diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java index 92400a1ee..f65685487 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java @@ -86,121 +86,10 @@ public class ModelConstants { public static final Qualifier PROVENANCE_ACTION_SET_QUALIFIER = qualifier( SYSIMPORT_ACTIONSET, SYSIMPORT_ACTIONSET, 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); - - public static final Qualifier DATASET_DEFAULT_RESULTTYPE = qualifier( - DATASET_RESULTTYPE_CLASSID, DATASET_RESULTTYPE_CLASSID, - DNET_RESULT_TYPOLOGIES); - - public static final Qualifier SOFTWARE_DEFAULT_RESULTTYPE = qualifier( - SOFTWARE_RESULTTYPE_CLASSID, SOFTWARE_RESULTTYPE_CLASSID, - DNET_RESULT_TYPOLOGIES); - - public static final Qualifier ORP_DEFAULT_RESULTTYPE = qualifier( - ORP_RESULTTYPE_CLASSID, ORP_RESULTTYPE_CLASSID, - DNET_RESULT_TYPOLOGIES); - public static final Qualifier REPOSITORY_PROVENANCE_ACTIONS = qualifier( SYSIMPORT_CROSSWALK_REPOSITORY, SYSIMPORT_CROSSWALK_REPOSITORY, DNET_PROVENANCE_ACTIONS); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/common/ModelSupport.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/common/ModelSupport.java index 3ee3ed5a1..b4d9683f5 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/common/ModelSupport.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/common/ModelSupport.java @@ -96,48 +96,6 @@ public class ModelSupport { idPrefixEntity.put("50", "result"); } - public static final Map 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 relationInverseMap, String relType, String subRelType, String relClass, String inverseRelClass) { relationInverseMap @@ -158,35 +116,6 @@ public class ModelSupport { } } - /** - * 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 @@ -364,17 +293,17 @@ public class ModelSupport { .join( source, target, - relType, - subRelType, - relClass)) + relType.toString(), + subRelType.toString(), + relClass.toString())) .orElse( String .join( source, target, - relType, - subRelType))) - .orElse(String.join(source, target, relType))) + relType.toString(), + subRelType.toString()))) + .orElse(String.join(source, target, relType.toString()))) .orElse(String.join(source, target))) .orElse(source)) .orElse(null); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index 967326b83..3aec286b2 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -16,6 +16,8 @@ import org.apache.commons.lang3.StringUtils; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; import com.github.sisyphsu.dateparser.DateParserUtils; import com.google.common.collect.Lists; import com.google.common.collect.Sets; @@ -38,6 +40,127 @@ public class GraphCleaningFunctions extends CleaningFunctions { public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5; + public static T cleanContext(T value, String contextId, String verifyParam) { + if (ModelSupport.isSubClass(value, Result.class)) { + final Result res = (Result) value; + if (shouldCleanContext(res, verifyParam)) { + res + .setContext( + res + .getContext() + .stream() + .filter(c -> !StringUtils.startsWith(c.getId().toLowerCase(), contextId)) + .collect(Collectors.toList())); + } + return (T) res; + } else { + return value; + } + } + + private static boolean shouldCleanContext(Result res, String verifyParam) { + boolean titleMatch = res + .getTitle() + .stream() + .filter( + t -> t + .getQualifier() + .getClassid() + .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) + .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase())); + + return titleMatch && Objects.nonNull(res.getContext()); + } + + public static T cleanCountry(T value, String[] verifyParam, Set hostedBy, + String collectedfrom, String country) { + if (ModelSupport.isSubClass(value, Result.class)) { + final Result res = (Result) value; + if (res.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) || + !res.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) { + return (T) res; + } + + List ids = getPidsAndAltIds(res).collect(Collectors.toList()); + if (ids + .stream() + .anyMatch( + p -> p + .getQualifier() + .getClassid() + .equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) { + res + .setCountry( + res + .getCountry() + .stream() + .filter( + c -> toTakeCountry(c, country)) + .collect(Collectors.toList())); + } + + return (T) res; + } else { + return value; + } + } + + private static Stream getPidsAndAltIds(T r) { + final Stream resultPids = Optional + .ofNullable(r.getPid()) + .map(Collection::stream) + .orElse(Stream.empty()); + + final Stream instancePids = Optional + .ofNullable(r.getInstance()) + .map( + instance -> instance + .stream() + .flatMap( + i -> Optional + .ofNullable(i.getPid()) + .map(Collection::stream) + .orElse(Stream.empty()))) + .orElse(Stream.empty()); + + final Stream instanceAltIds = Optional + .ofNullable(r.getInstance()) + .map( + instance -> instance + .stream() + .flatMap( + i -> Optional + .ofNullable(i.getAlternateIdentifier()) + .map(Collection::stream) + .orElse(Stream.empty()))) + .orElse(Stream.empty()); + + return Stream + .concat( + Stream.concat(resultPids, instancePids), + instanceAltIds); + } + + private static boolean pidInParam(String value, String[] verifyParam) { + for (String s : verifyParam) + if (value.startsWith(s)) + return true; + return false; + } + + private static boolean toTakeCountry(Country c, String country) { + // If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be + // inserted via propagation + if (!Optional.ofNullable(c.getDataInfo()).isPresent()) + return true; + if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent()) + return true; + return !(c + .getClassid() + .equalsIgnoreCase(country) && + c.getDataInfo().getInferenceprovenance().equals("propagation")); + } + public static T fixVocabularyNames(T value) { if (value instanceof Datasource) { // nothing to clean here diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index ffe2c3f69..dc625eb20 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -18,443 +18,443 @@ import eu.dnetlib.dhp.schema.oaf.common.AccessRightComparator; public class OafMapperUtils { - private OafMapperUtils() { - } + private OafMapperUtils() { + } - public static KeyValue keyValue(final String k, final String v) { - final KeyValue kv = new KeyValue(); - kv.setKey(k); - kv.setValue(v); - return kv; - } + public static KeyValue keyValue(final String k, final String v) { + final KeyValue kv = new KeyValue(); + kv.setKey(k); + kv.setValue(v); + return kv; + } - public static List listKeyValues(final String... s) { - if (s.length % 2 > 0) { - throw new IllegalArgumentException("Invalid number of parameters (k,v,k,v,....)"); - } + public static List listKeyValues(final String... s) { + if (s.length % 2 > 0) { + throw new IllegalArgumentException("Invalid number of parameters (k,v,k,v,....)"); + } - final List list = new ArrayList<>(); - for (int i = 0; i < s.length; i += 2) { - list.add(keyValue(s[i], s[i + 1])); - } - return list; - } + final List list = new ArrayList<>(); + for (int i = 0; i < s.length; i += 2) { + list.add(keyValue(s[i], s[i + 1])); + } + return list; + } - public static List listValues(Array values) throws SQLException { - if (Objects.isNull(values)) { - return null; - } - return Arrays - .stream((T[]) values.getArray()) - .filter(Objects::nonNull) - .distinct() - .collect(Collectors.toList()); - } + public static List listValues(Array values) throws SQLException { + if (Objects.isNull(values)) { + return null; + } + return Arrays + .stream((T[]) values.getArray()) + .filter(Objects::nonNull) + .distinct() + .collect(Collectors.toList()); + } - public static Qualifier unknown(final String schemeid) { - return qualifier(UNKNOWN, "Unknown", schemeid); - } + public static Qualifier unknown(final String schemeid) { + return qualifier(UNKNOWN, "Unknown", schemeid); + } - public static AccessRight accessRight( - final String classid, - final String classname, - final String schemeid) { - return accessRight(classid, classname, schemeid, null); - } + public static AccessRight accessRight( + final String classid, + final String classname, + final String schemeid) { + return accessRight(classid, classname, schemeid, null); + } - public static AccessRight accessRight( - final String classid, - final String classname, - final String schemeid, - final OpenAccessRoute openAccessRoute) { - final AccessRight accessRight = new AccessRight(); - accessRight.setClassid(classid); - accessRight.setClassname(classname); - accessRight.setSchemeid(schemeid); - accessRight.setOpenAccessRoute(openAccessRoute); - return accessRight; - } + public static AccessRight accessRight( + final String classid, + final String classname, + final String schemeid, + final OpenAccessRoute openAccessRoute) { + final AccessRight accessRight = new AccessRight(); + accessRight.setClassid(classid); + accessRight.setClassname(classname); + accessRight.setSchemeid(schemeid); + accessRight.setOpenAccessRoute(openAccessRoute); + return accessRight; + } - public static Qualifier qualifier( - final String classid, - final String classname, - final String schemeid) { - final Qualifier q = new Qualifier(); - q.setClassid(classid); - q.setClassname(classname); - q.setSchemeid(schemeid); - return q; - } + public static Qualifier qualifier( + final String classid, + final String classname, + final String schemeid) { + final Qualifier q = new Qualifier(); + q.setClassid(classid); + q.setClassname(classname); + q.setSchemeid(schemeid); + return q; + } - public static Qualifier qualifier(final Qualifier qualifier) { - final Qualifier q = new Qualifier(); - q.setClassid(qualifier.getClassid()); - q.setClassname(qualifier.getClassname()); - q.setSchemeid(qualifier.getSchemeid()); - return q; - } + public static Qualifier qualifier(final Qualifier qualifier) { + final Qualifier q = new Qualifier(); + q.setClassid(qualifier.getClassid()); + q.setClassname(qualifier.getClassname()); + q.setSchemeid(qualifier.getSchemeid()); + return q; + } - public static Subject subject( - final String value, - final String classid, - final String classname, - final String schemeid, - final DataInfo dataInfo) { + public static Subject subject( + final String value, + final String classid, + final String classname, + final String schemeid, + final DataInfo dataInfo) { - return subject(value, qualifier(classid, classname, schemeid), dataInfo); - } + return subject(value, qualifier(classid, classname, schemeid), dataInfo); + } - public static StructuredProperty structuredProperty( - final String value, - final String classid, - final String classname, - final String schemeid) { + public static StructuredProperty structuredProperty( + final String value, + final String classid, + final String classname, + final String schemeid) { - return structuredProperty(value, qualifier(classid, classname, schemeid)); - } + return structuredProperty(value, qualifier(classid, classname, schemeid)); + } - public static Subject subject( - final String value, - final Qualifier qualifier, - final DataInfo dataInfo) { - if (value == null) { - return null; - } - final Subject s = new Subject(); - s.setValue(value); - s.setQualifier(qualifier); - s.setDataInfo(dataInfo); - return s; - } + public static Subject subject( + final String value, + final Qualifier qualifier, + final DataInfo dataInfo) { + if (value == null) { + return null; + } + final Subject s = new Subject(); + s.setValue(value); + s.setQualifier(qualifier); + s.setDataInfo(dataInfo); + return s; + } - public static StructuredProperty structuredProperty( - final String value, - final Qualifier qualifier) { - if (value == null) { - return null; - } - final StructuredProperty sp = new StructuredProperty(); - sp.setValue(value); - sp.setQualifier(qualifier); - return sp; - } + public static StructuredProperty structuredProperty( + final String value, + final Qualifier qualifier) { + if (value == null) { + return null; + } + final StructuredProperty sp = new StructuredProperty(); + sp.setValue(value); + sp.setQualifier(qualifier); + return sp; + } - public static Publisher publisher(final String name) { - final Publisher p = new Publisher(); - p.setName(name); - return p; - } + public static Publisher publisher(final String name) { + final Publisher p = new Publisher(); + p.setName(name); + return p; + } - public static License license(final String url) { - final License l = new License(); - l.setUrl(url); - return l; - } + public static License license(final String url) { + final License l = new License(); + l.setUrl(url); + return l; + } - public static AuthorPid authorPid( - final String value, - final Qualifier qualifier, - final DataInfo dataInfo) { - if (value == null) { - return null; - } - final AuthorPid ap = new AuthorPid(); - ap.setValue(value); - ap.setQualifier(qualifier); - ap.setDataInfo(dataInfo); - return ap; - } + public static AuthorPid authorPid( + final String value, + final Qualifier qualifier, + final DataInfo dataInfo) { + if (value == null) { + return null; + } + final AuthorPid ap = new AuthorPid(); + ap.setValue(value); + ap.setQualifier(qualifier); + ap.setDataInfo(dataInfo); + return ap; + } - public static AuthorPid authorPid( - final String value, - final String classid, - final String schemeid, - final DataInfo dataInfo) { - if (value == null) { - return null; - } - final AuthorPid ap = new AuthorPid(); - ap.setValue(value); - ap.setQualifier(qualifier(classid, classid, schemeid)); - ap.setDataInfo(dataInfo); - return ap; - } + public static AuthorPid authorPid( + final String value, + final String classid, + final String schemeid, + final DataInfo dataInfo) { + if (value == null) { + return null; + } + final AuthorPid ap = new AuthorPid(); + ap.setValue(value); + ap.setQualifier(qualifier(classid, classid, schemeid)); + ap.setDataInfo(dataInfo); + return ap; + } - public static ExtraInfo extraInfo( - final String name, - final String value, - final String typology, - final String provenance, - final String trust) { - final ExtraInfo info = new ExtraInfo(); - info.setName(name); - info.setValue(value); - info.setTypology(typology); - info.setProvenance(provenance); - info.setTrust(trust); - return info; - } + public static ExtraInfo extraInfo( + final String name, + final String value, + final String typology, + final String provenance, + final String trust) { + final ExtraInfo info = new ExtraInfo(); + info.setName(name); + info.setValue(value); + info.setTypology(typology); + info.setProvenance(provenance); + info.setTrust(trust); + return info; + } - public static OAIProvenance oaiIProvenance( - final String identifier, - final String baseURL, - final String metadataNamespace, - final Boolean altered, - final String datestamp, - final String harvestDate) { + public static OAIProvenance oaiIProvenance( + final String identifier, + final String baseURL, + final String metadataNamespace, + final Boolean altered, + final String datestamp, + final String harvestDate) { - final OriginDescription desc = new OriginDescription(); - desc.setIdentifier(identifier); - desc.setBaseURL(baseURL); - desc.setMetadataNamespace(metadataNamespace); - desc.setAltered(altered); - desc.setDatestamp(datestamp); - desc.setHarvestDate(harvestDate); + final OriginDescription desc = new OriginDescription(); + desc.setIdentifier(identifier); + desc.setBaseURL(baseURL); + desc.setMetadataNamespace(metadataNamespace); + desc.setAltered(altered); + desc.setDatestamp(datestamp); + desc.setHarvestDate(harvestDate); - final OAIProvenance p = new OAIProvenance(); - p.setOriginDescription(desc); + final OAIProvenance p = new OAIProvenance(); + p.setOriginDescription(desc); - return p; - } + return p; + } - public static Journal journal( - final String name, - final String issnPrinted, - final String issnOnline, - final String issnLinking) { + public static Journal journal( + final String name, + final String issnPrinted, + final String issnOnline, + final String issnLinking) { - return hasIssn(issnPrinted, issnOnline, issnLinking) ? journal( - name, - issnPrinted, - issnOnline, - issnLinking, - null, - null, - null, - null, - null, - null, - null) : null; - } + return hasIssn(issnPrinted, issnOnline, issnLinking) ? journal( + name, + issnPrinted, + issnOnline, + issnLinking, + null, + null, + null, + null, + null, + null, + null) : null; + } - public static Journal journal( - final String name, - final String issnPrinted, - final String issnOnline, - final String issnLinking, - final String ep, - final String iss, - final String sp, - final String vol, - final String edition, - final String conferenceplace, - final String conferencedate) { + public static Journal journal( + final String name, + final String issnPrinted, + final String issnOnline, + final String issnLinking, + final String ep, + final String iss, + final String sp, + final String vol, + final String edition, + final String conferenceplace, + final String conferencedate) { - if (StringUtils.isNotBlank(name) || hasIssn(issnPrinted, issnOnline, issnLinking)) { - final Journal j = new Journal(); - j.setName(name); - j.setIssnPrinted(issnPrinted); - j.setIssnOnline(issnOnline); - j.setIssnLinking(issnLinking); - j.setEp(ep); - j.setIss(iss); - j.setSp(sp); - j.setVol(vol); - j.setEdition(edition); - j.setConferenceplace(conferenceplace); - j.setConferencedate(conferencedate); - return j; - } else { - return null; - } - } + if (StringUtils.isNotBlank(name) || hasIssn(issnPrinted, issnOnline, issnLinking)) { + final Journal j = new Journal(); + j.setName(name); + j.setIssnPrinted(issnPrinted); + j.setIssnOnline(issnOnline); + j.setIssnLinking(issnLinking); + j.setEp(ep); + j.setIss(iss); + j.setSp(sp); + j.setVol(vol); + j.setEdition(edition); + j.setConferenceplace(conferenceplace); + j.setConferencedate(conferencedate); + return j; + } else { + return null; + } + } - private static boolean hasIssn(String issnPrinted, String issnOnline, String issnLinking) { - return StringUtils.isNotBlank(issnPrinted) - || StringUtils.isNotBlank(issnOnline) - || StringUtils.isNotBlank(issnLinking); - } + private static boolean hasIssn(String issnPrinted, String issnOnline, String issnLinking) { + return StringUtils.isNotBlank(issnPrinted) + || StringUtils.isNotBlank(issnOnline) + || StringUtils.isNotBlank(issnLinking); + } - public static DataInfo dataInfo( - final float trust, - final String inferenceprovenance, - final boolean inferred, - final Qualifier provenanceaction) { - final DataInfo d = new DataInfo(); - d.setTrust(trust); - d.setInferenceprovenance(inferenceprovenance); - d.setInferred(inferred); - d.setProvenanceaction(provenanceaction); - return d; - } + public static DataInfo dataInfo( + final float trust, + final String inferenceprovenance, + final boolean inferred, + final Qualifier provenanceaction) { + final DataInfo d = new DataInfo(); + d.setTrust(trust); + d.setInferenceprovenance(inferenceprovenance); + d.setInferred(inferred); + d.setProvenanceaction(provenanceaction); + return d; + } - public static EntityDataInfo dataInfo( - final boolean invisible, - final boolean deletedbyinference, - final float trust, - final String inferenceprovenance, - final boolean inferred, - final Qualifier provenanceaction) { - final EntityDataInfo d = new EntityDataInfo(); - d.setTrust(trust); - d.setInvisible(invisible); - d.setDeletedbyinference(deletedbyinference); - d.setInferenceprovenance(inferenceprovenance); - d.setInferred(inferred); - d.setProvenanceaction(provenanceaction); - return d; - } + public static EntityDataInfo dataInfo( + final boolean invisible, + final boolean deletedbyinference, + final float trust, + final String inferenceprovenance, + final boolean inferred, + final Qualifier provenanceaction) { + final EntityDataInfo d = new EntityDataInfo(); + d.setTrust(trust); + d.setInvisible(invisible); + d.setDeletedbyinference(deletedbyinference); + d.setInferenceprovenance(inferenceprovenance); + d.setInferred(inferred); + d.setProvenanceaction(provenanceaction); + return d; + } - public static String asString(final Object o) { - return o == null ? "" : o.toString(); - } + public static String asString(final Object o) { + return o == null ? "" : o.toString(); + } - public static Predicate distinctByKey( - final Function keyExtractor) { - final Map seen = new ConcurrentHashMap<>(); - return t -> seen.putIfAbsent(keyExtractor.apply(t), Boolean.TRUE) == null; - } + public static Predicate distinctByKey( + final Function keyExtractor) { + final Map seen = new ConcurrentHashMap<>(); + return t -> seen.putIfAbsent(keyExtractor.apply(t), Boolean.TRUE) == null; + } - public static Qualifier createBestAccessRights(final List instanceList) { - return getBestAccessRights(instanceList); - } + public static Qualifier createBestAccessRights(final List instanceList) { + return getBestAccessRights(instanceList); + } - protected static Qualifier getBestAccessRights(final List instanceList) { - if (instanceList != null) { - final Optional min = instanceList - .stream() - .map(Instance::getAccessright) - .min(new AccessRightComparator<>()); + protected static Qualifier getBestAccessRights(final List instanceList) { + if (instanceList != null) { + final Optional min = instanceList + .stream() + .map(Instance::getAccessright) + .min(new AccessRightComparator<>()); - final Qualifier rights = min.map(OafMapperUtils::qualifier).orElseGet(Qualifier::new); + final Qualifier rights = min.map(OafMapperUtils::qualifier).orElseGet(Qualifier::new); - if (StringUtils.isBlank(rights.getClassid())) { - rights.setClassid(UNKNOWN); - } - if (StringUtils.isBlank(rights.getClassname()) - || UNKNOWN.equalsIgnoreCase(rights.getClassname())) { - rights.setClassname(NOT_AVAILABLE); - } - if (StringUtils.isBlank(rights.getSchemeid())) { - rights.setSchemeid(DNET_ACCESS_MODES); - } + if (StringUtils.isBlank(rights.getClassid())) { + rights.setClassid(UNKNOWN); + } + if (StringUtils.isBlank(rights.getClassname()) + || UNKNOWN.equalsIgnoreCase(rights.getClassname())) { + rights.setClassname(NOT_AVAILABLE); + } + if (StringUtils.isBlank(rights.getSchemeid())) { + rights.setSchemeid(DNET_ACCESS_MODES); + } - return rights; - } - return null; - } + return rights; + } + return null; + } - public static Measure newMeasureInstance(String id, String value, String key, DataInfo dataInfo) { - Measure m = new Measure(); - m.setId(id); - m.setUnit(Arrays.asList(unit(key, value, dataInfo))); - return m; - } + public static Measure newMeasureInstance(String id, String value, String key, DataInfo dataInfo) { + Measure m = new Measure(); + m.setId(id); + m.setUnit(Arrays.asList(unit(key, value, dataInfo))); + return m; + } - public static MeasureUnit unit(String key, String value, DataInfo dataInfo) { - MeasureUnit unit = new MeasureUnit(); - unit.setKey(key); - unit.setValue(value); - unit.setDataInfo(dataInfo); - return unit; - } + public static MeasureUnit unit(String key, String value, DataInfo dataInfo) { + MeasureUnit unit = new MeasureUnit(); + unit.setKey(key); + unit.setValue(value); + unit.setDataInfo(dataInfo); + return unit; + } - public static Relation getRelation(final String source, - final String target, - final String relType, - final String subRelType, - final String relClass, - final Entity entity) { - return getRelation(source, target, relType, subRelType, relClass, entity, null); - } + public static Relation getRelation(final String source, + final String target, + final Relation.RELTYPE relType, + final Relation.SUBRELTYPE subRelType, + final Relation.RELCLASS relClass, + final Entity entity) { + return getRelation(source, target, relType, subRelType, relClass, entity, null); + } - public static Relation getRelation(final String source, - final String target, - final String relType, - final String subRelType, - final String relClass, - final Entity entity, - final String validationDate) { + public static Relation getRelation(final String source, + final String target, + final Relation.RELTYPE relType, + final Relation.SUBRELTYPE subRelType, + final Relation.RELCLASS relClass, + final Entity entity, + final String validationDate) { - final List provenance = getProvenance( - entity.getCollectedfrom(), fromEntityDataInfo(entity.getDataInfo())); - return getRelation( - source, target, relType, subRelType, relClass, provenance, validationDate, null); - } + final List provenance = getProvenance( + entity.getCollectedfrom(), fromEntityDataInfo(entity.getDataInfo())); + return getRelation( + source, target, relType, subRelType, relClass, provenance, validationDate, null); + } - public static Relation getRelation(final String source, - final String target, - final String relType, - final String subRelType, - final String relClass, - final List provenance) { - return getRelation( - source, target, relType, subRelType, relClass, provenance, null, null); - } + public static Relation getRelation(final String source, + final String target, + final Relation.RELTYPE relType, + final Relation.SUBRELTYPE subRelType, + final Relation.RELCLASS relClass, + final List provenance) { + return getRelation( + source, target, relType, subRelType, relClass, provenance, null, null); + } - public static Relation getRelation(final String source, - final String target, - final String relType, - final String subRelType, - final String relClass, - final List provenance, - final List properties) { - return getRelation( - source, target, relType, subRelType, relClass, provenance, null, properties); - } + public static Relation getRelation(final String source, + final String target, + final Relation.RELTYPE relType, + final Relation.SUBRELTYPE subRelType, + final Relation.RELCLASS relClass, + final List provenance, + final List properties) { + return getRelation( + source, target, relType, subRelType, relClass, provenance, null, properties); + } - public static Relation getRelation(final String source, - final String target, - final String relType, - final String subRelType, - final String relClass, - final List provenance, - final String validationDate, - final List properties) { - final Relation rel = new Relation(); - rel.setRelType(relType); - rel.setSubRelType(subRelType); - rel.setRelClass(relClass); - rel.setSource(source); - rel.setTarget(target); - rel.setProvenance(provenance); - rel.setValidated(StringUtils.isNotBlank(validationDate)); - rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); - rel.setProperties(properties); - return rel; - } + public static Relation getRelation(final String source, + final String target, + final Relation.RELTYPE relType, + final Relation.SUBRELTYPE subRelType, + final Relation.RELCLASS relClass, + final List provenance, + final String validationDate, + final List properties) { + final Relation rel = new Relation(); + rel.setRelType(relType); + rel.setSubRelType(subRelType); + rel.setRelClass(relClass); + rel.setSource(source); + rel.setTarget(target); + rel.setProvenance(provenance); + rel.setValidated(StringUtils.isNotBlank(validationDate)); + rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); + rel.setProperties(properties); + return rel; + } - public static List getProvenance(final List collectedfrom, final DataInfo dataInfo) { - return collectedfrom - .stream() - .map(cf -> getProvenance(cf, dataInfo)) - .collect(Collectors.toList()); - } + public static List getProvenance(final List collectedfrom, final DataInfo dataInfo) { + return collectedfrom + .stream() + .map(cf -> getProvenance(cf, dataInfo)) + .collect(Collectors.toList()); + } - public static Provenance getProvenance(final KeyValue collectedfrom, final DataInfo dataInfo) { - final Provenance prov = new Provenance(); - prov.setCollectedfrom(collectedfrom); - prov.setDataInfo(dataInfo); - return prov; - } + public static Provenance getProvenance(final KeyValue collectedfrom, final DataInfo dataInfo) { + final Provenance prov = new Provenance(); + prov.setCollectedfrom(collectedfrom); + prov.setDataInfo(dataInfo); + return prov; + } - public static String getProvenance(DataInfo dataInfo) { - return Optional - .ofNullable(dataInfo) - .map( - d -> Optional - .ofNullable(d.getProvenanceaction()) - .map(Qualifier::getClassid) - .orElse("")) - .orElse(""); - } + public static String getProvenance(DataInfo dataInfo) { + return Optional + .ofNullable(dataInfo) + .map( + d -> Optional + .ofNullable(d.getProvenanceaction()) + .map(Qualifier::getClassid) + .orElse("")) + .orElse(""); + } - public static DataInfo fromEntityDataInfo(EntityDataInfo entityDataInfo) { - DataInfo dataInfo = new DataInfo(); - dataInfo.setTrust(entityDataInfo.getTrust()); - dataInfo.setInferenceprovenance(entityDataInfo.getInferenceprovenance()); - dataInfo.setInferred(entityDataInfo.getInferred()); - dataInfo.setProvenanceaction(entityDataInfo.getProvenanceaction()); - return dataInfo; - } + public static DataInfo fromEntityDataInfo(EntityDataInfo entityDataInfo) { + DataInfo dataInfo = new DataInfo(); + dataInfo.setTrust(entityDataInfo.getTrust()); + dataInfo.setInferenceprovenance(entityDataInfo.getInferenceprovenance()); + dataInfo.setInferred(entityDataInfo.getInferred()); + dataInfo.setProvenanceaction(entityDataInfo.getProvenanceaction()); + return dataInfo; + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java index a233ae764..55b483558 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java @@ -34,34 +34,34 @@ public class ResultTypeComparator implements Comparator { return 1; } - String lClass = left.getResulttype(); - String rClass = right.getResulttype(); + Result.RESULTTYPE lType = left.getResulttype(); + Result.RESULTTYPE rType = right.getResulttype(); - if (lClass.equals(rClass)) + if (lType.equals(rType)) return 0; - if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID)) + if (lType.equals(Result.RESULTTYPE.publication)) return -1; - if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID)) + if (rType.equals(Result.RESULTTYPE.publication)) return 1; - if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID)) + if (lType.equals(Result.RESULTTYPE.dataset)) return -1; - if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID)) + if (rType.equals(Result.RESULTTYPE.dataset)) return 1; - if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID)) + if (lType.equals(Result.RESULTTYPE.software)) return -1; - if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID)) + if (rType.equals(Result.RESULTTYPE.software)) return 1; - if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID)) + if (lType.equals(Result.RESULTTYPE.otherresearchproduct)) return -1; - if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID)) + if (rType.equals(Result.RESULTTYPE.otherresearchproduct)) return 1; // Else (but unlikely), lexicographical ordering will do. - return lClass.compareTo(rClass); + return lType.compareTo(rType); } protected HashSet getCollectedFromIds(Result left) { diff --git a/dhp-common/src/main/resources/eu/dnetlib/scholexplorer/relation/relations.json b/dhp-common/src/main/resources/eu/dnetlib/scholexplorer/relation/relations.json deleted file mode 100644 index 98e8daa18..000000000 --- a/dhp-common/src/main/resources/eu/dnetlib/scholexplorer/relation/relations.json +++ /dev/null @@ -1,158 +0,0 @@ -{ - "cites":{ - "original":"Cites", - "inverse":"IsCitedBy" - }, - "compiles":{ - "original":"Compiles", - "inverse":"IsCompiledBy" - }, - "continues":{ - "original":"Continues", - "inverse":"IsContinuedBy" - }, - "derives":{ - "original":"IsSourceOf", - "inverse":"IsDerivedFrom" - }, - "describes":{ - "original":"Describes", - "inverse":"IsDescribedBy" - }, - "documents":{ - "original":"Documents", - "inverse":"IsDocumentedBy" - }, - "hasmetadata":{ - "original":"HasMetadata", - "inverse":"IsMetadataOf" - }, - "hasassociationwith":{ - "original":"HasAssociationWith", - "inverse":"HasAssociationWith" - }, - "haspart":{ - "original":"HasPart", - "inverse":"IsPartOf" - }, - "hasversion":{ - "original":"HasVersion", - "inverse":"IsVersionOf" - }, - "iscitedby":{ - "original":"IsCitedBy", - "inverse":"Cites" - }, - "iscompiledby":{ - "original":"IsCompiledBy", - "inverse":"Compiles" - }, - "iscontinuedby":{ - "original":"IsContinuedBy", - "inverse":"Continues" - }, - "isderivedfrom":{ - "original":"IsDerivedFrom", - "inverse":"IsSourceOf" - }, - "isdescribedby":{ - "original":"IsDescribedBy", - "inverse":"Describes" - }, - "isdocumentedby":{ - "original":"IsDocumentedBy", - "inverse":"Documents" - }, - "isidenticalto":{ - "original":"IsIdenticalTo", - "inverse":"IsIdenticalTo" - }, - "ismetadatafor":{ - "original":"IsMetadataFor", - "inverse":"IsMetadataOf" - }, - "ismetadataof":{ - "original":"IsMetadataOf", - "inverse":"IsMetadataFor" - }, - "isnewversionof":{ - "original":"IsNewVersionOf", - "inverse":"IsPreviousVersionOf" - }, - "isobsoletedby":{ - "original":"IsObsoletedBy", - "inverse":"Obsoletes" - }, - "isoriginalformof":{ - "original":"IsOriginalFormOf", - "inverse":"IsVariantFormOf" - }, - "ispartof":{ - "original":"IsPartOf", - "inverse":"HasPart" - }, - "ispreviousversionof":{ - "original":"IsPreviousVersionOf", - "inverse":"IsNewVersionOf" - }, - "isreferencedby":{ - "original":"IsReferencedBy", - "inverse":"References" - }, - "isrelatedto":{ - "original":"IsRelatedTo", - "inverse":"IsRelatedTo" - }, - "isrequiredby":{ - "original":"IsRequiredBy", - "inverse":"Requires" - }, - "isreviewedby":{ - "original":"IsReviewedBy", - "inverse":"Reviews" - }, - "issourceof":{ - "original":"IsSourceOf", - "inverse":"IsDerivedFrom" - }, - "issupplementedby":{ - "original":"IsSupplementedBy", - "inverse":"IsSupplementTo" - }, - "issupplementto":{ - "original":"IsSupplementTo", - "inverse":"IsSupplementedBy" - }, - "isvariantformof":{ - "original":"IsVariantFormOf", - "inverse":"IsOriginalFormOf" - }, - "isversionof":{ - "original":"IsVersionOf", - "inverse":"HasVersion" - }, - "obsoletes":{ - "original":"Obsoletes", - "inverse":"IsObsoletedBy" - }, - "references":{ - "original":"References", - "inverse":"IsReferencedBy" - }, - "requires":{ - "original":"Requires", - "inverse":"IsRequiredBy" - }, - "related":{ - "original":"IsRelatedTo", - "inverse":"IsRelatedTo" - }, - "reviews":{ - "original":"Reviews", - "inverse":"IsReviewedBy" - }, - "unknown":{ - "original":"Unknown", - "inverse":"Unknown" - } -} \ No newline at end of file diff --git a/dhp-common/src/main/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala b/dhp-common/src/main/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala index 65a7f43af..db9ee80eb 100644 --- a/dhp-common/src/main/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala +++ b/dhp-common/src/main/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala @@ -22,19 +22,6 @@ object ScholixUtils extends Serializable { case class RelatedEntities(id: String, relatedDataset: Long, relatedPublication: Long) {} - val relations: Map[String, RelationVocabulary] = { - val input = Source - .fromInputStream( - getClass.getResourceAsStream("/eu/dnetlib/scholexplorer/relation/relations.json") - ) - .mkString - implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats - - lazy val json: json4s.JValue = parse(input) - - json.extract[Map[String, RelationVocabulary]] - } - def extractRelationDate(relation: Relation): String = { if (relation.getProperties == null || !relation.getProperties.isEmpty) @@ -288,11 +275,8 @@ object ScholixUtils extends Serializable { s.setPublisher(source.getPublisher) } - val semanticRelation = relations.getOrElse(relation.getRelClass.toLowerCase, null) - if (semanticRelation == null) - return null s.setRelationship( - new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse) + new ScholixRelationship(relation.getRelClass.toString, "datacite", relation.getRelClass.getInverse.toString) ) s.setSource(source) @@ -330,12 +314,10 @@ object ScholixUtils extends Serializable { s.setPublisher(l.asJava) } - val semanticRelation = relations.getOrElse(relation.getRelClass.toLowerCase, null) - if (semanticRelation == null) - return null s.setRelationship( - new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse) + new ScholixRelationship(relation.getRelClass.toString, "datacite", relation.getRelClass.getInverse.toString) ) + s.setSource(generateScholixResourceFromSummary(source)) s diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java index 12edfeac6..ec2007128 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java @@ -44,7 +44,7 @@ public class MergeUtilsTest { assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID)); final Result p1d2 = MergeUtils.merge(p1, d2); - assertEquals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, p1d2.getResulttype()); + assertEquals(Result.RESULTTYPE.publication, p1d2.getResulttype()); assertTrue(p1d2 instanceof Publication); assertEquals(p1.getId(), p1d2.getId()); } @@ -55,7 +55,7 @@ public class MergeUtilsTest { Dataset d1 = read("dataset_1.json", Dataset.class); final Result p2d1 = MergeUtils.merge(p2, d1); - assertEquals(ModelConstants.DATASET_RESULTTYPE_CLASSID, p2d1.getResulttype()); + assertEquals(Result.RESULTTYPE.dataset, p2d1.getResulttype()); assertTrue(p2d1 instanceof Dataset); assertEquals(d1.getId(), p2d1.getId()); assertEquals(2, p2d1.getCollectedfrom().size()); diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/CollectionUtils.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/CollectionUtils.scala index 46ae6b9de..71d9eeec5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/CollectionUtils.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/CollectionUtils.scala @@ -18,30 +18,21 @@ object CollectionUtils { def fixRelations(i: Oaf): List[Oaf] = { if (i.isInstanceOf[Entity]) - return List(i) + List(i) else { val r: Relation = i.asInstanceOf[Relation] - val currentRel = ModelSupport.findRelation(r.getRelClass) - if (currentRel != null) { - - // Cleaning relation - r.setRelType(currentRel.getRelType) - r.setSubRelType(currentRel.getSubReltype) - r.setRelClass(currentRel.getRelClass) - val inverse = new Relation - inverse.setSource(r.getTarget) - inverse.setTarget(r.getSource) - inverse.setRelType(currentRel.getRelType) - inverse.setSubRelType(currentRel.getSubReltype) - inverse.setRelClass(currentRel.getInverseRelClass) - inverse.setProvenance(r.getProvenance) - inverse.setProperties(r.getProperties) - inverse.setValidated(r.getValidated) - inverse.setValidationDate(r.getValidationDate) - return List(r, inverse) - } + val inverse = new Relation + inverse.setSource(r.getTarget) + inverse.setTarget(r.getSource) + inverse.setRelType(r.getRelType) + inverse.setSubRelType(r.getSubRelType) + inverse.setRelClass(r.getRelClass.getInverse) + inverse.setProvenance(r.getProvenance) + inverse.setProperties(r.getProperties) + inverse.setValidated(r.getValidated) + inverse.setValidationDate(r.getValidationDate) + List(r, inverse) } - List() } def saveDataset(dataset: Dataset[Oaf], targetPath: String): Unit = { diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/crossref/CrossrefUtility.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/crossref/CrossrefUtility.scala index 7c7c6df29..3831b1ad2 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/crossref/CrossrefUtility.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/crossref/CrossrefUtility.scala @@ -61,13 +61,15 @@ object CrossrefUtility { resultList } - private def createRelation(sourceId: String, targetId: String, relClass: String): Relation = { + private def createRelation(sourceId: String, targetId: String, relClass: Relation.RELCLASS): Relation = { val r = new Relation + + //TODO further inspect r.setSource(sourceId) r.setTarget(targetId) - r.setRelType(ModelConstants.RESULT_PROJECT) + r.setRelType(Relation.RELTYPE.resultProject) r.setRelClass(relClass) - r.setSubRelType(ModelConstants.OUTCOME) + r.setSubRelType(Relation.SUBRELTYPE.outcome) r.setProvenance(List(OafMapperUtils.getProvenance(CROSSREF_COLLECTED_FROM, null)).asJava) r } @@ -84,7 +86,7 @@ object CrossrefUtility { .filter(a => a != null && a.nonEmpty) .map(award => { val targetId = IdentifierFactory.createOpenaireId("project", s"$nsPrefix::$award", true) - createRelation(targetId, source.getId, ModelConstants.PRODUCES) + createRelation(targetId, source.getId, Relation.RELCLASS.produces) }) else List() } @@ -132,15 +134,15 @@ object CrossrefUtility { case "10.13039/501100000038" => val targetId = IdentifierFactory.createOpenaireId("project", "nserc_______::1e5e62235d094afd01cd56e65112fc63", false) - relList = relList ::: List(createRelation(targetId, result.getId, ModelConstants.PRODUCES)) + relList = relList ::: List(createRelation(targetId, result.getId, Relation.RELCLASS.produces)) case "10.13039/501100000155" => val targetId = IdentifierFactory.createOpenaireId("project", "sshrc_______::1e5e62235d094afd01cd56e65112fc63", false) - relList = relList ::: List(createRelation(targetId, result.getId, ModelConstants.PRODUCES)) + relList = relList ::: List(createRelation(targetId, result.getId, Relation.RELCLASS.produces)) case "10.13039/501100000024" => val targetId = IdentifierFactory.createOpenaireId("project", "cihr________::1e5e62235d094afd01cd56e65112fc63", false) - relList = relList ::: List(createRelation(targetId, result.getId, ModelConstants.PRODUCES)) + relList = relList ::: List(createRelation(targetId, result.getId, Relation.RELCLASS.produces)) case "10.13039/501100002848" => relList = relList ::: generateSimpleRelationFromAward(funder, "conicytf____", a => a, result) case "10.13039/501100003448" => @@ -153,7 +155,7 @@ object CrossrefUtility { relList = relList ::: generateSimpleRelationFromAward(funder, "miur________", a => a, result) val targetId = IdentifierFactory.createOpenaireId("project", "miur________::1e5e62235d094afd01cd56e65112fc63", false) - relList = relList ::: List(createRelation(targetId, result.getId, ModelConstants.PRODUCES)) + relList = relList ::: List(createRelation(targetId, result.getId, Relation.RELCLASS.produces)) case "10.13039/501100006588" | "10.13039/501100004488" => relList = relList ::: generateSimpleRelationFromAward( funder, @@ -171,7 +173,7 @@ object CrossrefUtility { relList = relList ::: generateSimpleRelationFromAward(funder, "wt__________", a => a, result) val targetId = IdentifierFactory.createOpenaireId("project", "wt__________::1e5e62235d094afd01cd56e65112fc63", false) - relList = relList ::: List(createRelation(targetId, result.getId, ModelConstants.PRODUCES)) + relList = relList ::: List(createRelation(targetId, result.getId, Relation.RELCLASS.produces)) case _ => logger.debug("no match for " + funder.DOI.get) } @@ -191,7 +193,7 @@ object CrossrefUtility { relList = relList ::: generateSimpleRelationFromAward(funder, "wt__________", a => a, result) val targetId = IdentifierFactory.createOpenaireId("project", "wt__________::1e5e62235d094afd01cd56e65112fc63", false) - relList = relList ::: List(createRelation(targetId, result.getId, ModelConstants.PRODUCES)) + relList = relList ::: List(createRelation(targetId, result.getId, Relation.RELCLASS.produces)) case _ => logger.debug("no match for " + funder.name) } diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteModelConstants.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteModelConstants.scala index ba08f2cd1..0d66dc006 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteModelConstants.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteModelConstants.scala @@ -78,124 +78,6 @@ object DataciteModelConstants { val DATACITE_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue(ModelConstants.DATACITE_ID, DATACITE_NAME) - val subRelTypeMapping: Map[String, OAFRelations] = Map( - ModelConstants.IS_SUPPLEMENTED_BY -> OAFRelations( - ModelConstants.IS_SUPPLEMENTED_BY, - ModelConstants.IS_SUPPLEMENT_TO, - ModelConstants.SUPPLEMENT - ), - ModelConstants.IS_SUPPLEMENT_TO -> OAFRelations( - ModelConstants.IS_SUPPLEMENT_TO, - ModelConstants.IS_SUPPLEMENTED_BY, - ModelConstants.SUPPLEMENT - ), - ModelConstants.HAS_PART -> OAFRelations( - ModelConstants.HAS_PART, - ModelConstants.IS_PART_OF, - ModelConstants.PART - ), - ModelConstants.IS_PART_OF -> OAFRelations( - ModelConstants.IS_PART_OF, - ModelConstants.HAS_PART, - ModelConstants.PART - ), - ModelConstants.IS_VERSION_OF -> OAFRelations( - ModelConstants.IS_VERSION_OF, - ModelConstants.HAS_VERSION, - ModelConstants.VERSION - ), - ModelConstants.HAS_VERSION -> OAFRelations( - ModelConstants.HAS_VERSION, - ModelConstants.IS_VERSION_OF, - ModelConstants.VERSION - ), - ModelConstants.IS_IDENTICAL_TO -> OAFRelations( - ModelConstants.IS_IDENTICAL_TO, - ModelConstants.IS_IDENTICAL_TO, - ModelConstants.RELATIONSHIP - ), - ModelConstants.IS_CONTINUED_BY -> OAFRelations( - ModelConstants.IS_CONTINUED_BY, - ModelConstants.CONTINUES, - ModelConstants.RELATIONSHIP - ), - ModelConstants.CONTINUES -> OAFRelations( - ModelConstants.CONTINUES, - ModelConstants.IS_CONTINUED_BY, - ModelConstants.RELATIONSHIP - ), - ModelConstants.IS_NEW_VERSION_OF -> OAFRelations( - ModelConstants.IS_NEW_VERSION_OF, - ModelConstants.IS_PREVIOUS_VERSION_OF, - ModelConstants.VERSION - ), - ModelConstants.IS_PREVIOUS_VERSION_OF -> OAFRelations( - ModelConstants.IS_PREVIOUS_VERSION_OF, - ModelConstants.IS_NEW_VERSION_OF, - ModelConstants.VERSION - ), - ModelConstants.IS_DOCUMENTED_BY -> OAFRelations( - ModelConstants.IS_DOCUMENTED_BY, - ModelConstants.DOCUMENTS, - ModelConstants.RELATIONSHIP - ), - ModelConstants.DOCUMENTS -> OAFRelations( - ModelConstants.DOCUMENTS, - ModelConstants.IS_DOCUMENTED_BY, - ModelConstants.RELATIONSHIP - ), - ModelConstants.IS_SOURCE_OF -> OAFRelations( - ModelConstants.IS_SOURCE_OF, - ModelConstants.IS_DERIVED_FROM, - ModelConstants.VERSION - ), - ModelConstants.IS_DERIVED_FROM -> OAFRelations( - ModelConstants.IS_DERIVED_FROM, - ModelConstants.IS_SOURCE_OF, - ModelConstants.VERSION - ), - ModelConstants.IS_VARIANT_FORM_OF -> OAFRelations( - ModelConstants.IS_VARIANT_FORM_OF, - ModelConstants.IS_DERIVED_FROM, - ModelConstants.VERSION - ), - ModelConstants.IS_OBSOLETED_BY -> OAFRelations( - ModelConstants.IS_OBSOLETED_BY, - ModelConstants.IS_NEW_VERSION_OF, - ModelConstants.VERSION - ), - ModelConstants.REVIEWS -> OAFRelations( - ModelConstants.REVIEWS, - ModelConstants.IS_REVIEWED_BY, - ModelConstants.REVIEW - ), - ModelConstants.IS_REVIEWED_BY -> OAFRelations( - ModelConstants.IS_REVIEWED_BY, - ModelConstants.REVIEWS, - ModelConstants.REVIEW - ), - ModelConstants.DOCUMENTS -> OAFRelations( - ModelConstants.DOCUMENTS, - ModelConstants.IS_DOCUMENTED_BY, - ModelConstants.RELATIONSHIP - ), - ModelConstants.IS_DOCUMENTED_BY -> OAFRelations( - ModelConstants.IS_DOCUMENTED_BY, - ModelConstants.DOCUMENTS, - ModelConstants.RELATIONSHIP - ), - ModelConstants.COMPILES -> OAFRelations( - ModelConstants.COMPILES, - ModelConstants.IS_COMPILED_BY, - ModelConstants.RELATIONSHIP - ), - ModelConstants.IS_COMPILED_BY -> OAFRelations( - ModelConstants.IS_COMPILED_BY, - ModelConstants.COMPILES, - ModelConstants.RELATIONSHIP - ) - ) - val datacite_filter: List[String] = { val stream: InputStream = getClass.getResourceAsStream(DATACITE_FILTER_PATH) require(stream != null) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index ecd957aa6..aee5b196c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -286,7 +286,7 @@ object DataciteToOAFTransformation { def generateRelation( sourceId: String, targetId: String, - relClass: String, + relClass: Relation.RELCLASS, collectedFrom: KeyValue, di: DataInfo ): Relation = { @@ -294,9 +294,9 @@ object DataciteToOAFTransformation { val r = new Relation r.setSource(sourceId) r.setTarget(targetId) - r.setRelType(ModelConstants.RESULT_PROJECT) + r.setRelType(Relation.RELTYPE.resultProject) r.setRelClass(relClass) - r.setSubRelType(ModelConstants.OUTCOME) + r.setSubRelType(Relation.SUBRELTYPE.outcome) r.setProvenance(Lists.newArrayList(OafMapperUtils.getProvenance(collectedFrom, di))) r } @@ -309,7 +309,7 @@ object DataciteToOAFTransformation { val p = match_pattern.get._2 val grantId = m.matcher(awardUri).replaceAll("$2") val targetId = s"$p${DHPUtils.md5(grantId)}" - List(generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, relDataInfo)) + List(generateRelation(sourceId, targetId, Relation.RELCLASS.isProducedBy, DATACITE_COLLECTED_FROM, relDataInfo)) } else List() @@ -622,8 +622,7 @@ object DataciteToOAFTransformation { ): List[Relation] = { val bidirectionalRels: List[Relation] = rels .filter(r => - subRelTypeMapping - .contains(r.relationType) && (r.relatedIdentifierType.equalsIgnoreCase("doi") || + Relation.RELCLASS.exists(r.relationType) && (r.relatedIdentifierType.equalsIgnoreCase("doi") || r.relatedIdentifierType.equalsIgnoreCase("pmid") || r.relatedIdentifierType.equalsIgnoreCase("arxiv")) ) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java deleted file mode 100644 index 10a3d4465..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java +++ /dev/null @@ -1,122 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class CleanContextSparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - - String jsonConfiguration = IOUtils - .toString( - CleanContextSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); - - String workingDir = parser.get("workingDir"); - log.info("workingDir: {}", workingDir); - - String contextId = parser.get("contextId"); - log.info("contextId: {}", contextId); - - String verifyParam = parser.get("verifyParam"); - log.info("verifyParam: {}", verifyParam); - - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); - - Class entityClazz = (Class) Class.forName(graphTableClassName); - - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - - cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingDir); - }); - } - - private static void cleanContext(SparkSession spark, String contextId, String verifyParam, - String inputPath, Class entityClazz, String workingDir) { - Dataset res = spark - .read() - .textFile(inputPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)); - - res.map((MapFunction) r -> { - if (!r - .getTitle() - .stream() - .filter( - t -> t - .getQualifier() - .getClassid() - .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) - .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) { - return r; - } - r - .setContext( - r - .getContext() - .stream() - .filter( - c -> !c.getId().split("::")[0] - .equalsIgnoreCase(contextId)) - .collect(Collectors.toList())); - return r; - }, Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingDir); - - spark - .read() - .textFile(workingDir) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(inputPath); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java index 29c8bb680..b98761c74 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java @@ -3,12 +3,20 @@ package eu.dnetlib.dhp.oa.graph.clean; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import java.util.Optional; +import java.util.*; +import java.util.stream.Stream; +import com.google.common.collect.Iterators; +import com.google.common.collect.Sets; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.common.ModelSupport; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -20,12 +28,16 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.action.model.MasterDuplicate; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Entity; import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import scala.Tuple2; public class CleanGraphSparkJob { @@ -33,79 +45,293 @@ public class CleanGraphSparkJob { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { + private ArgumentApplicationParser parser; + public CleanGraphSparkJob(ArgumentApplicationParser parser) { + this.parser = parser; + } + + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - CleanGraphSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json")); + .toString( + CleanGraphSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + ISLookUpService isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl); + + new CleanGraphSparkJob(parser).run(isSparkSessionManaged, isLookup); + } + + public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) + throws ISLookUpException, ClassNotFoundException { + String inputPath = parser.get("inputPath"); log.info("inputPath: {}", inputPath); String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - String isLookupUrl = parser.get("isLookupUrl"); - log.info("isLookupUrl: {}", isLookupUrl); - String graphTableClassName = parser.get("graphTableClassName"); log.info("graphTableClassName: {}", graphTableClassName); + String contextId = parser.get("contextId"); + log.info("contextId: {}", contextId); + + String verifyParam = parser.get("verifyParam"); + log.info("verifyParam: {}", verifyParam); + + String datasourcePath = parser.get("hostedBy"); + log.info("datasourcePath: {}", datasourcePath); + + String country = parser.get("country"); + log.info("country: {}", country); + + String[] verifyCountryParam = Optional + .ofNullable(parser.get("verifyCountryParam")) + .map(s -> s.split(";")) + .orElse(new String[] {}); + log.info("verifyCountryParam: {}", verifyCountryParam); + + String collectedfrom = parser.get("collectedfrom"); + log.info("collectedfrom: {}", collectedfrom); + + String dsMasterDuplicatePath = parser.get("masterDuplicatePath"); + log.info("masterDuplicatePath: {}", dsMasterDuplicatePath); + + Boolean deepClean = Optional + .ofNullable(parser.get("deepClean")) + .map(Boolean::valueOf) + .orElse(Boolean.FALSE); + log.info("deepClean: {}", deepClean); + Class entityClazz = (Class) Class.forName(graphTableClassName); - final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); - final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); SparkConf conf = new SparkConf(); + conf.setAppName(CleanGraphSparkJob.class.getSimpleName() + "#" + entityClazz.getSimpleName()); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration()); - cleanGraphTable(spark, vocs, inputPath, entityClazz, outputPath); - }); + conf, + isSparkSessionManaged, + spark -> { + HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration()); + cleanGraphTable( + spark, vocs, inputPath, entityClazz, outputPath, contextId, verifyParam, datasourcePath, country, + verifyCountryParam, collectedfrom, dsMasterDuplicatePath, deepClean); + }); } private static void cleanGraphTable( - SparkSession spark, - VocabularyGroup vocs, - String inputPath, - Class clazz, - String outputPath) { + SparkSession spark, + VocabularyGroup vocs, + String inputPath, + Class clazz, + String outputPath, String contextId, String verifyParam, String datasourcePath, String country, + String[] verifyCountryParam, String collectedfrom, String dsMasterDuplicatePath, + Boolean deepClean) { final CleaningRuleMap mapping = CleaningRuleMap.create(vocs); - readTableFromPath(spark, inputPath, clazz) - .map((MapFunction) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz)) - .map((MapFunction) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz)) - .map((MapFunction) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz)) - .filter((FilterFunction) GraphCleaningFunctions::filter) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + final Dataset cleaned_basic = readTableFromPath(spark, inputPath, clazz) + .map((MapFunction) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz)) + .map((MapFunction) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz)) + .map((MapFunction) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz)) + .filter((FilterFunction) GraphCleaningFunctions::filter); + + // read the master-duplicate tuples + Dataset md = spark + .read() + .textFile(dsMasterDuplicatePath) + .map(as(MasterDuplicate.class), Encoders.bean(MasterDuplicate.class)); + + // prepare the resolved CF|HB references with the corresponding EMPTY master ID + Dataset resolved = spark + .read() + .textFile(inputPath) + .map(as(clazz), Encoders.bean(clazz)) + .flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class)); + + if (Boolean.FALSE.equals(deepClean)) { + + if (Boolean.TRUE.equals(ModelSupport.isSubClass(clazz, Result.class))) { + save(fixCFHB(clazz, cleaned_basic, md, resolved), outputPath); + } else { + save(cleaned_basic, outputPath); + } + } else if (Boolean.TRUE.equals(ModelSupport.isSubClass(clazz, Result.class))) { + + // load the hostedby mapping + Set hostedBy = Sets + .newHashSet( + spark + .read() + .textFile(datasourcePath) + .collectAsList()); + + // perform the deep cleaning steps + final Dataset cleaned_deep = fixCFHB(clazz, cleaned_basic, md, resolved) + .map( + (MapFunction) value -> GraphCleaningFunctions.cleanContext(value, contextId, verifyParam), + Encoders.bean(clazz)) + .map( + (MapFunction) value -> GraphCleaningFunctions + .cleanCountry(value, verifyCountryParam, hostedBy, collectedfrom, country), + Encoders.bean(clazz)); + + save(cleaned_deep, outputPath); + } else { + save(cleaned_basic, outputPath); + } + } + + private static void save(final Dataset dataset, final String outputPath) { + dataset + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static Dataset fixCFHB(Class clazz, Dataset results, Dataset md, + Dataset resolved) { + + // set the EMPTY master ID/NAME + Dataset resolvedDs = resolved + .joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId"))) + .map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class)) + .filter((FilterFunction) m -> Objects.nonNull(m.getMasterId())); + + return results + .joinWith(resolvedDs, results.col("id").equalTo(resolvedDs.col("resultId")), "left") + .groupByKey( + (MapFunction, String>) t -> ((Result) t._1()).getId(), Encoders.STRING()) + .mapGroups(getMapGroupsFunction(), Encoders.bean(clazz)); } private static Dataset readTableFromPath( - SparkSession spark, String inputEntityPath, Class clazz) { + SparkSession spark, String inputEntityPath, Class clazz) { log.info("Reading Graph table from: {}", inputEntityPath); return spark - .read() - .textFile(inputEntityPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), - Encoders.bean(clazz)); + .read() + .textFile(inputEntityPath) + .map(as(clazz), Encoders.bean(clazz)); + } + + private static MapFunction as(Class clazz) { + return s -> OBJECT_MAPPER.readValue(s, clazz); + } + + private static FlatMapFunction flattenCfHbFn() { + return t -> { + if (!ModelSupport.isSubClass(t, Result.class)) { + return Iterators.emptyIterator(); + } + final Result r = (Result) t; + return Stream + .concat( + Optional + .ofNullable(r.getCollectedfrom()) + .map(cf -> cf.stream().map(KeyValue::getKey)) + .orElse(Stream.empty()), + Stream + .concat( + Optional + .ofNullable(r.getInstance()) + .map( + instances -> instances + .stream() + .map(i -> Optional.ofNullable(i.getHostedby()).map(KeyValue::getKey).orElse(""))) + .orElse(Stream.empty()) + .filter(StringUtils::isNotBlank), + Optional + .ofNullable(r.getInstance()) + .map( + instances -> instances + .stream() + .map( + i -> Optional + .ofNullable(i.getCollectedfrom()) + .map(KeyValue::getKey) + .orElse(""))) + .orElse(Stream.empty()) + .filter(StringUtils::isNotBlank))) + .distinct() + .filter(StringUtils::isNotBlank) + .map(cfHb -> asIdCfHbMapping(r.getId(), cfHb)) + .iterator(); + }; + } + + private static MapFunction, IdCfHbMapping> asIdCfHbMapping() { + return t -> { + final IdCfHbMapping mapping = t._1(); + Optional + .ofNullable(t._2()) + .ifPresent(t2 -> { + mapping.setMasterId(t2.getMasterId()); + mapping.setMasterName(t2.getMasterName()); + + }); + return mapping; + }; + } + + private static IdCfHbMapping asIdCfHbMapping(String resultId, String cfHb) { + IdCfHbMapping m = new IdCfHbMapping(resultId); + m.setCfhb(cfHb); + return m; + } + + private static MapGroupsFunction, T> getMapGroupsFunction() { + return new MapGroupsFunction, T>() { + @Override + public T call(String key, Iterator> values) { + final Tuple2 first = values.next(); + final T res = first._1(); + + updateResult(res, first._2()); + values.forEachRemaining(t -> updateResult(res, t._2())); + return res; + } + + private void updateResult(T t, IdCfHbMapping m) { + if (Objects.nonNull(m) && (ModelSupport.isSubClass(t, Result.class))) { + final Result res = (Result) t; + filter(res.getCollectedfrom()).forEach(kv -> updateKeyValue(kv, m)); + res.getInstance().forEach(i -> { + updateKeyValue(i.getHostedby(), m); + updateKeyValue(i.getCollectedfrom(), m); + }); + } + } + + private Stream filter(List kvs) { + return kvs + .stream() + .filter(kv -> StringUtils.isNotBlank(kv.getKey()) && StringUtils.isNotBlank(kv.getValue())); + } + + private void updateKeyValue(final KeyValue kv, final IdCfHbMapping a) { + if (Objects.nonNull(kv) && Objects.nonNull(kv.getKey()) && kv.getKey().equals(a.getCfhb())) { + kv.setKey(a.getMasterId()); + kv.setValue(a.getMasterName()); + } + } + + }; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GetDatasourceFromCountry.java similarity index 96% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GetDatasourceFromCountry.java index 1b110a279..923ecdb83 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GetDatasourceFromCountry.java @@ -1,10 +1,9 @@ -package eu.dnetlib.dhp.oa.graph.clean.country; +package eu.dnetlib.dhp.oa.graph.clean; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; -import java.util.List; import java.util.Optional; import org.apache.commons.io.IOUtils; @@ -21,7 +20,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/IdCfHbMapping.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/IdCfHbMapping.java similarity index 94% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/IdCfHbMapping.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/IdCfHbMapping.java index fad1129c5..a560360ba 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/IdCfHbMapping.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/IdCfHbMapping.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.oa.graph.clean.cfhb; +package eu.dnetlib.dhp.oa.graph.clean; import java.io.Serializable; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java deleted file mode 100644 index 531b415ed..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java +++ /dev/null @@ -1,227 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean.cfhb; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.util.Iterator; -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.stream.Collectors; -import java.util.stream.Stream; - -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.FlatMapFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.sql.*; -import org.apache.spark.sql.expressions.Aggregator; -import org.jetbrains.annotations.NotNull; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.common.action.model.MasterDuplicate; -import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.utils.DHPUtils; -import scala.Tuple2; - -public class CleanCfHbSparkJob { - - private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJob.class); - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - - String jsonConfiguration = IOUtils - .toString( - CleanCountrySparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_cfhb_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); - - String resolvedPath = parser.get("resolvedPath"); - log.info("resolvedPath: {}", resolvedPath); - - String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - String dsMasterDuplicatePath = parser.get("masterDuplicatePath"); - log.info("masterDuplicatePath: {}", dsMasterDuplicatePath); - - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); - - Class entityClazz = (Class) Class.forName(graphTableClassName); - - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration()); - HdfsSupport.remove(resolvedPath, spark.sparkContext().hadoopConfiguration()); - cleanCfHb( - spark, inputPath, entityClazz, resolvedPath, dsMasterDuplicatePath, outputPath); - }); - } - - private static void cleanCfHb(SparkSession spark, String inputPath, Class entityClazz, - String resolvedPath, String masterDuplicatePath, String outputPath) { - - // read the master-duplicate tuples - Dataset md = spark - .read() - .textFile(masterDuplicatePath) - .map(as(MasterDuplicate.class), Encoders.bean(MasterDuplicate.class)); - - // prepare the resolved CF|HB references with the corresponding EMPTY master ID - Dataset resolved = spark - .read() - .textFile(inputPath) - .map(as(entityClazz), Encoders.bean(entityClazz)) - .flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class)); - - // set the EMPTY master ID/NAME and save it - resolved - .joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId"))) - .map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class)) - .filter((FilterFunction) m -> Objects.nonNull(m.getMasterId())) - .write() - .mode(SaveMode.Overwrite) - .json(resolvedPath); - - // read again the resolved CF|HB mapping - Dataset resolvedDS = spark - .read() - .textFile(resolvedPath) - .map(as(IdCfHbMapping.class), Encoders.bean(IdCfHbMapping.class)); - - // read the result table - Dataset res = spark - .read() - .textFile(inputPath) - .map(as(entityClazz), Encoders.bean(entityClazz)); - - // Join the results with the resolved CF|HB mapping, apply the mapping and save it - res - .joinWith(resolvedDS, res.col("id").equalTo(resolvedDS.col("resultId")), "left") - .groupByKey((MapFunction, String>) t -> t._1().getId(), Encoders.STRING()) - .mapGroups(getMapGroupsFunction(), Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - private static MapFunction, IdCfHbMapping> asIdCfHbMapping() { - return t -> { - final IdCfHbMapping mapping = t._1(); - Optional - .ofNullable(t._2()) - .ifPresent(t2 -> { - mapping.setMasterId(t2.getMasterId()); - mapping.setMasterName(t2.getMasterName()); - - }); - return mapping; - }; - } - - private static FlatMapFunction flattenCfHbFn() { - return r -> Stream - .concat( - Optional - .ofNullable(r.getCollectedfrom()) - .map(cf -> cf.stream().map(KeyValue::getKey)) - .orElse(Stream.empty()), - Stream - .concat( - Optional - .ofNullable(r.getInstance()) - .map( - instances -> instances - .stream() - .map(i -> Optional.ofNullable(i.getHostedby()).map(KeyValue::getKey).orElse(""))) - .orElse(Stream.empty()) - .filter(StringUtils::isNotBlank), - Optional - .ofNullable(r.getInstance()) - .map( - instances -> instances - .stream() - .map( - i -> Optional - .ofNullable(i.getCollectedfrom()) - .map(KeyValue::getKey) - .orElse(""))) - .orElse(Stream.empty()) - .filter(StringUtils::isNotBlank))) - .distinct() - .filter(StringUtils::isNotBlank) - .map(cfHb -> asIdCfHbMapping(r.getId(), cfHb)) - .iterator(); - } - - private static MapGroupsFunction, T> getMapGroupsFunction() { - return new MapGroupsFunction, T>() { - @Override - public T call(String key, Iterator> values) { - final Tuple2 first = values.next(); - final T res = first._1(); - - updateResult(res, first._2()); - values.forEachRemaining(t -> updateResult(res, t._2())); - return res; - } - - private void updateResult(T res, IdCfHbMapping m) { - if (Objects.nonNull(m)) { - res.getCollectedfrom().forEach(kv -> updateKeyValue(kv, m)); - res.getInstance().forEach(i -> { - updateKeyValue(i.getHostedby(), m); - updateKeyValue(i.getCollectedfrom(), m); - }); - } - } - - private void updateKeyValue(final KeyValue kv, final IdCfHbMapping a) { - if (kv.getKey().equals(a.getCfhb())) { - kv.setKey(a.getMasterId()); - kv.setValue(a.getMasterName()); - } - } - - }; - } - - private static IdCfHbMapping asIdCfHbMapping(String resultId, String cfHb) { - IdCfHbMapping m = new IdCfHbMapping(resultId); - m.setCfhb(cfHb); - return m; - } - - private static MapFunction as(Class clazz) { - return s -> OBJECT_MAPPER.readValue(s, clazz); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java deleted file mode 100644 index 37e693de9..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java +++ /dev/null @@ -1,211 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean.country; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Collection; -import java.util.List; -import java.util.Optional; -import java.util.function.Function; -import java.util.stream.Collectors; -import java.util.stream.Stream; - -import javax.swing.text.html.Option; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * @author miriam.baglioni - * @Date 20/07/22 - */ -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; -import eu.dnetlib.dhp.schema.oaf.Country; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import eu.dnetlib.dhp.schema.oaf.utils.PidType; - -public class CleanCountrySparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class); - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - - String jsonConfiguration = IOUtils - .toString( - CleanCountrySparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); - - String workingDir = parser.get("workingDir"); - log.info("workingDir: {}", workingDir); - - String datasourcePath = parser.get("hostedBy"); - log.info("datasourcePath: {}", datasourcePath); - - String country = parser.get("country"); - log.info("country: {}", country); - - String[] verifyParam = parser.get("verifyParam").split(";"); - log.info("verifyParam: {}", verifyParam); - - String collectedfrom = parser.get("collectedfrom"); - log.info("collectedfrom: {}", collectedfrom); - - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); - - Class entityClazz = (Class) Class.forName(graphTableClassName); - - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - - cleanCountry( - spark, country, verifyParam, inputPath, entityClazz, workingDir, collectedfrom, datasourcePath); - }); - } - - private static void cleanCountry(SparkSession spark, String country, String[] verifyParam, - String inputPath, Class entityClazz, String workingDir, String collectedfrom, String datasourcePath) { - - List hostedBy = spark - .read() - .textFile(datasourcePath) - .collectAsList(); - - Dataset res = spark - .read() - .textFile(inputPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)); - - res.map((MapFunction) r -> { - if (r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) || - !r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) { - return r; - } - - List ids = getPidsAndAltIds(r).collect(Collectors.toList()); - if (ids - .stream() - .anyMatch( - p -> p - .getQualifier() - .getClassid() - .equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) { - r - .setCountry( - r - .getCountry() - .stream() - .filter( - c -> toTakeCountry(c, country)) - .collect(Collectors.toList())); - - } - - return r; - }, Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingDir); - - spark - .read() - .textFile(workingDir) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(inputPath); - } - - private static Stream getPidsAndAltIds(T r) { - final Stream resultPids = Optional - .ofNullable(r.getPid()) - .map(Collection::stream) - .orElse(Stream.empty()); - - final Stream instancePids = Optional - .ofNullable(r.getInstance()) - .map( - instance -> instance - .stream() - .flatMap( - i -> Optional - .ofNullable(i.getPid()) - .map(Collection::stream) - .orElse(Stream.empty()))) - .orElse(Stream.empty()); - - final Stream instanceAltIds = Optional - .ofNullable(r.getInstance()) - .map( - instance -> instance - .stream() - .flatMap( - i -> Optional - .ofNullable(i.getAlternateIdentifier()) - .map(Collection::stream) - .orElse(Stream.empty()))) - .orElse(Stream.empty()); - - return Stream - .concat( - Stream.concat(resultPids, instancePids), - instanceAltIds); - } - - private static boolean pidInParam(String value, String[] verifyParam) { - for (String s : verifyParam) - if (value.startsWith(s)) - return true; - return false; - } - - private static boolean toTakeCountry(Country c, String country) { - // If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be - // inserted via propagation - if (!Optional.ofNullable(c.getDataInfo()).isPresent()) - return true; - if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent()) - return true; - return !(c - .getClassid() - .equalsIgnoreCase(country) && - c.getDataInfo().getInferenceprovenance().equals("propagation")); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 683c2417b..f6bf053cd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -83,12 +83,57 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + yarn + cluster + Select datasource ID from country + eu.dnetlib.dhp.oa.graph.clean.GetDatasourceFromCountry + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=10000 + + --inputPath${graphInputPath} + --workingDir${workingDir}/working/hostedby + --country${country} + + + + + + + + eu.dnetlib.dhp.oa.graph.clean.MasterDuplicateAction + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + --hdfsPath${workingDir}/masterduplicate + --hdfsNameNode${nameNode} + + + + + + + @@ -115,12 +160,20 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=15000 --inputPath${graphInputPath}/publication --outputPath${graphOutputPath}/publication --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -141,12 +194,20 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=8000 --inputPath${graphInputPath}/dataset --outputPath${graphOutputPath}/dataset --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -167,12 +228,20 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=5000 --inputPath${graphInputPath}/otherresearchproduct --outputPath${graphOutputPath}/otherresearchproduct --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -193,12 +262,20 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=2000 --inputPath${graphInputPath}/software --outputPath${graphOutputPath}/software --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -219,12 +296,20 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=1000 --inputPath${graphInputPath}/datasource --outputPath${graphOutputPath}/datasource --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Datasource --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -245,12 +330,20 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=1000 --inputPath${graphInputPath}/organization --outputPath${graphOutputPath}/organization --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Organization --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -271,12 +364,20 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=2000 --inputPath${graphInputPath}/project --outputPath${graphOutputPath}/project --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Project --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} @@ -297,486 +398,26 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=20000 --inputPath${graphInputPath}/relation --outputPath${graphOutputPath}/relation --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Relation --isLookupUrl${isLookupUrl} + --contextId${contextId} + --verifyParam${verifyParam} + --country${country} + --verifyCountryParam${verifyCountryParam} + --hostedBy${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + --masterDuplicatePath${workingDir}/masterduplicate + --deepClean${shouldClean} - - - - - ${wf:conf('shouldClean') eq true} - - - - - - - - - - - - - - yarn - cluster - Clean publications context - eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/publication - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication - --workingDir${workingDir}/working/publication - --contextId${contextId} - --verifyParam${verifyParam} - - - - - - - - yarn - cluster - Clean datasets Context - eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/dataset - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset - --workingDir${workingDir}/working/dataset - --contextId${contextId} - --verifyParam${verifyParam} - - - - - - - - yarn - cluster - Clean otherresearchproducts context - eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/otherresearchproduct - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --workingDir${workingDir}/working/otherresearchproduct - --contextId${contextId} - --verifyParam${verifyParam} - - - - - - - - yarn - cluster - Clean softwares context - eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/software - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software - --workingDir${workingDir}/working/software - --contextId${contextId} - --verifyParam${verifyParam} - - - - - - - - - - yarn - cluster - Select datasource ID from country - eu.dnetlib.dhp.oa.graph.clean.country.GetDatasourceFromCountry - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath} - --workingDir${workingDir}/working/hostedby - --country${country} - - - - - - - - - - - - - - - yarn - cluster - Clean publication country - eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/publication - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication - --workingDir${workingDir}/working/publication - --country${country} - --verifyParam${verifyCountryParam} - --hostedBy${workingDir}/working/hostedby - --collectedfrom${collectedfrom} - - - - - - - - yarn - cluster - Clean dataset country - eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/dataset - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset - --workingDir${workingDir}/working/dataset - --country${country} - --verifyParam${verifyCountryParam} - --hostedBy${workingDir}/working/hostedby - --collectedfrom${collectedfrom} - - - - - - - - yarn - cluster - Clean otherresearchproduct country - eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/otherresearchproduct - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --workingDir${workingDir}/working/otherresearchproduct - --country${country} - --verifyParam${verifyCountryParam} - --hostedBy${workingDir}/working/hostedby - --collectedfrom${collectedfrom} - - - - - - - - yarn - cluster - Clean software country - eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/software - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software - --workingDir${workingDir}/working/software - --country${country} - --verifyParam${verifyCountryParam} - --hostedBy${workingDir}/working/hostedby - --collectedfrom${collectedfrom} - - - - - - - - - - ${wf:conf('shouldClean') eq true} - - - - - - - eu.dnetlib.dhp.oa.graph.clean.MasterDuplicateAction - --postgresUrl${postgresURL} - --postgresUser${postgresUser} - --postgresPassword${postgresPassword} - --hdfsPath${workingDir}/masterduplicate - --hdfsNameNode${nameNode} - - - - - - - - - - - - - - - yarn - cluster - patch publication cfhb - eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/publication - --resolvedPath${workingDir}/cfHbResolved/publication - --outputPath${workingDir}/cfHbPatched/publication - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication - --masterDuplicatePath${workingDir}/masterduplicate - - - - - - - - yarn - cluster - patch dataset cfhb - eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/dataset - --resolvedPath${workingDir}/cfHbResolved/dataset - --outputPath${workingDir}/cfHbPatched/dataset - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset - --masterDuplicatePath${workingDir}/masterduplicate - - - - - - - - yarn - cluster - patch otherresearchproduct cfhb - eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/otherresearchproduct - --resolvedPath${workingDir}/cfHbResolved/otherresearchproduct - --outputPath${workingDir}/cfHbPatched/otherresearchproduct - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --masterDuplicatePath${workingDir}/masterduplicate - - - - - - - - yarn - cluster - patch software cfhb - eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --inputPath${graphOutputPath}/software - --resolvedPath${workingDir}/cfHbResolved/software - --outputPath${workingDir}/cfHbPatched/software - --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software - --masterDuplicatePath${workingDir}/masterduplicate - - - - - - - - - - - - - - - - - - - - ${workingDir}/cfHbPatched/publication - ${graphOutputPath}/publication - - - - - - - - - - - ${workingDir}/cfHbPatched/dataset - ${graphOutputPath}/dataset - - - - - - - - - - - ${workingDir}/cfHbPatched/otherresearchproduct - ${graphOutputPath}/otherresearchproduct - - - - - - - - - - - ${workingDir}/cfHbPatched/software - ${graphOutputPath}/software - - - - - - + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json index 9cfed1e91..0a703763b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json @@ -28,5 +28,53 @@ "paramLongName": "graphTableClassName", "paramDescription": "class name moelling the graph table", "paramRequired": true + }, + { + "paramName": "ci", + "paramLongName": "contextId", + "paramDescription": "the id of the context to be removed", + "paramRequired": false + }, + { + "paramName": "vf", + "paramLongName": "verifyParam", + "paramDescription": "the parameter to be verified to remove the context", + "paramRequired": false + }, + { + "paramName": "c", + "paramLongName": "country", + "paramDescription": "the id of the context to be removed", + "paramRequired": false + }, + { + "paramName": "vfc", + "paramLongName": "verifyCountryParam", + "paramDescription": "the parameter to be verified to remove the country", + "paramRequired": false + }, + { + "paramName": "cf", + "paramLongName": "collectedfrom", + "paramDescription": "the collectedfrom value for which we should apply the cleaning", + "paramRequired": false + }, + { + "paramName": "hb", + "paramLongName": "hostedBy", + "paramDescription": "the set of datasources having the specified country in the graph searched for in the hostedby of the results", + "paramRequired": false + }, + { + "paramName": "md", + "paramLongName": "masterDuplicatePath", + "paramDescription": "path to the file on HDFS holding the datasource id tuples [master, duplicate]", + "paramRequired": false + }, + { + "paramName": "dc", + "paramLongName": "deepClean", + "paramDescription": "flag to activate further cleaning steps", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java deleted file mode 100644 index 91094f534..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java +++ /dev/null @@ -1,289 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; - -public class CleanContextTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(CleanContextTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(CleanContextTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(CleanContextTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void testResultClean() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") - .getPath(); - final String prefix = "gcube "; - - spark - .read() - .textFile(sourcePath) - .map( - (MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), - Encoders.bean(Publication.class)) - .write() - .json(workingDir.toString() + "/publication"); - - CleanContextSparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/publication", - "--graphTableClassName", Publication.class.getCanonicalName(), - "--workingDir", workingDir.toString() + "/working", - "--contextId", "sobigdata", - "--verifyParam", "gCube " - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - - Assertions.assertEquals(7, tmp.count()); - - // original result with sobigdata context and gcube as starting string in the main title for the publication - Assertions - .assertEquals( - 0, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) - .collect() - .get(0) - .getContext() - .size()); - - // original result with sobigdata context without gcube as starting string in the main title for the publication - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) - .collect() - .get(0) - .getContext() - .size()); - Assertions - .assertEquals( - "sobigdata::projects::2", - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) - .collect() - .get(0) - .getContext() - .get(0) - .getId()); - - // original result with sobigdata context with gcube as starting string in the subtitle - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) - .collect() - .get(0) - .getContext() - .size()); - Assertions - .assertEquals( - "sobigdata::projects::2", - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) - .collect() - .get(0) - .getContext() - .get(0) - .getId()); - List titles = tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) - .collect() - .get(0) - .getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); - Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); - - // original result with sobigdata context with gcube not as starting string in the main title - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) - .collect() - .get(0) - .getContext() - .size()); - Assertions - .assertEquals( - "sobigdata::projects::1", - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) - .collect() - .get(0) - .getContext() - .get(0) - .getId()); - titles = tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) - .collect() - .get(0) - .getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix)); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim())); - Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); - - // original result with sobigdata in context and also other contexts with gcube as starting string for the main - // title - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) - .collect() - .get(0) - .getContext() - .size()); - Assertions - .assertEquals( - "dh-ch", - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) - .collect() - .get(0) - .getContext() - .get(0) - .getId()); - titles = tmp - .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) - .collect() - .get(0) - .getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); - Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); - - // original result with multiple main title one of which whith gcube as starting string and with 2 contextes - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) - .collect() - .get(0) - .getContext() - .size()); - Assertions - .assertEquals( - "dh-ch", - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) - .collect() - .get(0) - .getContext() - .get(0) - .getId()); - titles = tmp - .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) - .collect() - .get(0) - .getTitle(); - Assertions.assertEquals(2, titles.size()); - Assertions - .assertTrue( - titles - .stream() - .anyMatch( - t -> t.getQualifier().getClassid().equals("main title") - && t.getValue().toLowerCase().startsWith(prefix))); - - // original result without sobigdata in context with gcube as starting string for the main title - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) - .collect() - .get(0) - .getContext() - .size()); - Assertions - .assertEquals( - "dh-ch", - tmp - .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) - .collect() - .get(0) - .getContext() - .get(0) - .getId()); - titles = tmp - .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) - .collect() - .get(0) - .getTitle(); - Assertions.assertEquals(2, titles.size()); - - Assertions - .assertTrue( - titles - .stream() - .anyMatch( - t -> t.getQualifier().getClassid().equals("main title") - && t.getValue().toLowerCase().startsWith(prefix))); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java deleted file mode 100644 index 3bc69cfd1..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java +++ /dev/null @@ -1,190 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * @author miriam.baglioni - * @Date 20/07/22 - */ -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Publication; - -public class CleanCountryTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(CleanCountryTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(CleanCountryTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(CleanCountryTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void testResultClean() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json") - .getPath(); - - spark - .read() - .textFile(sourcePath) - .map( - (MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), - Encoders.bean(Publication.class)) - .write() - .json(workingDir.toString() + "/publication"); - - CleanCountrySparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/publication", - "--graphTableClassName", Publication.class.getCanonicalName(), - "--workingDir", workingDir.toString() + "/working", - "--country", "NL", - "--verifyParam", "10.17632", - "--collectedfrom", "NARCIS", - "--hostedBy", getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") - .getPath() - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - - Assertions.assertEquals(8, tmp.count()); - - // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) - .collect() - .get(0) - .getCountry() - .size()); - - // original result with NL country and pid not starting with Mendely prefix - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) - .collect() - .get(0) - .getCountry() - .size()); - - // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not - // inserted with propagation - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) - .collect() - .get(0) - .getCountry() - .size()); - - // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with - // propagation - Assertions - .assertEquals( - 0, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6ag")) - .collect() - .get(0) - .getCountry() - .size()); - } - - @Test - public void testDatasetClean() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json") - .getPath(); - - spark - .read() - .textFile(sourcePath) - .map( - (MapFunction) r -> OBJECT_MAPPER.readValue(r, Dataset.class), - Encoders.bean(Dataset.class)) - .write() - .json(workingDir.toString() + "/dataset"); - - CleanCountrySparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/dataset", - "-graphTableClassName", Dataset.class.getCanonicalName(), - "-workingDir", workingDir.toString() + "/working", - "-country", "NL", - "-verifyParam", "10.17632", - "-collectedfrom", "NARCIS", - "-hostedBy", getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") - .getPath() - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - - Assertions.assertEquals(1, tmp.count()); - - Assertions.assertEquals(0, tmp.first().getCountry().size()); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java new file mode 100644 index 000000000..4bca10f1f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java @@ -0,0 +1,924 @@ + +package eu.dnetlib.dhp.oa.graph.clean; + +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.lenient; + +import java.io.File; +import java.io.IOException; +import java.net.URISyntaxException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.*; +import java.util.stream.Collectors; + +import org.apache.commons.cli.ParseException; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.commons.io.filefilter.FalseFileFilter; +import org.apache.commons.io.filefilter.TrueFileFilter; +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +public class CleanGraphSparkJobTest { + + private static final Logger log = LoggerFactory.getLogger(CleanGraphSparkJobTest.class); + + public static final ObjectMapper MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + @Mock + private ISLookUpService isLookUpService; + + private VocabularyGroup vocabularies; + + private CleaningRuleMap mapping; + + private static SparkSession spark; + + private static Path testBaseTmpPath; + + private static String graphInputPath; + + private static String graphOutputPath; + + private static String dsMasterDuplicatePath; + + @BeforeAll + public static void beforeAll() throws IOException, URISyntaxException { + testBaseTmpPath = Files.createTempDirectory(CleanGraphSparkJobTest.class.getSimpleName()); + log.info("using test base path {}", testBaseTmpPath); + + File basePath = Paths + .get( + Objects + .requireNonNull( + CleanGraphSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/graph")) + .toURI()) + .toFile(); + + List paths = FileUtils + .listFilesAndDirs(basePath, FalseFileFilter.FALSE, TrueFileFilter.TRUE) + .stream() + .filter(f -> !f.getAbsolutePath().endsWith("/graph")) + .collect(Collectors.toList()); + + for (File path : paths) { + String type = StringUtils.substringAfterLast(path.getAbsolutePath(), "/"); + FileUtils + .copyDirectory( + path, + testBaseTmpPath.resolve("input").resolve("graph").resolve(type).toFile()); + } + + FileUtils + .copyFileToDirectory( + Paths + .get( + CleanGraphSparkJobTest.class + .getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/masterduplicate.json") + .toURI()) + .toFile(), + testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toFile()); + + graphInputPath = testBaseTmpPath.resolve("input").resolve("graph").toString(); + graphOutputPath = testBaseTmpPath.resolve("output").resolve("graph").toString(); + dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString(); + + SparkConf conf = new SparkConf(); + conf.setAppName(CleanGraphSparkJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", testBaseTmpPath.toString()); + conf.set("hive.metastore.warehouse.dir", testBaseTmpPath.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .config(conf) + .getOrCreate(); + } + + @BeforeEach + public void setUp() throws ISLookUpException, IOException { + lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); + lenient() + .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) + .thenReturn(synonyms()); + + vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); + mapping = CleaningRuleMap.create(vocabularies); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(testBaseTmpPath.toFile()); + spark.stop(); + } + + @Test + void testCleanRelations() throws Exception { + + spark + .read() + .textFile(graphInputPath.toString() + "/relation") + .map(as(Relation.class), Encoders.bean(Relation.class)) + .collectAsList() + .forEach( + r -> assertFalse( + vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r.getRelClass()))); + + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/relation", + "--outputPath", graphOutputPath + "/relation", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Relation.class.getCanonicalName(), + "--deepClean", "false", + "--masterDuplicatePath", dsMasterDuplicatePath, + })).run(false, isLookUpService); + + spark + .read() + .textFile(graphOutputPath.toString() + "/relation") + .map(as(Relation.class), Encoders.bean(Relation.class)) + .collectAsList() + .forEach(r -> { + + assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r.getRelClass())); + assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_SUBRELTYPE).contains(r.getSubRelType())); + + assertEquals("iis", r.getProvenance().get(0).getDataInfo().getProvenanceaction().getClassid()); + assertEquals("Inferred by OpenAIRE", r.getProvenance().get(0).getDataInfo().getProvenanceaction().getClassname()); + }); + } + + @Test + void testFilter_invisible_true() throws Exception { + + assertNotNull(vocabularies); + assertNotNull(mapping); + + String json = IOUtils + .toString( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json"))); + Publication p_in = MAPPER.readValue(json, Publication.class); + + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + assertEquals(true, GraphCleaningFunctions.filter(p_in)); + } + + @Test + void testFilter_true_nothing_to_filter() throws Exception { + + assertNotNull(vocabularies); + assertNotNull(mapping); + + String json = IOUtils + .toString( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json"))); + Publication p_in = MAPPER.readValue(json, Publication.class); + + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + assertEquals(true, GraphCleaningFunctions.filter(p_in)); + } + + @Test + void testFilter_missing_invisible() throws Exception { + + assertNotNull(vocabularies); + assertNotNull(mapping); + + String json = IOUtils + .toString( + Objects + .requireNonNull( + getClass() + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json"))); + Publication p_in = MAPPER.readValue(json, Publication.class); + + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + assertEquals(true, GraphCleaningFunctions.filter(p_in)); + } + + @Test + void testCleaning_publication() throws Exception { + + final String id = "50|CSC_________::2250a70c903c6ac6e4c01438259e9375"; + + Publication p_in = read(spark, graphInputPath + "/publication", Publication.class) + .filter(String.format("id = '%s'", id)) + .first(); + + assertNull(p_in.getBestaccessright()); + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/publication", + "--outputPath", graphOutputPath + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "false", + "--masterDuplicatePath", dsMasterDuplicatePath, + })).run(false, isLookUpService); + + Publication p = read(spark, graphOutputPath + "/publication", Publication.class) + .filter(String.format("id = '%s'", id)) + .first(); + + assertNull(p.getPublisher()); + + assertEquals("und", p.getLanguage().getClassid()); + assertEquals("Undetermined", p.getLanguage().getClassname()); + + assertEquals("DE", p.getCountry().get(0).getClassid()); + assertEquals("Germany", p.getCountry().get(0).getClassname()); + + assertEquals("0018", p.getInstance().get(0).getInstancetype().getClassid()); + assertEquals("Annotation", p.getInstance().get(0).getInstancetype().getClassname()); + + assertEquals("0027", p.getInstance().get(1).getInstancetype().getClassid()); + assertEquals("Model", p.getInstance().get(1).getInstancetype().getClassname()); + + assertEquals("0038", p.getInstance().get(2).getInstancetype().getClassid()); + assertEquals("Other literature type", p.getInstance().get(2).getInstancetype().getClassname()); + + assertEquals("CLOSED", p.getInstance().get(0).getAccessright().getClassid()); + assertEquals("Closed Access", p.getInstance().get(0).getAccessright().getClassname()); + + Set pidTerms = vocabularies.getTerms(ModelConstants.DNET_PID_TYPES); + assertTrue( + p + .getPid() + .stream() + .map(StructuredProperty::getQualifier) + .allMatch(q -> pidTerms.contains(q.getClassid()))); + + List poi = p.getInstance(); + assertNotNull(poi); + assertEquals(3, poi.size()); + + final Instance poii = poi.get(0); + assertNotNull(poii); + assertNotNull(poii.getPid()); + + assertEquals(2, poii.getPid().size()); + + assertTrue( + poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x"))); + assertTrue(poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd"))); + + assertNotNull(poii.getAlternateIdentifier()); + assertEquals(1, poii.getAlternateIdentifier().size()); + + assertTrue( + poii + .getAlternateIdentifier() + .stream() + .anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); + + assertEquals(3, p.getTitle().size()); + + List titles = p + .getTitle() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toList()); + assertTrue(titles.contains("omic")); + assertTrue( + titles.contains("Optical response of strained- and unstrained-silicon cold-electron bolometers test")); + assertTrue(titles.contains("｢マキャベリ的知性と心の理論の進化論｣ リチャード・バーン， アンドリュー・ホワイトゥン 編／藤田和生， 山下博志， 友永雅巳 監訳")); + + assertEquals("CLOSED", p.getBestaccessright().getClassid()); + assertNull(p.getPublisher()); + + assertEquals("1970-10-07", p.getDateofacceptance()); + + assertEquals("0038", p.getInstance().get(2).getInstancetype().getClassid()); + assertEquals("Other literature type", p.getInstance().get(2).getInstancetype().getClassname()); + + final List pci = p.getInstance(); + assertNotNull(pci); + assertEquals(3, pci.size()); + + final Instance pcii = pci.get(0); + assertNotNull(pcii); + assertNotNull(pcii.getPid()); + + assertEquals(2, pcii.getPid().size()); + + assertTrue( + pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x"))); + assertTrue(pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd"))); + + assertNotNull(pcii.getAlternateIdentifier()); + assertEquals(1, pcii.getAlternateIdentifier().size()); + assertTrue( + pcii + .getAlternateIdentifier() + .stream() + .anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); + + assertNotNull(p.getSubject()); + + List fos_subjects = p + .getSubject() + .stream() + .filter(s -> ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid())) + .collect(Collectors.toList()); + + assertNotNull(fos_subjects); + assertEquals(2, fos_subjects.size()); + + assertTrue( + fos_subjects + .stream() + .anyMatch( + s -> "0101 mathematics".equals(s.getValue()) & + ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) & + "sysimport:crosswalk:datasetarchive" + .equals(s.getDataInfo().getProvenanceaction().getClassid()))); + + assertTrue( + fos_subjects + .stream() + .anyMatch( + s -> "0102 computer and information sciences".equals(s.getValue()) & + ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))); + + verify_keyword(p, "In Situ Hybridization"); + verify_keyword(p, "Avicennia"); + } + + @Test + void testCleanDoiBoost() throws IOException, ParseException, ISLookUpException, ClassNotFoundException { + verifyFiltering(1, "50|doi_________::b0baa0eb88a5788f0b8815560d2a32f2"); + } + + @Test + void testCleanDoiBoost2() throws IOException, ParseException, ISLookUpException, ClassNotFoundException { + verifyFiltering(1, "50|doi_________::4972b0ca81b96b225aed8038bb965656"); + } + + private void verifyFiltering(int expectedCount, String id) + throws ISLookUpException, ClassNotFoundException, IOException, ParseException { + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/publication", + "--outputPath", graphOutputPath + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "false", + "--masterDuplicatePath", dsMasterDuplicatePath, + })).run(false, isLookUpService); + + Dataset p = read(spark, graphOutputPath + "/publication", Publication.class) + .filter(String.format("id = '%s'", id)); + + assertEquals(expectedCount, p.count()); + } + + @Test + void testCleanContext() throws Exception { + final String prefix = "gcube "; + + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/publication", + "--outputPath", graphOutputPath + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "true", + "--contextId", "sobigdata", + "--verifyParam", "gCube ", + "--masterDuplicatePath", dsMasterDuplicatePath, + "--country", "NL", + "--verifyCountryParam", "10.17632", + "--collectedfrom", "NARCIS", + "--hostedBy", Objects + .requireNonNull( + getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")) + .getPath() + })).run(false, isLookUpService); + + Dataset pubs = read(spark, graphOutputPath + "/publication", Publication.class) + .filter((FilterFunction) p1 -> StringUtils.endsWith(p1.getId(), "_ctx")); + + assertEquals(7, pubs.count()); + + // original result with sobigdata context and gcube as starting string in the main title for the publication + assertEquals( + 0, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::0224aae28af558f21768dbc6439a_ctx")) + .first() + .getContext() + .size()); + + // original result with sobigdata context without gcube as starting string in the main title for the publication + assertEquals( + 1, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "sobigdata::projects::2", + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx")) + .first() + .getContext() + .get(0) + .getId()); + + // original result with sobigdata context with gcube as starting string in the subtitle + assertEquals( + 1, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "sobigdata::projects::2", + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) + .first() + .getContext() + .get(0) + .getId()); + + List titles = pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) + .first() + .getTitle(); + + assertEquals(1, titles.size()); + assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); + + // original result with sobigdata context with gcube not as starting string in the main title + assertEquals( + 1, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "sobigdata::projects::1", + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) + .first() + .getContext() + .get(0) + .getId()); + titles = pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) + .first() + .getTitle(); + + assertEquals(1, titles.size()); + assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim())); + assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + // original result with sobigdata in context and also other contexts with gcube as starting string for the main + // title + assertEquals( + 1, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "dh-ch", + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) + .first() + .getContext() + .get(0) + .getId()); + titles = pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) + .first() + .getTitle(); + + assertEquals(1, titles.size()); + assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + // original result with multiple main title one of which whith gcube as starting string and with 2 contextes + assertEquals( + 1, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "dh-ch", + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) + .first() + .getContext() + .get(0) + .getId()); + titles = pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) + .first() + .getTitle(); + + assertEquals(2, titles.size()); + assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); + + // original result without sobigdata in context with gcube as starting string for the main title + assertEquals( + 1, + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) + .first() + .getContext() + .size()); + assertEquals( + "dh-ch", + pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) + .first() + .getContext() + .get(0) + .getId()); + titles = pubs + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) + .first() + .getTitle(); + + assertEquals(2, titles.size()); + + assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); + + } + + @Test + void testCleanCfHbSparkJob() throws Exception { + + final Dataset pubs_in = read(spark, graphInputPath + "/publication", Publication.class); + final Publication p1_in = pubs_in + .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13b_cfhb'") + .first(); + assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", p1_in.getCollectedfrom().get(0).getKey()); + assertEquals("Bacterial Protein Interaction Database - DUP", p1_in.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", + p1_in.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "Bacterial Protein Interaction Database - DUP", p1_in.getInstance().get(0).getCollectedfrom().getValue()); + + final Publication p2_in = pubs_in + .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3a_cfhb'") + .first(); + assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", p2_in.getCollectedfrom().get(0).getKey()); + assertEquals("FILUR DATA - DUP", p2_in.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", + p2_in.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals("FILUR DATA - DUP", p2_in.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|re3data_____::6ffd7bc058f762912dc494cd9c175341", p2_in.getInstance().get(0).getHostedby().getKey()); + assertEquals("depositar - DUP", p2_in.getInstance().get(0).getHostedby().getValue()); + + final Publication p3_in = pubs_in + .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7d_cfhb'") + .first(); + assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getCollectedfrom().get(0).getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", p3_in.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", + p3_in.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getInstance().get(0).getHostedby().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getHostedby().getValue()); + + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/publication", + "--outputPath", graphOutputPath + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "true", + "--contextId", "sobigdata", + "--verifyParam", "gCube ", + "--masterDuplicatePath", dsMasterDuplicatePath, + "--country", "NL", + "--verifyCountryParam", "10.17632", + "--collectedfrom", "NARCIS", + "--hostedBy", Objects + .requireNonNull( + getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")) + .getPath() + })).run(false, isLookUpService); + + assertTrue(Files.exists(Paths.get(graphOutputPath, "publication"))); + + final Dataset pubs_out = read(spark, graphOutputPath + "/publication", Publication.class) + .filter((FilterFunction) p -> StringUtils.endsWith(p.getId(), "_cfhb")); + + assertEquals(3, pubs_out.count()); + + final Publication p1_out = pubs_out + .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13b_cfhb'") + .first(); + assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", p1_out.getCollectedfrom().get(0).getKey()); + assertEquals("Bacterial Protein Interaction Database", p1_out.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", + p1_out.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "Bacterial Protein Interaction Database", p1_out.getInstance().get(0).getCollectedfrom().getValue()); + + final Publication p2_out = pubs_out + .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3a_cfhb'") + .first(); + assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", p2_out.getCollectedfrom().get(0).getKey()); + assertEquals("FULIR Data", p2_out.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|re3data_____::fc1db64b3964826913b1e9eafe830490", + p2_out.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals("FULIR Data", p2_out.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|fairsharing_::3f647cadf56541fb9513cb63ec370187", p2_out.getInstance().get(0).getHostedby().getKey()); + assertEquals("depositar", p2_out.getInstance().get(0).getHostedby().getValue()); + + final Publication p3_out = pubs_out + .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7d_cfhb'") + .first(); + assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getCollectedfrom().get(0).getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", p3_out.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", + p3_out.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getInstance().get(0).getHostedby().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getHostedby().getValue()); + } + + @Test + void testCleanCountry() throws Exception { + + new CleanGraphSparkJob( + args( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", + new String[] { + "--inputPath", graphInputPath + "/publication", + "--outputPath", graphOutputPath + "/publication", + "--isLookupUrl", "lookupurl", + "--graphTableClassName", Publication.class.getCanonicalName(), + "--deepClean", "true", + "--contextId", "sobigdata", + "--verifyParam", "gCube ", + "--masterDuplicatePath", dsMasterDuplicatePath, + "--country", "NL", + "--verifyCountryParam", "10.17632", + "--collectedfrom", "NARCIS", + "--hostedBy", Objects + .requireNonNull( + getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")) + .getPath() + })).run(false, isLookUpService); + + final Dataset pubs_out = read(spark, graphOutputPath + "/publication", Publication.class) + .filter((FilterFunction) p -> StringUtils.endsWith(p.getId(), "_country")); + + assertEquals(8, pubs_out.count()); + + // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS + assertEquals( + 1, + pubs_out + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::0224aae28af558f21768dbc6_country")) + .first() + .getCountry() + .size()); + + // original result with NL country and pid not starting with Mendely prefix + assertEquals( + 1, + pubs_out + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1_country")) + .first() + .getCountry() + .size()); + + // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not + // inserted with propagation + assertEquals( + 1, + pubs_out + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c81248c335f0aa07e06817e_country")) + .first() + .getCountry() + .size()); + + // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with + // propagation + assertEquals( + 0, + pubs_out + .filter( + (FilterFunction) p -> p + .getId() + .equals("50|DansKnawCris::3c81248c335f0aa07e06817d_country")) + .first() + .getCountry() + .size()); + } + + private List vocs() throws IOException { + return IOUtils + .readLines( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"))); + } + + private List synonyms() throws IOException { + return IOUtils + .readLines( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"))); + } + + private org.apache.spark.sql.Dataset read(SparkSession spark, String path, Class clazz) { + return spark + .read() + .textFile(path) + .map(as(clazz), Encoders.bean(clazz)); + } + + private static MapFunction as(Class clazz) { + return s -> MAPPER.readValue(s, clazz); + } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + Objects + .requireNonNull( + CleanGraphSparkJobTest.class.getResourceAsStream(path))); + } + + private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { + ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs)); + parser.parseArgument(args); + return parser; + } + + private static void verify_keyword(Publication p_cleaned, String subject) { + Optional s1 = p_cleaned + .getSubject() + .stream() + .filter(s -> s.getValue().equals(subject)) + .findFirst(); + + assertTrue(s1.isPresent()); + assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassid()); + assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassname()); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java index 3e9bce675..92fa38719 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java @@ -13,7 +13,6 @@ import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.io.IOUtils; -import org.apache.hadoop.hdfs.server.datanode.fsdataset.impl.MappableBlock; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; @@ -59,7 +58,7 @@ public class GraphCleaningFunctionsTest { void testCleanRelations() throws Exception { List lines = IOUtils - .readLines(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/relation.json")); + .readLines(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/graph/relation/relation.json")); for (String json : lines) { Relation r_in = MAPPER.readValue(json, Relation.class); assertNotNull(r_in); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java deleted file mode 100644 index 9096180ef..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java +++ /dev/null @@ -1,213 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean.cfhb; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; - -import java.io.File; -import java.io.IOException; -import java.net.URISyntaxException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Publication; - -public class CleanCfHbSparkJobTest { - - private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJobTest.class); - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path testBaseTmpPath; - - private static String resolvedPath; - - private static String graphInputPath; - - private static String graphOutputPath; - - private static String dsMasterDuplicatePath; - - @BeforeAll - public static void beforeAll() throws IOException, URISyntaxException { - - testBaseTmpPath = Files.createTempDirectory(CleanCfHbSparkJobTest.class.getSimpleName()); - log.info("using test base path {}", testBaseTmpPath); - - final File entitiesSources = Paths - .get(CleanCfHbSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities").toURI()) - .toFile(); - - FileUtils - .copyDirectory( - entitiesSources, - testBaseTmpPath.resolve("input").resolve("entities").toFile()); - - FileUtils - .copyFileToDirectory( - Paths - .get( - CleanCfHbSparkJobTest.class - .getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/masterduplicate.json") - .toURI()) - .toFile(), - testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toFile()); - - graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString(); - resolvedPath = testBaseTmpPath.resolve("workingDir").resolve("cfHbResolved").toString(); - graphOutputPath = testBaseTmpPath.resolve("workingDir").resolve("cfHbPatched").toString(); - dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString(); - - SparkConf conf = new SparkConf(); - conf.setAppName(CleanCfHbSparkJobTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("spark.ui.enabled", "false"); - - spark = SparkSession - .builder() - .appName(CleanCfHbSparkJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(testBaseTmpPath.toFile()); - spark.stop(); - } - - @Test - void testCleanCfHbSparkJob() throws Exception { - final String outputPath = graphOutputPath + "/dataset"; - final String inputPath = graphInputPath + "/dataset"; - - org.apache.spark.sql.Dataset records = read(spark, inputPath, Dataset.class); - Dataset d = records - .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'") - .first(); - assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", d.getCollectedfrom().get(0).getKey()); - assertEquals("Bacterial Protein Interaction Database - DUP", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals( - "Bacterial Protein Interaction Database - DUP", d.getInstance().get(0).getCollectedfrom().getValue()); - - d = records - .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3adc37a'") - .first(); - assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", d.getCollectedfrom().get(0).getKey()); - assertEquals("FILUR DATA - DUP", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals("FILUR DATA - DUP", d.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|re3data_____::6ffd7bc058f762912dc494cd9c175341", d.getInstance().get(0).getHostedby().getKey()); - assertEquals("depositar - DUP", d.getInstance().get(0).getHostedby().getValue()); - - d = records - .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'") - .first(); - assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals( - "DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue()); - - CleanCfHbSparkJob - .main( - new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", inputPath, - "--outputPath", outputPath, - "--resolvedPath", resolvedPath + "/dataset", - "--graphTableClassName", Dataset.class.getCanonicalName(), - "--masterDuplicatePath", dsMasterDuplicatePath - }); - - assertTrue(Files.exists(Paths.get(graphOutputPath, "dataset"))); - - records = read(spark, outputPath, Dataset.class); - - assertEquals(3, records.count()); - - d = records - .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'") - .first(); - assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", d.getCollectedfrom().get(0).getKey()); - assertEquals("Bacterial Protein Interaction Database", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals("Bacterial Protein Interaction Database", d.getInstance().get(0).getCollectedfrom().getValue()); - - d = records - .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3adc37a'") - .first(); - assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", d.getCollectedfrom().get(0).getKey()); - assertEquals("FULIR Data", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|re3data_____::fc1db64b3964826913b1e9eafe830490", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals("FULIR Data", d.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|fairsharing_::3f647cadf56541fb9513cb63ec370187", d.getInstance().get(0).getHostedby().getKey()); - assertEquals("depositar", d.getInstance().get(0).getHostedby().getValue()); - - d = records - .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'") - .first(); - assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals( - "DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue()); - - d = records - .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'") - .first(); - assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey()); - assertEquals( - "DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue()); - assertEquals( - "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey()); - assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue()); - } - - private org.apache.spark.sql.Dataset read(SparkSession spark, String path, Class clazz) { - return spark - .read() - .textFile(path) - .map(as(clazz), Encoders.bean(clazz)); - } - - private static MapFunction as(Class clazz) { - return s -> OBJECT_MAPPER.readValue(s, clazz); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities/dataset/dataset.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities/dataset/dataset.json deleted file mode 100644 index bf2f2d963..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities/dataset/dataset.json +++ /dev/null @@ -1,3 +0,0 @@ -{"author":[{"affiliation":[],"fullname":"Greenough, B","name":"B","pid":[],"rank":1,"surname":"Greenough"}],"bestaccessright":{"classid":"UNKNOWN","classname":"not 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