diff --git a/dhp-schemas/pom.xml b/dhp-schemas/pom.xml index a8535fc93..bf92e1549 100644 --- a/dhp-schemas/pom.xml +++ b/dhp-schemas/pom.xml @@ -22,15 +22,6 @@ commons-io commons-io - - com.googlecode.protobuf-java-format - protobuf-java-format - - - - eu.dnetlib - dnet-openaire-data-protos - diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProducts.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java similarity index 91% rename from dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProducts.java rename to dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java index 35fe541af..5f32b8895 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProducts.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java @@ -3,7 +3,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; import java.util.List; -public class OtherResearchProducts extends Result implements Serializable { +public class OtherResearchProduct extends Result implements Serializable { private List> contactperson; diff --git a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/proto/TestParseProtoJson.java b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/proto/TestParseProtoJson.java deleted file mode 100644 index 7f5139631..000000000 --- a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/proto/TestParseProtoJson.java +++ /dev/null @@ -1,23 +0,0 @@ -package eu.dnetlib.dhp.schema.proto; - -import com.googlecode.protobuf.format.JsonFormat; -import eu.dnetlib.data.proto.OafProtos; -import org.apache.commons.io.IOUtils; -import org.junit.Test; - -public class TestParseProtoJson { - - @Test - public void testParse() throws Exception { - final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/schema/proto/hugeRecord.json")); - - final OafProtos.Oaf.Builder oafBuilder = OafProtos.Oaf.newBuilder(); - - JsonFormat jf = new JsonFormat(); - jf.merge(IOUtils.toInputStream(json), oafBuilder); - - OafProtos.Oaf oaf = oafBuilder.build(); - System.out.println(jf.printToString(oaf)); - } - -} diff --git a/dhp-schemas/src/test/resources/eu/dnetlib/dhp/schema/proto/hugeRecord.json b/dhp-schemas/src/test/resources/eu/dnetlib/dhp/schema/proto/hugeRecord.json deleted file mode 100644 index ac9ebb2cf..000000000 --- a/dhp-schemas/src/test/resources/eu/dnetlib/dhp/schema/proto/hugeRecord.json +++ /dev/null @@ -1,1294 +0,0 @@ -{ - "kind": "relation", - "dataInfo": { - "provenanceaction": { - "classid": "iis", - "classname": "iis", - "schemename": "dnet:provenanceActions", - "schemeid": "dnet:provenanceActions" - }, - "trust": "0.9", - "inferred": true, - "inferenceprovenance": "iis::document_affiliations" - }, - "lastupdatetimestamp": 1559901970310, - "entity": { - "type": "result", - "id": "50|dedup_wf_001::00000016db3c44b536e40fde7dc8876b", - "originalId": [ - "oai:recercat.cat:2072/246120", - "oai:upcommons.upc.edu:2099.1/24887" - ], - "collectedfrom": [ - { - "key": "10|opendoar____::966b6dfb6b0819cc10644bea3115cf20", - "value": "UPCommons. 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} - ] - }, - "storagedate": { - "value": "v" - }, - "device": { - "value": "v" - }, - "size": { - "value": "v" - }, - "version": { - "value": "v" - }, - "lastmetadataupdate": { - "value": "v" - }, - "metadataversionnumber": { - "value": "v" - }, - "publisher": { - "value": "Universitat Polit\u00e8cnica de Catalunya" - }, - "embargoenddate": { - "value": "" - }, - "refereed": { - "value": "" - }, - "documentationUrl": [ - { - "value": "" - } - ], - "license": [ - { - "qualifier": { - "classid": "main title", - "classname": "main title", - "schemeid": "dnet:dataCite_title", - "schemename": "dnet:dataCite_title" - }, - "value": "Protecci\u00f3n de la legalidad urban\u00edstica" - } - ], - "codeRepositoryUrl": { - "value": "" - }, - "programmingLanguage": { - "classid": "eng", - "classname": "English", - "schemeid": "dnet:languages", - "schemename": "dnet:languages" - }, - "contactperson": [ - { - "value": "" - } - ], - "contactgroup": [ - { - "value": "" - } - ], - "tool": [ - { - "value": "" - } - ], - "source": [ - { - "value": "El presente Trabajo Final de Grado con modalidad B (pr\u00e1cticum) ha tenido como objetivo\ndentro del \u00c1rea de Urbanismo y Vivienda del Ayuntamiento de Corbera de Llobregat, realizar\nun seguimiento de los procedimientos administrativos sobre la Protecci\u00f3n de la Legalidad\nUrban\u00edstica, con el fin de la sistematizaci\u00f3n, ordenaci\u00f3n e identificaci\u00f3n de la informaci\u00f3n\ndocumental contenida en aquellos expedientes resultantes de incoaci\u00f3n, gestionando la\nidentificaci\u00f3n de los procedimientos administrativos, asegurando de esta manera la\nresoluci\u00f3n futura en t\u00e9rminos de validez y eficacia.\nEn el desarrollo de este proyecto, se har\u00e1 referencia a las normativas aplicadas a la\nProtecci\u00f3n de la Legalidad Urban\u00edstica, que tienen por finalidad prevenir e impedir cualquier\nforma de transgresi\u00f3n de la legalidad jur\u00eddico-urban\u00edstica y, en caso de llegar a producirse\nesta, restaurar la realidad urban\u00edstica infringida mediante la reposici\u00f3n de la realidad f\u00edsica\nalterada o trasformada al estado anterior a la actuaci\u00f3n ilegal y, en su caso, la anulaci\u00f3n de\nlos actos administrativos en los que pueda ampararse dicha actuaci\u00f3n ilegal.\nPara dar mejor compresi\u00f3n a todo lo que es el procedimiento administrativo, y con toda la\nteor\u00eda, se ha llegado a los concretos expedientes implicados en las ilegalidades urban\u00edsticas,\ncon todos los hitos procedimentales que han sido pertinentes una vez que han sido\nincoados." - } - ], - "fulltext": [ - { - "value": "El presente Trabajo Final de Grado con modalidad B (pr\u00e1cticum) ha tenido como objetivo\ndentro del \u00c1rea de Urbanismo y Vivienda del Ayuntamiento de Corbera de Llobregat, realizar\nun seguimiento de los procedimientos administrativos sobre la Protecci\u00f3n de la Legalidad\nUrban\u00edstica, con el fin de la sistematizaci\u00f3n, ordenaci\u00f3n e identificaci\u00f3n de la informaci\u00f3n\ndocumental contenida en aquellos expedientes resultantes de incoaci\u00f3n, gestionando la\nidentificaci\u00f3n de los procedimientos administrativos, asegurando de esta manera la\nresoluci\u00f3n futura en t\u00e9rminos de validez y eficacia.\nEn el desarrollo de este proyecto, se har\u00e1 referencia a las normativas aplicadas a la\nProtecci\u00f3n de la Legalidad Urban\u00edstica, que tienen por finalidad prevenir e impedir cualquier\nforma de transgresi\u00f3n de la legalidad jur\u00eddico-urban\u00edstica y, en caso de llegar a producirse\nesta, restaurar la realidad urban\u00edstica infringida mediante la reposici\u00f3n de la realidad f\u00edsica\nalterada o trasformada al estado anterior a la actuaci\u00f3n ilegal y, en su caso, la anulaci\u00f3n de\nlos actos administrativos en los que pueda ampararse dicha actuaci\u00f3n ilegal.\nPara dar mejor compresi\u00f3n a todo lo que es el procedimiento administrativo, y con toda la\nteor\u00eda, se ha llegado a los concretos expedientes implicados en las ilegalidades urban\u00edsticas,\ncon todos los hitos procedimentales que han sido pertinentes una vez que han sido\nincoados." - } - ], - "coverage": [ - { - "value": "El presente Trabajo Final de Grado con modalidad B (pr\u00e1cticum) ha tenido como objetivo\ndentro del \u00c1rea de Urbanismo y Vivienda del Ayuntamiento de Corbera de Llobregat, realizar\nun seguimiento de los procedimientos administrativos sobre la Protecci\u00f3n de la Legalidad\nUrban\u00edstica, con el fin de la sistematizaci\u00f3n, ordenaci\u00f3n e identificaci\u00f3n de la informaci\u00f3n\ndocumental contenida en aquellos expedientes resultantes de incoaci\u00f3n, gestionando la\nidentificaci\u00f3n de los procedimientos administrativos, asegurando de esta manera la\nresoluci\u00f3n futura en t\u00e9rminos de validez y eficacia.\nEn el desarrollo de este proyecto, se har\u00e1 referencia a las normativas aplicadas a la\nProtecci\u00f3n de la Legalidad Urban\u00edstica, que tienen por finalidad prevenir e impedir cualquier\nforma de transgresi\u00f3n de la legalidad jur\u00eddico-urban\u00edstica y, en caso de llegar a producirse\nesta, restaurar la realidad urban\u00edstica infringida mediante la reposici\u00f3n de la realidad f\u00edsica\nalterada o trasformada al estado anterior a la actuaci\u00f3n ilegal y, en su caso, la anulaci\u00f3n de\nlos actos administrativos en los que pueda ampararse dicha actuaci\u00f3n ilegal.\nPara dar mejor compresi\u00f3n a todo lo que es el procedimiento administrativo, y con toda la\nteor\u00eda, se ha llegado a los concretos expedientes implicados en las ilegalidades urban\u00edsticas,\ncon todos los hitos procedimentales que han sido pertinentes una vez que han sido\nincoados." - } - ], - "description": [ - { - "value": "El presente Trabajo Final de Grado con modalidad B (pr\u00e1cticum) ha tenido como objetivo\ndentro del \u00c1rea de Urbanismo y Vivienda del Ayuntamiento de Corbera de Llobregat, realizar\nun seguimiento de los procedimientos administrativos sobre la Protecci\u00f3n de la Legalidad\nUrban\u00edstica, con el fin de la sistematizaci\u00f3n, ordenaci\u00f3n e identificaci\u00f3n de la informaci\u00f3n\ndocumental contenida en aquellos expedientes resultantes de incoaci\u00f3n, gestionando la\nidentificaci\u00f3n de los procedimientos administrativos, asegurando de esta manera la\nresoluci\u00f3n futura en t\u00e9rminos de validez y eficacia.\nEn el desarrollo de este proyecto, se har\u00e1 referencia a las normativas aplicadas a la\nProtecci\u00f3n de la Legalidad Urban\u00edstica, que tienen por finalidad prevenir e impedir cualquier\nforma de transgresi\u00f3n de la legalidad jur\u00eddico-urban\u00edstica y, en caso de llegar a producirse\nesta, restaurar la realidad urban\u00edstica infringida mediante la reposici\u00f3n de la realidad f\u00edsica\nalterada o trasformada al estado anterior a la actuaci\u00f3n ilegal y, en su caso, la anulaci\u00f3n de\nlos actos administrativos en los que pueda ampararse dicha actuaci\u00f3n ilegal.\nPara dar mejor compresi\u00f3n a todo lo que es el procedimiento administrativo, y con toda la\nteor\u00eda, se ha llegado a los concretos expedientes implicados en las ilegalidades urban\u00edsticas,\ncon todos los hitos procedimentales que han sido pertinentes una vez que han sido\nincoados." - 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Departament d'Organitzaci\u00f3 d'Empreses" - }, - { - "value": "Larrubia Garc\u00eda, Yolanda" - }, - { - "value": "Universitat Polit\u00e8cnica de Catalunya. 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"target": "50|dedup_wf_001::1fc35b70379be0de4eb30ba700b0e2c8", - "relType": "resultOrganization", - "source": "20|____________::14bcdabd409ac067c7c90ecf15599ef7", - "child": false, - "datasourceOrganization": { - "provision": { - "relMetadata": { - "semantics": { - "classid": "isAuthorInstitutionOf", - "classname": "isAuthorInstitutionOf", - "schemename": "dnet:result_organization_relations", - "schemeid": "dnet:result_organization_relations" - } - } - } - }, - "projectOrganization": { - "participation": { - "relMetadata": { - "semantics": { - "classid": "isAuthorInstitutionOf", - "classname": "isAuthorInstitutionOf", - "schemename": "dnet:result_organization_relations", - "schemeid": "dnet:result_organization_relations" - } - } - } - }, - "resultOrganization": { - "affiliation": { - "relMetadata": { - "semantics": { - "classid": "isAuthorInstitutionOf", - "classname": "isAuthorInstitutionOf", - "schemename": "dnet:result_organization_relations", - "schemeid": "dnet:result_organization_relations" - } - } - } - }, - "resultProject": { - "outcome": { - "relMetadata": { - "semantics": { - "classid": "isAuthorInstitutionOf", - "classname": "isAuthorInstitutionOf", - "schemename": "dnet:result_organization_relations", - "schemeid": "dnet:result_organization_relations" - } - } - } - }, - "resultResult": { - "similarity": { - "type": "STANDARD", - "relMetadata": { - "semantics": { - "classid": "hasAmongTopNSimilarDocuments", - "classname": "hasAmongTopNSimilarDocuments", - "schemename": "dnet:result_result_relations", - "schemeid": "dnet:result_result_relations" - } - }, - "similarity": 0.79513913 - }, - "publicationDataset": { - "relMetadata": { - "semantics": { - "classid": "isRelatedTo", - "classname": "isRelatedTo", - "schemeid": "dnet:result_result_relations", - "schemename": "dnet:result_result_relations" - } - } - }, - "dedup": { - "relMetadata": { - "semantics": { - "classid": "isMergedIn", - "classname": "isMergedIn", - "schemeid": "dnet:result_result_relations", - "schemename": "dnet:result_result_relations" - } - } - }, - "dedupSimilarity": { - "relMetadata": { - "semantics": { - "classid": "isSimilarTo", - "classname": "isSimilarTo", - "schemeid": "dnet:result_result_relations", - "schemename": "dnet:result_result_relations" - } - } - }, - "supplement": { - "relMetadata": { - "semantics": { - "classid": "supplement", - "classname": "supplement", - "schemeid": "dnet:result_result_relations", - "schemename": "dnet:result_result_relations" - } - } - }, - "part": { - "relMetadata": { - "semantics": { - "classid": "isPartOf", - "classname": "isPartOf", - "schemeid": "dnet:result_result_relations", - "schemename": "dnet:result_result_relations" - } - } - }, - "relationship": { - "relMetadata": { - "semantics": { - "classid": "isRelatedTo", - "classname": "isRelatedTo", - "schemeid": "dnet:result_result_relations", - "schemename": "dnet:result_result_relations" - } - } - }, - "softwareSoftware": { - "relMetadata": { - "semantics": { - "classid": "isVersionOf", - "classname": "isVersionOf", - "schemeid": "dnet:result_result_relations", - "schemename": "dnet:result_result_relations" - } - } - } - }, - "organizationOrganization": { - "dedup": { - "relMetadata": { - "semantics": { - "classid": "isMergedIn", - "classname": "isMergedIn", - "schemeid": "dnet:result_result_relations", - "schemename": "dnet:result_result_relations" - } - } - }, - "dedupSimilarity": { - "relMetadata": { - "semantics": { - "classid": "isSimilarTo", - "classname": "isSimilarTo", - "schemeid": "dnet:result_result_relations", - "schemename": "dnet:result_result_relations" - } - } - } - }, - "collectedfrom": [ - { - "key": "a", - "value": "b", - "dataInfo": { - "provenanceaction": { - "classid": "iis", - "classname": "iis", - "schemename": "dnet:provenanceActions", - "schemeid": "dnet:provenanceActions" - }, - "trust": "0.9", - "inferred": true, - "inferenceprovenance": "iis::document_affiliations" - } - } - ] - } -} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 4a4492cee..9a434492f 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -21,16 +21,6 @@ spark-sql_2.11 - - eu.dnetlib - dnet-openaire-data-protos - - - - com.googlecode.protobuf-java-format - protobuf-java-format - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoConverter.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoConverter.java deleted file mode 100644 index 6cf64923e..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoConverter.java +++ /dev/null @@ -1,269 +0,0 @@ -package eu.dnetlib.dhp.graph; - -import eu.dnetlib.data.proto.*; -import eu.dnetlib.dhp.schema.oaf.*; - -import java.io.Serializable; -import java.util.stream.Collectors; - -import static eu.dnetlib.dhp.graph.ProtoUtils.*; - -public class ProtoConverter implements Serializable { - - public static Oaf convert(String s) { - try { - OafProtos.Oaf oaf = ProtoUtils.parse(s); - - if (oaf.getKind() == KindProtos.Kind.entity) - return convertEntity(oaf); - else { - return convertRelation(oaf); - } - } catch (Throwable e) { - throw new RuntimeException("error on getting " + s, e); - } - } - - private static Relation convertRelation(OafProtos.Oaf oaf) { - final OafProtos.OafRel r = oaf.getRel(); - final Relation rel = new Relation(); - rel.setDataInfo(mapDataInfo(oaf.getDataInfo())); - rel.setLastupdatetimestamp(oaf.getLastupdatetimestamp()); - rel.setSource(r.getSource()); - rel.setTarget(r.getTarget()); - rel.setRelType(r.getRelType().toString()); - rel.setSubRelType(r.getSubRelType().toString()); - rel.setRelClass(r.getRelClass()); - rel.setCollectedFrom(r.getCollectedfromCount() > 0 ? - r.getCollectedfromList().stream() - .map(kv -> mapKV(kv)) - .collect(Collectors.toList()) : null); - return rel; - } - - private static OafEntity convertEntity(OafProtos.Oaf oaf) { - - switch (oaf.getEntity().getType()) { - case result: - return convertResult(oaf); - case project: - return convertProject(oaf); - case datasource: - return convertDataSource(oaf); - case organization: - return convertOrganization(oaf); - default: - throw new RuntimeException("received unknown type"); - } - } - - private static Organization convertOrganization(OafProtos.Oaf oaf) { - final OrganizationProtos.Organization.Metadata m = oaf.getEntity().getOrganization().getMetadata(); - final Organization org = setOaf(new Organization(), oaf); - setEntity(org, oaf); - org.setLegalshortname(mapStringField(m.getLegalshortname())); - org.setLegalname(mapStringField(m.getLegalname())); - org.setAlternativeNames(m.getAlternativeNamesList(). - stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - org.setWebsiteurl(mapStringField(m.getWebsiteurl())); - org.setLogourl(mapStringField(m.getLogourl())); - org.setEclegalbody(mapStringField(m.getEclegalbody())); - org.setEclegalperson(mapStringField(m.getEclegalperson())); - org.setEcnonprofit(mapStringField(m.getEcnonprofit())); - org.setEcresearchorganization(mapStringField(m.getEcresearchorganization())); - org.setEchighereducation(mapStringField(m.getEchighereducation())); - org.setEcinternationalorganizationeurinterests(mapStringField(m.getEcinternationalorganizationeurinterests())); - org.setEcinternationalorganization(mapStringField(m.getEcinternationalorganization())); - org.setEcenterprise(mapStringField(m.getEcenterprise())); - org.setEcsmevalidated(mapStringField(m.getEcsmevalidated())); - org.setEcnutscode(mapStringField(m.getEcnutscode())); - org.setCountry(mapQualifier(m.getCountry())); - - return org; - } - - private static Datasource convertDataSource(OafProtos.Oaf oaf) { - final DatasourceProtos.Datasource.Metadata m = oaf.getEntity().getDatasource().getMetadata(); - final Datasource datasource = setOaf(new Datasource(), oaf); - setEntity(datasource, oaf); - datasource.setAccessinfopackage(m.getAccessinfopackageList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - datasource.setCertificates(mapStringField(m.getCertificates())); - datasource.setCitationguidelineurl(mapStringField(m.getCitationguidelineurl())); - datasource.setContactemail(mapStringField(m.getContactemail())); - datasource.setDatabaseaccessrestriction(mapStringField(m.getDatabaseaccessrestriction())); - datasource.setDatabaseaccesstype(mapStringField(m.getDatabaseaccesstype())); - datasource.setDataprovider(mapBoolField(m.getDataprovider())); - datasource.setDatasourcetype(mapQualifier(m.getDatasourcetype())); - datasource.setDatauploadrestriction(mapStringField(m.getDatauploadrestriction())); - datasource.setCitationguidelineurl(mapStringField(m.getCitationguidelineurl())); - datasource.setDatauploadtype(mapStringField(m.getDatauploadtype())); - datasource.setDateofvalidation(mapStringField(m.getDateofvalidation())); - datasource.setDescription(mapStringField(m.getDescription())); - datasource.setEnglishname(mapStringField(m.getEnglishname())); - datasource.setLatitude(mapStringField(m.getLatitude())); - datasource.setLongitude(mapStringField(m.getLongitude())); - datasource.setLogourl(mapStringField(m.getLogourl())); - datasource.setMissionstatementurl(mapStringField(m.getMissionstatementurl())); - datasource.setNamespaceprefix(mapStringField(m.getNamespaceprefix())); - datasource.setOdcontenttypes(m.getOdcontenttypesList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - datasource.setOdlanguages(m.getOdlanguagesList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - datasource.setOdnumberofitems(mapStringField(m.getOdnumberofitems())); - datasource.setOdnumberofitemsdate(mapStringField(m.getOdnumberofitemsdate())); - datasource.setOdpolicies(mapStringField(m.getOdpolicies())); - datasource.setOfficialname(mapStringField(m.getOfficialname())); - datasource.setOpenairecompatibility(mapQualifier(m.getOpenairecompatibility())); - datasource.setPidsystems(mapStringField(m.getPidsystems())); - datasource.setPolicies(m.getPoliciesList() - .stream() - .map(ProtoUtils::mapKV) - .collect(Collectors.toList())); - datasource.setQualitymanagementkind(mapStringField(m.getQualitymanagementkind())); - datasource.setReleaseenddate(mapStringField(m.getReleaseenddate())); - datasource.setServiceprovider(mapBoolField(m.getServiceprovider())); - datasource.setReleasestartdate(mapStringField(m.getReleasestartdate())); - datasource.setSubjects(m.getSubjectsList() - .stream() - .map(ProtoUtils::mapStructuredProperty) - .collect(Collectors.toList())); - datasource.setVersioning(mapBoolField(m.getVersioning())); - datasource.setWebsiteurl(mapStringField(m.getWebsiteurl())); - datasource.setJournal(mapJournal(m.getJournal())); - - - return datasource; - } - - private static Project convertProject(OafProtos.Oaf oaf) { - final ProjectProtos.Project.Metadata m = oaf.getEntity().getProject().getMetadata(); - final Project project = setOaf(new Project(), oaf); - setEntity(project, oaf); - project.setAcronym(mapStringField(m.getAcronym())); - project.setCallidentifier(mapStringField(m.getCallidentifier())); - project.setCode(mapStringField(m.getCode())); - project.setContactemail(mapStringField(m.getContactemail())); - project.setContactfax(mapStringField(m.getContactfax())); - project.setContactfullname(mapStringField(m.getContactfullname())); - project.setContactphone(mapStringField(m.getContactphone())); - project.setContracttype(mapQualifier(m.getContracttype())); - project.setCurrency(mapStringField(m.getCurrency())); - project.setDuration(mapStringField(m.getDuration())); - project.setEcarticle29_3(mapStringField(m.getEcarticle293())); - project.setEcsc39(mapStringField(m.getEcsc39())); - project.setOamandatepublications(mapStringField(m.getOamandatepublications())); - project.setStartdate(mapStringField(m.getStartdate())); - project.setEnddate(mapStringField(m.getEnddate())); - project.setFundedamount(m.getFundedamount()); - project.setTotalcost(m.getTotalcost()); - project.setKeywords(mapStringField(m.getKeywords())); - project.setSubjects(m.getSubjectsList().stream() - .map(sp -> mapStructuredProperty(sp)) - .collect(Collectors.toList())); - project.setTitle(mapStringField(m.getTitle())); - project.setWebsiteurl(mapStringField(m.getWebsiteurl())); - project.setFundingtree(m.getFundingtreeList().stream() - .map(f -> mapStringField(f)) - .collect(Collectors.toList())); - project.setJsonextrainfo(mapStringField(m.getJsonextrainfo())); - project.setSummary(mapStringField(m.getSummary())); - project.setOptional1(mapStringField(m.getOptional1())); - project.setOptional2(mapStringField(m.getOptional2())); - return project; - } - - private static Result convertResult(OafProtos.Oaf oaf) { - switch (oaf.getEntity().getResult().getMetadata().getResulttype().getClassid()) { - - case "dataset": - return createDataset(oaf); - case "publication": - return createPublication(oaf); - case "software": - return createSoftware(oaf); - case "other": - return createORP(oaf); - default: - throw new RuntimeException("received unknown type: " + oaf.getEntity().getResult().getMetadata().getResulttype().getClassid()); - } - } - - private static Software createSoftware(OafProtos.Oaf oaf) { - ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata(); - Software software = setOaf(new Software(), oaf); - setEntity(software, oaf); - setResult(software, oaf); - - software.setDocumentationUrl(m.getDocumentationUrlList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - software.setLicense(m.getLicenseList() - .stream() - .map(ProtoUtils::mapStructuredProperty) - .collect(Collectors.toList())); - software.setCodeRepositoryUrl(ProtoUtils.mapStringField(m.getCodeRepositoryUrl())); - software.setProgrammingLanguage(ProtoUtils.mapQualifier(m.getProgrammingLanguage())); - return software; - } - - private static OtherResearchProducts createORP(OafProtos.Oaf oaf) { - ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata(); - OtherResearchProducts otherResearchProducts = setOaf(new OtherResearchProducts(), oaf); - setEntity(otherResearchProducts, oaf); - setResult(otherResearchProducts, oaf); - otherResearchProducts.setContactperson(m.getContactpersonList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - otherResearchProducts.setContactgroup(m.getContactgroupList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - otherResearchProducts.setTool(m.getToolList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - - return otherResearchProducts; - } - - private static Publication createPublication(OafProtos.Oaf oaf) { - - ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata(); - Publication publication = setOaf(new Publication(), oaf); - setEntity(publication, oaf); - setResult(publication, oaf); - publication.setJournal(mapJournal(m.getJournal())); - return publication; - } - - private static Dataset createDataset(OafProtos.Oaf oaf) { - - ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata(); - Dataset dataset = setOaf(new Dataset(), oaf); - setEntity(dataset, oaf); - setResult(dataset, oaf); - dataset.setStoragedate(ProtoUtils.mapStringField(m.getStoragedate())); - dataset.setDevice(ProtoUtils.mapStringField(m.getDevice())); - dataset.setSize(ProtoUtils.mapStringField(m.getSize())); - dataset.setVersion(ProtoUtils.mapStringField(m.getVersion())); - dataset.setLastmetadataupdate(ProtoUtils.mapStringField(m.getLastmetadataupdate())); - dataset.setMetadataversionnumber(ProtoUtils.mapStringField(m.getMetadataversionnumber())); - dataset.setGeolocation(m.getGeolocationList() - .stream() - .map(ProtoUtils::mapGeolocation) - .collect(Collectors.toList())); - return dataset; - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoUtils.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoUtils.java deleted file mode 100644 index 41e0baa57..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoUtils.java +++ /dev/null @@ -1,251 +0,0 @@ -package eu.dnetlib.dhp.graph; - -import com.googlecode.protobuf.format.JsonFormat; -import eu.dnetlib.data.proto.FieldTypeProtos; -import eu.dnetlib.data.proto.OafProtos; -import eu.dnetlib.data.proto.ResultProtos; -import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.commons.io.IOUtils; - -import java.io.IOException; -import java.util.stream.Collectors; - -public class ProtoUtils { - - public static OafProtos.Oaf parse(String json) throws IOException { - final OafProtos.Oaf.Builder builder = OafProtos.Oaf.newBuilder(); - - final JsonFormat jf = new JsonFormat(); - jf.merge(IOUtils.toInputStream(json), builder); - - return builder.build(); - } - - public static T setOaf(T oaf, OafProtos.Oaf o) { - oaf.setDataInfo(mapDataInfo(o.getDataInfo())); - oaf.setLastupdatetimestamp(o.getLastupdatetimestamp()); - return oaf; - } - - public static T setEntity(T entity, OafProtos.Oaf oaf) { - //setting Entity fields - final OafProtos.OafEntity e = oaf.getEntity(); - entity.setId(e.getId()); - entity.setOriginalId(e.getOriginalIdList()); - entity.setCollectedfrom(e.getCollectedfromList() - .stream() - .map(ProtoUtils::mapKV) - .collect(Collectors.toList())); - entity.setPid(e.getPidList().stream() - .map(ProtoUtils::mapStructuredProperty) - .collect(Collectors.toList())); - entity.setDateofcollection(entity.getDateofcollection()); - entity.setDateoftransformation(entity.getDateoftransformation()); - entity.setExtraInfo(e.getExtraInfoList() - .stream() - .map(ProtoUtils::mapExtraInfo) - .collect(Collectors.toList())); - return entity; - } - - public static T setResult(T entity, OafProtos.Oaf oaf) { - //setting Entity fields - final ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata(); - entity.setAuthor(m.getAuthorList() - .stream() - .map(ProtoUtils::mapAuthor) - .collect(Collectors.toList())); - entity.setResulttype(mapQualifier(m.getResulttype())); - entity.setLanguage(ProtoUtils.mapQualifier(m.getLanguage())); - entity.setCountry(m.getCountryList() - .stream() - .map(ProtoUtils::mapQualifier) - .collect(Collectors.toList())); - entity.setSubject(m.getSubjectList() - .stream() - .map(ProtoUtils::mapStructuredProperty) - .collect(Collectors.toList())); - entity.setTitle(m.getTitleList() - .stream() - .map(ProtoUtils::mapStructuredProperty) - .collect(Collectors.toList())); - entity.setRelevantdate(m.getRelevantdateList() - .stream() - .map(ProtoUtils::mapStructuredProperty) - .collect(Collectors.toList())); - entity.setDescription(m.getDescriptionList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - entity.setDateofacceptance(ProtoUtils.mapStringField(m.getDateofacceptance())); - entity.setPublisher(ProtoUtils.mapStringField(m.getPublisher())); - entity.setEmbargoenddate(ProtoUtils.mapStringField(m.getEmbargoenddate())); - entity.setSource(m.getSourceList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - entity.setFulltext(m.getFulltextList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - entity.setFormat(m.getFormatList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - entity.setContributor(m.getContributorList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - entity.setResourcetype(ProtoUtils.mapQualifier(m.getResourcetype())); - entity.setCoverage(m.getCoverageList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - entity.setRefereed(mapStringField(m.getRefereed())); - entity.setContext(m.getContextList() - .stream() - .map(ProtoUtils::mapContext) - .collect(Collectors.toList())); - - return entity; - } - - private static Context mapContext(ResultProtos.Result.Context context) { - - final Context entity = new Context(); - entity.setId(context.getId()); - entity.setDataInfo(context.getDataInfoList() - .stream() - .map(ProtoUtils::mapDataInfo) - .collect(Collectors.toList())); - return entity; - } - - - public static KeyValue mapKV(FieldTypeProtos.KeyValue kv) { - final KeyValue keyValue = new KeyValue(); - keyValue.setKey(kv.getKey()); - keyValue.setValue(kv.getValue()); - keyValue.setDataInfo(mapDataInfo(kv.getDataInfo())); - return keyValue; - } - - public static DataInfo mapDataInfo(FieldTypeProtos.DataInfo d) { - final DataInfo dataInfo = new DataInfo(); - dataInfo.setDeletedbyinference(d.getDeletedbyinference()); - dataInfo.setInferenceprovenance(d.getInferenceprovenance()); - dataInfo.setInferred(d.getInferred()); - dataInfo.setInvisible(d.getInvisible()); - dataInfo.setProvenanceaction(mapQualifier(d.getProvenanceaction())); - return dataInfo; - } - - public static Qualifier mapQualifier(FieldTypeProtos.Qualifier q) { - final Qualifier qualifier = new Qualifier(); - qualifier.setClassid(q.getClassid()); - qualifier.setClassname(q.getClassname()); - qualifier.setSchemeid(q.getSchemeid()); - qualifier.setSchemename(q.getSchemename()); - return qualifier; - } - - public static StructuredProperty mapStructuredProperty(FieldTypeProtos.StructuredProperty sp) { - final StructuredProperty structuredProperty = new StructuredProperty(); - structuredProperty.setValue(sp.getValue()); - structuredProperty.setQualifier(mapQualifier(sp.getQualifier())); - structuredProperty.setDataInfo(mapDataInfo(sp.getDataInfo())); - return structuredProperty; - } - - public static ExtraInfo mapExtraInfo(FieldTypeProtos.ExtraInfo extraInfo) { - final ExtraInfo entity = new ExtraInfo(); - entity.setName(extraInfo.getName()); - entity.setTypology(extraInfo.getTypology()); - entity.setProvenance(extraInfo.getProvenance()); - entity.setTrust(extraInfo.getTrust()); - entity.setValue(extraInfo.getValue()); - return entity; - } - - public static OAIProvenance mapOAIProvenance(FieldTypeProtos.OAIProvenance oaiProvenance) { - final OAIProvenance entity = new OAIProvenance(); - entity.setOriginDescription(mapOriginalDescription(oaiProvenance.getOriginDescription())); - return entity; - } - - public static OriginDescription mapOriginalDescription(FieldTypeProtos.OAIProvenance.OriginDescription originDescription) { - final OriginDescription originDescriptionResult = new OriginDescription(); - originDescriptionResult.setHarvestDate(originDescription.getHarvestDate()); - originDescriptionResult.setAltered(originDescription.getAltered()); - originDescriptionResult.setBaseURL(originDescription.getBaseURL()); - originDescriptionResult.setIdentifier(originDescription.getIdentifier()); - originDescriptionResult.setDatestamp(originDescription.getDatestamp()); - originDescriptionResult.setMetadataNamespace(originDescription.getMetadataNamespace()); - return originDescriptionResult; - } - - public static Field mapStringField(FieldTypeProtos.StringField s) { - final Field stringField = new Field<>(); - stringField.setValue(s.getValue()); - stringField.setDataInfo(mapDataInfo(s.getDataInfo())); - return stringField; - } - - public static Field mapBoolField(FieldTypeProtos.BoolField b) { - final Field booleanField = new Field<>(); - booleanField.setValue(b.getValue()); - booleanField.setDataInfo(mapDataInfo(b.getDataInfo())); - return booleanField; - } - - public static Field mapIntField(FieldTypeProtos.IntField b) { - final Field entity = new Field<>(); - entity.setValue(b.getValue()); - entity.setDataInfo(mapDataInfo(b.getDataInfo())); - return entity; - } - - public static Journal mapJournal(FieldTypeProtos.Journal j) { - final Journal journal = new Journal(); - journal.setConferencedate(j.getConferencedate()); - journal.setConferenceplace(j.getConferenceplace()); - journal.setEdition(j.getEdition()); - journal.setEp(j.getEp()); - journal.setIss(j.getIss()); - journal.setIssnLinking(j.getIssnLinking()); - journal.setIssnOnline(j.getIssnOnline()); - journal.setIssnPrinted(j.getIssnPrinted()); - journal.setName(j.getName()); - journal.setSp(j.getSp()); - journal.setVol(j.getVol()); - journal.setDataInfo(mapDataInfo(j.getDataInfo())); - return journal; - } - - public static Author mapAuthor(FieldTypeProtos.Author author) { - final Author entity = new Author(); - entity.setFullname(author.getFullname()); - entity.setName(author.getName()); - entity.setSurname(author.getSurname()); - entity.setRank(author.getRank()); - entity.setPid(author.getPidList() - .stream() - .map(ProtoUtils::mapKV) - .collect(Collectors.toList())); - entity.setAffiliation(author.getAffiliationList() - .stream() - .map(ProtoUtils::mapStringField) - .collect(Collectors.toList())); - return entity; - - } - - public static GeoLocation mapGeolocation(ResultProtos.Result.GeoLocation geoLocation) { - final GeoLocation entity = new GeoLocation(); - entity.setPoint(geoLocation.getPoint()); - entity.setBox(geoLocation.getBox()); - entity.setPlace(geoLocation.getPlace()); - return entity; - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/SparkGraphImporterJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/SparkGraphImporterJob.java index 625b34223..f081b4ca9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/SparkGraphImporterJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/SparkGraphImporterJob.java @@ -1,5 +1,7 @@ package eu.dnetlib.dhp.graph; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Maps; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.IOUtils; @@ -7,11 +9,12 @@ import org.apache.commons.lang.StringUtils; import org.apache.hadoop.io.Text; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import scala.Tuple2; +import java.util.Map; + public class SparkGraphImporterJob { public static void main(String[] args) throws Exception { @@ -27,44 +30,33 @@ public class SparkGraphImporterJob { final String inputPath = parser.get("input"); final String outputPath = parser.get("outputDir"); - final String filter = parser.get("filter"); - - // Read the input file and convert it into RDD of serializable object final JavaRDD> inputRDD = sc.sequenceFile(inputPath, Text.class, Text.class) .map(item -> new Tuple2<>(item._1.toString(), item._2.toString())); - final JavaRDD oafRdd = inputRDD.filter(s -> !StringUtils.isBlank(s._2()) && !s._1().contains("@update")).map(Tuple2::_2).map(ProtoConverter::convert); + final Map types = Maps.newHashMap(); + types.put("datasource", Datasource.class); + types.put("organization", Organization.class); + types.put("project", Project.class); + types.put("dataset", Dataset.class); + types.put("otherresearchproduct", OtherResearchProduct.class); + types.put("software", Software.class); + types.put("publication", Publication.class); + types.put("relation", Relation.class); - final Encoder organizationEncoder = Encoders.bean(Organization.class); - final Encoder projectEncoder = Encoders.bean(Project.class); - final Encoder datasourceEncoder = Encoders.bean(Datasource.class); + types.forEach((name, clazz) -> { + if (StringUtils.isNotBlank(filter) || filter.toLowerCase().contains(name)) { + spark.createDataset(inputRDD + .filter(s -> s._1().equals(clazz.getName())) + .map(Tuple2::_2) + .map(s -> new ObjectMapper().readValue(s, clazz)) + .rdd(), Encoders.bean(clazz)) + .write() + .save(outputPath + "/" + name); + } + }); - final Encoder datasetEncoder = Encoders.bean(eu.dnetlib.dhp.schema.oaf.Dataset.class); - final Encoder publicationEncoder = Encoders.bean(Publication.class); - final Encoder softwareEncoder = Encoders.bean(Software.class); - final Encoder otherResearchProductsEncoder = Encoders.bean(OtherResearchProducts.class); - - final Encoder relationEncoder = Encoders.bean(Relation.class); - - if (filter == null|| filter.toLowerCase().contains("organization")) - spark.createDataset(oafRdd.filter(s -> s instanceof Organization).map(s -> (Organization) s).rdd(), organizationEncoder).write().save(outputPath + "/organizations"); - if (filter == null|| filter.toLowerCase().contains("project")) - spark.createDataset(oafRdd.filter(s -> s instanceof Project).map(s -> (Project) s).rdd(), projectEncoder).write().save(outputPath + "/projects"); - if (filter == null|| filter.toLowerCase().contains("datasource")) - spark.createDataset(oafRdd.filter(s -> s instanceof Datasource).map(s -> (Datasource) s).rdd(), datasourceEncoder).write().save(outputPath + "/datasources"); - if (filter == null|| filter.toLowerCase().contains("dataset")) - spark.createDataset(oafRdd.filter(s -> s instanceof eu.dnetlib.dhp.schema.oaf.Dataset).map(s -> (eu.dnetlib.dhp.schema.oaf.Dataset) s).rdd(), datasetEncoder).write().save(outputPath + "/datasets"); - - if (filter == null|| filter.toLowerCase().contains("publication")) - spark.createDataset(oafRdd.filter(s -> s instanceof Publication).map(s -> (Publication) s).rdd(), publicationEncoder).write().save(outputPath + "/publications"); - if (filter == null|| filter.toLowerCase().contains("software")) - spark.createDataset(oafRdd.filter(s -> s instanceof Software).map(s -> (Software) s).rdd(), softwareEncoder).write().save(outputPath + "/software"); - if (filter == null|| filter.toLowerCase().contains("otherresearchproduct")) - spark.createDataset(oafRdd.filter(s -> s instanceof OtherResearchProducts).map(s -> (OtherResearchProducts) s).rdd(), otherResearchProductsEncoder).write().save(outputPath + "/otherResearchProducts"); - if (filter == null|| filter.toLowerCase().contains("relation")) - spark.createDataset(oafRdd.filter(s -> s instanceof Relation).map(s -> (Relation) s).rdd(), relationEncoder).write().save(outputPath + "/relations"); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/graph/ProtoConverterTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/graph/ProtoConverterTest.java deleted file mode 100644 index 8afd0cda6..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/graph/ProtoConverterTest.java +++ /dev/null @@ -1,111 +0,0 @@ -package eu.dnetlib.dhp.graph; - -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.commons.io.IOUtils; -import org.junit.Test; - -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; - -public class ProtoConverterTest { - - - @Test - public void convertDatasourceTest() throws Exception { - final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/graph/datasource.json")); - - Oaf result = ProtoConverter.convert(json); - assertNotNull(result); - assertTrue(result instanceof Datasource); - Datasource ds = (Datasource) result; - assertNotNull(ds.getId()); - - System.out.println(ds.getId()); - - - ObjectMapper mapper = new ObjectMapper(); - System.out.println(mapper.writeValueAsString(result)); - } - - - @Test - public void convertOrganizationTest() throws Exception { - - final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/graph/organization.json")); - - Oaf result = ProtoConverter.convert(json); - assertNotNull(result); - assertTrue(result instanceof Organization); - Organization ds = (Organization) result; - assertNotNull(ds.getId()); - - System.out.println(ds.getId()); - - - ObjectMapper mapper = new ObjectMapper(); - System.out.println(mapper.writeValueAsString(result)); - - } - - @Test - public void convertPublicationTest() throws Exception { - final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/graph/publication.json")); - - Oaf result = ProtoConverter.convert(json); - - assertNotNull(result); - assertTrue(result instanceof Publication); - Publication p = (Publication) result; - - ObjectMapper mapper = new ObjectMapper(); - System.out.println(mapper.writeValueAsString(p)); - - } - - @Test - public void convertDatasetTest() throws Exception { - final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/graph/dataset.json")); - - Oaf result = ProtoConverter.convert(json); - - assertNotNull(result); - assertTrue(result instanceof Dataset); - Dataset d = (Dataset) result; - - ObjectMapper mapper = new ObjectMapper(); - System.out.println(mapper.writeValueAsString(d)); - - } - - @Test - public void convertORPTest() throws Exception { - final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/graph/orp.json")); - - Oaf result = ProtoConverter.convert(json); - - assertNotNull(result); - assertTrue(result instanceof OtherResearchProducts); - OtherResearchProducts orp = (OtherResearchProducts) result; - - ObjectMapper mapper = new ObjectMapper(); - System.out.println(mapper.writeValueAsString(orp)); - - } - - @Test - public void convertSoftware() throws Exception { - final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/graph/software.json")); - - Oaf result = ProtoConverter.convert(json); - - assertNotNull(result); - assertTrue(result instanceof Software); - Software s = (Software) result; - - ObjectMapper mapper = new ObjectMapper(); - System.out.println(mapper.writeValueAsString(s)); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/graph/dataset.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/graph/dataset.json deleted file mode 100644 index 05ba555dd..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/graph/dataset.json +++ /dev/null @@ -1 +0,0 @@ -{"kind":1,"dataInfo":{"deletedbyinference":true,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemename":"dnet:provenanceActions","schemeid":"dnet:provenanceActions"},"inferred":true,"inferenceprovenance":"dedup-similarity-result-levenstein","invisible":false,"trust":"0.9"},"entity":{"pid":[{"qualifier":{"classid":"doi","classname":"doi","schemename":"dnet:pid_types","schemeid":"dnet:pid_types"},"value":"10.5517/cc11xr4v"}],"result":{"instance":[{"url":["http://dx.doi.org/10.5517/cc11xr4v"],"collectedfrom":{"value":"scholExplorer","key":"10|openaire____::e034d6a11054f5ade9221ebac484e864"},"hostedby":{"value":"Unknown Repository","key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c"},"accessright":{"classid":"UNKNOWN","classname":"not available","schemename":"dnet:access_modes","schemeid":"dnet:access_modes"},"instancetype":{"classid":"0000","classname":"Unknown","schemename":"dnet:publication_resource","schemeid":"dnet:publication_resource"}}],"metadata":{"publisher":{"value":"Cambridge Crystallographic Data Centre"},"description":[{"value":"An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. 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To search their archives and sign-up for them, please visit the following URLs:\n\nDiscussion: http://lists.idyll.org/listinfo/khmer\nAnnouncements: http://lists.idyll.org/listinfo/khmer-announce\nWe chat at https://gitter.im/dib-lab/khmer and the maintainers can be contacted at khmer-project@idyll.org.\n\nFor getting help with please see this guide: http://khmer.readthedocs.org/user/getting-help.html\n\nIMPORTANT NOTE: CITE US!\n\nkhmer is research software, so you should cite us when you use it in scientific publications! Please see the CITATION file for citation information.\n\nINSTALL INSTRUCTIONS:\n\nkhmer requires a 64-bit operating system and Python 2.7.x. Linux users will need the Python development libraries and gcc. OS X users may need XCode installed.\n\nIn short:\n\npip install khmer to download, build, and install the latest stable version.\n\nFor more details see doc/install.txt\n\nThe use of a virtualenv is recommended, see https://virtualenv.readthedocs.org/en/latest/installation.html\n\nkhmer is under the BSD license; see doc/LICENSE.txt. Distribution, modification and redistribution, incorporation into other software, and pretty much everything else is allowed.\n\nMRC 2014-05-14"}],"license":[{"value":""}],"title":[{"qualifier":{"classid":"main title","classname":"main title","schemename":"dnet:dataCite_title","schemeid":"dnet:dataCite_title"},"value":"Khmer: Khmer/ The Khmer Software Package: Enabling Efficient Nucleotide Sequence Analysis"}],"programmingLanguage":{"classid":"","classname":"","schemename":"dnet:programming_languages","schemeid":"dnet:programming_languages"},"author":[{"fullname":"C. 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