dump representations, defined under the package `eu.dnetlib.dhp.schema.dump.oaf`
- the scholexplorer content representation, defined under the package `eu.dnetlib.dhp.schema.sx` - the scholexplorer content representation, defined under the package `eu.dnetlib.dhp.schema.sx`
- the contents acquired from the netadata aggregation subsystem, defined under the package `eu.dnetlib.dhp.schema.mdstore` - the contents acquired from the metadata aggregation subsystem, defined under the package `eu.dnetlib.dhp.schema.mdstore`
- the ORCID common schemas, defined under the package `eu.dnetlib.dhp.schema.orcid` - the ORCID common schemas, defined under the package `eu.dnetlib.dhp.schema.orcid`
Te serialization of such objects (data store files) are used to pass data between workflow nodes in the processing pipeline. Te serialization of such objects (data store files) are used to pass data between workflow nodes in the processing pipeline.

2
pom.xml
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@ -5,7 +5,7 @@
<groupId>eu.dnetlib.dhp</groupId> <groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId> <artifactId>dhp-schemas</artifactId>
<packaging>jar</packaging> <packaging>jar</packaging>
<version>3.15.1-SNAPSHOT</version> <version>4.0.0-SNAPSHOT</version>
<licenses> <licenses>
<license> <license>

69
src/main/java/eu/dnetlib/dhp/schema/common/AccessRightComparator.java
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@ -1,69 +0,0 @@
package eu.dnetlib.dhp.schema.common;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class AccessRightComparator<T extends Qualifier> implements Comparator<T> {
@Override
public int compare(T left, T right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
String lClass = left.getClassid();
String rClass = right.getClassid();
if (lClass.equals(rClass))
return 0;
if (lClass.equals("OPEN SOURCE"))
return -1;
if (rClass.equals("OPEN SOURCE"))
return 1;
if (lClass.equals("OPEN"))
return -1;
if (rClass.equals("OPEN"))
return 1;
if (lClass.equals("6MONTHS"))
return -1;
if (rClass.equals("6MONTHS"))
return 1;
if (lClass.equals("12MONTHS"))
return -1;
if (rClass.equals("12MONTHS"))
return 1;
if (lClass.equals("EMBARGO"))
return -1;
if (rClass.equals("EMBARGO"))
return 1;
if (lClass.equals("RESTRICTED"))
return -1;
if (rClass.equals("RESTRICTED"))
return 1;
if (lClass.equals("CLOSED"))
return -1;
if (rClass.equals("CLOSED"))
return 1;
if (lClass.equals("UNKNOWN"))
return -1;
if (rClass.equals("UNKNOWN"))
return 1;
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
}

21
src/main/java/eu/dnetlib/dhp/schema/common/EntityType.java
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@ -1,21 +0,0 @@
package eu.dnetlib.dhp.schema.common;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
/** Actual entity types in the Graph */
public enum EntityType {
publication, dataset, otherresearchproduct, software, datasource, organization, project;
/**
* Resolves the EntityType, given the relative class name
*
* @param clazz the given class name
* @param <T> actual OafEntity subclass
* @return the EntityType associated to the given class
*/
public static <T extends OafEntity> EntityType fromClass(Class<T> clazz) {
return EntityType.valueOf(clazz.getSimpleName().toLowerCase());
}
}

7
src/main/java/eu/dnetlib/dhp/schema/common/MainEntityType.java
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@ -1,7 +0,0 @@
package eu.dnetlib.dhp.schema.common;
/** Main entity types in the Graph */
public enum MainEntityType {
result, datasource, organization, project
}

250
src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
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@ -1,250 +0,0 @@
package eu.dnetlib.dhp.schema.common;
import eu.dnetlib.dhp.schema.oaf.AccessRight;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class ModelConstants {
private ModelConstants() {}
public static final String ORCID = "orcid";
public static final String ORCID_PENDING = "orcid_pending";
public static final String ORCID_CLASSNAME = "Open Researcher and Contributor ID";
public static final String ORCID_DS = ORCID.toUpperCase();
public static final String CROSSREF_ID = "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2";
public static final String DATACITE_ID = "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254";
public static final String ZENODO_OD_ID = "10|opendoar____::358aee4cc897452c00244351e4d91f69";
public static final String ZENODO_R3_ID = "10|re3data_____::7b0ad08687b2c960d5aeef06f811d5e6";
public static final String EUROPE_PUBMED_CENTRAL_ID = "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c";
public static final String PUBMED_CENTRAL_ID = "10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357";
public static final String ARXIV_ID = "10|opendoar____::6f4922f45568161a8cdf4ad2299f6d23";
public static final String ROHUB_ID = "10|fairsharing_::1b69ebedb522700034547abc5652ffac";
public static final String OPENORGS_NAME = "OpenOrgs Database";
public static final String OPENOCITATIONS_NAME = "OpenCitations";
public static final String OPENOCITATIONS_ID = "10|openaire____::c06df618c5de1c786535ccf3f8b7b059";
public static final String OPEN_APC_NAME = "OpenAPC Global Initiative";
public static final String OPEN_APC_ID = "10|apc_________::e2b1600b229fc30663c8a1f662debddf";
// VOCABULARY VALUE
public static final String ACCESS_RIGHT_OPEN = "OPEN";
public static final String ACCESS_RIGHT_EMBARGO = "EMBARGO";
public static final String ACCESS_RIGHT_CLOSED = "CLOSED";
public static final String DNET_SUBJECT_KEYWORD = "keyword";
public static final String DNET_SUBJECT_FOS_CLASSID = "FOS";
public static final String DNET_SUBJECT_FOS_CLASSNAME = "Fields of Science and Technology classification";
public static final String DNET_SUBJECT_TYPOLOGIES = "dnet:subject_classification_typologies";
public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies";
public static final String DNET_PUBLICATION_RESOURCE = "dnet:publication_resource";
public static final String DNET_ACCESS_MODES = "dnet:access_modes";
public static final String DNET_LANGUAGES = "dnet:languages";
public static final String DNET_PID_TYPES = "dnet:pid_types";
public static final String DNET_DATACITE_DATE = "dnet:dataCite_date";
public static final String DNET_DATACITE_TITLE = "dnet:dataCite_title";
public static final String DNET_DATA_CITE_RESOURCE = "dnet:dataCite_resource";
public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
public static final String DNET_COUNTRY_TYPE = "dnet:countries";
public static final String DNET_REVIEW_LEVELS = "dnet:review_levels";
public static final String DNET_PROGRAMMING_LANGUAGES = "dnet:programming_languages";
public static final String DNET_EXTERNAL_REFERENCE_TYPE = "dnet:externalReference_typologies";
public static final String DNET_RELATION_RELTYPE = "dnet:relation_relType";
public static final String DNET_RELATION_SUBRELTYPE = "dnet:relation_subRelType";
public static final String DNET_RELATION_RELCLASS = "dnet:relation_relClass";
public static final String PEER_REVIEWED_CLASSNAME = "nonPeerReviewed";
public static final String NON_PEER_REVIEWED_CLASSNAME = "nonPeerReviewed";
public static final String PEER_REVIEWED_CLASSID = "0001";
public static final String NON_PEER_REVIEWED_CLASSID = "0002";
public static final String SYSIMPORT_CROSSWALK_REPOSITORY = "sysimport:crosswalk:repository";
public static final String SYSIMPORT_CROSSWALK_ENTITYREGISTRY = "sysimport:crosswalk:entityregistry";
public static final String SYSIMPORT_ACTIONSET = "sysimport:actionset";
public static final String SYSIMPORT_ORCID_NO_DOI = "sysimport:actionset:orcidworks-no-doi";
public static final String USER_CLAIM = "user:claim";
public static final String HARVESTED = "Harvested";
public static final String PROVENANCE_DEDUP = "sysimport:dedup";
public static final String PROVENANCE_ENRICH = "sysimport:enrich";
public static final Qualifier PROVENANCE_ACTION_SET_QUALIFIER = qualifier(
SYSIMPORT_ACTIONSET, SYSIMPORT_ACTIONSET, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS);
public static final String DATASET_RESULTTYPE_CLASSID = "dataset";
public static final String PUBLICATION_RESULTTYPE_CLASSID = "publication";
public static final String SOFTWARE_RESULTTYPE_CLASSID = "software";
public static final String ORP_RESULTTYPE_CLASSID = "other";
public static final String RESULT_RESULT = "resultResult"; // relType
/**
* @deprecated Use {@link ModelConstants#RELATIONSHIP} instead.
*/
@Deprecated
public static final String PUBLICATION_DATASET = "publicationDataset"; // subreltype
public static final String SUPPLEMENT = "supplement"; // subreltype
public static final String IS_SUPPLEMENT_TO = "IsSupplementTo";
public static final String IS_SUPPLEMENTED_BY = "IsSupplementedBy";
public static final String PART = "part"; // subreltype
public static final String IS_PART_OF = "IsPartOf";
public static final String HAS_PART = "HasPart";
public static final String RELATIONSHIP = "relationship"; // subreltype
public static final String IS_RELATED_TO = "IsRelatedTo";
public static final String IS_IDENTICAL_TO = "IsIdenticalTo";
public static final String REFERENCES = "References";
public static final String IS_REFERENCED_BY = "IsReferencedBy";
public static final String CONTINUES = "Continues";
public static final String IS_CONTINUED_BY = "IsContinuedBy";
public static final String DOCUMENTS = "Documents";
public static final String IS_DOCUMENTED_BY = "IsDocumentedBy";
public static final String IS_SOURCE_OF = "IsSourceOf";
public static final String IS_DERIVED_FROM = "IsDerivedFrom";
public static final String COMPILES = "Compiles";
public static final String IS_COMPILED_BY = "IsCompiledBy";
public static final String DESCRIBES = "Describes";
public static final String IS_DESCRIBED_BY = "IsDescribedBy";
public static final String IS_METADATA_FOR = "IsMetadataFor";
public static final String IS_METADATA_OF = "IsMetadataOf";
public static final String HAS_ASSOCIATION_WITH = "HasAssociationWith";
public static final String IS_REQUIRED_BY = "IsRequiredBy";
public static final String REQUIRES = "Requires";
public static final String CITATION = "citation"; // subreltype
public static final String CITES = "Cites";
public static final String IS_CITED_BY = "IsCitedBy";
public static final String REVIEW = "review"; // subreltype
public static final String REVIEWS = "Reviews";
public static final String IS_REVIEWED_BY = "IsReviewedBy";
public static final String VERSION = "version"; // subreltype
public static final String IS_VERSION_OF = "IsVersionOf";
public static final String HAS_VERSION = "HasVersion";
public static final String IS_PREVIOUS_VERSION_OF = "IsPreviousVersionOf";
public static final String IS_NEW_VERSION_OF = "IsNewVersionOf";
public static final String IS_VARIANT_FORM_OF = "IsVariantFormOf";
public static final String IS_ORIGINAL_FORM_OF = "IsOriginalFormOf";
public static final String IS_OBSOLETED_BY = "IsObsoletedBy";
public static final String OBSOLETES = "Obsoletes";
public static final String RESULT_PROJECT = "resultProject"; // relType
public static final String OUTCOME = "outcome"; // subreltype
public static final String IS_PRODUCED_BY = "isProducedBy";
public static final String PRODUCES = "produces";
public static final String DATASOURCE_ORGANIZATION = "datasourceOrganization"; // relType
public static final String PROVISION = "provision"; // subreltype
public static final String IS_PROVIDED_BY = "isProvidedBy";
public static final String PROVIDES = "provides";
public static final String PROJECT_ORGANIZATION = "projectOrganization"; // relType
public static final String PARTICIPATION = "participation"; // subreltype
public static final String HAS_PARTICIPANT = "hasParticipant";
public static final String IS_PARTICIPANT = "isParticipant";
public static final String RESULT_ORGANIZATION = "resultOrganization"; // relType
public static final String AFFILIATION = "affiliation"; // subreltype
public static final String IS_AUTHOR_INSTITUTION_OF = "isAuthorInstitutionOf";
public static final String HAS_AUTHOR_INSTITUTION = "hasAuthorInstitution";
public static final String ORG_ORG_RELTYPE = "organizationOrganization"; // relType
public static final String IS_PARENT_OF = "IsParentOf";
public static final String IS_CHILD_OF = "IsChildOf";
public static final String DEDUP = "dedup"; // subreltype
public static final String MERGES = "merges";
public static final String IS_MERGED_IN = "isMergedIn";
public static final String SIMILARITY = "similarity"; // subreltype
public static final String IS_SIMILAR_TO = "isSimilarTo";
public static final String IS_AMONG_TOP_N_SIMILAR_DOCS = "IsAmongTopNSimilarDocuments";
public static final String HAS_AMONG_TOP_N_SIMILAR_DOCS = "HasAmongTopNSimilarDocuments";
public static final String IS_DIFFERENT_FROM = "isDifferentFrom";
public static final String UNKNOWN = "UNKNOWN";
public static final String NOT_AVAILABLE = "not available";
public static final Qualifier PUBLICATION_DEFAULT_RESULTTYPE = qualifier(
PUBLICATION_RESULTTYPE_CLASSID, PUBLICATION_RESULTTYPE_CLASSID,
DNET_RESULT_TYPOLOGIES, DNET_RESULT_TYPOLOGIES);
public static final Qualifier DATASET_DEFAULT_RESULTTYPE = qualifier(
DATASET_RESULTTYPE_CLASSID, DATASET_RESULTTYPE_CLASSID,
DNET_RESULT_TYPOLOGIES, DNET_RESULT_TYPOLOGIES);
public static final Qualifier SOFTWARE_DEFAULT_RESULTTYPE = qualifier(
SOFTWARE_RESULTTYPE_CLASSID, SOFTWARE_RESULTTYPE_CLASSID,
DNET_RESULT_TYPOLOGIES, DNET_RESULT_TYPOLOGIES);
public static final Qualifier ORP_DEFAULT_RESULTTYPE = qualifier(
ORP_RESULTTYPE_CLASSID, ORP_RESULTTYPE_CLASSID,
DNET_RESULT_TYPOLOGIES, DNET_RESULT_TYPOLOGIES);
public static final Qualifier REPOSITORY_PROVENANCE_ACTIONS = qualifier(
SYSIMPORT_CROSSWALK_REPOSITORY, SYSIMPORT_CROSSWALK_REPOSITORY,
DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS);
public static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = qualifier(
SYSIMPORT_CROSSWALK_ENTITYREGISTRY, SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS);
public static final String UNKNOWN_REPOSITORY_ORIGINALID = "openaire____::1256f046-bf1f-4afc-8b47-d0b147148b18";
public static final KeyValue UNKNOWN_REPOSITORY = keyValue(
"10|openaire____::55045bd2a65019fd8e6741a755395c8c", "Unknown Repository");
public static final Qualifier UNKNOWN_COUNTRY = qualifier(UNKNOWN, "Unknown", DNET_COUNTRY_TYPE, DNET_COUNTRY_TYPE);
public static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
"main title", "main title", DNET_DATACITE_TITLE, DNET_DATACITE_TITLE);
public static final AccessRight OPEN_ACCESS_RIGHT() {
final AccessRight result = new AccessRight();
result.setClassid(ACCESS_RIGHT_OPEN);
result.setClassid(ACCESS_RIGHT_OPEN);
result.setSchemeid(ModelConstants.DNET_ACCESS_MODES);
result.setSchemename(ModelConstants.DNET_ACCESS_MODES);
return result;
}
private static Qualifier qualifier(
final String classid,
final String classname,
final String schemeid,
final String schemename) {
final Qualifier q = new Qualifier();
q.setClassid(classid);
q.setClassname(classname);
q.setSchemeid(schemeid);
q.setSchemename(schemename);
return q;
}
private static KeyValue keyValue(final String key, final String value) {
final KeyValue kv = new KeyValue();
kv.setKey(key);
kv.setValue(value);
kv.setDataInfo(new DataInfo());
return kv;
}
}

412
src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java
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@ -1,412 +0,0 @@
package eu.dnetlib.dhp.schema.common;
import static com.google.common.base.Preconditions.checkArgument;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.text.ParseException;
import java.util.Date;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.function.Function;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.lang3.StringUtils;
import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.oaf.*;
/** Oaf model utility methods. */
public class ModelSupport {
/** Defines the mapping between the actual entity type and the main entity type */
private static final Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
static {
entityMapping.put(EntityType.publication, MainEntityType.result);
entityMapping.put(EntityType.dataset, MainEntityType.result);
entityMapping.put(EntityType.otherresearchproduct, MainEntityType.result);
entityMapping.put(EntityType.software, MainEntityType.result);
entityMapping.put(EntityType.datasource, MainEntityType.datasource);
entityMapping.put(EntityType.organization, MainEntityType.organization);
entityMapping.put(EntityType.project, MainEntityType.project);
}
/**
* Defines the mapping between the actual entity types and the relative classes implementing them
*/
public static final Map<EntityType, Class> entityTypes = Maps.newHashMap();
static {
entityTypes.put(EntityType.datasource, Datasource.class);
entityTypes.put(EntityType.organization, Organization.class);
entityTypes.put(EntityType.project, Project.class);
entityTypes.put(EntityType.dataset, Dataset.class);
entityTypes.put(EntityType.otherresearchproduct, OtherResearchProduct.class);
entityTypes.put(EntityType.software, Software.class);
entityTypes.put(EntityType.publication, Publication.class);
}
public static final Map<String, Class> oafTypes = Maps.newHashMap();
static {
oafTypes.put("datasource", Datasource.class);
oafTypes.put("organization", Organization.class);
oafTypes.put("project", Project.class);
oafTypes.put("dataset", Dataset.class);
oafTypes.put("otherresearchproduct", OtherResearchProduct.class);
oafTypes.put("software", Software.class);
oafTypes.put("publication", Publication.class);
oafTypes.put("relation", Relation.class);
}
public static final Map<Class, String> idPrefixMap = Maps.newHashMap();
static {
idPrefixMap.put(Datasource.class, "10");
idPrefixMap.put(Organization.class, "20");
idPrefixMap.put(Project.class, "40");
idPrefixMap.put(Dataset.class, "50");
idPrefixMap.put(OtherResearchProduct.class, "50");
idPrefixMap.put(Software.class, "50");
idPrefixMap.put(Publication.class, "50");
}
public static final Map<String, String> entityIdPrefix = Maps.newHashMap();
static {
entityIdPrefix.put("datasource", "10");
entityIdPrefix.put("organization", "20");
entityIdPrefix.put("project", "40");
entityIdPrefix.put("result", "50");
}
public static final Map<String, String> idPrefixEntity = Maps.newHashMap();
static {
idPrefixEntity.put("10", "datasource");
idPrefixEntity.put("20", "organization");
idPrefixEntity.put("40", "project");
idPrefixEntity.put("50", "result");
}
public static final Map<String, RelationInverse> relationInverseMap = Maps.newHashMap();
static {
set(relationInverseMap, PROJECT_ORGANIZATION, PARTICIPATION, IS_PARTICIPANT, HAS_PARTICIPANT);
set(relationInverseMap, RESULT_ORGANIZATION, AFFILIATION, IS_AUTHOR_INSTITUTION_OF, HAS_AUTHOR_INSTITUTION);
set(relationInverseMap, ORG_ORG_RELTYPE, DEDUP, IS_MERGED_IN, MERGES);
set(relationInverseMap, ORG_ORG_RELTYPE, DEDUP, IS_SIMILAR_TO, IS_SIMILAR_TO);
set(relationInverseMap, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, PRODUCES);
set(relationInverseMap, DATASOURCE_ORGANIZATION, PROVISION, IS_PROVIDED_BY, PROVIDES);
set(relationInverseMap, RESULT_RESULT, SIMILARITY, IS_AMONG_TOP_N_SIMILAR_DOCS, HAS_AMONG_TOP_N_SIMILAR_DOCS);
set(relationInverseMap, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, IS_SUPPLEMENTED_BY);
set(relationInverseMap, RESULT_RESULT, PART, IS_PART_OF, HAS_PART);
set(relationInverseMap, RESULT_RESULT, DEDUP, IS_MERGED_IN, MERGES);
set(relationInverseMap, RESULT_RESULT, DEDUP, IS_SIMILAR_TO, IS_SIMILAR_TO);
set(relationInverseMap, RESULT_RESULT, CITATION, IS_CITED_BY, CITES);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_IDENTICAL_TO, IS_IDENTICAL_TO);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_REFERENCED_BY, REFERENCES);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_CONTINUED_BY, CONTINUES);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_DOCUMENTED_BY, DOCUMENTS);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_DERIVED_FROM, IS_SOURCE_OF);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, IS_RELATED_TO);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_COMPILED_BY, COMPILES);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_DESCRIBED_BY, DESCRIBES);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_METADATA_FOR, IS_METADATA_OF);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, HAS_ASSOCIATION_WITH, HAS_ASSOCIATION_WITH);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_REQUIRED_BY, REQUIRES);
set(relationInverseMap, RESULT_RESULT, VERSION, IS_PREVIOUS_VERSION_OF, IS_NEW_VERSION_OF);
set(relationInverseMap, RESULT_RESULT, VERSION, IS_VARIANT_FORM_OF, IS_ORIGINAL_FORM_OF);
set(relationInverseMap, RESULT_RESULT, VERSION, IS_OBSOLETED_BY, OBSOLETES);
set(relationInverseMap, RESULT_RESULT, VERSION, IS_VERSION_OF, HAS_VERSION);
set(relationInverseMap, RESULT_RESULT, REVIEW, IS_REVIEWED_BY, REVIEWS);
}
private static void set(Map<String, RelationInverse> relationInverseMap, String relType, String subRelType, String relClass, String inverseRelClass) {
relationInverseMap
.put(
rel(relType, subRelType, relClass), new RelationInverse()
.setInverseRelClass(inverseRelClass)
.setRelClass(relClass)
.setRelType(relType)
.setSubReltype(subRelType));
if (!relClass.equals(inverseRelClass)) {
relationInverseMap
.put(
rel(relType, subRelType, inverseRelClass), new RelationInverse()
.setInverseRelClass(relClass)
.setRelClass(inverseRelClass)
.setRelType(relType)
.setSubReltype(subRelType));
}
}
/**
* Helper method: lookup relation inverse, given the direct relation encoding (case insensitive)
* @param encoding
* @return the relation inverse descriptor, throws @IllegalArgumentException when not found.
*/
public static RelationInverse findInverse(String encoding) {
return ModelSupport.relationInverseMap
.entrySet()
.stream()
.filter(r -> encoding.equalsIgnoreCase(r.getKey()))
.findFirst()
.map(r -> r.getValue())
.orElseThrow(() -> new IllegalArgumentException("invalid relationship: " + encoding));
}
/**
* Helper method: fina a relation filtering by a relation name
* @param relationName
* @return
*/
public static RelationInverse findRelation(final String relationName) {
return relationInverseMap.values()
.stream()
.filter(r -> relationName.equalsIgnoreCase(r.getRelClass()))
.findFirst()
.orElse(null);
}
/**
* Helper method: combines the relation attributes
* @param relType
* @param subRelType
* @param relClass
* @return
*/
public static String rel(String relType, String subRelType, String relClass) {
return String.format("%s_%s_%s", relType, subRelType, relClass);
}
private static final String schemeTemplate = "dnet:%s_%s_relations";
public static final String DATE_FORMAT = "yyyy-MM-dd";
private ModelSupport() {
}
public static <E extends OafEntity> String getIdPrefix(Class<E> clazz) {
return idPrefixMap.get(clazz);
}
/**
* Checks subclass-superclass relationship.
*
* @param subClazzObject Subclass object instance
* @param superClazzObject Superclass object instance
* @param <X> Subclass type
* @param <Y> Superclass type
* @return True if X is a subclass of Y
*/
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
X subClazzObject, Y superClazzObject) {
return isSubClass(subClazzObject.getClass(), superClazzObject.getClass());
}
/**
* Checks subclass-superclass relationship.
*
* @param subClazzObject Subclass object instance
* @param superClazz Superclass class
* @param <X> Subclass type
* @param <Y> Superclass type
* @return True if X is a subclass of Y
*/
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
X subClazzObject, Class<Y> superClazz) {
return isSubClass(subClazzObject.getClass(), superClazz);
}
/**
* Checks subclass-superclass relationship.
*
* @param subClazz Subclass class
* @param superClazz Superclass class
* @param <X> Subclass type
* @param <Y> Superclass type
* @return True if X is a subclass of Y
*/
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
Class<X> subClazz, Class<Y> superClazz) {
return superClazz.isAssignableFrom(subClazz);
}
/**
* Lists all the OAF model classes
*
* @param <T>
* @return
*/
public static <T extends Oaf> Class<T>[] getOafModelClasses() {
return new Class[] {
Author.class,
Context.class,
Country.class,
DataInfo.class,
Dataset.class,
Datasource.class,
ExternalReference.class,
ExtraInfo.class,
Field.class,
GeoLocation.class,
Instance.class,
AccessRight.class,
OpenAccessRoute.class,
Journal.class,
KeyValue.class,
Oaf.class,
OafEntity.class,
OAIProvenance.class,
Organization.class,
OriginDescription.class,
OtherResearchProduct.class,
Project.class,
Publication.class,
Qualifier.class,
Relation.class,
Result.class,
Software.class,
StructuredProperty.class
};
}
public static String getMainType(final EntityType type) {
return entityMapping.get(type).name();
}
public static boolean isResult(EntityType type) {
return MainEntityType.result.name().equals(getMainType(type));
}
public static String getScheme(final String sourceType, final String targetType) {
return String
.format(
schemeTemplate,
entityMapping.get(EntityType.valueOf(sourceType)).name(),
entityMapping.get(EntityType.valueOf(targetType)).name());
}
public static <T extends Oaf> String tableIdentifier(String dbName, String tableName) {
checkArgument(StringUtils.isNotBlank(dbName), "DB name cannot be empty");
checkArgument(StringUtils.isNotBlank(tableName), "table name cannot be empty");
return String.format("%s.%s", dbName, tableName);
}
public static <T extends Oaf> String tableIdentifier(String dbName, Class<T> clazz) {
checkArgument(Objects.nonNull(clazz), "clazz is needed to derive the table name, thus cannot be null");
return tableIdentifier(dbName, clazz.getSimpleName().toLowerCase());
}
public static <T extends Oaf> Function<T, String> idFn() {
return x -> {
if (isSubClass(x, Relation.class)) {
return idFnForRelation(x);
}
return idFnForOafEntity(x);
};
}
private static <T extends Oaf> String idFnForRelation(T t) {
Relation r = (Relation) t;
return Optional
.ofNullable(r.getSource())
.map(
source -> Optional
.ofNullable(r.getTarget())
.map(
target -> Optional
.ofNullable(r.getRelType())
.map(
relType -> Optional
.ofNullable(r.getSubRelType())
.map(
subRelType -> Optional
.ofNullable(r.getRelClass())
.map(
relClass -> String
.join(
source,
target,
relType,
subRelType,
relClass))
.orElse(
String
.join(
source,
target,
relType,
subRelType)))
.orElse(String.join(source, target, relType)))
.orElse(String.join(source, target)))
.orElse(source))
.orElse(null);
}
private static <T extends Oaf> String idFnForOafEntity(T t) {
return ((OafEntity) t).getId();
}
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest()));
} catch (final NoSuchAlgorithmException e) {
throw new IllegalStateException(e);
}
}
public static String generateIdentifier(final String originalId, final String nsPrefix) {
return String.format("%s::%s", nsPrefix, md5(originalId));
}
public static String oldest(String dateA, String dateB) throws ParseException {
if (StringUtils.isBlank(dateA)) {
return dateB;
}
if (StringUtils.isBlank(dateB)) {
return dateA;
}
if (StringUtils.isNotBlank(dateA) && StringUtils.isNotBlank(dateB)) {
final Date a = DateParserUtils.parseDate(dateA);
final Date b = DateParserUtils.parseDate(dateB);
if (Objects.nonNull(a) && Objects.nonNull(b)) {
return a.before(b) ? dateA : dateB;
} else {
return null;
}
} else {
return null;
}
}
}

44
src/main/java/eu/dnetlib/dhp/schema/common/RefereedComparator.java
View File

@ -1,44 +0,0 @@
package eu.dnetlib.dhp.schema.common;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class RefereedComparator implements Comparator<Qualifier> {
@Override
public int compare(Qualifier left, Qualifier right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
String lClass = left.getClassid();
String rClass = right.getClassid();
if (lClass.equals(rClass))
return 0;
if (lClass.equals(ModelConstants.PEER_REVIEWED_CLASSID))
return -1;
if (rClass.equals(ModelConstants.PEER_REVIEWED_CLASSID))
return 1;
if (lClass.equals(ModelConstants.NON_PEER_REVIEWED_CLASSID))
return -1;
if (rClass.equals(ModelConstants.NON_PEER_REVIEWED_CLASSID))
return 1;
if (lClass.equals(ModelConstants.UNKNOWN))
return -1;
if (rClass.equals(ModelConstants.UNKNOWN))
return 1;
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
}

46
src/main/java/eu/dnetlib/dhp/schema/common/RelationInverse.java
View File

@ -1,46 +0,0 @@
package eu.dnetlib.dhp.schema.common;
public class RelationInverse {
private String relClass;
private String inverseRelClass;
private String relType;
private String subReltype;
public String getRelType() {
return relType;
}
public RelationInverse setRelType(String relType) {
this.relType = relType;
return this;
}
public String getSubReltype() {
return subReltype;
}
public RelationInverse setSubReltype(String subReltype) {
this.subReltype = subReltype;
return this;
}
public String getRelClass() {
return relClass;
}
public RelationInverse setRelClass(String relClass) {
this.relClass = relClass;
return this;
}
public String getInverseRelClass() {
return inverseRelClass;
}
public RelationInverse setInverseRelClass(String inverseRelClass) {
this.inverseRelClass = inverseRelClass;
return this;
}
}

5
src/main/java/eu/dnetlib/dhp/schema/mdstore/MetadataRecord.java
View File

@ -3,8 +3,6 @@ package eu.dnetlib.dhp.schema.mdstore;
import java.io.Serializable; import java.io.Serializable;
import eu.dnetlib.dhp.schema.common.ModelSupport;
/** /**
* This class models a record in a Metadata store collection on HDFS * This class models a record in a Metadata store collection on HDFS
*/ */
@ -38,6 +36,7 @@ public class MetadataRecord implements Serializable {
} }
public MetadataRecord( public MetadataRecord(
String id,
String originalId, String originalId,
String encoding, String encoding,
Provenance provenance, Provenance provenance,
@ -49,7 +48,7 @@ public class MetadataRecord implements Serializable {
this.provenance = provenance; this.provenance = provenance;
this.body = body; this.body = body;
this.dateOfCollection = dateOfCollection; this.dateOfCollection = dateOfCollection;
this.id = ModelSupport.generateIdentifier(originalId, this.provenance.getNsPrefix()); this.id = id;
} }
public String getId() { public String getId() {

21
src/main/java/eu/dnetlib/dhp/schema/oaf/Author.java
View File

@ -15,9 +15,7 @@ public class Author implements Serializable {
// START WITH 1 // START WITH 1
private Integer rank; private Integer rank;
private List<StructuredProperty> pid; private List<AuthorPid> pid;
private List<Field<String>> affiliation;
public String getFullname() { public String getFullname() {
return fullname; return fullname;
@ -51,22 +49,14 @@ public class Author implements Serializable {
this.rank = rank; this.rank = rank;
} }
public List<StructuredProperty> getPid() { public List<AuthorPid> getPid() {
return pid; return pid;
} }
public void setPid(List<StructuredProperty> pid) { public void setPid(List<AuthorPid> pid) {
this.pid = pid; this.pid = pid;
} }
public List<Field<String>> getAffiliation() {
return affiliation;
}
public void setAffiliation(List<Field<String>> affiliation) {
this.affiliation = affiliation;
}
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) if (this == o)
@ -78,13 +68,12 @@ public class Author implements Serializable {
&& Objects.equals(name, author.name) && Objects.equals(name, author.name)
&& Objects.equals(surname, author.surname) && Objects.equals(surname, author.surname)
&& Objects.equals(rank, author.rank) && Objects.equals(rank, author.rank)
&& Objects.equals(pid, author.pid) && Objects.equals(pid, author.pid);
&& Objects.equals(affiliation, author.affiliation);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash(fullname, name, surname, rank, pid, affiliation); return Objects.hash(fullname, name, surname, rank, pid);
} }
} }

16
src/main/java/eu/dnetlib/dhp/schema/oaf/AuthorPid.java Normal file
View File

@ -0,0 +1,16 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
public class AuthorPid extends StructuredProperty implements Serializable {
private DataInfo dataInfo;
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
}

30
src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java
View File

@ -6,21 +6,11 @@ import java.util.Objects;
public class DataInfo implements Serializable { public class DataInfo implements Serializable {
private Boolean invisible = false;
private Boolean inferred; private Boolean inferred;
private Boolean deletedbyinference = false; private Float trust;
private String trust;
private String inferenceprovenance; private String inferenceprovenance;
private Qualifier provenanceaction; private Qualifier provenanceaction;
public Boolean getInvisible() {
return invisible;
}
public void setInvisible(Boolean invisible) {
this.invisible = invisible;
}
public Boolean getInferred() { public Boolean getInferred() {
return inferred; return inferred;
} }
@ -29,19 +19,11 @@ public class DataInfo implements Serializable {
this.inferred = inferred; this.inferred = inferred;
} }
public Boolean getDeletedbyinference() { public Float getTrust() {
return deletedbyinference;
}
public void setDeletedbyinference(Boolean deletedbyinference) {
this.deletedbyinference = deletedbyinference;
}
public String getTrust() {
return trust; return trust;
} }
public void setTrust(String trust) { public void setTrust(Float trust) {
this.trust = trust; this.trust = trust;
} }
@ -68,9 +50,7 @@ public class DataInfo implements Serializable {
if (o == null || getClass() != o.getClass()) if (o == null || getClass() != o.getClass())
return false; return false;
DataInfo dataInfo = (DataInfo) o; DataInfo dataInfo = (DataInfo) o;
return Objects.equals(invisible, dataInfo.invisible) return Objects.equals(inferred, dataInfo.inferred)
&& Objects.equals(inferred, dataInfo.inferred)
&& Objects.equals(deletedbyinference, dataInfo.deletedbyinference)
&& Objects.equals(trust, dataInfo.trust) && Objects.equals(trust, dataInfo.trust)
&& Objects.equals(inferenceprovenance, dataInfo.inferenceprovenance) && Objects.equals(inferenceprovenance, dataInfo.inferenceprovenance)
&& Objects.equals(provenanceaction, dataInfo.provenanceaction); && Objects.equals(provenanceaction, dataInfo.provenanceaction);
@ -80,6 +60,6 @@ public class DataInfo implements Serializable {
public int hashCode() { public int hashCode() {
return Objects return Objects
.hash( .hash(
invisible, inferred, deletedbyinference, trust, inferenceprovenance, provenanceaction); inferred, trust, inferenceprovenance, provenanceaction);
} }
} }

71
src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java
View File

@ -4,74 +4,72 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Dataset extends Result implements Serializable { public class Dataset extends Result implements Serializable {
private Field<String> storagedate; private String storagedate;
// candidate for removal // candidate for removal
private Field<String> device; private String device;
private Field<String> size; private String size;
private Field<String> version; private String version;
private Field<String> lastmetadataupdate; private String lastmetadataupdate;
private Field<String> metadataversionnumber; private String metadataversionnumber;
private List<GeoLocation> geolocation; private List<GeoLocation> geolocation;
public Dataset() { public Dataset() {
setResulttype(ModelConstants.DATASET_DEFAULT_RESULTTYPE); setResulttype(RESULTTYPE.dataset);
} }
public Field<String> getStoragedate() { public String getStoragedate() {
return storagedate; return storagedate;
} }
public void setStoragedate(Field<String> storagedate) { public void setStoragedate(String storagedate) {
this.storagedate = storagedate; this.storagedate = storagedate;
} }
public Field<String> getDevice() { public String getDevice() {
return device; return device;
} }
public void setDevice(Field<String> device) { public void setDevice(String device) {
this.device = device; this.device = device;
} }
public Field<String> getSize() { public String getSize() {
return size; return size;
} }
public void setSize(Field<String> size) { public void setSize(String size) {
this.size = size; this.size = size;
} }
public Field<String> getVersion() { public String getVersion() {
return version; return version;
} }
public void setVersion(Field<String> version) { public void setVersion(String version) {
this.version = version; this.version = version;
} }
public Field<String> getLastmetadataupdate() { public String getLastmetadataupdate() {
return lastmetadataupdate; return lastmetadataupdate;
} }
public void setLastmetadataupdate(Field<String> lastmetadataupdate) { public void setLastmetadataupdate(String lastmetadataupdate) {
this.lastmetadataupdate = lastmetadataupdate; this.lastmetadataupdate = lastmetadataupdate;
} }
public Field<String> getMetadataversionnumber() { public String getMetadataversionnumber() {
return metadataversionnumber; return metadataversionnumber;
} }
public void setMetadataversionnumber(Field<String> metadataversionnumber) { public void setMetadataversionnumber(String metadataversionnumber) {
this.metadataversionnumber = metadataversionnumber; this.metadataversionnumber = metadataversionnumber;
} }
@ -82,35 +80,4 @@ public class Dataset extends Result implements Serializable {
public void setGeolocation(List<GeoLocation> geolocation) { public void setGeolocation(List<GeoLocation> geolocation) {
this.geolocation = geolocation; this.geolocation = geolocation;
} }
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Dataset.class.isAssignableFrom(e.getClass())) {
return;
}
final Dataset d = (Dataset) e;
storagedate = d.getStoragedate() != null && compareTrust(this, e) < 0 ? d.getStoragedate() : storagedate;
device = d.getDevice() != null && compareTrust(this, e) < 0 ? d.getDevice() : device;
size = d.getSize() != null && compareTrust(this, e) < 0 ? d.getSize() : size;
version = d.getVersion() != null && compareTrust(this, e) < 0 ? d.getVersion() : version;
lastmetadataupdate = d.getLastmetadataupdate() != null && compareTrust(this, e) < 0
? d.getLastmetadataupdate()
: lastmetadataupdate;
metadataversionnumber = d.getMetadataversionnumber() != null && compareTrust(this, e) < 0
? d.getMetadataversionnumber()
: metadataversionnumber;
geolocation = mergeLists(geolocation, d.getGeolocation());
mergeOAFDataInfo(d);
}
} }

243
src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java
View File

@ -4,11 +4,8 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
public class Datasource extends OafEntity implements Serializable { public class Datasource extends Entity implements Serializable {
/**
*
*/
private static final long serialVersionUID = 1019089598408414496L; private static final long serialVersionUID = 1019089598408414496L;
@Deprecated @Deprecated
@ -23,83 +20,83 @@ public class Datasource extends OafEntity implements Serializable {
private Qualifier openairecompatibility; private Qualifier openairecompatibility;
private Field<String> officialname; private String officialname;
private Field<String> englishname; private String englishname;
private Field<String> websiteurl; private String websiteurl;
private Field<String> logourl; private String logourl;
private Field<String> contactemail; private String contactemail;
private Field<String> namespaceprefix; private String namespaceprefix;
private Field<String> latitude; private String latitude;
private Field<String> longitude; private String longitude;
private Field<String> dateofvalidation; private String dateofvalidation;
private Field<String> description; private String description;
private List<StructuredProperty> subjects; private List<StructuredProperty> subjects;
// opendoar specific fields (od*) // opendoar specific fields (od*)
@Deprecated @Deprecated
private Field<String> odnumberofitems; private String odnumberofitems;
@Deprecated @Deprecated
private Field<String> odnumberofitemsdate; private String odnumberofitemsdate;
@Deprecated @Deprecated
private Field<String> odpolicies; private String odpolicies;
@Deprecated @Deprecated
private List<Field<String>> odlanguages; private List<String> odlanguages;
private List<String> languages; private List<String> languages;
@Deprecated @Deprecated
private List<Field<String>> odcontenttypes; private List<String> odcontenttypes;
private List<Field<String>> accessinfopackage; private List<String> accessinfopackage;
// re3data fields // re3data fields
private Field<String> releasestartdate; private String releasestartdate;
private Field<String> releaseenddate; private String releaseenddate;
private Field<String> missionstatementurl; private String missionstatementurl;
@Deprecated @Deprecated
private Field<Boolean> dataprovider; private Boolean dataprovider;
@Deprecated @Deprecated
private Field<Boolean> serviceprovider; private Boolean serviceprovider;
// {open, restricted or closed} // {open, restricted or closed}
private Field<String> databaseaccesstype; private String databaseaccesstype;
// {open, restricted or closed} // {open, restricted or closed}
private Field<String> datauploadtype; private String datauploadtype;
// {feeRequired, registration, other} // {feeRequired, registration, other}
private Field<String> databaseaccessrestriction; private String databaseaccessrestriction;
// {feeRequired, registration, other} // {feeRequired, registration, other}
private Field<String> datauploadrestriction; private String datauploadrestriction;
@Deprecated @Deprecated
private Field<Boolean> versioning; private Boolean versioning;
private Boolean versioncontrol; private Boolean versioncontrol;
private Field<String> citationguidelineurl; private String citationguidelineurl;
private Field<String> pidsystems; private String pidsystems;
private Field<String> certificates; private String certificates;
@Deprecated @Deprecated
private List<KeyValue> policies; private List<KeyValue> policies;
@ -146,7 +143,7 @@ public class Datasource extends OafEntity implements Serializable {
return datasourcetype; return datasourcetype;
} }
public void setDatasourcetype(final Qualifier datasourcetype) { public void setDatasourcetype(Qualifier datasourcetype) {
this.datasourcetype = datasourcetype; this.datasourcetype = datasourcetype;
} }
@ -154,7 +151,7 @@ public class Datasource extends OafEntity implements Serializable {
return datasourcetypeui; return datasourcetypeui;
} }
public void setDatasourcetypeui(final Qualifier datasourcetypeui) { public void setDatasourcetypeui(Qualifier datasourcetypeui) {
this.datasourcetypeui = datasourcetypeui; this.datasourcetypeui = datasourcetypeui;
} }
@ -178,87 +175,87 @@ public class Datasource extends OafEntity implements Serializable {
return openairecompatibility; return openairecompatibility;
} }
public void setOpenairecompatibility(final Qualifier openairecompatibility) { public void setOpenairecompatibility(Qualifier openairecompatibility) {
this.openairecompatibility = openairecompatibility; this.openairecompatibility = openairecompatibility;
} }
public Field<String> getOfficialname() { public String getOfficialname() {
return officialname; return officialname;
} }
public void setOfficialname(final Field<String> officialname) { public void setOfficialname(String officialname) {
this.officialname = officialname; this.officialname = officialname;
} }
public Field<String> getEnglishname() { public String getEnglishname() {
return englishname; return englishname;
} }
public void setEnglishname(final Field<String> englishname) { public void setEnglishname(String englishname) {
this.englishname = englishname; this.englishname = englishname;
} }
public Field<String> getWebsiteurl() { public String getWebsiteurl() {
return websiteurl; return websiteurl;
} }
public void setWebsiteurl(final Field<String> websiteurl) { public void setWebsiteurl(String websiteurl) {
this.websiteurl = websiteurl; this.websiteurl = websiteurl;
} }
public Field<String> getLogourl() { public String getLogourl() {
return logourl; return logourl;
} }
public void setLogourl(final Field<String> logourl) { public void setLogourl(String logourl) {
this.logourl = logourl; this.logourl = logourl;
} }
public Field<String> getContactemail() { public String getContactemail() {
return contactemail; return contactemail;
} }
public void setContactemail(final Field<String> contactemail) { public void setContactemail(String contactemail) {
this.contactemail = contactemail; this.contactemail = contactemail;
} }
public Field<String> getNamespaceprefix() { public String getNamespaceprefix() {
return namespaceprefix; return namespaceprefix;
} }
public void setNamespaceprefix(final Field<String> namespaceprefix) { public void setNamespaceprefix(String namespaceprefix) {
this.namespaceprefix = namespaceprefix; this.namespaceprefix = namespaceprefix;
} }
public Field<String> getLatitude() { public String getLatitude() {
return latitude; return latitude;
} }
public void setLatitude(final Field<String> latitude) { public void setLatitude(String latitude) {
this.latitude = latitude; this.latitude = latitude;
} }
public Field<String> getLongitude() { public String getLongitude() {
return longitude; return longitude;
} }
public void setLongitude(final Field<String> longitude) { public void setLongitude(String longitude) {
this.longitude = longitude; this.longitude = longitude;
} }
public Field<String> getDateofvalidation() { public String getDateofvalidation() {
return dateofvalidation; return dateofvalidation;
} }
public void setDateofvalidation(final Field<String> dateofvalidation) { public void setDateofvalidation(String dateofvalidation) {
this.dateofvalidation = dateofvalidation; this.dateofvalidation = dateofvalidation;
} }
public Field<String> getDescription() { public String getDescription() {
return description; return description;
} }
public void setDescription(final Field<String> description) { public void setDescription(String description) {
this.description = description; this.description = description;
} }
@ -266,39 +263,39 @@ public class Datasource extends OafEntity implements Serializable {
return subjects; return subjects;
} }
public void setSubjects(final List<StructuredProperty> subjects) { public void setSubjects(List<StructuredProperty> subjects) {
this.subjects = subjects; this.subjects = subjects;
} }
public Field<String> getOdnumberofitems() { public String getOdnumberofitems() {
return odnumberofitems; return odnumberofitems;
} }
public void setOdnumberofitems(final Field<String> odnumberofitems) { public void setOdnumberofitems(String odnumberofitems) {
this.odnumberofitems = odnumberofitems; this.odnumberofitems = odnumberofitems;
} }
public Field<String> getOdnumberofitemsdate() { public String getOdnumberofitemsdate() {
return odnumberofitemsdate; return odnumberofitemsdate;
} }
public void setOdnumberofitemsdate(final Field<String> odnumberofitemsdate) { public void setOdnumberofitemsdate(String odnumberofitemsdate) {
this.odnumberofitemsdate = odnumberofitemsdate; this.odnumberofitemsdate = odnumberofitemsdate;
} }
public Field<String> getOdpolicies() { public String getOdpolicies() {
return odpolicies; return odpolicies;
} }
public void setOdpolicies(final Field<String> odpolicies) { public void setOdpolicies(String odpolicies) {
this.odpolicies = odpolicies; this.odpolicies = odpolicies;
} }
public List<Field<String>> getOdlanguages() { public List<String> getOdlanguages() {
return odlanguages; return odlanguages;
} }
public void setOdlanguages(final List<Field<String>> odlanguages) { public void setOdlanguages(List<String> odlanguages) {
this.odlanguages = odlanguages; this.odlanguages = odlanguages;
} }
@ -306,103 +303,103 @@ public class Datasource extends OafEntity implements Serializable {
return languages; return languages;
} }
public void setLanguages(final List<String> languages) { public void setLanguages(List<String> languages) {
this.languages = languages; this.languages = languages;
} }
public List<Field<String>> getOdcontenttypes() { public List<String> getOdcontenttypes() {
return odcontenttypes; return odcontenttypes;
} }
public void setOdcontenttypes(final List<Field<String>> odcontenttypes) { public void setOdcontenttypes(List<String> odcontenttypes) {
this.odcontenttypes = odcontenttypes; this.odcontenttypes = odcontenttypes;
} }
public List<Field<String>> getAccessinfopackage() { public List<String> getAccessinfopackage() {
return accessinfopackage; return accessinfopackage;
} }
public void setAccessinfopackage(final List<Field<String>> accessinfopackage) { public void setAccessinfopackage(List<String> accessinfopackage) {
this.accessinfopackage = accessinfopackage; this.accessinfopackage = accessinfopackage;
} }
public Field<String> getReleasestartdate() { public String getReleasestartdate() {
return releasestartdate; return releasestartdate;
} }
public void setReleasestartdate(final Field<String> releasestartdate) { public void setReleasestartdate(String releasestartdate) {
this.releasestartdate = releasestartdate; this.releasestartdate = releasestartdate;
} }
public Field<String> getReleaseenddate() { public String getReleaseenddate() {
return releaseenddate; return releaseenddate;
} }
public void setReleaseenddate(final Field<String> releaseenddate) { public void setReleaseenddate(String releaseenddate) {
this.releaseenddate = releaseenddate; this.releaseenddate = releaseenddate;
} }
public Field<String> getMissionstatementurl() { public String getMissionstatementurl() {
return missionstatementurl; return missionstatementurl;
} }
public void setMissionstatementurl(final Field<String> missionstatementurl) { public void setMissionstatementurl(String missionstatementurl) {
this.missionstatementurl = missionstatementurl; this.missionstatementurl = missionstatementurl;
} }
public Field<Boolean> getDataprovider() { public Boolean getDataprovider() {
return dataprovider; return dataprovider;
} }
public void setDataprovider(final Field<Boolean> dataprovider) { public void setDataprovider(Boolean dataprovider) {
this.dataprovider = dataprovider; this.dataprovider = dataprovider;
} }
public Field<Boolean> getServiceprovider() { public Boolean getServiceprovider() {
return serviceprovider; return serviceprovider;
} }
public void setServiceprovider(final Field<Boolean> serviceprovider) { public void setServiceprovider(Boolean serviceprovider) {
this.serviceprovider = serviceprovider; this.serviceprovider = serviceprovider;
} }
public Field<String> getDatabaseaccesstype() { public String getDatabaseaccesstype() {
return databaseaccesstype; return databaseaccesstype;
} }
public void setDatabaseaccesstype(final Field<String> databaseaccesstype) { public void setDatabaseaccesstype(String databaseaccesstype) {
this.databaseaccesstype = databaseaccesstype; this.databaseaccesstype = databaseaccesstype;
} }
public Field<String> getDatauploadtype() { public String getDatauploadtype() {
return datauploadtype; return datauploadtype;
} }
public void setDatauploadtype(final Field<String> datauploadtype) { public void setDatauploadtype(String datauploadtype) {
this.datauploadtype = datauploadtype; this.datauploadtype = datauploadtype;
} }
public Field<String> getDatabaseaccessrestriction() { public String getDatabaseaccessrestriction() {
return databaseaccessrestriction; return databaseaccessrestriction;
} }
public void setDatabaseaccessrestriction(final Field<String> databaseaccessrestriction) { public void setDatabaseaccessrestriction(String databaseaccessrestriction) {
this.databaseaccessrestriction = databaseaccessrestriction; this.databaseaccessrestriction = databaseaccessrestriction;
} }
public Field<String> getDatauploadrestriction() { public String getDatauploadrestriction() {
return datauploadrestriction; return datauploadrestriction;
} }
public void setDatauploadrestriction(final Field<String> datauploadrestriction) { public void setDatauploadrestriction(String datauploadrestriction) {
this.datauploadrestriction = datauploadrestriction; this.datauploadrestriction = datauploadrestriction;
} }
public Field<Boolean> getVersioning() { public Boolean getVersioning() {
return versioning; return versioning;
} }
public void setVersioning(final Field<Boolean> versioning) { public void setVersioning(Boolean versioning) {
this.versioning = versioning; this.versioning = versioning;
} }
@ -414,27 +411,27 @@ public class Datasource extends OafEntity implements Serializable {
this.versioncontrol = versioncontrol; this.versioncontrol = versioncontrol;
} }
public Field<String> getCitationguidelineurl() { public String getCitationguidelineurl() {
return citationguidelineurl; return citationguidelineurl;
} }
public void setCitationguidelineurl(final Field<String> citationguidelineurl) { public void setCitationguidelineurl(String citationguidelineurl) {
this.citationguidelineurl = citationguidelineurl; this.citationguidelineurl = citationguidelineurl;
} }
public Field<String> getPidsystems() { public String getPidsystems() {
return pidsystems; return pidsystems;
} }
public void setPidsystems(final Field<String> pidsystems) { public void setPidsystems(String pidsystems) {
this.pidsystems = pidsystems; this.pidsystems = pidsystems;
} }
public Field<String> getCertificates() { public String getCertificates() {
return certificates; return certificates;
} }
public void setCertificates(final Field<String> certificates) { public void setCertificates(String certificates) {
this.certificates = certificates; this.certificates = certificates;
} }
@ -442,7 +439,7 @@ public class Datasource extends OafEntity implements Serializable {
return policies; return policies;
} }
public void setPolicies(final List<KeyValue> policies) { public void setPolicies(List<KeyValue> policies) {
this.policies = policies; this.policies = policies;
} }
@ -450,7 +447,7 @@ public class Datasource extends OafEntity implements Serializable {
return journal; return journal;
} }
public void setJournal(final Journal journal) { public void setJournal(Journal journal) {
this.journal = journal; this.journal = journal;
} }
@ -458,7 +455,7 @@ public class Datasource extends OafEntity implements Serializable {
return researchentitytypes; return researchentitytypes;
} }
public void setResearchentitytypes(final List<String> researchentitytypes) { public void setResearchentitytypes(List<String> researchentitytypes) {
this.researchentitytypes = researchentitytypes; this.researchentitytypes = researchentitytypes;
} }
@ -466,7 +463,7 @@ public class Datasource extends OafEntity implements Serializable {
return providedproducttypes; return providedproducttypes;
} }
public void setProvidedproducttypes(final List<String> providedproducttypes) { public void setProvidedproducttypes(List<String> providedproducttypes) {
this.providedproducttypes = providedproducttypes; this.providedproducttypes = providedproducttypes;
} }
@ -474,7 +471,7 @@ public class Datasource extends OafEntity implements Serializable {
return jurisdiction; return jurisdiction;
} }
public void setJurisdiction(final Qualifier jurisdiction) { public void setJurisdiction(Qualifier jurisdiction) {
this.jurisdiction = jurisdiction; this.jurisdiction = jurisdiction;
} }
@ -482,7 +479,7 @@ public class Datasource extends OafEntity implements Serializable {
return thematic; return thematic;
} }
public void setThematic(final Boolean thematic) { public void setThematic(Boolean thematic) {
this.thematic = thematic; this.thematic = thematic;
} }
@ -490,7 +487,7 @@ public class Datasource extends OafEntity implements Serializable {
return contentpolicies; return contentpolicies;
} }
public void setContentpolicies(final List<Qualifier> contentpolicies) { public void setContentpolicies(List<Qualifier> contentpolicies) {
this.contentpolicies = contentpolicies; this.contentpolicies = contentpolicies;
} }
@ -530,10 +527,26 @@ public class Datasource extends OafEntity implements Serializable {
return consenttermsofuse; return consenttermsofuse;
} }
public void setConsenttermsofuse(final Boolean consenttermsofuse) { public void setConsenttermsofuse(Boolean consenttermsofuse) {
this.consenttermsofuse = consenttermsofuse; this.consenttermsofuse = consenttermsofuse;
} }
public Boolean getFulltextdownload() {
return fulltextdownload;
}
public void setFulltextdownload(Boolean fulltextdownload) {
this.fulltextdownload = fulltextdownload;
}
public String getConsenttermsofusedate() {
return consenttermsofusedate;
}
public void setConsenttermsofusedate(String consenttermsofusedate) {
this.consenttermsofusedate = consenttermsofusedate;
}
public String getLastconsenttermsofusedate() { public String getLastconsenttermsofusedate() {
return lastconsenttermsofusedate; return lastconsenttermsofusedate;
} }
@ -542,22 +555,6 @@ public class Datasource extends OafEntity implements Serializable {
this.lastconsenttermsofusedate = lastconsenttermsofusedate; this.lastconsenttermsofusedate = lastconsenttermsofusedate;
} }
public Boolean getFulltextdownload() {
return fulltextdownload;
}
public void setFulltextdownload(final Boolean fulltextdownload) {
this.fulltextdownload = fulltextdownload;
}
public String getConsenttermsofusedate() {
return consenttermsofusedate;
}
public void setConsenttermsofusedate(final String consenttermsofusedate) {
this.consenttermsofusedate = consenttermsofusedate;
}
public List<EoscIfGuidelines> getEoscifguidelines() { public List<EoscIfGuidelines> getEoscifguidelines() {
return eoscifguidelines; return eoscifguidelines;
} }
@ -565,10 +562,4 @@ public class Datasource extends OafEntity implements Serializable {
public void setEoscifguidelines(List<EoscIfGuidelines> eoscifguidelines) { public void setEoscifguidelines(List<EoscIfGuidelines> eoscifguidelines) {
this.eoscifguidelines = eoscifguidelines; this.eoscifguidelines = eoscifguidelines;
} }
@Override
public void mergeFrom(final OafEntity e) {
super.mergeFrom(e);
}
} }

92
src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java → src/main/java/eu/dnetlib/dhp/schema/oaf/Entity.java
View File

@ -5,21 +5,49 @@ import java.io.Serializable;
import java.util.*; import java.util.*;
import java.util.stream.Collectors; import java.util.stream.Collectors;
public abstract class OafEntity extends Oaf implements Serializable { public abstract class Entity extends Oaf implements Serializable {
private String id; private String id;
private List<String> originalId; private List<String> originalId;
/**
* The list of datasource id/name pairs providing this Oaf.
*/
private List<KeyValue> collectedfrom;
private Long lastupdatetimestamp;
private List<StructuredProperty> pid; private List<StructuredProperty> pid;
private String dateofcollection; private String dateofcollection;
private String dateoftransformation; private String dateoftransformation;
/**
* The Measures.
*/
private List<Measure> measures;
private List<ExtraInfo> extraInfo; private List<ExtraInfo> extraInfo;
private OAIProvenance oaiprovenance; private EntityDataInfo dataInfo;
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public Long getLastupdatetimestamp() {
return lastupdatetimestamp;
}
public void setLastupdatetimestamp(Long lastupdatetimestamp) {
this.lastupdatetimestamp = lastupdatetimestamp;
}
public String getId() { public String getId() {
return id; return id;
@ -57,6 +85,24 @@ public abstract class OafEntity extends Oaf implements Serializable {
return dateoftransformation; return dateoftransformation;
} }
/**
* Gets measures.
*
* @return the measures
*/
public List<Measure> getMeasures() {
return measures;
}
/**
* Sets measures.
*
* @param measures the measures
*/
public void setMeasures(List<Measure> measures) {
this.measures = measures;
}
public void setDateoftransformation(String dateoftransformation) { public void setDateoftransformation(String dateoftransformation) {
this.dateoftransformation = dateoftransformation; this.dateoftransformation = dateoftransformation;
} }
@ -69,43 +115,12 @@ public abstract class OafEntity extends Oaf implements Serializable {
this.extraInfo = extraInfo; this.extraInfo = extraInfo;
} }
public OAIProvenance getOaiprovenance() { public EntityDataInfo getDataInfo() {
return oaiprovenance; return dataInfo;
} }
public void setOaiprovenance(OAIProvenance oaiprovenance) { public void setDataInfo(EntityDataInfo dataInfo) {
this.oaiprovenance = oaiprovenance; this.dataInfo = dataInfo;
}
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
originalId = mergeLists(originalId, e.getOriginalId());
pid = mergeLists(pid, e.getPid());
if (e.getDateofcollection() != null && compareTrust(this, e) < 0)
dateofcollection = e.getDateofcollection();
if (e.getDateoftransformation() != null && compareTrust(this, e) < 0)
dateoftransformation = e.getDateoftransformation();
extraInfo = mergeLists(extraInfo, e.getExtraInfo());
if (e.getOaiprovenance() != null && compareTrust(this, e) < 0)
oaiprovenance = e.getOaiprovenance();
}
@SafeVarargs
protected final <T> List<T> mergeLists(final List<T>... lists) {
return Arrays
.stream(lists)
.filter(Objects::nonNull)
.flatMap(List::stream)
.filter(Objects::nonNull)
.distinct()
.collect(Collectors.toList());
} }
@Override @Override
@ -116,7 +131,7 @@ public abstract class OafEntity extends Oaf implements Serializable {
return false; return false;
if (!super.equals(o)) if (!super.equals(o))
return false; return false;
OafEntity oafEntity = (OafEntity) o; Entity oafEntity = (Entity) o;
return Objects.equals(id, oafEntity.id); return Objects.equals(id, oafEntity.id);
} }
@ -124,4 +139,5 @@ public abstract class OafEntity extends Oaf implements Serializable {
public int hashCode() { public int hashCode() {
return Objects.hash(super.hashCode(), id); return Objects.hash(super.hashCode(), id);
} }
} }

82
src/main/java/eu/dnetlib/dhp/schema/oaf/EntityDataInfo.java Normal file
View File

@ -0,0 +1,82 @@
package eu.dnetlib.dhp.schema.oaf;
import java.util.Objects;
public class EntityDataInfo {
private Boolean inferred;
private Float trust;
private String inferenceprovenance;
private Qualifier provenanceaction;
private Boolean invisible = false;
private Boolean deletedbyinference = false;
public Boolean getInferred() {
return inferred;
}
public void setInferred(Boolean inferred) {
this.inferred = inferred;
}
public Float getTrust() {
return trust;
}
public void setTrust(Float trust) {
this.trust = trust;
}
public String getInferenceprovenance() {
return inferenceprovenance;
}
public void setInferenceprovenance(String inferenceprovenance) {
this.inferenceprovenance = inferenceprovenance;
}
public Qualifier getProvenanceaction() {
return provenanceaction;
}
public void setProvenanceaction(Qualifier provenanceaction) {
this.provenanceaction = provenanceaction;
}
public Boolean getInvisible() {
return invisible;
}
public void setInvisible(Boolean invisible) {
this.invisible = invisible;
}
public Boolean getDeletedbyinference() {
return deletedbyinference;
}
public void setDeletedbyinference(Boolean deletedbyinference) {
this.deletedbyinference = deletedbyinference;
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
EntityDataInfo dataInfo = (EntityDataInfo) o;
return Objects.equals(inferred, dataInfo.inferred)
&& Objects.equals(trust, dataInfo.trust)
&& Objects.equals(inferenceprovenance, dataInfo.inferenceprovenance)
&& Objects.equals(provenanceaction, dataInfo.provenanceaction)
&& Objects.equals(deletedbyinference, dataInfo.deletedbyinference)
&& Objects.equals(invisible, dataInfo.invisible);
}
@Override
public int hashCode() {
return Objects.hash(
inferred, trust, inferenceprovenance, provenanceaction, deletedbyinference, invisible);
}
}

16
src/main/java/eu/dnetlib/dhp/schema/oaf/ExternalReference.java
View File

@ -27,9 +27,6 @@ public class ExternalReference implements Serializable {
// maps the oaf:reference/@query attribute // maps the oaf:reference/@query attribute
private String query; private String query;
// ExternalReferences might be also inferred
private DataInfo dataInfo;
public String getSitename() { public String getSitename() {
return sitename; return sitename;
} }
@ -86,14 +83,6 @@ public class ExternalReference implements Serializable {
this.query = query; this.query = query;
} }
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) if (this == o)
@ -106,15 +95,14 @@ public class ExternalReference implements Serializable {
&& Objects.equals(url, that.url) && Objects.equals(url, that.url)
&& Objects.equals(qualifier, that.qualifier) && Objects.equals(qualifier, that.qualifier)
&& Objects.equals(refidentifier, that.refidentifier) && Objects.equals(refidentifier, that.refidentifier)
&& Objects.equals(query, that.query) && Objects.equals(query, that.query);
&& Objects.equals(dataInfo, that.dataInfo);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects return Objects
.hash( .hash(
sitename, label, url, qualifier, refidentifier, query, dataInfo); sitename, label, url, qualifier, refidentifier, query);
} }
} }

45
src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java
View File

@ -1,45 +0,0 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
import java.util.Objects;
public class Field<T> implements Serializable {
private T value;
private DataInfo dataInfo;
public T getValue() {
return value;
}
public void setValue(T value) {
this.value = value;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
@Override
public int hashCode() {
return getValue() == null ? 0 : getValue().hashCode();
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Field<T> other = (Field<T>) obj;
return Objects.equals(getValue(), other.getValue());
}
}

44
src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java
View File

@ -6,7 +6,7 @@ import java.util.List;
public class Instance implements Serializable { public class Instance implements Serializable {
private Field<String> license; private License license;
private AccessRight accessright; private AccessRight accessright;
@ -16,6 +16,8 @@ public class Instance implements Serializable {
private List<String> url; private List<String> url;
private List<String> fulltext;
// other research products specifc // other research products specifc
private String distributionlocation; private String distributionlocation;
@ -25,25 +27,23 @@ public class Instance implements Serializable {
private List<StructuredProperty> alternateIdentifier; private List<StructuredProperty> alternateIdentifier;
private Field<String> dateofacceptance; private String dateofacceptance;
// ( article | book ) processing charges. Defined here to cope with possible wrongly typed // ( article | book ) processing charges. Defined here to cope with possible wrongly typed
// results // results
private Field<String> processingchargeamount; private String processingchargeamount;
// currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly // currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly
// typed results // typed results
private Field<String> processingchargecurrency; private String processingchargecurrency;
private Qualifier refereed; // peer-review status private Qualifier refereed; // peer-review status
private List<Measure> measures; public License getLicense() {
public Field<String> getLicense() {
return license; return license;
} }
public void setLicense(Field<String> license) { public void setLicense(License license) {
this.license = license; this.license = license;
} }
@ -79,6 +79,14 @@ public class Instance implements Serializable {
this.url = url; this.url = url;
} }
public List<String> getFulltext() {
return fulltext;
}
public void setFulltext(List<String> fulltext) {
this.fulltext = fulltext;
}
public String getDistributionlocation() { public String getDistributionlocation() {
return distributionlocation; return distributionlocation;
} }
@ -103,11 +111,11 @@ public class Instance implements Serializable {
this.pid = pid; this.pid = pid;
} }
public Field<String> getDateofacceptance() { public String getDateofacceptance() {
return dateofacceptance; return dateofacceptance;
} }
public void setDateofacceptance(Field<String> dateofacceptance) { public void setDateofacceptance(String dateofacceptance) {
this.dateofacceptance = dateofacceptance; this.dateofacceptance = dateofacceptance;
} }
@ -119,19 +127,19 @@ public class Instance implements Serializable {
this.alternateIdentifier = alternateIdentifier; this.alternateIdentifier = alternateIdentifier;
} }
public Field<String> getProcessingchargeamount() { public String getProcessingchargeamount() {
return processingchargeamount; return processingchargeamount;
} }
public void setProcessingchargeamount(Field<String> processingchargeamount) { public void setProcessingchargeamount(String processingchargeamount) {
this.processingchargeamount = processingchargeamount; this.processingchargeamount = processingchargeamount;
} }
public Field<String> getProcessingchargecurrency() { public String getProcessingchargecurrency() {
return processingchargecurrency; return processingchargecurrency;
} }
public void setProcessingchargecurrency(Field<String> processingchargecurrency) { public void setProcessingchargecurrency(String processingchargecurrency) {
this.processingchargecurrency = processingchargecurrency; this.processingchargecurrency = processingchargecurrency;
} }
@ -143,14 +151,6 @@ public class Instance implements Serializable {
this.refereed = refereed; this.refereed = refereed;
} }
public List<Measure> getMeasures() {
return measures;
}
public void setMeasures(List<Measure> measures) {
this.measures = measures;
}
public String toComparableString() { public String toComparableString() {
return String return String
.format( .format(

16
src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java
View File

@ -28,8 +28,6 @@ public class Journal implements Serializable {
private String conferencedate; private String conferencedate;
private DataInfo dataInfo;
public String getName() { public String getName() {
return name; return name;
} }
@ -118,14 +116,6 @@ public class Journal implements Serializable {
this.conferencedate = conferencedate; this.conferencedate = conferencedate;
} }
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) if (this == o)
@ -143,8 +133,7 @@ public class Journal implements Serializable {
&& Objects.equals(vol, journal.vol) && Objects.equals(vol, journal.vol)
&& Objects.equals(edition, journal.edition) && Objects.equals(edition, journal.edition)
&& Objects.equals(conferenceplace, journal.conferenceplace) && Objects.equals(conferenceplace, journal.conferenceplace)
&& Objects.equals(conferencedate, journal.conferencedate) && Objects.equals(conferencedate, journal.conferencedate);
&& Objects.equals(dataInfo, journal.dataInfo);
} }
@Override @Override
@ -161,7 +150,6 @@ public class Journal implements Serializable {
vol, vol,
edition, edition,
conferenceplace, conferenceplace,
conferencedate, conferencedate);
dataInfo);
} }
} }

10
src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java
View File

@ -13,8 +13,6 @@ public class KeyValue implements Serializable {
private String value; private String value;
private DataInfo dataInfo;
public String getKey() { public String getKey() {
return key; return key;
} }
@ -31,14 +29,6 @@ public class KeyValue implements Serializable {
this.value = value; this.value = value;
} }
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public String toComparableString() { public String toComparableString() {
return isBlank() return isBlank()
? "" ? ""

24
src/main/java/eu/dnetlib/dhp/schema/oaf/License.java Normal file
View File

@ -0,0 +1,24 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
public class License implements Serializable {
private String url;
public License() {
}
public License(String url) {
this.url = url;
}
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
}

12
src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java
View File

@ -17,10 +17,10 @@ public class Measure implements Serializable {
private String id; private String id;
/** /**
* List of units associated with this measure. KeyValue provides a pair to store the label (key) and the value, plus * List of units associated with this measure. MeasureUnit provides a pair to store the label (key) and the value, plus
* common provenance information. * common provenance information.
*/ */
private List<KeyValue> unit; private List<MeasureUnit> unit;
public String getId() { public String getId() {
return id; return id;
@ -30,18 +30,14 @@ public class Measure implements Serializable {
this.id = id; this.id = id;
} }
public List<KeyValue> getUnit() { public List<MeasureUnit> getUnit() {
return unit; return unit;
} }
public void setUnit(List<KeyValue> unit) { public void setUnit(List<MeasureUnit> unit) {
this.unit = unit; this.unit = unit;
} }
public void mergeFrom(Measure m) {
// TODO
}
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) if (this == o)

14
src/main/java/eu/dnetlib/dhp/schema/oaf/MeasureUnit.java Normal file
View File

@ -0,0 +1,14 @@
package eu.dnetlib.dhp.schema.oaf;
public class MeasureUnit extends KeyValue {
private DataInfo dataInfo;
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
}

104
src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java
View File

@ -1,108 +1,6 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.Collection;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.stream.Collectors;
import java.util.stream.Stream;
public abstract class Oaf implements Serializable { public class Oaf implements Serializable {
/**
* The list of datasource id/name pairs providing this relationship.
*/
protected List<KeyValue> collectedfrom;
private DataInfo dataInfo;
private Long lastupdatetimestamp;
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public Long getLastupdatetimestamp() {
return lastupdatetimestamp;
}
public void setLastupdatetimestamp(Long lastupdatetimestamp) {
this.lastupdatetimestamp = lastupdatetimestamp;
}
public void mergeFrom(Oaf o) {
if (Objects.isNull(o)) {
return;
}
setCollectedfrom(
Stream
.concat(
Optional
.ofNullable(getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()),
Optional
.ofNullable(o.getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()))
.distinct() // relies on KeyValue.equals
.collect(Collectors.toList()));
setLastupdatetimestamp(
Math
.max(
Optional.ofNullable(getLastupdatetimestamp()).orElse(0L),
Optional.ofNullable(o.getLastupdatetimestamp()).orElse(0L)));
}
public void mergeOAFDataInfo(Oaf o) {
Optional.ofNullable(o)
.ifPresent(other -> Optional.ofNullable(other.getDataInfo())
.ifPresent(otherDataInfo -> Optional.ofNullable(this.getDataInfo())
.ifPresent(thisDataInfo -> {
if (compareTrust(this, other) < 0 || thisDataInfo.getInvisible()) {
setDataInfo(otherDataInfo);
}
})));
}
protected String extractTrust(Oaf e) {
if (e == null || e.getDataInfo() == null || e.getDataInfo().getTrust() == null)
return "0.0";
return e.getDataInfo().getTrust();
}
protected int compareTrust(Oaf a, Oaf b) {
return extractTrust(a).compareTo(extractTrust(b));
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
Oaf oaf = (Oaf) o;
return Objects.equals(getDataInfo(), oaf.getDataInfo())
&& Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp);
}
@Override
public int hashCode() {
return Objects.hash(dataInfo, lastupdatetimestamp);
}
} }

136
src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java
View File

@ -4,158 +4,158 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
public class Organization extends OafEntity implements Serializable { public class Organization extends Entity implements Serializable {
private Field<String> legalshortname; private String legalshortname;
private Field<String> legalname; private String legalname;
private List<Field<String>> alternativeNames; private List<String> alternativeNames;
private Field<String> websiteurl; private String websiteurl;
private Field<String> logourl; private String logourl;
private Field<String> eclegalbody; private String eclegalbody;
private Field<String> eclegalperson; private String eclegalperson;
private Field<String> ecnonprofit; private String ecnonprofit;
private Field<String> ecresearchorganization; private String ecresearchorganization;
private Field<String> echighereducation; private String echighereducation;
private Field<String> ecinternationalorganizationeurinterests; private String ecinternationalorganizationeurinterests;
private Field<String> ecinternationalorganization; private String ecinternationalorganization;
private Field<String> ecenterprise; private String ecenterprise;
private Field<String> ecsmevalidated; private String ecsmevalidated;
private Field<String> ecnutscode; private String ecnutscode;
private Qualifier country; private Qualifier country;
public Field<String> getLegalshortname() { public String getLegalshortname() {
return legalshortname; return legalshortname;
} }
public void setLegalshortname(Field<String> legalshortname) { public void setLegalshortname(String legalshortname) {
this.legalshortname = legalshortname; this.legalshortname = legalshortname;
} }
public Field<String> getLegalname() { public String getLegalname() {
return legalname; return legalname;
} }
public void setLegalname(Field<String> legalname) { public void setLegalname(String legalname) {
this.legalname = legalname; this.legalname = legalname;
} }
public List<Field<String>> getAlternativeNames() { public List<String> getAlternativeNames() {
return alternativeNames; return alternativeNames;
} }
public void setAlternativeNames(List<Field<String>> alternativeNames) { public void setAlternativeNames(List<String> alternativeNames) {
this.alternativeNames = alternativeNames; this.alternativeNames = alternativeNames;
} }
public Field<String> getWebsiteurl() { public String getWebsiteurl() {
return websiteurl; return websiteurl;
} }
public void setWebsiteurl(Field<String> websiteurl) { public void setWebsiteurl(String websiteurl) {
this.websiteurl = websiteurl; this.websiteurl = websiteurl;
} }
public Field<String> getLogourl() { public String getLogourl() {
return logourl; return logourl;
} }
public void setLogourl(Field<String> logourl) { public void setLogourl(String logourl) {
this.logourl = logourl; this.logourl = logourl;
} }
public Field<String> getEclegalbody() { public String getEclegalbody() {
return eclegalbody; return eclegalbody;
} }
public void setEclegalbody(Field<String> eclegalbody) { public void setEclegalbody(String eclegalbody) {
this.eclegalbody = eclegalbody; this.eclegalbody = eclegalbody;
} }
public Field<String> getEclegalperson() { public String getEclegalperson() {
return eclegalperson; return eclegalperson;
} }
public void setEclegalperson(Field<String> eclegalperson) { public void setEclegalperson(String eclegalperson) {
this.eclegalperson = eclegalperson; this.eclegalperson = eclegalperson;
} }
public Field<String> getEcnonprofit() { public String getEcnonprofit() {
return ecnonprofit; return ecnonprofit;
} }
public void setEcnonprofit(Field<String> ecnonprofit) { public void setEcnonprofit(String ecnonprofit) {
this.ecnonprofit = ecnonprofit; this.ecnonprofit = ecnonprofit;
} }
public Field<String> getEcresearchorganization() { public String getEcresearchorganization() {
return ecresearchorganization; return ecresearchorganization;
} }
public void setEcresearchorganization(Field<String> ecresearchorganization) { public void setEcresearchorganization(String ecresearchorganization) {
this.ecresearchorganization = ecresearchorganization; this.ecresearchorganization = ecresearchorganization;
} }
public Field<String> getEchighereducation() { public String getEchighereducation() {
return echighereducation; return echighereducation;
} }
public void setEchighereducation(Field<String> echighereducation) { public void setEchighereducation(String echighereducation) {
this.echighereducation = echighereducation; this.echighereducation = echighereducation;
} }
public Field<String> getEcinternationalorganizationeurinterests() { public String getEcinternationalorganizationeurinterests() {
return ecinternationalorganizationeurinterests; return ecinternationalorganizationeurinterests;
} }
public void setEcinternationalorganizationeurinterests( public void setEcinternationalorganizationeurinterests(
Field<String> ecinternationalorganizationeurinterests) { String ecinternationalorganizationeurinterests) {
this.ecinternationalorganizationeurinterests = ecinternationalorganizationeurinterests; this.ecinternationalorganizationeurinterests = ecinternationalorganizationeurinterests;
} }
public Field<String> getEcinternationalorganization() { public String getEcinternationalorganization() {
return ecinternationalorganization; return ecinternationalorganization;
} }
public void setEcinternationalorganization(Field<String> ecinternationalorganization) { public void setEcinternationalorganization(String ecinternationalorganization) {
this.ecinternationalorganization = ecinternationalorganization; this.ecinternationalorganization = ecinternationalorganization;
} }
public Field<String> getEcenterprise() { public String getEcenterprise() {
return ecenterprise; return ecenterprise;
} }
public void setEcenterprise(Field<String> ecenterprise) { public void setEcenterprise(String ecenterprise) {
this.ecenterprise = ecenterprise; this.ecenterprise = ecenterprise;
} }
public Field<String> getEcsmevalidated() { public String getEcsmevalidated() {
return ecsmevalidated; return ecsmevalidated;
} }
public void setEcsmevalidated(Field<String> ecsmevalidated) { public void setEcsmevalidated(String ecsmevalidated) {
this.ecsmevalidated = ecsmevalidated; this.ecsmevalidated = ecsmevalidated;
} }
public Field<String> getEcnutscode() { public String getEcnutscode() {
return ecnutscode; return ecnutscode;
} }
public void setEcnutscode(Field<String> ecnutscode) { public void setEcnutscode(String ecnutscode) {
this.ecnutscode = ecnutscode; this.ecnutscode = ecnutscode;
} }
@ -167,48 +167,4 @@ public class Organization extends OafEntity implements Serializable {
this.country = country; this.country = country;
} }
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Organization.class.isAssignableFrom(e.getClass())) {
return;
}
final Organization o = (Organization) e;
legalshortname = o.getLegalshortname() != null && compareTrust(this, e) < 0
? o.getLegalshortname()
: legalshortname;
legalname = o.getLegalname() != null && compareTrust(this, e) < 0 ? o.getLegalname() : legalname;
alternativeNames = mergeLists(o.getAlternativeNames(), alternativeNames);
websiteurl = o.getWebsiteurl() != null && compareTrust(this, e) < 0 ? o.getWebsiteurl() : websiteurl;
logourl = o.getLogourl() != null && compareTrust(this, e) < 0 ? o.getLogourl() : logourl;
eclegalbody = o.getEclegalbody() != null && compareTrust(this, e) < 0 ? o.getEclegalbody() : eclegalbody;
eclegalperson = o.getEclegalperson() != null && compareTrust(this, e) < 0
? o.getEclegalperson()
: eclegalperson;
ecnonprofit = o.getEcnonprofit() != null && compareTrust(this, e) < 0 ? o.getEcnonprofit() : ecnonprofit;
ecresearchorganization = o.getEcresearchorganization() != null && compareTrust(this, e) < 0
? o.getEcresearchorganization()
: ecresearchorganization;
echighereducation = o.getEchighereducation() != null && compareTrust(this, e) < 0
? o.getEchighereducation()
: echighereducation;
ecinternationalorganizationeurinterests = o.getEcinternationalorganizationeurinterests() != null
&& compareTrust(this, e) < 0
? o.getEcinternationalorganizationeurinterests()
: ecinternationalorganizationeurinterests;
ecinternationalorganization = o.getEcinternationalorganization() != null && compareTrust(this, e) < 0
? o.getEcinternationalorganization()
: ecinternationalorganization;
ecenterprise = o.getEcenterprise() != null && compareTrust(this, e) < 0
? o.getEcenterprise()
: ecenterprise;
ecsmevalidated = o.getEcsmevalidated() != null && compareTrust(this, e) < 0
? o.getEcsmevalidated()
: ecsmevalidated;
ecnutscode = o.getEcnutscode() != null && compareTrust(this, e) < 0 ? o.getEcnutscode() : ecnutscode;
country = o.getCountry() != null && compareTrust(this, e) < 0 ? o.getCountry() : country;
mergeOAFDataInfo(o);
}
} }

38
src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java
View File

@ -4,57 +4,39 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class OtherResearchProduct extends Result implements Serializable { public class OtherResearchProduct extends Result implements Serializable {
private List<Field<String>> contactperson; private List<String> contactperson;
private List<Field<String>> contactgroup; private List<String> contactgroup;
private List<Field<String>> tool; private List<String> tool;
public OtherResearchProduct() { public OtherResearchProduct() {
setResulttype(ModelConstants.ORP_DEFAULT_RESULTTYPE); setResulttype(RESULTTYPE.otherresearchproduct);
} }
public List<Field<String>> getContactperson() { public List<String> getContactperson() {
return contactperson; return contactperson;
} }
public void setContactperson(List<Field<String>> contactperson) { public void setContactperson(List<String> contactperson) {
this.contactperson = contactperson; this.contactperson = contactperson;
} }
public List<Field<String>> getContactgroup() { public List<String> getContactgroup() {
return contactgroup; return contactgroup;
} }
public void setContactgroup(List<Field<String>> contactgroup) { public void setContactgroup(List<String> contactgroup) {
this.contactgroup = contactgroup; this.contactgroup = contactgroup;
} }
public List<Field<String>> getTool() { public List<String> getTool() {
return tool; return tool;
} }
public void setTool(List<Field<String>> tool) { public void setTool(List<String> tool) {
this.tool = tool; this.tool = tool;
} }
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!OtherResearchProduct.class.isAssignableFrom(e.getClass())) {
return;
}
OtherResearchProduct o = (OtherResearchProduct) e;
contactperson = mergeLists(contactperson, o.getContactperson());
contactgroup = mergeLists(contactgroup, o.getContactgroup());
tool = mergeLists(tool, o.getTool());
mergeOAFDataInfo(e);
}
} }

198
src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java
View File

@ -4,57 +4,55 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import org.apache.commons.lang3.StringUtils; public class Project extends Entity implements Serializable {
public class Project extends OafEntity implements Serializable { private String websiteurl;
private Field<String> websiteurl; private String code;
private Field<String> code; private String acronym;
private Field<String> acronym; private String title;
private Field<String> title; private String startdate;
private Field<String> startdate; private String enddate;
private Field<String> enddate; private String callidentifier;
private Field<String> callidentifier; private String keywords;
private Field<String> keywords; private String duration;
private Field<String> duration; private String ecsc39;
private Field<String> ecsc39; private String oamandatepublications;
private Field<String> oamandatepublications; private String ecarticle29_3;
private Field<String> ecarticle29_3;
private List<StructuredProperty> subjects; private List<StructuredProperty> subjects;
private List<Field<String>> fundingtree; private List<String> fundingtree;
private Qualifier contracttype; private Qualifier contracttype;
private Field<String> optional1; private String optional1;
private Field<String> optional2; private String optional2;
private Field<String> jsonextrainfo; private String jsonextrainfo;
private Field<String> contactfullname; private String contactfullname;
private Field<String> contactfax; private String contactfax;
private Field<String> contactphone; private String contactphone;
private Field<String> contactemail; private String contactemail;
private Field<String> summary; private String summary;
private Field<String> currency; private String currency;
private Float totalcost; private Float totalcost;
@ -64,7 +62,7 @@ public class Project extends OafEntity implements Serializable {
private String h2020topicdescription; private String h2020topicdescription;
private List<H2020Classification> h2020classification; private List<H2020Classification>h2020classification;
public String getH2020topicdescription() { public String getH2020topicdescription() {
return h2020topicdescription; return h2020topicdescription;
@ -90,99 +88,99 @@ public class Project extends OafEntity implements Serializable {
this.h2020classification = h2020classification; this.h2020classification = h2020classification;
} }
public Field<String> getWebsiteurl() { public String getWebsiteurl() {
return websiteurl; return websiteurl;
} }
public void setWebsiteurl(Field<String> websiteurl) { public void setWebsiteurl( String websiteurl) {
this.websiteurl = websiteurl; this.websiteurl = websiteurl;
} }
public Field<String> getCode() { public String getCode() {
return code; return code;
} }
public void setCode(Field<String> code) { public void setCode( String code) {
this.code = code; this.code = code;
} }
public Field<String> getAcronym() { public String getAcronym() {
return acronym; return acronym;
} }
public void setAcronym(Field<String> acronym) { public void setAcronym( String acronym) {
this.acronym = acronym; this.acronym = acronym;
} }
public Field<String> getTitle() { public String getTitle() {
return title; return title;
} }
public void setTitle(Field<String> title) { public void setTitle( String title) {
this.title = title; this.title = title;
} }
public Field<String> getStartdate() { public String getStartdate() {
return startdate; return startdate;
} }
public void setStartdate(Field<String> startdate) { public void setStartdate( String startdate) {
this.startdate = startdate; this.startdate = startdate;
} }
public Field<String> getEnddate() { public String getEnddate() {
return enddate; return enddate;
} }
public void setEnddate(Field<String> enddate) { public void setEnddate( String enddate) {
this.enddate = enddate; this.enddate = enddate;
} }
public Field<String> getCallidentifier() { public String getCallidentifier() {
return callidentifier; return callidentifier;
} }
public void setCallidentifier(Field<String> callidentifier) { public void setCallidentifier( String callidentifier) {
this.callidentifier = callidentifier; this.callidentifier = callidentifier;
} }
public Field<String> getKeywords() { public String getKeywords() {
return keywords; return keywords;
} }
public void setKeywords(Field<String> keywords) { public void setKeywords( String keywords) {
this.keywords = keywords; this.keywords = keywords;
} }
public Field<String> getDuration() { public String getDuration() {
return duration; return duration;
} }
public void setDuration(Field<String> duration) { public void setDuration( String duration) {
this.duration = duration; this.duration = duration;
} }
public Field<String> getEcsc39() { public String getEcsc39() {
return ecsc39; return ecsc39;
} }
public void setEcsc39(Field<String> ecsc39) { public void setEcsc39( String ecsc39) {
this.ecsc39 = ecsc39; this.ecsc39 = ecsc39;
} }
public Field<String> getOamandatepublications() { public String getOamandatepublications() {
return oamandatepublications; return oamandatepublications;
} }
public void setOamandatepublications(Field<String> oamandatepublications) { public void setOamandatepublications( String oamandatepublications) {
this.oamandatepublications = oamandatepublications; this.oamandatepublications = oamandatepublications;
} }
public Field<String> getEcarticle29_3() { public String getEcarticle29_3() {
return ecarticle29_3; return ecarticle29_3;
} }
public void setEcarticle29_3(Field<String> ecarticle29_3) { public void setEcarticle29_3( String ecarticle29_3) {
this.ecarticle29_3 = ecarticle29_3; this.ecarticle29_3 = ecarticle29_3;
} }
@ -194,11 +192,11 @@ public class Project extends OafEntity implements Serializable {
this.subjects = subjects; this.subjects = subjects;
} }
public List<Field<String>> getFundingtree() { public List< String> getFundingtree() {
return fundingtree; return fundingtree;
} }
public void setFundingtree(List<Field<String>> fundingtree) { public void setFundingtree(List< String> fundingtree) {
this.fundingtree = fundingtree; this.fundingtree = fundingtree;
} }
@ -210,75 +208,75 @@ public class Project extends OafEntity implements Serializable {
this.contracttype = contracttype; this.contracttype = contracttype;
} }
public Field<String> getOptional1() { public String getOptional1() {
return optional1; return optional1;
} }
public void setOptional1(Field<String> optional1) { public void setOptional1( String optional1) {
this.optional1 = optional1; this.optional1 = optional1;
} }
public Field<String> getOptional2() { public String getOptional2() {
return optional2; return optional2;
} }
public void setOptional2(Field<String> optional2) { public void setOptional2( String optional2) {
this.optional2 = optional2; this.optional2 = optional2;
} }
public Field<String> getJsonextrainfo() { public String getJsonextrainfo() {
return jsonextrainfo; return jsonextrainfo;
} }
public void setJsonextrainfo(Field<String> jsonextrainfo) { public void setJsonextrainfo( String jsonextrainfo) {
this.jsonextrainfo = jsonextrainfo; this.jsonextrainfo = jsonextrainfo;
} }
public Field<String> getContactfullname() { public String getContactfullname() {
return contactfullname; return contactfullname;
} }
public void setContactfullname(Field<String> contactfullname) { public void setContactfullname( String contactfullname) {
this.contactfullname = contactfullname; this.contactfullname = contactfullname;
} }
public Field<String> getContactfax() { public String getContactfax() {
return contactfax; return contactfax;
} }
public void setContactfax(Field<String> contactfax) { public void setContactfax( String contactfax) {
this.contactfax = contactfax; this.contactfax = contactfax;
} }
public Field<String> getContactphone() { public String getContactphone() {
return contactphone; return contactphone;
} }
public void setContactphone(Field<String> contactphone) { public void setContactphone( String contactphone) {
this.contactphone = contactphone; this.contactphone = contactphone;
} }
public Field<String> getContactemail() { public String getContactemail() {
return contactemail; return contactemail;
} }
public void setContactemail(Field<String> contactemail) { public void setContactemail( String contactemail) {
this.contactemail = contactemail; this.contactemail = contactemail;
} }
public Field<String> getSummary() { public String getSummary() {
return summary; return summary;
} }
public void setSummary(Field<String> summary) { public void setSummary( String summary) {
this.summary = summary; this.summary = summary;
} }
public Field<String> getCurrency() { public String getCurrency() {
return currency; return currency;
} }
public void setCurrency(Field<String> currency) { public void setCurrency( String currency) {
this.currency = currency; this.currency = currency;
} }
@ -298,64 +296,4 @@ public class Project extends OafEntity implements Serializable {
this.fundedamount = fundedamount; this.fundedamount = fundedamount;
} }
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Project.class.isAssignableFrom(e.getClass())) {
return;
}
Project p = (Project) e;
websiteurl = p.getWebsiteurl() != null && compareTrust(this, e) < 0 ? p.getWebsiteurl() : websiteurl;
code = p.getCode() != null && compareTrust(this, e) < 0 ? p.getCode() : code;
acronym = p.getAcronym() != null && compareTrust(this, e) < 0 ? p.getAcronym() : acronym;
title = p.getTitle() != null && compareTrust(this, e) < 0 ? p.getTitle() : title;
startdate = p.getStartdate() != null && compareTrust(this, e) < 0 ? p.getStartdate() : startdate;
enddate = p.getEnddate() != null && compareTrust(this, e) < 0 ? p.getEnddate() : enddate;
callidentifier = p.getCallidentifier() != null && compareTrust(this, e) < 0
? p.getCallidentifier()
: callidentifier;
keywords = p.getKeywords() != null && compareTrust(this, e) < 0 ? p.getKeywords() : keywords;
duration = p.getDuration() != null && compareTrust(this, e) < 0 ? p.getDuration() : duration;
ecsc39 = p.getEcsc39() != null && compareTrust(this, e) < 0 ? p.getEcsc39() : ecsc39;
oamandatepublications = p.getOamandatepublications() != null && compareTrust(this, e) < 0
? p.getOamandatepublications()
: oamandatepublications;
ecarticle29_3 = p.getEcarticle29_3() != null && compareTrust(this, e) < 0
? p.getEcarticle29_3()
: ecarticle29_3;
subjects = mergeLists(subjects, p.getSubjects());
fundingtree = mergeLists(fundingtree, p.getFundingtree());
contracttype = p.getContracttype() != null && compareTrust(this, e) < 0
? p.getContracttype()
: contracttype;
optional1 = p.getOptional1() != null && compareTrust(this, e) < 0 ? p.getOptional1() : optional1;
optional2 = p.getOptional2() != null && compareTrust(this, e) < 0 ? p.getOptional2() : optional2;
jsonextrainfo = p.getJsonextrainfo() != null && compareTrust(this, e) < 0
? p.getJsonextrainfo()
: jsonextrainfo;
contactfullname = p.getContactfullname() != null && compareTrust(this, e) < 0
? p.getContactfullname()
: contactfullname;
contactfax = p.getContactfax() != null && compareTrust(this, e) < 0 ? p.getContactfax() : contactfax;
contactphone = p.getContactphone() != null && compareTrust(this, e) < 0
? p.getContactphone()
: contactphone;
contactemail = p.getContactemail() != null && compareTrust(this, e) < 0
? p.getContactemail()
: contactemail;
summary = p.getSummary() != null && compareTrust(this, e) < 0 ? p.getSummary() : summary;
currency = p.getCurrency() != null && compareTrust(this, e) < 0 ? p.getCurrency() : currency;
if (p.getH2020topiccode() != null && StringUtils.isEmpty(h2020topiccode)){
h2020topiccode = p.getH2020topiccode();
h2020topicdescription = p.getH2020topicdescription();
}
h2020classification = mergeLists(h2020classification, p.getH2020classification());
mergeOAFDataInfo(e);
}
} }

26
src/main/java/eu/dnetlib/dhp/schema/oaf/Provenance.java Normal file
View File

@ -0,0 +1,26 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
public class Provenance implements Serializable {
private KeyValue collectedfrom;
private DataInfo dataInfo;
public KeyValue getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(KeyValue collectedfrom) {
this.collectedfrom = collectedfrom;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
}

29
src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java
View File

@ -3,37 +3,10 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Publication extends Result implements Serializable { public class Publication extends Result implements Serializable {
// publication specific
private Journal journal;
public Publication() { public Publication() {
setResulttype(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE); setResulttype(RESULTTYPE.publication);
} }
public Journal getJournal() {
return journal;
}
public void setJournal(Journal journal) {
this.journal = journal;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Publication.class.isAssignableFrom(e.getClass())) {
return;
}
Publication p = (Publication) e;
if (p.getJournal() != null && compareTrust(this, e) < 0)
journal = p.getJournal();
mergeOAFDataInfo(e);
}
} }

23
src/main/java/eu/dnetlib/dhp/schema/oaf/Publisher.java Normal file
View File

@ -0,0 +1,23 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
public class Publisher implements Serializable {
private String name;
public Publisher() {
}
public Publisher(String name) {
this.name = name;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
}

33
src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java
View File

@ -2,17 +2,18 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonIgnore;
import com.google.common.base.Joiner;
public class Qualifier implements Serializable { public class Qualifier implements Serializable {
private String classid; private String classid;
private String classname; private String classname;
private String schemeid; private String schemeid;
private String schemename;
public String getClassid() { public String getClassid() {
return classid; return classid;
@ -38,32 +39,12 @@ public class Qualifier implements Serializable {
this.schemeid = schemeid; this.schemeid = schemeid;
} }
public String getSchemename() {
return schemename;
}
public void setSchemename(String schemename) {
this.schemename = schemename;
}
public String toComparableString() { public String toComparableString() {
return isBlank() return Joiner
? "" .on("::")
: String .join(
.format( Stream.of(getClassid(), getClassname(), getSchemeid())
"%s::%s::%s::%s", .filter(StringUtils::isNotBlank).iterator());
classid != null ? classid : "",
classname != null ? classname : "",
schemeid != null ? schemeid : "",
schemename != null ? schemename : "");
}
@JsonIgnore
public boolean isBlank() {
return StringUtils.isBlank(classid)
&& StringUtils.isBlank(classname)
&& StringUtils.isBlank(schemeid)
&& StringUtils.isBlank(schemename);
} }
@Override @Override

537
src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java
View File

@ -1,168 +1,451 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import static com.google.common.base.Preconditions.checkArgument; import java.beans.Transient;
import java.io.Serializable;
import java.text.ParseException; import java.util.*;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import eu.dnetlib.dhp.schema.common.ModelSupport;
/** /**
* Relation models any edge between two nodes in the OpenAIRE graph. It has a source id and a target id pointing to * Relation models any edge between two nodes in the OpenAIRE graph. It has a source id and a target id pointing to
* graph node identifiers and it is further characterised by the semantic of the link through the fields relType, * graph node identifiers, and it is further characterised by the semantic of the link through the fields relType,
* subRelType and relClass. Provenance information is modeled according to the dataInfo element and collectedFrom, while * subRelType and relClass. Provenance information is modeled according to the dataInfo element and collectedFrom, while
* individual relationship types can provide extra information via the properties field. * individual relationship types can provide extra information via the properties field.
*/ */
public class Relation extends Oaf { public class Relation extends Oaf implements Serializable {
/**
* Main relationship classifier, values include 'resultResult', 'resultProject', 'resultOrganization', etc.
*/
private String relType;
/** public enum RELTYPE {
* Further classifies a relationship, values include 'affiliation', 'similarity', 'supplement', etc. resultResult,
*/ resultProject,
private String subRelType; resultOrganization,
projectOrganization,
datasourceOrganization,
organizationOrganization;
}
/** public enum SUBRELTYPE {
* Indicates the direction of the relationship, values include 'isSupplementTo', 'isSupplementedBy', 'merges, affiliation,
* 'isMergedIn'. citation,
*/ dedup,
private String relClass; outcome,
part,
participation,
provision,
relationship,
review,
similarity,
supplement,
version;
public static boolean exists(String subreltype) {
try {
SUBRELTYPE.valueOf(subreltype);
return true;
} catch (IllegalArgumentException | NullPointerException e) {
return false;
}
}
}
/** public enum RELCLASS {
* The source entity id. IsVersionOf,
*/ IsSourceOf,
private String source; isMergedIn,
IsIdenticalTo,
Documents,
IsAmongTopNSimilarDocuments,
IsSupplementedBy,
IsObsoletedBy,
Continues,
IsParentOf,
IsReferencedBy,
IsCitedBy,
Compiles,
IsPreviousVersionOf,
HasPart,
IsDocumentedBy,
HasAmongTopNSimilarDocuments,
isParticipant,
hasAuthorInstitution,
IsRelatedTo,
Requires,
Describes,
IsReviewedBy,
IsContinuedBy,
provides,
IsChildOf,
IsDescribedBy,
IsNewVersionOf,
IsPartOf,
HasVersion,
hasParticipant,
isAuthorInstitutionOf,
IsVariantFormOf,
isProducedBy,
IsMetadataFor,
HasAssociationWith,
Cites,
IsRequiredBy,
IsOriginalFormOf,
IsSupplementTo,
IsMetadataOf,
References,
IsCompiledBy,
isProvidedBy,
merges,
IsDerivedFrom,
Obsoletes,
Reviews,
isSimilarTo,
isDifferentFrom,
produces;
/** public static boolean exists(String relclass) {
* The target entity id. try {
*/ RELCLASS.valueOf(relclass);
private String target; return true;
} catch (IllegalArgumentException | NullPointerException e) {
return false;
}
}
@Transient
public SUBRELTYPE getSubRel() {
switch (this) {
case isParticipant:
case hasParticipant:
return SUBRELTYPE.participation;
case isAuthorInstitutionOf:
case hasAuthorInstitution:
return SUBRELTYPE.affiliation;
case isMergedIn:
case merges:
case isSimilarTo:
case isDifferentFrom:
return SUBRELTYPE.dedup;
case isProducedBy:
case produces:
return SUBRELTYPE.outcome;
case isProvidedBy:
case provides:
return SUBRELTYPE.provision;
case IsAmongTopNSimilarDocuments:
case HasAmongTopNSimilarDocuments:
return SUBRELTYPE.similarity;
case IsSupplementedBy:
case IsSupplementTo:
return SUBRELTYPE.supplement;
case IsPartOf:
case HasPart:
return SUBRELTYPE.part;
case IsCitedBy:
case Cites:
return SUBRELTYPE.citation;
case IsIdenticalTo:
case IsReferencedBy:
case References:
case IsContinuedBy:
case Continues:
case IsDocumentedBy:
case Documents:
case IsDerivedFrom:
case IsSourceOf:
case IsRelatedTo:
case IsCompiledBy:
case Compiles:
case IsDescribedBy:
case Describes:
case IsMetadataFor:
case IsMetadataOf:
case HasAssociationWith:
case IsRequiredBy:
case Requires:
case IsChildOf:
case IsParentOf:
return SUBRELTYPE.relationship;
case IsPreviousVersionOf:
case IsNewVersionOf:
case IsVariantFormOf:
case IsOriginalFormOf:
case IsObsoletedBy:
case Obsoletes:
case IsVersionOf:
case HasVersion:
return SUBRELTYPE.version;
case IsReviewedBy:
case Reviews:
return SUBRELTYPE.review;
}
// makes the compiler happy
throw new IllegalArgumentException("missing SubRel mapping for" + this);
}
/** /**
* Was this relationship authoritatively validated? * This mehtod is an implementation of the valueOF case insensitive
*/ * @param value the input Value
private Boolean validated; * @return the RELCLASS
*/
public static RELCLASS lookUp(String value) {
Optional<RELCLASS> rvlaue = Arrays.stream(RELCLASS.values()).filter(e -> e.name().equalsIgnoreCase(value)).findAny();
if (rvlaue.isPresent())
return rvlaue.get();
throw new IllegalArgumentException("value: "+value+" not found");
}
/** @Transient
* When was this relationship authoritatively validated. public RELCLASS getInverse() {
*/ switch (this) {
private String validationDate; case IsVersionOf:
return HasVersion;
case IsSourceOf:
return IsDerivedFrom;
case isMergedIn:
return merges;
case IsIdenticalTo:
return IsIdenticalTo;
case Documents:
return IsDocumentedBy;
case IsAmongTopNSimilarDocuments:
return HasAmongTopNSimilarDocuments;
case IsSupplementedBy:
return IsSupplementTo;
case IsObsoletedBy:
return Obsoletes;
case Continues:
return IsContinuedBy;
case IsParentOf:
return IsChildOf;
case IsReferencedBy:
return References;
case IsCitedBy:
return Cites;
case Compiles:
return IsCompiledBy;
case IsPreviousVersionOf:
return IsNewVersionOf;
case HasPart:
return IsPartOf;
case IsDocumentedBy:
return Documents;
case HasAmongTopNSimilarDocuments:
return IsAmongTopNSimilarDocuments;
case isParticipant:
return hasParticipant;
case hasAuthorInstitution:
return isAuthorInstitutionOf;
case IsRelatedTo:
return IsRelatedTo;
case Requires:
return IsRequiredBy;
case Describes:
return IsDescribedBy;
case IsReviewedBy:
return Reviews;
case IsContinuedBy:
return Continues;
case provides:
return isProvidedBy;
case IsChildOf:
return IsParentOf;
case IsDescribedBy:
return Describes;
case IsNewVersionOf:
return IsPreviousVersionOf;
case IsPartOf:
return HasPart;
case HasVersion:
return IsVersionOf;
case hasParticipant:
return isParticipant;
case isAuthorInstitutionOf:
return hasAuthorInstitution;
case IsVariantFormOf:
return IsOriginalFormOf;
case isProducedBy:
return produces;
case IsMetadataFor:
return IsMetadataOf;
case Cites:
return IsCitedBy;
case IsRequiredBy:
return Requires;
case IsOriginalFormOf:
return IsVariantFormOf;
case IsSupplementTo:
return IsSupplementedBy;
case IsMetadataOf:
return IsMetadataFor;
case References:
return IsReferencedBy;
case IsCompiledBy:
return Compiles;
case isProvidedBy:
return provides;
case merges:
return isMergedIn;
case IsDerivedFrom:
return IsSourceOf;
case Obsoletes:
return IsObsoletedBy;
case Reviews:
return IsReviewedBy;
case produces:
return isProducedBy;
case isSimilarTo:
return isSimilarTo;
case isDifferentFrom:
return isDifferentFrom;
}
// makes the compiler happy
throw new IllegalArgumentException("missing inverse mapping for" + this);
}
}
/** /**
* List of relation specific properties. Values include 'similarityLevel', indicating the similarity score between a * Main relationship classifier, values include 'resultResult', 'resultProject', 'resultOrganization', etc.
* pair of publications. */
*/ private RELTYPE relType;
private List<KeyValue> properties = new ArrayList<>();
public String getRelType() { /**
return relType; * Further classifies a relationship, values include 'affiliation', 'similarity', 'supplement', etc.
} */
private SUBRELTYPE subRelType;
public void setRelType(final String relType) { /**
this.relType = relType; * Indicates the direction of the relationship, values include 'isSupplementTo', 'isSupplementedBy', 'merges,
} * 'isMergedIn'.
*/
private RELCLASS relClass;
public String getSubRelType() { /**
return subRelType; * The source entity id.
} */
private String source;
public void setSubRelType(final String subRelType) { /**
this.subRelType = subRelType; * The target entity id.
} */
private String target;
public String getRelClass() { /**
return relClass; * Was this relationship authoritatively validated?
} */
private Boolean validated;
public void setRelClass(final String relClass) { /**
this.relClass = relClass; * When was this relationship authoritatively validated.
} */
private String validationDate;
public String getSource() { private List<Provenance> provenance;
return source;
}
public void setSource(final String source) { /**
this.source = source; * List of relation specific properties. Values include 'similarityLevel', indicating the similarity score between a
} * pair of publications.
*/
private List<KeyValue> properties = new ArrayList<>();
public String getTarget() { public RELTYPE getRelType() {
return target; return relType;
} }
public void setTarget(final String target) { public void setRelType(final RELTYPE relType) {
this.target = target; this.relType = relType;
} }
public List<KeyValue> getProperties() { public SUBRELTYPE getSubRelType() {
return properties; return subRelType;
} }
public void setProperties(List<KeyValue> properties) { public void setSubRelType(final SUBRELTYPE subRelType) {
this.properties = properties; this.subRelType = subRelType;
} }
public Boolean getValidated() { public RELCLASS getRelClass() {
return Objects.nonNull(validated) && validated; return relClass;
} }
public void setValidated(Boolean validated) { public void setRelClass(final RELCLASS relClass) {
this.validated = validated; this.relClass = relClass;
} }
public String getValidationDate() { public String getSource() {
return validationDate; return source;
} }
public void setValidationDate(String validationDate) { public void setSource(final String source) {
this.validationDate = validationDate; this.source = source;
} }
public void mergeFrom(final Relation r) { public String getTarget() {
return target;
}
checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal"); public void setTarget(final String target) {
checkArgument(Objects.equals(getTarget(), r.getTarget()), "target ids must be equal"); this.target = target;
checkArgument(Objects.equals(getRelType(), r.getRelType()), "relType(s) must be equal"); }
checkArgument(
Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal");
checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal");
setValidated(getValidated() || r.getValidated()); public List<KeyValue> getProperties() {
try { return properties;
setValidationDate(ModelSupport.oldest(getValidationDate(), r.getValidationDate())); }
} catch (ParseException e) {
throw new IllegalArgumentException(String
.format(
"invalid validation date format in relation [s:%s, t:%s]: %s", getSource(), getTarget(),
getValidationDate()));
}
super.mergeFrom(r); public void setProperties(List<KeyValue> properties) {
} this.properties = properties;
}
@Override public Boolean getValidated() {
public boolean equals(Object o) { return Objects.nonNull(validated) && validated;
if (this == o) }
return true;
if (o == null || getClass() != o.getClass())
return false;
Relation relation = (Relation) o;
return relType.equals(relation.relType)
&& subRelType.equals(relation.subRelType)
&& relClass.equals(relation.relClass)
&& source.equals(relation.source)
&& target.equals(relation.target);
}
@Override public void setValidated(Boolean validated) {
public int hashCode() { this.validated = validated;
return Objects.hash(relType, subRelType, relClass, source, target, collectedfrom); }
}
public String getValidationDate() {
return validationDate;
}
public void setValidationDate(String validationDate) {
this.validationDate = validationDate;
}
public List<Provenance> getProvenance() {
return provenance;
}
public void setProvenance(List<Provenance> provenance) {
this.provenance = provenance;
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
Relation relation = (Relation) o;
return relType.equals(relation.relType)
&& subRelType.equals(relation.subRelType)
&& relClass.equals(relation.relClass)
&& source.equals(relation.source)
&& target.equals(relation.target);
}
public Relation inverse() {
final Relation inverse = new Relation();
inverse.setSource(this.target);
inverse.setTarget(this.source);
inverse.setRelClass(this.relClass.getInverse());
inverse.setRelType(this.relType);
inverse.setSubRelType(this.subRelType);
inverse.setProperties(this.properties);
inverse.setValidated(validated);
inverse.setProvenance(provenance);
inverse.setValidationDate(validationDate);
return inverse;
}
@Override
public int hashCode() {
return Objects.hash(relType, subRelType, relClass, source, target, provenance);
}
} }

460
src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
View File

@ -2,38 +2,29 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.*; import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
/** /**
* The type Result. * The type Result.
*/ */
public class Result extends OafEntity implements Serializable { public class Result extends Entity implements Serializable {
public enum RESULTTYPE {
publication,
dataset,
software,
otherresearchproduct
}
/** /**
* ( article | book ) processing charges. * ( article | book ) processing charges.
*/ */
private String processingchargeamount;
private Field<String> processingchargeamount;
/** /**
* currency - alphabetic code describe in ISO-4217. * currency - alphabetic code describe in ISO-4217.
*/ */
private Field<String> processingchargecurrency; private String processingchargecurrency;
/**
* The Measures.
*/
private List<Measure> measures;
/** /**
* The Author. * The Author.
@ -41,15 +32,13 @@ public class Result extends OafEntity implements Serializable {
private List<Author> author; private List<Author> author;
/** /**
* The Resulttype. * The Resulttype. It allows subclassing results into publications | datasets | software | orp
*/ */
// resulttype allows subclassing results into publications | datasets | software private RESULTTYPE resulttype;
private Qualifier resulttype;
/** /**
* The Language. * The Language.
*/ */
// common fields
private Qualifier language; private Qualifier language;
/** /**
@ -75,42 +64,42 @@ public class Result extends OafEntity implements Serializable {
/** /**
* The Description. * The Description.
*/ */
private List<Field<String>> description; private List<String> description;
/** /**
* The Dateofacceptance. * The Dateofacceptance.
*/ */
private Field<String> dateofacceptance; private String dateofacceptance;
/** /**
* The Publisher. * The Publisher.
*/ */
private Field<String> publisher; private Publisher publisher;
/** /**
* The Embargoenddate. * The Embargoenddate.
*/ */
private Field<String> embargoenddate; private String embargoenddate;
/** /**
* The Source. * The Source.
*/ */
private List<Field<String>> source; private List<String> source;
/** /**
* The Fulltext. * The Fulltext.
*/ */
private List<Field<String>> fulltext; // remove candidate private List<String> fulltext;
/** /**
* The Format. * The Format.
*/ */
private List<Field<String>> format; private List<String> format;
/** /**
* The Contributor. * The Contributor.
*/ */
private List<Field<String>> contributor; private List<String> contributor;
/** /**
* The Resourcetype. * The Resourcetype.
@ -120,13 +109,15 @@ public class Result extends OafEntity implements Serializable {
/** /**
* The Coverage. * The Coverage.
*/ */
private List<Field<String>> coverage; private List<String> coverage;
/** /**
* The Bestaccessright. * The Bestaccessright.
*/ */
private Qualifier bestaccessright; private Qualifier bestaccessright;
private Journal journal;
/** /**
* The Context. * The Context.
*/ */
@ -147,37 +138,21 @@ public class Result extends OafEntity implements Serializable {
*/ */
private List<EoscIfGuidelines> eoscifguidelines; private List<EoscIfGuidelines> eoscifguidelines;
/** private OAIProvenance oaiprovenance;
* Gets measures.
*
* @return the measures
*/
public List<Measure> getMeasures() {
return measures;
}
/** public String getProcessingchargeamount() {
* Sets measures.
*
* @param measures the measures
*/
public void setMeasures(List<Measure> measures) {
this.measures = measures;
}
public Field<String> getProcessingchargeamount() {
return processingchargeamount; return processingchargeamount;
} }
public void setProcessingchargeamount(Field<String> processingchargeamount) { public void setProcessingchargeamount(String processingchargeamount) {
this.processingchargeamount = processingchargeamount; this.processingchargeamount = processingchargeamount;
} }
public Field<String> getProcessingchargecurrency() { public String getProcessingchargecurrency() {
return processingchargecurrency; return processingchargecurrency;
} }
public void setProcessingchargecurrency(Field<String> processingchargecurrency) { public void setProcessingchargecurrency(String processingchargecurrency) {
this.processingchargecurrency = processingchargecurrency; this.processingchargecurrency = processingchargecurrency;
} }
@ -204,7 +179,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @return the resulttype * @return the resulttype
*/ */
public Qualifier getResulttype() { public RESULTTYPE getResulttype() {
return resulttype; return resulttype;
} }
@ -213,7 +188,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @param resulttype the resulttype * @param resulttype the resulttype
*/ */
public void setResulttype(Qualifier resulttype) { public void setResulttype(RESULTTYPE resulttype) {
this.resulttype = resulttype; this.resulttype = resulttype;
} }
@ -312,7 +287,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @return the description * @return the description
*/ */
public List<Field<String>> getDescription() { public List<String> getDescription() {
return description; return description;
} }
@ -321,7 +296,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @param description the description * @param description the description
*/ */
public void setDescription(List<Field<String>> description) { public void setDescription(List<String> description) {
this.description = description; this.description = description;
} }
@ -330,7 +305,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @return the dateofacceptance * @return the dateofacceptance
*/ */
public Field<String> getDateofacceptance() { public String getDateofacceptance() {
return dateofacceptance; return dateofacceptance;
} }
@ -339,7 +314,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @param dateofacceptance the dateofacceptance * @param dateofacceptance the dateofacceptance
*/ */
public void setDateofacceptance(Field<String> dateofacceptance) { public void setDateofacceptance(String dateofacceptance) {
this.dateofacceptance = dateofacceptance; this.dateofacceptance = dateofacceptance;
} }
@ -348,7 +323,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @return the publisher * @return the publisher
*/ */
public Field<String> getPublisher() { public Publisher getPublisher() {
return publisher; return publisher;
} }
@ -357,7 +332,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @param publisher the publisher * @param publisher the publisher
*/ */
public void setPublisher(Field<String> publisher) { public void setPublisher(Publisher publisher) {
this.publisher = publisher; this.publisher = publisher;
} }
@ -366,7 +341,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @return the embargoenddate * @return the embargoenddate
*/ */
public Field<String> getEmbargoenddate() { public String getEmbargoenddate() {
return embargoenddate; return embargoenddate;
} }
@ -375,7 +350,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @param embargoenddate the embargoenddate * @param embargoenddate the embargoenddate
*/ */
public void setEmbargoenddate(Field<String> embargoenddate) { public void setEmbargoenddate(String embargoenddate) {
this.embargoenddate = embargoenddate; this.embargoenddate = embargoenddate;
} }
@ -384,7 +359,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @return the source * @return the source
*/ */
public List<Field<String>> getSource() { public List<String> getSource() {
return source; return source;
} }
@ -393,7 +368,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @param source the source * @param source the source
*/ */
public void setSource(List<Field<String>> source) { public void setSource(List<String> source) {
this.source = source; this.source = source;
} }
@ -402,7 +377,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @return the fulltext * @return the fulltext
*/ */
public List<Field<String>> getFulltext() { public List<String> getFulltext() {
return fulltext; return fulltext;
} }
@ -411,7 +386,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @param fulltext the fulltext * @param fulltext the fulltext
*/ */
public void setFulltext(List<Field<String>> fulltext) { public void setFulltext(List<String> fulltext) {
this.fulltext = fulltext; this.fulltext = fulltext;
} }
@ -420,7 +395,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @return the format * @return the format
*/ */
public List<Field<String>> getFormat() { public List<String> getFormat() {
return format; return format;
} }
@ -429,7 +404,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @param format the format * @param format the format
*/ */
public void setFormat(List<Field<String>> format) { public void setFormat(List<String> format) {
this.format = format; this.format = format;
} }
@ -438,7 +413,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @return the contributor * @return the contributor
*/ */
public List<Field<String>> getContributor() { public List<String> getContributor() {
return contributor; return contributor;
} }
@ -447,7 +422,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @param contributor the contributor * @param contributor the contributor
*/ */
public void setContributor(List<Field<String>> contributor) { public void setContributor(List<String> contributor) {
this.contributor = contributor; this.contributor = contributor;
} }
@ -474,7 +449,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @return the coverage * @return the coverage
*/ */
public List<Field<String>> getCoverage() { public List<String> getCoverage() {
return coverage; return coverage;
} }
@ -483,7 +458,7 @@ public class Result extends OafEntity implements Serializable {
* *
* @param coverage the coverage * @param coverage the coverage
*/ */
public void setCoverage(List<Field<String>> coverage) { public void setCoverage(List<String> coverage) {
this.coverage = coverage; this.coverage = coverage;
} }
@ -505,6 +480,14 @@ public class Result extends OafEntity implements Serializable {
this.bestaccessright = bestaccessright; this.bestaccessright = bestaccessright;
} }
public Journal getJournal() {
return journal;
}
public void setJournal(Journal journal) {
this.journal = journal;
}
/** /**
* Gets context. * Gets context.
* *
@ -567,332 +550,11 @@ public class Result extends OafEntity implements Serializable {
this.eoscifguidelines = eoscifguidelines; this.eoscifguidelines = eoscifguidelines;
} }
/** public OAIProvenance getOaiprovenance() {
* Is an enrichment boolean. return oaiprovenance;
*
* @param e the e
* @return the boolean
*/
public static boolean isAnEnrichment(OafEntity e) {
return e.getDataInfo()!= null &&
e.getDataInfo().getProvenanceaction()!= null
&& ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid());
} }
public void setOaiprovenance(OAIProvenance oaiprovenance) {
/** this.oaiprovenance = oaiprovenance;
* Normalize pid string.
*
* @param pid the pid
* @return the string
*/
private static String extractKeyFromPid(final StructuredProperty pid) {
if (pid == null)
return null;
final StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid);
return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue());
}
/**
* Valid pid boolean.
*
* @param p the p
* @return the boolean
*/
private static boolean validPid(final StructuredProperty p) {
return p.getValue()!= null && p.getQualifier()!= null && p.getQualifier().getClassid()!=null;
}
/**
* This method converts the list of instance enrichments
* into a Map where the key is the normalized identifier
* and the value is the instance itself
*
* @param ri the list of enrichment instances
* @return the result map
*/
public static Map<String, Instance> toInstanceMap(final List<Instance> ri) {
return ri
.stream()
.filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null)
.flatMap(i -> {
final List<Pair<String, Instance>> result = new ArrayList<>();
if (i.getPid() != null)
i.getPid().stream().filter(Result::validPid).forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
if (i.getAlternateIdentifier() != null)
i.getAlternateIdentifier().stream().filter(Result::validPid).forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
return result.stream();
}).collect(Collectors.toMap(
Pair::getLeft,
Pair::getRight,
(a, b) -> a
));
}
/**
* This utility method finds the list of enrichment instances
* that match one or more PIDs in the input list
*
* @param pids the list of PIDs
* @param enrichments the List of enrichment instances having the same pid
* @return the list
*/
private static List<Instance> findEnrichmentsByPID(final List<StructuredProperty> pids, final Map<String,Instance> enrichments) {
if (pids == null || enrichments == null)
return null;
return pids
.stream()
.map(Result::extractKeyFromPid)
.map(enrichments::get)
.filter(Objects::nonNull)
.collect(Collectors.toList());
}
/**
* This method apply enrichment on a single instance
* The enrichment consists of replacing values on
* single attribute only if in the current instance is missing
* The only repeatable field enriched is measures
*
* @param currentInstance the current instance
* @param enrichment the enrichment instance
*/
private static void applyEnrichment(final Instance currentInstance, final Instance enrichment) {
if (currentInstance == null || enrichment == null)
return;
//ENRICH accessright
if (enrichment.getAccessright()!=null && currentInstance.getAccessright() == null)
currentInstance.setAccessright(enrichment.getAccessright());
//ENRICH license
if (enrichment.getLicense()!=null && currentInstance.getLicense() == null)
currentInstance.setLicense(enrichment.getLicense());
//ENRICH instanceType
if (enrichment.getInstancetype()!=null && currentInstance.getInstancetype() == null)
currentInstance.setInstancetype(enrichment.getInstancetype());
//ENRICH hostedby
if (enrichment.getHostedby()!=null && currentInstance.getHostedby() == null)
currentInstance.setHostedby(enrichment.getHostedby());
//ENRICH distributionlocation
if (enrichment.getDistributionlocation()!=null && currentInstance.getDistributionlocation() == null)
currentInstance.setDistributionlocation(enrichment.getDistributionlocation());
//ENRICH collectedfrom
if (enrichment.getCollectedfrom()!=null && currentInstance.getCollectedfrom() == null)
currentInstance.setCollectedfrom(enrichment.getCollectedfrom());
//ENRICH dateofacceptance
if (enrichment.getDateofacceptance()!=null && currentInstance.getDateofacceptance() == null)
currentInstance.setDateofacceptance(enrichment.getDateofacceptance());
//ENRICH processingchargeamount
if (enrichment.getProcessingchargeamount()!=null && currentInstance.getProcessingchargeamount() == null)
currentInstance.setProcessingchargeamount(enrichment.getProcessingchargeamount());
//ENRICH refereed
if (enrichment.getRefereed()!=null && currentInstance.getRefereed() == null)
currentInstance.setRefereed(enrichment.getRefereed());
//ENRICH measures
if (enrichment.getMeasures()!=null)
if (currentInstance.getMeasures() == null)
currentInstance.setMeasures(enrichment.getMeasures());
else
enrichment.getMeasures().forEach(currentInstance.getMeasures()::add);
}
/**
* This main method apply the enrichment of the instances
*
* @param toEnrichInstances the instances that could be enriched
* @param enrichmentInstances the enrichment instances
* @return list of instances possibly enriched
*/
private static List<Instance> enrichInstances(final List<Instance> toEnrichInstances,final List<Instance> enrichmentInstances) {
final List<Instance> enrichmentResult = new ArrayList<>();
if (toEnrichInstances == null) {
return enrichmentResult;
}
if (enrichmentInstances == null) {
return enrichmentResult;
}
Map<String, Instance> ri = toInstanceMap(enrichmentInstances);
toEnrichInstances.forEach(i -> {
final List<Instance> e = findEnrichmentsByPID(i.getPid(), ri);
if (e!= null && e.size()> 0) {
e.forEach(enr -> applyEnrichment(i, enr));
} else {
final List<Instance> a = findEnrichmentsByPID(i.getAlternateIdentifier(), ri);
if (a!= null && a.size()> 0) {
a.forEach(enr -> applyEnrichment(i, enr));
}
}
enrichmentResult.add(i);
});
return enrichmentResult;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Result.class.isAssignableFrom(e.getClass())) {
return;
}
Result r = (Result) e;
if(processingchargeamount == null || StringUtils.isBlank(processingchargeamount.getValue() )){
processingchargeamount = r.getProcessingchargeamount();
processingchargecurrency = r.getProcessingchargecurrency();
}
measures = mergeLists(measures, r.getMeasures());
eoscifguidelines = mergeLists(eoscifguidelines, r.getEoscifguidelines());
if( !isAnEnrichment(this) && !isAnEnrichment(e))
instance = mergeLists(instance, r.getInstance());
else {
final List<Instance> enrichmentInstances = isAnEnrichment(this) ? instance : r.getInstance();
final List<Instance> enrichedInstances= isAnEnrichment(this) ? r.getInstance(): instance;
if (isAnEnrichment(this))
setDataInfo(e.getDataInfo());
instance = enrichInstances(enrichedInstances,enrichmentInstances);
}
if (r.getBestaccessright() != null
&& new AccessRightComparator().compare(r.getBestaccessright(), bestaccessright) < 0)
bestaccessright = r.getBestaccessright();
if (r.getResulttype() != null && compareTrust(this, r) < 0)
resulttype = r.getResulttype();
if (r.getLanguage() != null && compareTrust(this, r) < 0)
language = r.getLanguage();
if (Objects.nonNull(r.getDateofacceptance())) {
if (Objects.isNull(getDateofacceptance())) {
dateofacceptance = r.getDateofacceptance();
} else if (compareTrust(this, r) < 0) {
dateofacceptance = r.getDateofacceptance();
}
}
country = mergeLists(country, r.getCountry());
subject = mergeLists(subject, r.getSubject());
// merge title lists: main title with higher trust and distinct between the others
StructuredProperty baseMainTitle = null;
if (title != null) {
baseMainTitle = getMainTitle(title);
if (baseMainTitle != null) {
final StructuredProperty p = baseMainTitle;
title = title.stream().filter(t -> t != p).collect(Collectors.toList());
}
}
StructuredProperty newMainTitle = null;
if (r.getTitle() != null) {
newMainTitle = getMainTitle(r.getTitle());
if (newMainTitle != null) {
final StructuredProperty p = newMainTitle;
r.setTitle(r.getTitle().stream().filter(t -> t != p).collect(Collectors.toList()));
}
}
if (newMainTitle != null && compareTrust(this, r) < 0) {
baseMainTitle = newMainTitle;
}
title = mergeLists(title, r.getTitle());
if (title != null && baseMainTitle != null) {
title.add(baseMainTitle);
}
relevantdate = mergeLists(relevantdate, r.getRelevantdate());
description = longestLists(description, r.getDescription());
if (r.getPublisher() != null && compareTrust(this, r) < 0)
publisher = r.getPublisher();
if (r.getEmbargoenddate() != null && compareTrust(this, r) < 0)
embargoenddate = r.getEmbargoenddate();
source = mergeLists(source, r.getSource());
fulltext = mergeLists(fulltext, r.getFulltext());
format = mergeLists(format, r.getFormat());
contributor = mergeLists(contributor, r.getContributor());
if (r.getResourcetype() != null)
resourcetype = r.getResourcetype();
coverage = mergeLists(coverage, r.getCoverage());
context = mergeLists(context, r.getContext());
externalReference = mergeLists(externalReference, r.getExternalReference());
}
/**
* Longest lists list.
*
* @param a the a
* @param b the b
* @return the list
*/
private List<Field<String>> longestLists(List<Field<String>> a, List<Field<String>> b) {
if (a == null || b == null)
return a == null ? b : a;
if (a.size() == b.size()) {
int msa = a
.stream()
.filter(i -> i != null && i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
int msb = b
.stream()
.filter(i -> i != null && i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
return msa > msb ? a : b;
}
return a.size() > b.size() ? a : b;
}
/**
* Gets main title.
*
* @param titles the titles
* @return the main title
*/
private StructuredProperty getMainTitle(List<StructuredProperty> 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 t : titles) {
if (t.getQualifier() != null && t.getQualifier().getClassid() != null)
if (t.getQualifier().getClassid().equals("main title"))
return t;
}
return null;
} }
} }

51
src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java
View File

@ -4,45 +4,32 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Software extends Result implements Serializable { public class Software extends Result implements Serializable {
private List<Field<String>> documentationUrl; private List<String> documentationUrl;
// candidate for removal // candidate for removal
private List<StructuredProperty> license; private String codeRepositoryUrl;
// candidate for removal
private Field<String> codeRepositoryUrl;
private Qualifier programmingLanguage; private Qualifier programmingLanguage;
public Software() { public Software() {
setResulttype(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE); setResulttype(RESULTTYPE.software);
} }
public List<Field<String>> getDocumentationUrl() { public List<String> getDocumentationUrl() {
return documentationUrl; return documentationUrl;
} }
public void setDocumentationUrl(List<Field<String>> documentationUrl) { public void setDocumentationUrl(List<String> documentationUrl) {
this.documentationUrl = documentationUrl; this.documentationUrl = documentationUrl;
} }
public List<StructuredProperty> getLicense() { public String getCodeRepositoryUrl() {
return license;
}
public void setLicense(List<StructuredProperty> license) {
this.license = license;
}
public Field<String> getCodeRepositoryUrl() {
return codeRepositoryUrl; return codeRepositoryUrl;
} }
public void setCodeRepositoryUrl(Field<String> codeRepositoryUrl) { public void setCodeRepositoryUrl(String codeRepositoryUrl) {
this.codeRepositoryUrl = codeRepositoryUrl; this.codeRepositoryUrl = codeRepositoryUrl;
} }
@ -53,28 +40,4 @@ public class Software extends Result implements Serializable {
public void setProgrammingLanguage(Qualifier programmingLanguage) { public void setProgrammingLanguage(Qualifier programmingLanguage) {
this.programmingLanguage = programmingLanguage; this.programmingLanguage = programmingLanguage;
} }
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Software.class.isAssignableFrom(e.getClass())) {
return;
}
final Software s = (Software) e;
documentationUrl = mergeLists(documentationUrl, s.getDocumentationUrl());
license = mergeLists(license, s.getLicense());
codeRepositoryUrl = s.getCodeRepositoryUrl() != null && compareTrust(this, s) < 0
? s.getCodeRepositoryUrl()
: codeRepositoryUrl;
programmingLanguage = s.getProgrammingLanguage() != null && compareTrust(this, s) < 0
? s.getProgrammingLanguage()
: programmingLanguage;
mergeOAFDataInfo(e);
}
} }

12
src/main/java/eu/dnetlib/dhp/schema/oaf/StructuredProperty.java
View File

@ -14,8 +14,6 @@ public class StructuredProperty implements Serializable {
private Qualifier qualifier; private Qualifier qualifier;
private DataInfo dataInfo;
public String getValue() { public String getValue() {
return value; return value;
} }
@ -32,18 +30,10 @@ public class StructuredProperty implements Serializable {
this.qualifier = qualifier; this.qualifier = qualifier;
} }
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public String toComparableString() { public String toComparableString() {
return Stream return Stream
.of( .of(
getQualifier().toComparableString(), Optional.ofNullable(getQualifier()).map(q -> q.toComparableString()).orElse(""),
Optional.ofNullable(getValue()).map(String::toLowerCase).orElse("")) Optional.ofNullable(getValue()).map(String::toLowerCase).orElse(""))
.filter(StringUtils::isNotBlank) .filter(StringUtils::isNotBlank)
.collect(Collectors.joining("||")); .collect(Collectors.joining("||"));

10
src/main/java/eu/dnetlib/dhp/schema/oaf/Subject.java
View File

@ -3,4 +3,14 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
public class Subject extends StructuredProperty implements Serializable { public class Subject extends StructuredProperty implements Serializable {
private DataInfo dataInfo;
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
} }

74
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java
View File

@ -1,74 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.HashSet;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class CleaningFunctions {
public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10\\.)";
public static final String DOI_PREFIX = "10.";
public static final Set<String> PID_BLACKLIST = new HashSet<>();
static {
PID_BLACKLIST.add("none");
PID_BLACKLIST.add("na");
}
public CleaningFunctions() {}
/**
* Utility method that filter PID values on a per-type basis.
* @param s the PID whose value will be checked.
* @return false if the pid matches the filter criteria, true otherwise.
*/
public static boolean pidFilter(StructuredProperty s) {
final String pidValue = s.getValue();
if (Objects.isNull(s.getQualifier()) ||
StringUtils.isBlank(pidValue) ||
StringUtils.isBlank(pidValue.replaceAll("(?:\\n|\\r|\\t|\\s)", ""))) {
return false;
}
if (CleaningFunctions.PID_BLACKLIST.contains(pidValue)) {
return false;
}
return !PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue);
}
/**
* Utility method that normalises PID values on a per-type basis.
* @param pid the PID whose value will be normalised.
* @return the PID containing the normalised value.
*/
public static StructuredProperty normalizePidValue(StructuredProperty pid) {
pid.setValue(
normalizePidValue(
pid.getQualifier().getClassid(),
pid.getValue()));
return pid;
}
public static String normalizePidValue(String pidType, String pidValue) {
String value = Optional
.ofNullable(pidValue)
.map(String::trim)
.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
switch (pidType) {
// TODO add cleaning for more PID types as needed
case "doi":
return value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX);
}
return value;
}
}

292
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java
View File

@ -1,292 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static com.google.common.base.Preconditions.checkArgument;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.util.*;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.HashBiMap;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
/**
* Factory class for OpenAIRE identifiers in the Graph
*/
public class IdentifierFactory implements Serializable {
public static final String ID_SEPARATOR = "::";
public static final String ID_PREFIX_SEPARATOR = "|";
public static final int ID_PREFIX_LEN = 12;
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] considered authoritative for that PID_TYPE.
* The id of the record (source_::id) will be rewritten as pidType_::id)
*/
public static final Map<PidType, HashBiMap<String, String>> PID_AUTHORITY = Maps.newHashMap();
static {
PID_AUTHORITY.put(PidType.doi, HashBiMap.create());
PID_AUTHORITY.get(PidType.doi).put(CROSSREF_ID, "Crossref");
PID_AUTHORITY.get(PidType.doi).put(DATACITE_ID, "Datacite");
PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "ZENODO");
PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "Zenodo");
PID_AUTHORITY.put(PidType.pmc, HashBiMap.create());
PID_AUTHORITY.get(PidType.pmc).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
PID_AUTHORITY.get(PidType.pmc).put(PUBMED_CENTRAL_ID, "PubMed Central");
PID_AUTHORITY.put(PidType.pmid, HashBiMap.create());
PID_AUTHORITY.get(PidType.pmid).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
PID_AUTHORITY.get(PidType.pmid).put(PUBMED_CENTRAL_ID, "PubMed Central");
PID_AUTHORITY.put(PidType.arXiv, HashBiMap.create());
PID_AUTHORITY.get(PidType.arXiv).put(ARXIV_ID, "arXiv.org e-Print Archive");
PID_AUTHORITY.put(PidType.w3id, HashBiMap.create());
PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ROHub");
}
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, PID SUBSTRING] considered as delegated authority for that
* PID_TYPE. Example, Zenodo is delegated to forge DOIs that contain the 'zenodo' word.
*
* If a record with the same id (same pid) comes from 2 data sources, the one coming from a delegated source wins. E.g. Zenodo records win over those from Datacite.
* See also https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/187 and the class dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
*/
public static final Map<PidType, Map<String, String>> DELEGATED_PID_AUTHORITY = Maps.newHashMap();
static {
DELEGATED_PID_AUTHORITY.put(PidType.doi, new HashMap<>());
DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "zenodo");
DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "zenodo");
DELEGATED_PID_AUTHORITY.put(PidType.w3id, new HashMap<>());
DELEGATED_PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ro-id");
}
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] whose records are considered enrichment for the graph.
* Their OpenAIRE ID is built from the declared PID type. Are merged with their corresponding record, identified by
* the same OpenAIRE id.
*/
public static final Map<PidType, HashBiMap<String, String>> ENRICHMENT_PROVIDER = Maps.newHashMap();
static {
ENRICHMENT_PROVIDER.put(PidType.doi, HashBiMap.create());
ENRICHMENT_PROVIDER.get(PidType.doi).put(OPEN_APC_ID, OPEN_APC_NAME);
}
public static Set<String> delegatedAuthorityDatasourceIds() {
return DELEGATED_PID_AUTHORITY.values()
.stream()
.flatMap(m -> m.keySet().stream())
.collect(Collectors.toCollection(HashSet::new));
}
public static List<StructuredProperty> getPids(List<StructuredProperty> pid, KeyValue collectedFrom) {
return pidFromInstance(pid, collectedFrom, true).distinct().collect(Collectors.toList());
}
public static <T extends Result> String createDOIBoostIdentifier(T entity) {
if (entity == null)
return null;
StructuredProperty pid = null;
if (entity.getPid() != null) {
pid = entity
.getPid()
.stream()
.filter(Objects::nonNull)
.filter(s -> s.getQualifier() != null && "doi".equalsIgnoreCase(s.getQualifier().getClassid()))
.filter(CleaningFunctions::pidFilter)
.findAny()
.orElse(null);
} else {
if (entity.getInstance() != null) {
pid = entity
.getInstance()
.stream()
.filter(i -> i.getPid() != null)
.flatMap(i -> i.getPid().stream())
.filter(CleaningFunctions::pidFilter)
.findAny()
.orElse(null);
}
}
if (pid != null)
return idFromPid(entity, pid, true);
return null;
}
/**
* Creates an identifier from the most relevant PID (if available) provided by a known PID authority in the given
* entity T. Returns entity.id when none of the PIDs meet the selection criteria is available.
*
* @param entity the entity providing PIDs and a default ID.
* @param <T> the specific entity type. Currently Organization and Result subclasses are supported.
* @param md5 indicates whether should hash the PID value or not.
* @return an identifier from the most relevant PID, entity.id otherwise
*/
public static <T extends OafEntity> String createIdentifier(T entity, boolean md5) {
checkArgument(StringUtils.isNoneBlank(entity.getId()), "missing entity identifier");
final Map<String, Set<StructuredProperty>> pids = extractPids(entity);
return pids
.values()
.stream()
.flatMap(Set::stream)
.min(new PidComparator<>(entity))
.map(
min -> Optional
.ofNullable(pids.get(min.getQualifier().getClassid()))
.map(
p -> p
.stream()
.sorted(new PidValueComparator())
.findFirst()
.map(s -> idFromPid(entity, s, md5))
.orElseGet(entity::getId))
.orElseGet(entity::getId))
.orElseGet(entity::getId);
}
private static <T extends OafEntity> Map<String, Set<StructuredProperty>> extractPids(T entity) {
if (entity instanceof Result) {
return Optional
.ofNullable(((Result) entity).getInstance())
.map(IdentifierFactory::mapPids)
.orElse(new HashMap<>());
} else {
return entity
.getPid()
.stream()
.map(CleaningFunctions::normalizePidValue)
.filter(CleaningFunctions::pidFilter)
.collect(
Collectors
.groupingBy(
p -> p.getQualifier().getClassid(),
Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
}
}
private static Map<String, Set<StructuredProperty>> mapPids(List<Instance> instance) {
return instance
.stream()
.map(i -> pidFromInstance(i.getPid(), i.getCollectedfrom(), false))
.flatMap(Function.identity())
.collect(
Collectors
.groupingBy(
p -> p.getQualifier().getClassid(),
Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
}
private static Stream<StructuredProperty> pidFromInstance(List<StructuredProperty> pid, KeyValue collectedFrom,
boolean mapHandles) {
return Optional
.ofNullable(pid)
.map(
pp -> pp
.stream()
// filter away PIDs provided by a DS that is not considered an authority for the
// given PID Type
.filter(p -> shouldFilterPidByCriteria(collectedFrom, p, mapHandles))
.map(CleaningFunctions::normalizePidValue)
.filter(p -> isNotFromDelegatedAuthority(collectedFrom, p))
.filter(CleaningFunctions::pidFilter))
.orElse(Stream.empty());
}
private static boolean shouldFilterPidByCriteria(KeyValue collectedFrom, StructuredProperty p, boolean mapHandles) {
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
if (Objects.isNull(collectedFrom)) {
return false;
}
boolean isEnrich = Optional
.ofNullable(ENRICHMENT_PROVIDER.get(pType))
.map(enrich -> enrich.containsKey(collectedFrom.getKey())
|| enrich.containsValue(collectedFrom.getValue()))
.orElse(false);
boolean isAuthority = Optional
.ofNullable(PID_AUTHORITY.get(pType))
.map(authorities -> authorities.containsKey(collectedFrom.getKey())
|| authorities.containsValue(collectedFrom.getValue()))
.orElse(false);
return (mapHandles && pType.equals(PidType.handle)) || isEnrich || isAuthority;
}
private static boolean isNotFromDelegatedAuthority(KeyValue collectedFrom, StructuredProperty p) {
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
final Map<String, String> da = DELEGATED_PID_AUTHORITY.get(pType);
if (Objects.isNull(da)) {
return true;
}
if (!da.containsKey(collectedFrom.getKey())) {
return true;
}
return StringUtils.contains(p.getValue(), da.get(collectedFrom.getKey()));
}
/**
* @see {@link IdentifierFactory#createIdentifier(OafEntity, boolean)}
*/
public static <T extends OafEntity> String createIdentifier(T entity) {
return createIdentifier(entity, true);
}
private static <T extends OafEntity> String idFromPid(T entity, StructuredProperty s, boolean md5) {
return idFromPid(ModelSupport.getIdPrefix(entity.getClass()), s.getQualifier().getClassid(), s.getValue(), md5);
}
public static String idFromPid(String numericPrefix, String pidType, String pidValue, boolean md5) {
return new StringBuilder()
.append(numericPrefix)
.append(ID_PREFIX_SEPARATOR)
.append(createPrefix(pidType))
.append(ID_SEPARATOR)
.append(md5 ? md5(pidValue) : pidValue)
.toString();
}
// create the prefix (length = 12)
private static String createPrefix(String pidType) {
StringBuilder prefix = new StringBuilder(StringUtils.left(pidType, ID_PREFIX_LEN));
while (prefix.length() < ID_PREFIX_LEN) {
prefix.append("_");
}
return prefix.substring(0, ID_PREFIX_LEN);
}
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) {
return null;
}
}
}

24
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java
View File

@ -1,24 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
public class ModelHardLimits {
private ModelHardLimits() {}
public static final String LAYOUT = "index";
public static final String INTERPRETATION = "openaire";
public static final String SEPARATOR = "-";
public static final int MAX_EXTERNAL_ENTITIES = 50;
public static final int MAX_AUTHORS = 200;
public static final int MAX_AUTHOR_FULLNAME_LENGTH = 1000;
public static final int MAX_TITLE_LENGTH = 5000;
public static final int MAX_TITLES = 10;
public static final int MAX_ABSTRACT_LENGTH = 150000;
public static final int MAX_INSTANCES = 10;
public static String getCollectionName(String format) {
return format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
}
}

38
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OrganizationPidComparator.java
View File

@ -1,38 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class OrganizationPidComparator implements Comparator<StructuredProperty> {
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
if (lClass.equals(PidType.openorgs))
return -1;
if (rClass.equals(PidType.openorgs))
return 1;
if (lClass.equals(PidType.GRID))
return -1;
if (rClass.equals(PidType.GRID))
return 1;
if (lClass.equals(PidType.mag_id))
return -1;
if (rClass.equals(PidType.mag_id))
return 1;
if (lClass.equals(PidType.urn))
return -1;
if (rClass.equals(PidType.urn))
return 1;
return 0;
}
}

8
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklist.java
View File

@ -1,8 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.HashMap;
import java.util.HashSet;
public class PidBlacklist extends HashMap<String, HashSet<String>> {
}

39
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklistProvider.java
View File

@ -1,39 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.io.IOException;
import java.util.HashSet;
import java.util.Optional;
import java.util.Set;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class PidBlacklistProvider {
private static final PidBlacklist blacklist;
static {
try {
String json = IOUtils.toString(IdentifierFactory.class.getResourceAsStream("pid_blacklist.json"));
blacklist = new ObjectMapper().readValue(json, PidBlacklist.class);
} catch (IOException e) {
throw new RuntimeException(e);
}
}
public static PidBlacklist getBlacklist() {
return blacklist;
}
public static Set<String> getBlacklist(String pidType) {
return Optional
.ofNullable(getBlacklist().get(pidType))
.orElse(new HashSet<>());
}
private PidBlacklistProvider() {}
}

48
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidComparator.java
View File

@ -1,48 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class PidComparator<T extends OafEntity> implements Comparator<StructuredProperty> {
private final T entity;
public PidComparator(T entity) {
this.entity = entity;
}
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
if (ModelSupport.isSubClass(entity, Result.class)) {
return compareResultPids(left, right);
}
if (ModelSupport.isSubClass(entity, Organization.class)) {
return compareOrganizationtPids(left, right);
}
// Else (but unlikely), lexicographical ordering will do.
return left.getQualifier().getClassid().compareTo(right.getQualifier().getClassid());
}
private int compareResultPids(StructuredProperty left, StructuredProperty right) {
return new ResultPidComparator().compare(left, right);
}
private int compareOrganizationtPids(StructuredProperty left, StructuredProperty right) {
return new OrganizationPidComparator().compare(left, right);
}
}

79
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidType.java
View File

@ -1,79 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import org.apache.commons.lang3.EnumUtils;
public enum PidType {
/**
* The DOI syntax shall be made up of a DOI prefix and a DOI suffix separated by a forward slash.
*
* There is no defined limit on the length of the DOI name, or of the DOI prefix or DOI suffix.
*
* The DOI name is case-insensitive and can incorporate any printable characters from the legal graphic characters
* of Unicode. Further constraints on character use (e.g. use of language-specific alphanumeric characters) can be
* defined for an application by the ISO 26324 Registration Authority.
*
*
* DOI prefix: The DOI prefix shall be composed of a directory indicator followed by a registrant code.
* These two components shall be separated by a full stop (period). The directory indicator shall be "10" and
* distinguishes the entire set of character strings (prefix and suffix) as digital object identifiers within the
* resolution system.
*
* Registrant code: The second element of the DOI prefix shall be the registrant code. The registrant code is a
* unique string assigned to a registrant.
*
* DOI suffix: The DOI suffix shall consist of a character string of any length chosen by the registrant.
* Each suffix shall be unique to the prefix element that precedes it. The unique suffix can be a sequential number,
* or it might incorporate an identifier generated from or based on another system used by the registrant
* (e.g. ISAN, ISBN, ISRC, ISSN, ISTC, ISNI; in such cases, a preferred construction for such a suffix can be
* specified, as in Example 1).
*
* Source: https://www.doi.org/doi_handbook/2_Numbering.html#2.2
*/
doi,
/**
* PubMed Unique Identifier (PMID)
*
* This field is a 1-to-8 digit accession number with no leading zeros. It is present on all records and is the
* accession number for managing and disseminating records. PMIDs are not reused after records are deleted.
*
* Beginning in February 2012 PMIDs include extensions following a decimal point to account for article versions
* (e.g., 21804956.2). All citations are considered version 1 until replaced. The extended PMID is not displayed
* on the MEDLINE format.
*
* View the citation in abstract format in PubMed to access additional versions when available (see the article in
* the Jan-Feb 2012 NLM Technical Bulletin).
*
* Source: https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid
*/
pmid,
/**
* This field contains the unique identifier for the cited article in PubMed Central. The identifier begins with the
* prefix PMC.
*
* Source: https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmc
*/
pmc, handle, arXiv, nct, pdb, w3id,
// Organization
openorgs, corda, corda_h2020, GRID, mag_id, urn,
// Used by dedup
undefined, original;
public static boolean isValid(String type) {
return EnumUtils.isValidEnum(PidType.class, type);
}
public static PidType tryValueOf(String s) {
try {
return PidType.valueOf(s);
} catch (Exception e) {
return PidType.original;
}
}
}

33
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java
View File

@ -1,33 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import java.util.Optional;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class PidValueComparator implements Comparator<StructuredProperty> {
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
StructuredProperty l = CleaningFunctions.normalizePidValue(left);
StructuredProperty r = CleaningFunctions.normalizePidValue(right);
return Optional
.ofNullable(l.getValue())
.map(
lv -> Optional
.ofNullable(r.getValue())
.map(rv -> lv.compareTo(rv))
.orElse(-1))
.orElse(1);
}
}

53
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultPidComparator.java
View File

@ -1,53 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class ResultPidComparator implements Comparator<StructuredProperty> {
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
if (lClass.equals(PidType.doi))
return -1;
if (rClass.equals(PidType.doi))
return 1;
if (lClass.equals(PidType.pmid))
return -1;
if (rClass.equals(PidType.pmid))
return 1;
if (lClass.equals(PidType.pmc))
return -1;
if (rClass.equals(PidType.pmc))
return 1;
if (lClass.equals(PidType.handle))
return -1;
if (rClass.equals(PidType.handle))
return 1;
if (lClass.equals(PidType.arXiv))
return -1;
if (rClass.equals(PidType.arXiv))
return 1;
if (lClass.equals(PidType.nct))
return -1;
if (rClass.equals(PidType.nct))
return 1;
if (lClass.equals(PidType.pdb))
return -1;
if (rClass.equals(PidType.pdb))
return 1;
return 0;
}
}

77
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java
View File

@ -1,77 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Optional;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Result;
public class ResultTypeComparator implements Comparator<Result> {
@Override
public int compare(Result left, Result right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
HashSet<String> lCf = getCollectedFromIds(left);
HashSet<String> rCf = getCollectedFromIds(right);
if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
return -1;
}
if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
return 1;
}
String lClass = left.getResulttype().getClassid();
String rClass = right.getResulttype().getClassid();
if (lClass.equals(rClass))
return 0;
if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return 1;
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
protected HashSet<String> getCollectedFromIds(Result left) {
return Optional
.ofNullable(left.getCollectedfrom())
.map(
cf -> cf
.stream()
.map(KeyValue::getKey)
.collect(Collectors.toCollection(HashSet::new)))
.orElse(new HashSet<>());
}
}

100
src/main/java/eu/dnetlib/dhp/schema/sx/OafUtils.scala
View File

@ -1,100 +0,0 @@
package eu.dnetlib.dhp.schema.sx
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Field, KeyValue, Qualifier, StructuredProperty}
object OafUtils {
def generateKeyValue(key: String, value: String): KeyValue = {
val kv: KeyValue = new KeyValue()
kv.setKey(key)
kv.setValue(value)
kv.setDataInfo(generateDataInfo("0.9"))
kv
}
def generateDataInfo(trust: String = "0.9", invisible: Boolean = false): DataInfo = {
val di = new DataInfo
di.setDeletedbyinference(false)
di.setInferred(false)
di.setInvisible(invisible)
di.setTrust(trust)
di.setProvenanceaction(createQualifier(ModelConstants.SYSIMPORT_ACTIONSET, ModelConstants.DNET_PROVENANCE_ACTIONS))
di
}
def createQualifier(cls: String, sch: String): Qualifier = {
createQualifier(cls, cls, sch, sch)
}
def createQualifier(classId: String, className: String, schemeId: String, schemeName: String): Qualifier = {
val q: Qualifier = new Qualifier
q.setClassid(classId)
q.setClassname(className)
q.setSchemeid(schemeId)
q.setSchemename(schemeName)
q
}
def createAccessRight(classId: String, className: String, schemeId: String, schemeName: String): AccessRight = {
val accessRight: AccessRight = new AccessRight
accessRight.setClassid(classId)
accessRight.setClassname(className)
accessRight.setSchemeid(schemeId)
accessRight.setSchemename(schemeName)
accessRight
}
def asField[T](value: T): Field[T] = {
val tmp = new Field[T]
tmp.setValue(value)
tmp
}
def createSP(value: String, classId: String,className:String, schemeId: String, schemeName:String): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId,className, schemeId, schemeName))
sp.setValue(value)
sp
}
def createSP(value: String, classId: String,className:String, schemeId: String, schemeName:String, dataInfo: DataInfo): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId,className, schemeId, schemeName))
sp.setValue(value)
sp.setDataInfo(dataInfo)
sp
}
def createSP(value: String, classId: String, schemeId: String): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId, schemeId))
sp.setValue(value)
sp
}
def createSP(value: String, classId: String, schemeId: String, dataInfo: DataInfo): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId, schemeId))
sp.setValue(value)
sp.setDataInfo(dataInfo)
sp
}
}

5
src/main/resources/eu/dnetlib/dhp/schema/oaf/utils/pid_blacklist.json
View File

File diff suppressed because one or more lines are too long

7
src/test/java/eu/dnetlib/dhp/schema/action/AtomicActionTest.java
View File

@ -10,7 +10,6 @@ import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
/** @author claudio.atzori */ /** @author claudio.atzori */
@ -23,9 +22,9 @@ class AtomicActionTest {
Relation rel = new Relation(); Relation rel = new Relation();
rel.setSource("1"); rel.setSource("1");
rel.setTarget("2"); rel.setTarget("2");
rel.setRelType(ModelConstants.RESULT_RESULT); rel.setRelType(Relation.RELTYPE.resultResult);
rel.setSubRelType(ModelConstants.DEDUP); rel.setSubRelType(Relation.SUBRELTYPE.dedup);
rel.setRelClass(ModelConstants.MERGES); rel.setRelClass(Relation.RELCLASS.merges);
AtomicAction aa1 = new AtomicAction(Relation.class, rel); AtomicAction aa1 = new AtomicAction(Relation.class, rel);

53
src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java
View File

@ -1,53 +0,0 @@
package eu.dnetlib.dhp.schema.common;
import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
public class ModelSupportTest {
@Nested
class IsSubClass {
@Test
void shouldReturnFalseWhenSubClassDoesNotExtendSuperClass() {
// when
Boolean result = ModelSupport.isSubClass(Relation.class, OafEntity.class);
// then
assertFalse(result);
}
@Test
void shouldReturnTrueWhenSubClassExtendsSuperClass() {
// when
Boolean result = ModelSupport.isSubClass(Result.class, OafEntity.class);
// then
assertTrue(result);
}
}
@Nested
class InverseRelation {
@Test
void findRelations() throws IOException {
assertNotNull(ModelSupport.findRelation("isMetadataFor"));
assertNotNull(ModelSupport.findRelation("ismetadatafor"));
assertNotNull(ModelSupport.findRelation("ISMETADATAFOR"));
assertNotNull(ModelSupport.findRelation("isRelatedTo"));
}
}
}

5
src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java
View File

@ -39,7 +39,6 @@ class MeasureTest {
List<Measure> m = Lists.newArrayList(popularity, influence); List<Measure> m = Lists.newArrayList(popularity, influence);
String s = OBJECT_MAPPER.writeValueAsString(m); String s = OBJECT_MAPPER.writeValueAsString(m);
System.out.println(s);
List<Measure> mm = OBJECT_MAPPER.readValue(s, new TypeReference<List<Measure>>() { List<Measure> mm = OBJECT_MAPPER.readValue(s, new TypeReference<List<Measure>>() {
}); });
@ -47,8 +46,8 @@ class MeasureTest {
Assertions.assertNotNull(mm); Assertions.assertNotNull(mm);
} }
private KeyValue unit(String key, String value) { private MeasureUnit unit(String key, String value) {
KeyValue unit = new KeyValue(); MeasureUnit unit = new MeasureUnit();
unit.setKey(key); unit.setKey(key);
unit.setValue(value); unit.setValue(value);
return unit; return unit;

682
src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java
View File

@ -1,682 +0,0 @@
package eu.dnetlib.dhp.schema.oaf;
import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException;
import java.io.InputStream;
import java.time.format.DateTimeParseException;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
/**
* The type Merge test.
*/
class MergeTest {
/**
* The Oaf.
*/
OafEntity oaf;
/**
* Sets up.
*/
@BeforeEach
public void setUp() {
oaf = new Publication();
}
/**
* Merge lists test.
*/
@Test
@SuppressWarnings("unchecked")
void mergeListsTest() {
// string list merge test
List<String> a = Arrays.asList("a", "b", "c", "e");
List<String> b = Arrays.asList("a", "b", "c", "d");
List<String> c = null;
System.out.println("merge result 1 = " + oaf.mergeLists(a, b));
System.out.println("merge result 2 = " + oaf.mergeLists(a, c));
System.out.println("merge result 3 = " + oaf.mergeLists(c, c));
}
/**
* Merge publication collected from test.
*/
@Test
void mergePublicationCollectedFromTest() {
Publication a = publication();
Publication b = publication();
a.setCollectedfrom(Arrays.asList(setKV("a", "open"), setKV("b", "closed")));
b.setCollectedfrom(Arrays.asList(setKV("A", "open"), setKV("b", "Open")));
a.mergeFrom(b);
assertNotNull(a.getCollectedfrom());
assertEquals(3, a.getCollectedfrom().size());
}
/**
* Load resource result list.
*
* @param <T> the type parameter
* @param path the path
* @param clazz the clazz
* @return the list
* @throws Exception the exception
*/
private <T extends Result> List<Result> loadResourceResult(final String path, final Class<T> clazz ) throws Exception {
final ObjectMapper mapper = new ObjectMapper();
final InputStream str = Objects.requireNonNull(getClass().getResourceAsStream(path));
// LOAD test publications
return IOUtils.readLines(str).stream().map(s -> {
try {
return mapper.readValue(s, clazz);
} catch (IOException e) {
return null;
}
}).filter(Objects::nonNull).collect(Collectors.toList());
}
/**
* Apply to any test list result the same pid of the enrichment instance
*
* @param source the source
* @param enrichment the enrichment
* @param overrideAlternateIdentifier the override alternate identifier
*/
private void updatePidIntoPublicationInstance(final List<Result> source, final List<Result>enrichment, final boolean overrideAlternateIdentifier) {
for(int i = 0 ; i< source.size(); i++) {
final Result currentPub = source.get(i);
final Result currentEnrichment = enrichment.get(i);
final Instance currentInstance = Objects.requireNonNull(currentPub.getInstance()).get(0);
if (overrideAlternateIdentifier)
currentInstance.setAlternateIdentifier(Objects.requireNonNull(currentEnrichment.getInstance()).get(0).getPid());
else
currentInstance.setPid(Objects.requireNonNull(currentEnrichment.getInstance()).get(0).getPid());
}
}
private void applyAndVerifyEnrichment(final List<Result> l1, final List<Result> l2) {
// Apply Merge and verify that enrichments works
for(int i = 0 ; i< l1.size(); i++) {
final Result currentPub = l2.get(i);
final Result currentEnrichment = l1.get(i);
currentPub.mergeFrom(currentEnrichment);
assertEquals(1, currentPub.getInstance().size());
final Instance currentInstance = Objects.requireNonNull(currentPub.getInstance()).get(0);
assertNotNull(currentInstance.getMeasures());
assertNotNull(currentPub.getTitle());
assertFalse(Result.isAnEnrichment(currentPub));
}
}
/**
* Test the merge of the APC at the level of the result and the instance.
*
* @throws Exception the exception
*/
@Test
void testAPCMerge() throws Exception {
List<Result> publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publication_apc.json", Publication.class);
System.out.println(publications.size());
publications.forEach(p -> assertEquals(1, p.getInstance().size()));
publications.forEach(p -> assertTrue(p.getProcessingchargeamount() != null ));
publications.forEach(p -> assertTrue(p.getProcessingchargecurrency() != null ));
publications.forEach(p -> assertTrue(StringUtils.isNotBlank(p.getProcessingchargeamount().getValue() )));
publications.forEach(p -> assertTrue(StringUtils.isNotBlank(p.getProcessingchargecurrency().getValue() )));
publications.forEach(p -> p.getInstance().stream()
.forEach(i -> assertTrue(i.getProcessingchargeamount() != null)));
publications.forEach(p -> p.getInstance().stream()
.forEach(i -> assertTrue(i.getProcessingchargecurrency() != null)));
publications.forEach(p -> p.getInstance().stream()
.forEach(i -> assertTrue(StringUtils.isNotBlank(i.getProcessingchargeamount().getValue()))));
publications.forEach(p -> p.getInstance().stream()
.forEach(i -> assertTrue(StringUtils.isNotBlank(i.getProcessingchargecurrency().getValue()))));
Result p1 = publications.get(0);
Result p2 = publications.get(1);
p1.mergeFrom(p2);
assertEquals("1721.47", p1.getProcessingchargeamount().getValue());
assertEquals("EUR", p1.getProcessingchargecurrency().getValue());
assertEquals(2 , p1.getInstance().size());
p1.getInstance().stream().forEach(i -> assertTrue(i.getProcessingchargeamount() != null));
p1.getInstance().stream().forEach(i -> assertTrue(i.getProcessingchargecurrency() != null));
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargeamount().getValue().equals("2000.47"));
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargeamount().getValue().equals("1721.47"));
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargecurrency().getValue().equals("EUR"));
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargecurrency().getValue().equals("USD"));
System.out.println(new ObjectMapper().writeValueAsString(p1));
}
@Test
void testAPCMerge2() throws Exception {
List<Result> publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publication_apc2.json", Publication.class);
System.out.println(publications.size());
publications.forEach(p -> assertEquals(1, p.getInstance().size()));
assertTrue(publications.get(0).getProcessingchargeamount() != null );
assertTrue(publications.get(0).getProcessingchargecurrency() != null );
assertTrue(publications.get(1).getProcessingchargeamount() == null );
Result p1 = publications.get(1);
Result p2 = publications.get(0);
//merge visible record with OpenAPC
p1.mergeFrom(p2);
assertFalse(p1.getDataInfo().getInvisible());
assertEquals("1721.47", p1.getProcessingchargeamount().getValue());
assertEquals("EUR", p1.getProcessingchargecurrency().getValue());
assertEquals(2 , p1.getInstance().size());
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargeamount() != null);
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargecurrency() != null);
assertEquals("1721.47", p1.getInstance().stream().filter(i -> i.getProcessingchargeamount() != null)
.collect(Collectors.toList()).get(0).getProcessingchargeamount().getValue());
assertEquals("EUR", p1.getInstance().stream().filter(i -> i.getProcessingchargeamount() != null)
.collect(Collectors.toList()).get(0).getProcessingchargecurrency().getValue());
assertFalse(p1.getDataInfo().getInvisible());
System.out.println(new ObjectMapper().writeValueAsString(p1));
//merge OpenAPC with visible record
p2.mergeFrom(p1);
assertFalse(p2.getDataInfo().getInvisible());
assertEquals("1721.47", p2.getProcessingchargeamount().getValue());
assertEquals("EUR", p2.getProcessingchargecurrency().getValue());
assertEquals(2 , p2.getInstance().size());
p2.getInstance().stream().anyMatch(i -> i.getProcessingchargeamount() != null);
p2.getInstance().stream().anyMatch(i -> i.getProcessingchargecurrency() != null);
assertEquals("1721.47", p2.getInstance().stream().filter(i -> i.getProcessingchargeamount() != null)
.collect(Collectors.toList()).get(0).getProcessingchargeamount().getValue());
assertEquals("EUR", p2.getInstance().stream().filter(i -> i.getProcessingchargeamount() != null)
.collect(Collectors.toList()).get(0).getProcessingchargecurrency().getValue());
}
/**
* Test enrichment function.
*
* @throws Exception the exception
*/
@Test
void testEnrichment() throws Exception {
// 1 TEST UPDATING PID INSTANCE AND MERGE CURRENT PUBLICATION WITH ENRICHMENT
// LOAD test publications
List<Result> publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publications.json", Publication.class);
// Assert that each publication has only one instance and inside that all the measure field is empty
publications.forEach(p -> {
assertEquals(1, p.getInstance().size());
final Instance currentInstance = Objects.requireNonNull(p.getInstance()).get(0);
assertNull(currentInstance.getMeasures());
});
// LOAD test enrichments
List<Result> enrichment = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json", Result.class);
updatePidIntoPublicationInstance(publications, enrichment, false);
applyAndVerifyEnrichment(publications, enrichment);
// 2 TEST UPDATING ALTERNATE ID INSTANCE AND MERGE CURRENT PUBLICATION WITH ENRICHMENT
publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publications.json", Publication.class);
enrichment = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json", Result.class);
updatePidIntoPublicationInstance(publications, enrichment, true);
applyAndVerifyEnrichment(publications, enrichment);
// 3 TEST UPDATING PID INSTANCE AND MERGE ENRICHMENT WITH CURRENT PUBLICATION
publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publications.json", Publication.class);
enrichment = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json", Result.class);
updatePidIntoPublicationInstance(publications, enrichment, false);
applyAndVerifyEnrichment( enrichment, publications);
// 4 TEST UPDATING ALTERNATE ID INSTANCE AND MERGE ENRICHMENT WITH CURRENT PUBLICATION
publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publications.json", Publication.class);
enrichment = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json", Result.class);
updatePidIntoPublicationInstance(publications, enrichment, true);
applyAndVerifyEnrichment( enrichment, publications);
}
/**
* Merge publication date of acceptance test both present.
*/
@Test
void mergePublicationDateOfAcceptanceTest_bothPresent() {
Publication a = publication();
Publication b = publication();
a.setDateofacceptance(field("2021-06-18"));
b.setDateofacceptance(field("2021-06-19"));
a.mergeFrom(b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-18", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test both present 1.
*/
@Test
void mergePublicationDateOfAcceptanceTest_bothPresent_1() {
Publication a = publication("0.8");
Publication b = publication("0.9");
a.setDateofacceptance(field("2021-06-18"));
b.setDateofacceptance(field("2021-06-19"));
a.mergeFrom(b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test both present 2.
*/
@Test
void mergePublicationDateOfAcceptanceTest_bothPresent_2() {
Publication a = publication("0.9");
Publication b = publication("0.8");
a.setDateofacceptance(field("2021-06-18"));
b.setDateofacceptance(field("2021-06-19"));
a.mergeFrom(b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-18", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test left missing.
*/
@Test
void mergePublicationDateOfAcceptanceTest_leftMissing() {
Publication a = publication();
Publication b = publication();
b.setDateofacceptance(field("2021-06-19"));
a.mergeFrom(b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test left missing 1.
*/
@Test
void mergePublicationDateOfAcceptanceTest_leftMissing_1() {
Publication a = publication("0.9");
Publication b = publication("0.8");
b.setDateofacceptance(field("2021-06-19"));
a.mergeFrom(b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test left missing 2.
*/
@Test
void mergePublicationDateOfAcceptanceTest_leftMissing_2() {
Publication a = publication("0.8");
Publication b = publication("0.9");
b.setDateofacceptance(field("2021-06-19"));
a.mergeFrom(b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test right missing.
*/
@Test
void mergePublicationDateOfAcceptanceTest_rightMissing() {
Publication a = publication();
Publication b = publication();
a.setDateofacceptance(field("2021-06-19"));
a.mergeFrom(b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test right missing 1.
*/
@Test
void mergePublicationDateOfAcceptanceTest_rightMissing_1() {
Publication a = publication("0.8");
Publication b = publication("0.9");
a.setDateofacceptance(field("2021-06-19"));
a.mergeFrom(b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test right missing 2.
*/
@Test
void mergePublicationDateOfAcceptanceTest_rightMissing_2() {
Publication a = publication("0.9");
Publication b = publication("0.8");
a.setDateofacceptance(field("2021-06-19"));
a.mergeFrom(b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication subject test.
*/
@Test
void mergePublicationSubjectTest() {
Publication a = publication();
Publication b = publication();
a.setSubject(Arrays.asList(setSub("a", "open", "classe"), setSub("b", "open", "classe")));
b.setSubject(Arrays.asList(setSub("A", "open", "classe"), setSub("c", "open", "classe")));
a.mergeFrom(b);
assertNotNull(a.getSubject());
assertEquals(3, a.getSubject().size());
}
/**
* Merge publication EoscIfGuidelines test.
*/
@Test
void mergePublicationEoscIfGuidelinesTest() {
Publication a = publication();
Publication b = publication();
a.setEoscifguidelines(Lists.newArrayList(eoscifg("a", "label a", "https://aaa.aa", "semRelA")));
b.setEoscifguidelines(Lists.newArrayList(eoscifg("a", "label a", "https://aaa.aa", "semRelA")));
a.mergeFrom(b);
assertNotNull(a.getEoscifguidelines());
assertEquals(1, a.getEoscifguidelines().size());
a.getEoscifguidelines().clear();
b.getEoscifguidelines().clear();
a.setEoscifguidelines(Lists.newArrayList(eoscifg("a", "label a", "https://aaa.aa", "semRelA")));
b.setEoscifguidelines(Lists.newArrayList(eoscifg("a", "label a", "https://aaa.aa", "semRelA")));
b.mergeFrom(a);
assertNotNull(a.getEoscifguidelines());
assertEquals(1, a.getEoscifguidelines().size());
EoscIfGuidelines e = b.getEoscifguidelines().get(0);
assertEquals("a", e.getCode());
assertEquals("label a", e.getLabel());
assertEquals("https://aaa.aa", e.getUrl());
assertEquals("semRelA", e.getSemanticRelation());
a.getEoscifguidelines().clear();
b.getEoscifguidelines().clear();
a.setEoscifguidelines(Lists.newArrayList(eoscifg("a", "label a", "https://aaa.aa", "semRelA")));
b.setEoscifguidelines(Lists.newArrayList(eoscifg("b", "label b", "https://bbb.bb", "semRelB")));
a.mergeFrom(b);
assertNotNull(a.getEoscifguidelines());
assertEquals(2, a.getEoscifguidelines().size());
}
private EoscIfGuidelines eoscifg(String code, String label, String url, String semrel) {
EoscIfGuidelines e = new EoscIfGuidelines();
e.setCode(code);
e.setLabel(label);
e.setUrl(url);
e.setSemanticRelation(semrel);
return e;
}
/**
* Merge relation test.
*/
@Test
void mergeRelationTest() {
Relation a = createRel(null, null);
Relation b = createRel(null, null);
a.mergeFrom(b);
assertEquals(a, b);
a = createRel(true, null);
b = createRel(null, null);
a.mergeFrom(b);
assertEquals(true, a.getValidated());
a = createRel(true, null);
b = createRel(false, null);
a.mergeFrom(b);
assertEquals(true, a.getValidated());
a = createRel(true, null);
b = createRel(true, "2016-04-05T12:41:19.202Z");
a.mergeFrom(b);
assertEquals("2016-04-05T12:41:19.202Z", a.getValidationDate());
a = createRel(true, "2016-05-07T12:41:19.202Z");
b = createRel(true, "2016-04-05T12:41:19.202Z");
a.mergeFrom(b);
assertEquals("2016-04-05T12:41:19.202Z", a.getValidationDate());
a = createRel(true, "2020-09-10 11:08:52");
b = createRel(true, "2021-09-10 11:08:52");
a.mergeFrom(b);
assertEquals("2020-09-10 11:08:52", a.getValidationDate());
a = createRel(true, "2021-03-16T10:32:42Z");
b = createRel(true, "2020-03-16T10:32:42Z");
a.mergeFrom(b);
assertEquals("2020-03-16T10:32:42Z", a.getValidationDate());
}
/**
* Merge relation test parse exception.
*/
@Test
void mergeRelationTestParseException() {
assertThrows(DateTimeParseException.class, () -> {
Relation a = createRel(true, "Once upon a time ...");
Relation b = createRel(true, "... in a far away land");
a.mergeFrom(b);
});
}
/**
* Create rel relation.
*
* @param validated the validated
* @param validationDate the validation date
* @return the relation
*/
private Relation createRel(Boolean validated, String validationDate) {
Relation rel = new Relation();
rel.setSource("1");
rel.setTarget("2");
rel.setRelType("reltype");
rel.setSubRelType("subreltype");
rel.setRelClass("relclass");
rel.setValidated(validated);
rel.setValidationDate(validationDate);
return rel;
}
/**
* Sets kv.
*
* @param key the key
* @param value the value
* @return the kv
*/
private KeyValue setKV(final String key, final String value) {
KeyValue k = new KeyValue();
k.setKey(key);
k.setValue(value);
return k;
}
private Subject setSub(final String value, final String schema, final String classname) {
Subject s = new Subject();
s.setValue(value);
Qualifier q = new Qualifier();
q.setClassname(classname);
q.setClassid(classname);
q.setSchemename(schema);
q.setSchemeid(schema);
s.setQualifier(q);
return s;
}
/**
* Sets sp.
*
* @param value the value
* @param schema the schema
* @param classname the classname
* @return the sp
*/
private StructuredProperty setSP(
final String value, final String schema, final String classname) {
StructuredProperty s = new StructuredProperty();
s.setValue(value);
Qualifier q = new Qualifier();
q.setClassname(classname);
q.setClassid(classname);
q.setSchemename(schema);
q.setSchemeid(schema);
s.setQualifier(q);
return s;
}
/**
* Field field.
*
* @param <T> the type parameter
* @param value the value
* @return the field
*/
private <T> Field<T> field(T value) {
Field<T> f = new Field();
f.setValue(value);
return f;
}
/**
* Publication publication.
*
* @return the publication
*/
private Publication publication() {
Publication p = new Publication();
p.setDataInfo(df("0.9"));
return p;
}
/**
* Publication publication.
*
* @param trust the trust
* @return the publication
*/
private Publication publication(String trust) {
Publication p = new Publication();
p.setDataInfo(df(trust));
return p;
}
/**
* Df data info.
*
* @param trust the trust
* @return the data info
*/
private DataInfo df(String trust) {
DataInfo d = new DataInfo();
d.setTrust(trust);
return d;
}
}

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src/test/java/eu/dnetlib/dhp/schema/oaf/RelationTest.java Normal file
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package eu.dnetlib.dhp.schema.oaf;
import static org.junit.jupiter.api.Assertions.*;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
public class RelationTest {
@Test
public void checkExistRelType() {
assertTrue(Relation.SUBRELTYPE.exists(Relation.SUBRELTYPE.dedup.toString()));
assertFalse(Relation.SUBRELTYPE.exists("foo"));
}
@Test
public void checkSubRelType() {
Relation.RELCLASS rc = Relation.RELCLASS.merges;
assertEquals(Relation.SUBRELTYPE.dedup, rc.getSubRel());
for (Relation.RELCLASS value : Relation.RELCLASS.values()) {
System.out.printf("%s => %s\n", value, value.getSubRel());
}
}
@Test
public void lookRelClassUpTest() {
Assertions.assertEquals(Relation.RELCLASS.Compiles, Relation.RELCLASS.lookUp("compiles"));
Assertions.assertEquals(Relation.RELCLASS.IsMetadataFor, Relation.RELCLASS.lookUp("isMetaDATAFOr"));
Assertions.assertThrows(IllegalArgumentException.class, () -> Relation.RELCLASS.lookUp("hello"));
}
}

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src/test/java/eu/dnetlib/dhp/schema/oaf/utils/BlackListProviderTest.java
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package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Set;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
class BlackListProviderTest {
@Test
void blackListTest() {
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist());
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist().get("doi"));
Assertions.assertTrue(PidBlacklistProvider.getBlacklist().get("doi").size() > 0);
final Set<String> xxx = PidBlacklistProvider.getBlacklist("xxx");
Assertions.assertNotNull(xxx);
Assertions.assertEquals(0, xxx.size());
}
}

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package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import java.io.IOException;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Publication;
class IdentifierFactoryTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@Test
void testCreateIdentifierForPublication() throws IOException {
verifyIdentifier(
"publication_doi1.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
verifyIdentifier(
"publication_doi2.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
verifyIdentifier(
"publication_doi3.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
verifyIdentifier(
"publication_doi4.json", "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66", true);
verifyIdentifier(
"publication_doi5.json", "50|doi_________::3bef95c0ca26dd55451fc8839ea69d27", true);
verifyIdentifier(
"publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true);
verifyIdentifier(
"publication_pmc2.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
verifyIdentifier(
"publication_openapc.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
verifyIdentifier("publication_3.json", defaultID, true);
verifyIdentifier("publication_4.json", defaultID, true);
verifyIdentifier("publication_5.json", defaultID, true);
}
@Test
void testCreateIdentifierForPublicationNoHash() throws IOException {
verifyIdentifier("publication_doi1.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
verifyIdentifier("publication_doi2.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
verifyIdentifier("publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
verifyIdentifier(
"publication_urn1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
verifyIdentifier("publication_3.json", defaultID, false);
verifyIdentifier("publication_4.json", defaultID, false);
verifyIdentifier("publication_5.json", defaultID, false);
}
@Test
void testCreateIdentifierForROHub() throws IOException {
verifyIdentifier(
"orp-rohub.json", "50|w3id________::afc7592914ae190a50570db90f55f9c2", true);
}
protected void verifyIdentifier(String filename, String expectedID, boolean md5) throws IOException {
final String json = IOUtils.toString(getClass().getResourceAsStream(filename));
final Publication pub = OBJECT_MAPPER.readValue(json, Publication.class);
String id = IdentifierFactory.createIdentifier(pub, md5);
System.out.println(id);
assertNotNull(id);
assertEquals(expectedID, id);
}
}

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{"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____::081b82f96300b6a6e3d282bad31cb6e2", "value" : "Crossref"} ]}

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src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/dataset_2.json
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"value": "10.1016/j.cmet.2010.03.013"
},
{
"qualifier": {"classid": "handle"},
"value": "11012/83840"
}
]
},
{
"collectedfrom": {
"key": "10|opendoar____::2852",
"value": "Digital library of Brno University of Technology"
},
"pid": [
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
},
{
"qualifier": {"classid": "handle"},
"value": "11012/83840"
}
]
}
]
}

37
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi5.json
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@ -1,37 +0,0 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.5281/zenodo.5121485"
}
]
},
{
"collectedfrom": {
"key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
"value": "Europe PubMed Central"
},
"pid": [
{
"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"
}
]
}
]
}

31
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_openapc.json
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@ -1,31 +0,0 @@
{
"id": "50|openapc_____::000023f9cb6e3a247c764daec4273cbc",
"resuttype": {
"classid": "publication"
},
"instance": [
{
"collectedfrom": {
"key": "10|apc_________::e2b1600b229fc30663c8a1f662debddf",
"value": "OpenAPC Global Initiative"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
},
{
"qualifier": {"classid": "pmid"},
"value": "25811027"
}
],
"url":["https://doi.org/10.1155/2015/439379"]
}
]
}

17
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc1.json
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@ -1,17 +0,0 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"pid": [
{
"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"
}
]
}

21
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json
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@ -1,21 +0,0 @@
{
"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
"value": "Europe PubMed Central"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
},
{
"qualifier":{"classid":"pmc"},
"value":"21459329"
}
]
}
]
}

23
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_urn1.json
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@ -1,23 +0,0 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"pid": [
{
"qualifier": {
"classid": "urn"
},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {
"classid": "scp-number"
},
"value": "79953761260"
},
{
"qualifier": {
"classid": "pmcid"
},
"value": "21459329"
}
]
}

12
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publications.json
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