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added hash map for relationship entityType id prefix, and relation inverse

This commit is contained in:
Miriam Baglioni 2020-04-29 18:14:52 +02:00
parent b85ad7012a
commit 869f576273
4 changed files with 490 additions and 1 deletions

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@ -50,6 +50,172 @@ public class ModelSupport {
oafTypes.put("relation", Relation.class);
}
public static final Map<String, String> entityIdPrefix = Maps.newHashMap();
static {
entityIdPrefix.put("datasource", "10");
entityIdPrefix.put("organization", "20");
entityIdPrefix.put("project", "40");
entityIdPrefix.put("result","50");
}
public static final Map<String, RelationInverse> relationInverseMap = Maps.newHashMap();
static {
relationInverseMap.put("personResult_authorship_isAuthorOf", new RelationInverse()
.setRelation("isAuthorOf")
.setInverse("hasAuthor")
.setRelType("personResult")
.setSubReltype("authorship"));
relationInverseMap.put("personResult_authorship_hasAuthor", new RelationInverse()
.setInverse("isAuthorOf")
.setRelation("hasAuthor")
.setRelType("personResult")
.setSubReltype("authorship"));
relationInverseMap.put("projectOrganization_participation_isParticipant", new RelationInverse()
.setRelation("isParticipant")
.setInverse("hasParticipant")
.setRelType("projectOrganization")
.setSubReltype("participation"));
relationInverseMap.put("projectOrganization_participation_hasParticipant", new RelationInverse()
.setInverse("isParticipant")
.setRelation("hasParticipant")
.setRelType("projectOrganization")
.setSubReltype("participation"));
relationInverseMap.put("resultOrganization_affiliation_hasAuthorInstitution", new RelationInverse()
.setRelation("hasAuthorInstitution")
.setInverse("isAuthorInstitutionOf")
.setRelType("resultOrganization")
.setSubReltype("affiliation"));
relationInverseMap.put("resultOrganization_affiliation_isAuthorInstitutionOf", new RelationInverse()
.setInverse("hasAuthorInstitution")
.setRelation("isAuthorInstitutionOf")
.setRelType("resultOrganization")
.setSubReltype("affiliation"));
relationInverseMap.put("organizationOrganization_dedup_merges", new RelationInverse()
.setRelation("merges")
.setInverse("isMergedIn")
.setRelType("organizationOrganization")
.setSubReltype("dedup"));
relationInverseMap.put("organizationOrganization_dedup_isMergedIn", new RelationInverse()
.setInverse("merges")
.setRelation("isMergedIn")
.setRelType("organizationOrganization")
.setSubReltype("dedup"));
relationInverseMap.put("organizationOrganization_dedupSimilarity_isSimilarTo", new RelationInverse()
.setInverse("isSimilarTo")
.setRelation("isSimilarTo")
.setRelType("organizationOrganization")
.setSubReltype("dedupSimilarity"));
relationInverseMap.put("resultProject_outcome_isProducedBy", new RelationInverse()
.setRelation("isProducedBy")
.setInverse("produces")
.setRelType("resultProject")
.setSubReltype("outcome"));
relationInverseMap.put("resultProject_outcome_produces", new RelationInverse()
.setInverse("isProducedBy")
.setRelation("produces")
.setRelType("resultProject")
.setSubReltype("outcome"));
relationInverseMap.put("projectPerson_contactPerson_isContact", new RelationInverse()
.setRelation("isContact")
.setInverse("hasContact")
.setRelType("projectPerson")
.setSubReltype("contactPerson"));
relationInverseMap.put("projectPerson_contactPerson_hasContact", new RelationInverse()
.setInverse("isContact")
.setRelation("hasContact")
.setRelType("personPerson")
.setSubReltype("coAuthorship"));
relationInverseMap.put("personPerson_coAuthorship_isCoauthorOf", new RelationInverse()
.setInverse("isCoAuthorOf")
.setRelation("isCoAuthorOf")
.setRelType("personPerson")
.setSubReltype("coAuthorship"));
relationInverseMap.put("personPerson_dedup_merges", new RelationInverse()
.setInverse("isMergedIn")
.setRelation("merges")
.setRelType("personPerson")
.setSubReltype("dedup"));
relationInverseMap.put("personPerson_dedup_isMergedIn", new RelationInverse()
.setInverse("merges")
.setRelation("isMergedIn")
.setRelType("personPerson")
.setSubReltype("dedup"));
relationInverseMap.put("personPerson_dedupSimilarity_isSimilarTo", new RelationInverse()
.setInverse("isSimilarTo")
.setRelation("isSimilarTo")
.setRelType("personPerson")
.setSubReltype("dedupSimilarity"));
relationInverseMap.put("datasourceOrganization_provision_isProvidedBy", new RelationInverse()
.setInverse("provides")
.setRelation("isProvidedBy")
.setRelType("datasourceOrganization")
.setSubReltype("provision"));
relationInverseMap.put("datasourceOrganization_provision_provides", new RelationInverse()
.setInverse("isProvidedBy")
.setRelation("provides")
.setRelType("datasourceOrganization")
.setSubReltype("provision"));
relationInverseMap.put("resultResult_similarity_hasAmongTopNSimilarDocuments", new RelationInverse()
.setInverse("isAmongTopNSimilarDocuments")
.setRelation("hasAmongTopNSimilarDocuments")
.setRelType("resultResult")
.setSubReltype("similarity"));
relationInverseMap.put("resultResult_similarity_isAmongTopNSimilarDocuments", new RelationInverse()
.setInverse("hasAmongTopNSimilarDocuments")
.setRelation("isAmongTopNSimilarDocuments")
.setRelType("resultResult")
.setSubReltype("similarity"));
relationInverseMap.put("resultResult_relationship_isRelatedTo", new RelationInverse()
.setInverse("isRelatedTo")
.setRelation("isRelatedTo")
.setRelType("resultResult")
.setSubReltype("relationship"));
relationInverseMap.put("resultResult_similarity_isAmongTopNSimilarDocuments", new RelationInverse()
.setInverse("hasAmongTopNSimilarDocuments")
.setRelation("isAmongTopNSimilarDocuments")
.setRelType("resultResult")
.setSubReltype("similarity"));
relationInverseMap.put("resultResult_supplement_isSupplementTo", new RelationInverse()
.setInverse("isSupplementedBy")
.setRelation("isSupplementTo")
.setRelType("resultResult")
.setSubReltype("supplement"));
relationInverseMap.put("resultResult_supplement_isSupplementedBy", new RelationInverse()
.setInverse("isSupplementTo")
.setRelation("isSupplementedBy")
.setRelType("resultResult")
.setSubReltype("supplement"));
relationInverseMap.put("resultResult_part_isPartOf", new RelationInverse()
.setInverse("hasPart")
.setRelation("isPartOf")
.setRelType("resultResult")
.setSubReltype("part"));
relationInverseMap.put("resultResult_part_hasPart", new RelationInverse()
.setInverse("isPartOf")
.setRelation("hasPart")
.setRelType("resultResult")
.setSubReltype("part"));
relationInverseMap.put("resultResult_dedup_merges", new RelationInverse()
.setInverse("isMergedIn")
.setRelation("merges")
.setRelType("resultResult")
.setSubReltype("dedup"));
relationInverseMap.put("resultResult_dedup_isMergedIn", new RelationInverse()
.setInverse("merges")
.setRelation("isMergedIn")
.setRelType("resultResult")
.setSubReltype("dedup"));
relationInverseMap.put("resultResult_dedupSimilarity_isSimilarTo", new RelationInverse()
.setInverse("isSimilarTo")
.setRelation("isSimilarTo")
.setRelType("resultResult")
.setSubReltype("dedupSimilarity"));
}
private static final String schemeTemplate = "dnet:%s_%s_relations";
private ModelSupport() {}

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@ -1,4 +1,46 @@
package eu.dnetlib.dhp.schema.common;
public class RelationInverse {
private String relation;
private String inverse;
private String relType;
private String subReltype;
public String getRelType() {
return relType;
}
public RelationInverse setRelType(String relType) {
this.relType = relType;
return this;
}
public String getSubReltype() {
return subReltype;
}
public RelationInverse setSubReltype(String subReltype) {
this.subReltype = subReltype;
return this;
}
public String getRelation() {
return relation;
}
public RelationInverse setRelation(String relation) {
this.relation = relation;
return this;
}
public String getInverse() {
return inverse;
}
public RelationInverse setInverse(String inverse) {
this.inverse = inverse;
return this;
}
}

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@ -0,0 +1,54 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
</property>
<property>
<name>sparkExecutorNumber</name>
<value>4</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>sparkDriverMemory</name>
<value>15G</value>
</property>
<property>
<name>sparkExecutorMemory</name>
<value>6G</value>
</property>
<property>
<name>sparkExecutorCores</name>
<value>1</value>
</property>
</configuration>

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@ -0,0 +1,227 @@
<workflow-app name="bulk_tagging" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>isLookUpUrl</name>
<description>the isLookup service endpoint</description>
</property>
<property>
<name>pathMap</name>
<description>the json path associated to each selection field</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
</parameters>
<start to="reset-outputpath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset-outputpath">
<fs>
<delete path='${outputPath}/relation'/>
<delete path='${outputPath}/publication'/>
<delete path='${outputPath}/dataset'/>
<delete path='${outputPath}/otherresearchproduct'/>
<delete path='${outputPath}/software'/>
<delete path='${outputPath}/organization'/>
<delete path='${outputPath}/project'/>
<delete path='${outputPath}/datasource'/>
</fs>
<ok to="copy_entities"/>
<error to="Kill"/>
</action>
<fork name="copy_entities">
<path start="copy_relation"/>
<path start="copy_organization"/>
<path start="copy_projects"/>
<path start="copy_datasources"/>
</fork>
<action name="copy_relation">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<arg>${nameNode}/${sourcePath}/relation</arg>
<arg>${nameNode}/${outputPath}/relation</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<action name="copy_organization">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<arg>${nameNode}/${sourcePath}/organization</arg>
<arg>${nameNode}/${outputPath}/organization</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<action name="copy_projects">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<arg>${nameNode}/${sourcePath}/project</arg>
<arg>${nameNode}/${outputPath}/project</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<action name="copy_datasources">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<arg>${nameNode}/${sourcePath}/datasource</arg>
<arg>${nameNode}/${outputPath}/datasource</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<join name="copy_wait" to="fork_exec_bulktag"/>
<fork name="fork_exec_bulktag">
<path start="join_bulktag_publication"/>
<path start="join_bulktag_dataset"/>
<path start="join_bulktag_otherresearchproduct"/>
<path start="join_bulktag_software"/>
</fork>
<action name="join_bulktag_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>bulkTagging-publication</name>
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob2</class>
<jar>dhp-bulktag-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_bulktag_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>bulkTagging-dataset</name>
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob2</class>
<jar>dhp-bulktag-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_bulktag_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>bulkTagging-orp</name>
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob2</class>
<jar>dhp-bulktag-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_bulktag_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>bulkTagging-software</name>
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob2</class>
<jar>dhp-bulktag-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<join name="wait" to="End"/>
<end name="End"/>
</workflow-app>