master #11
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@ -50,6 +50,172 @@ public class ModelSupport {
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oafTypes.put("relation", Relation.class);
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oafTypes.put("relation", Relation.class);
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}
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}
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public static final Map<String, String> entityIdPrefix = Maps.newHashMap();
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static {
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entityIdPrefix.put("datasource", "10");
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entityIdPrefix.put("organization", "20");
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entityIdPrefix.put("project", "40");
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entityIdPrefix.put("result","50");
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}
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public static final Map<String, RelationInverse> relationInverseMap = Maps.newHashMap();
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static {
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relationInverseMap.put("personResult_authorship_isAuthorOf", new RelationInverse()
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.setRelation("isAuthorOf")
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.setInverse("hasAuthor")
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.setRelType("personResult")
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.setSubReltype("authorship"));
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relationInverseMap.put("personResult_authorship_hasAuthor", new RelationInverse()
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.setInverse("isAuthorOf")
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.setRelation("hasAuthor")
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.setRelType("personResult")
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.setSubReltype("authorship"));
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relationInverseMap.put("projectOrganization_participation_isParticipant", new RelationInverse()
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.setRelation("isParticipant")
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.setInverse("hasParticipant")
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.setRelType("projectOrganization")
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.setSubReltype("participation"));
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relationInverseMap.put("projectOrganization_participation_hasParticipant", new RelationInverse()
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.setInverse("isParticipant")
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.setRelation("hasParticipant")
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.setRelType("projectOrganization")
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.setSubReltype("participation"));
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relationInverseMap.put("resultOrganization_affiliation_hasAuthorInstitution", new RelationInverse()
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.setRelation("hasAuthorInstitution")
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.setInverse("isAuthorInstitutionOf")
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.setRelType("resultOrganization")
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.setSubReltype("affiliation"));
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relationInverseMap.put("resultOrganization_affiliation_isAuthorInstitutionOf", new RelationInverse()
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.setInverse("hasAuthorInstitution")
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.setRelation("isAuthorInstitutionOf")
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.setRelType("resultOrganization")
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.setSubReltype("affiliation"));
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relationInverseMap.put("organizationOrganization_dedup_merges", new RelationInverse()
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.setRelation("merges")
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.setInverse("isMergedIn")
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.setRelType("organizationOrganization")
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.setSubReltype("dedup"));
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relationInverseMap.put("organizationOrganization_dedup_isMergedIn", new RelationInverse()
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.setInverse("merges")
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.setRelation("isMergedIn")
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.setRelType("organizationOrganization")
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.setSubReltype("dedup"));
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relationInverseMap.put("organizationOrganization_dedupSimilarity_isSimilarTo", new RelationInverse()
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.setInverse("isSimilarTo")
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.setRelation("isSimilarTo")
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.setRelType("organizationOrganization")
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.setSubReltype("dedupSimilarity"));
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relationInverseMap.put("resultProject_outcome_isProducedBy", new RelationInverse()
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.setRelation("isProducedBy")
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.setInverse("produces")
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.setRelType("resultProject")
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.setSubReltype("outcome"));
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relationInverseMap.put("resultProject_outcome_produces", new RelationInverse()
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.setInverse("isProducedBy")
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.setRelation("produces")
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.setRelType("resultProject")
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.setSubReltype("outcome"));
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relationInverseMap.put("projectPerson_contactPerson_isContact", new RelationInverse()
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.setRelation("isContact")
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.setInverse("hasContact")
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.setRelType("projectPerson")
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.setSubReltype("contactPerson"));
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relationInverseMap.put("projectPerson_contactPerson_hasContact", new RelationInverse()
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.setInverse("isContact")
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.setRelation("hasContact")
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.setRelType("personPerson")
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.setSubReltype("coAuthorship"));
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relationInverseMap.put("personPerson_coAuthorship_isCoauthorOf", new RelationInverse()
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.setInverse("isCoAuthorOf")
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.setRelation("isCoAuthorOf")
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.setRelType("personPerson")
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.setSubReltype("coAuthorship"));
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relationInverseMap.put("personPerson_dedup_merges", new RelationInverse()
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.setInverse("isMergedIn")
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.setRelation("merges")
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.setRelType("personPerson")
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.setSubReltype("dedup"));
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relationInverseMap.put("personPerson_dedup_isMergedIn", new RelationInverse()
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.setInverse("merges")
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.setRelation("isMergedIn")
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.setRelType("personPerson")
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.setSubReltype("dedup"));
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relationInverseMap.put("personPerson_dedupSimilarity_isSimilarTo", new RelationInverse()
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.setInverse("isSimilarTo")
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.setRelation("isSimilarTo")
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.setRelType("personPerson")
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.setSubReltype("dedupSimilarity"));
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relationInverseMap.put("datasourceOrganization_provision_isProvidedBy", new RelationInverse()
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.setInverse("provides")
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.setRelation("isProvidedBy")
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.setRelType("datasourceOrganization")
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.setSubReltype("provision"));
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relationInverseMap.put("datasourceOrganization_provision_provides", new RelationInverse()
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.setInverse("isProvidedBy")
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.setRelation("provides")
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.setRelType("datasourceOrganization")
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.setSubReltype("provision"));
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relationInverseMap.put("resultResult_similarity_hasAmongTopNSimilarDocuments", new RelationInverse()
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.setInverse("isAmongTopNSimilarDocuments")
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.setRelation("hasAmongTopNSimilarDocuments")
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.setRelType("resultResult")
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.setSubReltype("similarity"));
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relationInverseMap.put("resultResult_similarity_isAmongTopNSimilarDocuments", new RelationInverse()
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.setInverse("hasAmongTopNSimilarDocuments")
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.setRelation("isAmongTopNSimilarDocuments")
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.setRelType("resultResult")
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.setSubReltype("similarity"));
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relationInverseMap.put("resultResult_relationship_isRelatedTo", new RelationInverse()
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.setInverse("isRelatedTo")
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.setRelation("isRelatedTo")
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.setRelType("resultResult")
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.setSubReltype("relationship"));
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relationInverseMap.put("resultResult_similarity_isAmongTopNSimilarDocuments", new RelationInverse()
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.setInverse("hasAmongTopNSimilarDocuments")
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.setRelation("isAmongTopNSimilarDocuments")
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.setRelType("resultResult")
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.setSubReltype("similarity"));
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relationInverseMap.put("resultResult_supplement_isSupplementTo", new RelationInverse()
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.setInverse("isSupplementedBy")
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.setRelation("isSupplementTo")
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.setRelType("resultResult")
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.setSubReltype("supplement"));
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relationInverseMap.put("resultResult_supplement_isSupplementedBy", new RelationInverse()
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.setInverse("isSupplementTo")
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.setRelation("isSupplementedBy")
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.setRelType("resultResult")
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.setSubReltype("supplement"));
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relationInverseMap.put("resultResult_part_isPartOf", new RelationInverse()
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.setInverse("hasPart")
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.setRelation("isPartOf")
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.setRelType("resultResult")
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.setSubReltype("part"));
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relationInverseMap.put("resultResult_part_hasPart", new RelationInverse()
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.setInverse("isPartOf")
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.setRelation("hasPart")
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.setRelType("resultResult")
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.setSubReltype("part"));
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relationInverseMap.put("resultResult_dedup_merges", new RelationInverse()
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.setInverse("isMergedIn")
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.setRelation("merges")
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.setRelType("resultResult")
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.setSubReltype("dedup"));
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relationInverseMap.put("resultResult_dedup_isMergedIn", new RelationInverse()
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.setInverse("merges")
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.setRelation("isMergedIn")
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.setRelType("resultResult")
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.setSubReltype("dedup"));
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relationInverseMap.put("resultResult_dedupSimilarity_isSimilarTo", new RelationInverse()
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.setInverse("isSimilarTo")
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.setRelation("isSimilarTo")
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.setRelType("resultResult")
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.setSubReltype("dedupSimilarity"));
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}
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private static final String schemeTemplate = "dnet:%s_%s_relations";
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private static final String schemeTemplate = "dnet:%s_%s_relations";
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private ModelSupport() {}
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private ModelSupport() {}
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@ -1,4 +1,46 @@
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package eu.dnetlib.dhp.schema.common;
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package eu.dnetlib.dhp.schema.common;
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public class RelationInverse {
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public class RelationInverse {
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private String relation;
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private String inverse;
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private String relType;
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private String subReltype;
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public String getRelType() {
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return relType;
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}
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public RelationInverse setRelType(String relType) {
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this.relType = relType;
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return this;
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}
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public String getSubReltype() {
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return subReltype;
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}
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public RelationInverse setSubReltype(String subReltype) {
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this.subReltype = subReltype;
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return this;
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}
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public String getRelation() {
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return relation;
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}
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public RelationInverse setRelation(String relation) {
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this.relation = relation;
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return this;
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}
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public String getInverse() {
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return inverse;
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}
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public RelationInverse setInverse(String inverse) {
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this.inverse = inverse;
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return this;
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}
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}
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}
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@ -0,0 +1,54 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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<property>
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<name>hive_metastore_uris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
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</property>
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<property>
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<name>sparkExecutorNumber</name>
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<value>4</value>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<value>/user/spark/spark2ApplicationHistory</value>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<value>15G</value>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<value>6G</value>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<value>1</value>
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</property>
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</configuration>
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@ -0,0 +1,227 @@
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<workflow-app name="bulk_tagging" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the source path</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>isLookUpUrl</name>
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<description>the isLookup service endpoint</description>
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</property>
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<property>
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<name>pathMap</name>
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<description>the json path associated to each selection field</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>the output path</description>
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</property>
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</parameters>
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<start to="reset-outputpath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="reset-outputpath">
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<fs>
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<delete path='${outputPath}/relation'/>
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<delete path='${outputPath}/publication'/>
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<delete path='${outputPath}/dataset'/>
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<delete path='${outputPath}/otherresearchproduct'/>
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<delete path='${outputPath}/software'/>
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<delete path='${outputPath}/organization'/>
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<delete path='${outputPath}/project'/>
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<delete path='${outputPath}/datasource'/>
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</fs>
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<ok to="copy_entities"/>
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<error to="Kill"/>
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</action>
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<fork name="copy_entities">
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<path start="copy_relation"/>
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<path start="copy_organization"/>
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<path start="copy_projects"/>
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<path start="copy_datasources"/>
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</fork>
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<action name="copy_relation">
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<distcp xmlns="uri:oozie:distcp-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<arg>${nameNode}/${sourcePath}/relation</arg>
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<arg>${nameNode}/${outputPath}/relation</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<action name="copy_organization">
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<distcp xmlns="uri:oozie:distcp-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<arg>${nameNode}/${sourcePath}/organization</arg>
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<arg>${nameNode}/${outputPath}/organization</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<action name="copy_projects">
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<distcp xmlns="uri:oozie:distcp-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<arg>${nameNode}/${sourcePath}/project</arg>
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<arg>${nameNode}/${outputPath}/project</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="copy_datasources">
|
||||||
|
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<arg>${nameNode}/${sourcePath}/datasource</arg>
|
||||||
|
<arg>${nameNode}/${outputPath}/datasource</arg>
|
||||||
|
</distcp>
|
||||||
|
<ok to="copy_wait"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<join name="copy_wait" to="fork_exec_bulktag"/>
|
||||||
|
|
||||||
|
<fork name="fork_exec_bulktag">
|
||||||
|
<path start="join_bulktag_publication"/>
|
||||||
|
<path start="join_bulktag_dataset"/>
|
||||||
|
<path start="join_bulktag_otherresearchproduct"/>
|
||||||
|
<path start="join_bulktag_software"/>
|
||||||
|
</fork>
|
||||||
|
<action name="join_bulktag_publication">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>bulkTagging-publication</name>
|
||||||
|
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob2</class>
|
||||||
|
<jar>dhp-bulktag-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--num-executors=${sparkExecutorNumber}
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
|
||||||
|
<arg>--pathMap</arg><arg>${pathMap}</arg>
|
||||||
|
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="wait"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
<action name="join_bulktag_dataset">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>bulkTagging-dataset</name>
|
||||||
|
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob2</class>
|
||||||
|
<jar>dhp-bulktag-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--num-executors=${sparkExecutorNumber}
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
|
||||||
|
<arg>--pathMap</arg><arg>${pathMap}</arg>
|
||||||
|
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="wait"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
<action name="join_bulktag_otherresearchproduct">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>bulkTagging-orp</name>
|
||||||
|
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob2</class>
|
||||||
|
<jar>dhp-bulktag-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--num-executors=${sparkExecutorNumber}
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
|
||||||
|
<arg>--pathMap</arg><arg>${pathMap}</arg>
|
||||||
|
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="wait"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
<action name="join_bulktag_software">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>bulkTagging-software</name>
|
||||||
|
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob2</class>
|
||||||
|
<jar>dhp-bulktag-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--num-executors=${sparkExecutorNumber}
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
|
||||||
|
<arg>--pathMap</arg><arg>${pathMap}</arg>
|
||||||
|
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="wait"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
<join name="wait" to="End"/>
|
||||||
|
<end name="End"/>
|
||||||
|
</workflow-app>
|
||||||
Loading…
Reference in New Issue