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[Enrichment WF] second attempt to make it run in a single step

This commit is contained in:
Miriam Baglioni 2022-04-07 18:58:55 +02:00
parent 7406c88276
commit 9bd5310112
32 changed files with 248 additions and 407 deletions
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6
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java
View File

@ -97,6 +97,12 @@ public class SparkCountryPropagationJob {
.mode(SaveMode.Overwrite)
.json(outputPath);
readPath(spark,outputPath,resultClazz)
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(sourcePath);
}
private static <R extends Result> MapFunction<Tuple2<R, ResultCountrySet>, R> getCountryMergeFn() {

6
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java
View File

@ -99,6 +99,12 @@ public class SparkResultToCommunityFromOrganizationJob {
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
readPath(spark,outputPath,resultClazz)
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(inputPath);
}
private static <R extends Result> MapFunction<Tuple2<R, ResultCommunityList>, R> resultCommunityFn() {

6
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java
View File

@ -100,6 +100,12 @@ public class SparkResultToCommunityThroughSemRelJob {
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
readPath(spark, outputPath, resultClazz)
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(inputPath);
}
private static <R extends Result> MapFunction<Tuple2<R, ResultCommunityList>, R> contextUpdaterFn() {

4
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java
View File

@ -119,13 +119,13 @@ public class SparkResultToOrganizationFromIstRepoJob {
"left_outer")
.flatMap(createRelationFn(), Encoders.bean(Relation.class))
.write()
.mode(SaveMode.Append)
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
readPath(spark, outputPath, Relation.class)
.write()
.mode(SaveMode.Overwrite)
.mode(SaveMode.Append)
.option("compression","gzip")
.json(inputPath.substring(0, inputPath.indexOf("/") + 1) + "relation");
}

1
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/SparkResultToOrganizationFromSemRel.java
View File

@ -225,7 +225,6 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
, Encoders.bean(Relation.class))
.write()
.mode(SaveMode.Append)
.option("compression", "gzip")
.json(outputPath);

9
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/oozie_app/import.txt
View File

@ -1,4 +1,9 @@
## This is a classpath-based import file (this header is required)
orcid_propagation classpath eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app
dump_funder classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app
dump_community classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app
bulk_tagging classpath eu/dnetlib/dhp/wf/subworkflows/bulktag/oozie_app
affiliation_inst_repo classpath eu/dnetlib/dhp/wf/subworkflows/resulttoorganizationfrominstrepo/oozie_app
affiliation_semantic_relation classpath eu/dnetlib/dhp/wf/subworkflows/resuttoorganizationfromsemrel/oozie_app
community_organization classpath eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromorganization/oozie_app
result_project classpath eu/dnetlib/dhp/wf/subworkflows/projecttoresult/oozie_app
community_sem_rel classpath eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromsemrel/oozie_app
country_propagation classpath eu/dnetlib/dhp/wf/subworkflows/countrypropagation/oozie_app

148
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/oozie_app/workflow.xml
View File

@ -6,14 +6,33 @@
<description>the source path</description>
</property>
<property>
<name>allowedsemrels</name>
<name>allowedsemrelsorginstrepo</name>
<description>the semantic relationships allowed for propagation</description>
</property>
<property>
<name>allowedsemrelsresultproject</name>
<description>the allowed semantics </description>
</property>
<property>
<name>allowedsemrelscommunitysemrel</name>
<description>the semantic relationships allowed for propagation</description>
</property>
<property>
<name>whitelist</name>
<description>the white list</description>
</property>
<property>
<name>allowedtypes</name>
<description>the allowed types</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
<property>
<name>organizationtoresultcommunitymap</name>
<description>organization community map</description>
</property>
<property>
<name>isLookUpUrl</name>
<description>the isLookup service endpoint</description>
@ -117,7 +136,7 @@
</property>
<property>
<name>allowedsemrels</name>
<value>${allowedsemrels}</value>
<value>${allowedsemrelsorginstrepo}</value>
</property>
<property>
<name>outputPath</name>
@ -159,7 +178,7 @@
<action name="affiliation_inst_repo">
<sub-workflow>
<app-path>${wf:appPath()}/bulk_tagging
<app-path>${wf:appPath()}/affiliation_inst_repo
</app-path>
<propagate-configuration/>
<configuration>
@ -177,10 +196,129 @@
</property>
</configuration>
</sub-workflow>
<ok to="bulk_tagging" />
<ok to="affiliation_semantic_relation" />
<error to="Kill" />
</action>
<action name="affiliation_semantic_relation">
<sub-workflow>
<app-path>${wf:appPath()}/affiliation_semantic_relation
</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>sourcePath</name>
<value>${outputPath}</value>
</property>
<property>
<name>outputPath</name>
<value>${outputPath}</value>
</property>
</configuration>
</sub-workflow>
<ok to="community_organization" />
<error to="Kill" />
</action>
<action name="community_organization">
<sub-workflow>
<app-path>${wf:appPath()}/community_organization
</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>sourcePath</name>
<value>${outputPath}</value>
</property>
<property>
<name>outputPath</name>
<value>${outputPath}</value>
</property>
<property>
<name>organizationtoresultcommunitymap</name>
<value>${organizationtoresultcommunitymap}</value>
</property>
</configuration>
</sub-workflow>
<ok to="result_project" />
<error to="Kill" />
</action>
<action name="result_project">
<sub-workflow>
<app-path>${wf:appPath()}/result_project
</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>sourcePath</name>
<value>${outputPath}</value>
</property>
<property>
<name>outputPath</name>
<value>${outputPath}</value>
</property>
<property>
<name>allowedsemrels</name>
<value>${allowedsemrelsresultproject}</value>
</property>
</configuration>
</sub-workflow>
<ok to="community_sem_rel" />
<error to="Kill" />
</action>
<action name="community_sem_rel">
<sub-workflow>
<app-path>${wf:appPath()}/result_project
</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>sourcePath</name>
<value>${outputPath}</value>
</property>
<property>
<name>outputPath</name>
<value>${workingDir}/communitysemrel</value>
</property>
<property>
<name>allowedsemrels</name>
<value>${allowedsemrelscommunitysemrel}</value>
</property>
</configuration>
</sub-workflow>
<ok to="country_propagation" />
<error to="Kill" />
</action>
<action name="country_propagation">
<sub-workflow>
<app-path>${wf:appPath()}/country_propagation
</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>sourcePath</name>
<value>${outputPath}</value>
</property>
<property>
<name>outputPath</name>
<value>${workingDir}/country/result</value>
</property>
<property>
<name>whitelist</name>
<value>${whitelist}</value>
</property>
<property>
<name>allowedtypes</name>
<value>${allowedtupes}</value>
</property>
</configuration>
</sub-workflow>
<ok to="End" />
<error to="Kill" />
</action>
<end name="End"/>

8
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/bulktag/oozie_app/workflow.xml
View File

@ -62,7 +62,7 @@
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--workingPath</arg><arg>${workingPath}/publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/bulktag/publication</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
@ -89,7 +89,7 @@
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--workingPath</arg><arg>${workingPath}/dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/bulktag/dataset</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
@ -116,7 +116,7 @@
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--workingPath</arg><arg>${workingPath}/otherresearchproduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/bulktag/otherresearchproduct</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
@ -143,7 +143,7 @@
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--workingPath</arg><arg>${workingPath}/software</arg>
<arg>--outputPath</arg><arg>${workingDir}/bulktag/software</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/countrypropagation/input_countrypropagation_parameters.json
View File

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/countrypropagation/input_prepareassoc_parameters.json
View File

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareresultcountry_parameters.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/countrypropagation/input_prepareresultcountry_parameters.json
View File

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/config-default.xml → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/countrypropagation/oozie_app/config-default.xml
View File

79
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/countrypropagation/oozie_app/workflow.xml
View File

@ -41,55 +41,10 @@
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<ok to="prepare_datasource_country_association"/>
<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">
<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">
<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">
<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">
<arg>${nameNode}/${sourcePath}/datasource</arg>
<arg>${nameNode}/${outputPath}/datasource</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<join name="copy_wait" to="prepare_datasource_country_association"/>
<action name="prepare_datasource_country_association">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -110,7 +65,7 @@
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--whitelist</arg><arg>${whitelist}</arg>
<arg>--allowedtypes</arg><arg>${allowedtypes}</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg>
<arg>--outputPath</arg><arg>${workingDir}/country/preparedInfo</arg>
</spark>
<ok to="fork_join_prepare_result_country"/>
<error to="Kill"/>
@ -144,10 +99,10 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/publication</arg>
<arg>--workingPath</arg><arg>${workingDir}/workingP</arg>
<arg>--outputPath</arg><arg>${workingDir}/country/publication</arg>
<arg>--workingPath</arg><arg>${workingDir}/country/workingP</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country/preparedInfo</arg>
</spark>
<ok to="wait_prepare"/>
<error to="Kill"/>
@ -174,10 +129,10 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/dataset</arg>
<arg>--workingPath</arg><arg>${workingDir}/workingD</arg>
<arg>--outputPath</arg><arg>${workingDir}/country/dataset</arg>
<arg>--workingPath</arg><arg>${workingDir}/country/workingD</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country/preparedInfo</arg>
</spark>
<ok to="wait_prepare"/>
<error to="Kill"/>
@ -204,10 +159,10 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--workingPath</arg><arg>${workingDir}/workingO</arg>
<arg>--outputPath</arg><arg>${workingDir}/country/otherresearchproduct</arg>
<arg>--workingPath</arg><arg>${workingDir}/country/workingO</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country/preparedInfo</arg>
</spark>
<ok to="wait_prepare"/>
<error to="Kill"/>
@ -234,10 +189,10 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--outputPath</arg><arg>${workingDir}/software</arg>
<arg>--workingPath</arg><arg>${workingDir}/workingS</arg>
<arg>--outputPath</arg><arg>${workingDir}/country/software</arg>
<arg>--workingPath</arg><arg>${workingDir}/country/workingS</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country/preparedInfo</arg>
</spark>
<ok to="wait_prepare"/>
<error to="Kill"/>
@ -273,7 +228,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/publication</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country/publication</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
@ -303,7 +258,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/dataset</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country/dataset</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
@ -333,7 +288,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country/otherresearchproduct</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>

20
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/orcidtoresultfromsemrel/oozie_app/workflow.xml
View File

@ -72,7 +72,7 @@
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/orcidprop/preparedInfo/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
</spark>
<ok to="wait"/>
@ -100,7 +100,7 @@
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/orcidprop/preparedInfo/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
</spark>
<ok to="wait"/>
@ -128,7 +128,7 @@
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/orcidprop/preparedInfo/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
</spark>
<ok to="wait"/>
@ -156,7 +156,7 @@
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/orcidprop/preparedInfo/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
</spark>
<ok to="wait"/>
@ -183,8 +183,8 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/orcidprop/preparedInfo/targetOrcidAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/orcidprop/preparedInfo/mergedOrcidAssoc</arg>
</spark>
<ok to="fork-join-exec-propagation"/>
<error to="Kill"/>
@ -219,7 +219,7 @@
--conf spark.hadoop.mapreduce.reduce.speculative=false
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcidprop/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
@ -250,7 +250,7 @@
--conf spark.hadoop.mapreduce.map.speculative=false
--conf spark.hadoop.mapreduce.reduce.speculative=false
</spark-opts>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcidprop/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
@ -281,7 +281,7 @@
--conf spark.hadoop.mapreduce.map.speculative=false
--conf spark.hadoop.mapreduce.reduce.speculative=false
</spark-opts>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcidprop/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
@ -312,7 +312,7 @@
--conf spark.hadoop.mapreduce.map.speculative=false
--conf spark.hadoop.mapreduce.reduce.speculative=false
</spark-opts>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcidprop/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/input_prepareprojecttoresult_parameters.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/projecttoresult/input_prepareprojecttoresult_parameters.json
View File

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/input_projecttoresult_parameters.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/projecttoresult/input_projecttoresult_parameters.json
View File

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/config-default.xml → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/projecttoresult/oozie_app/config-default.xml
View File

103
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/projecttoresult/oozie_app/workflow.xml
View File

@ -25,105 +25,12 @@
</configuration>
</global>
<start to="reset_outputpath"/>
<start to="prepare_project_results_association"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset_outputpath">
<fs>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<error to="Kill"/>
</action>
<fork name="copy_entities">
<path start="copy_relation"/>
<path start="copy_publication"/>
<path start="copy_dataset"/>
<path start="copy_orp"/>
<path start="copy_software"/>
<path start="copy_organization"/>
<path start="copy_projects"/>
<path start="copy_datasources"/>
</fork>
<action name="copy_relation">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/relation</arg>
<arg>${nameNode}/${outputPath}/relation</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_publication">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/publication</arg>
<arg>${nameNode}/${outputPath}/publication</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_dataset">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/dataset</arg>
<arg>${nameNode}/${outputPath}/dataset</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_orp">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/otherresearchproduct</arg>
<arg>${nameNode}/${outputPath}/otherresearchproduct</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_software">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/software</arg>
<arg>${nameNode}/${outputPath}/software</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_organization">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/organization</arg>
<arg>${nameNode}/${outputPath}/organization</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_projects">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/project</arg>
<arg>${nameNode}/${outputPath}/project</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_datasources">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/datasource</arg>
<arg>${nameNode}/${outputPath}/datasource</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<join name="wait" to="prepare_project_results_association"/>
<action name="prepare_project_results_association">
<spark xmlns="uri:oozie:spark-action:0.2">
@ -144,8 +51,8 @@
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--potentialUpdatePath</arg><arg>${workingDir}/preparedInfo/potentialUpdates</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
<arg>--potentialUpdatePath</arg><arg>${workingDir}/resultproject/preparedInfo/potentialUpdates</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/resultproject/preparedInfo/alreadyLinked</arg>
</spark>
<ok to="apply_propagation"/>
<error to="Kill"/>
@ -172,8 +79,8 @@
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--outputPath</arg><arg>${outputPath}/relation</arg>
<arg>--potentialUpdatePath</arg><arg>${workingDir}/preparedInfo/potentialUpdates</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
<arg>--potentialUpdatePath</arg><arg>${workingDir}/resultproject/preparedInfo/potentialUpdates</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/resultproject/preparedInfo/alreadyLinked</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttocommunityfromorganization/input_communitytoresult_parameters.json
View File

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json
View File

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/config-default.xml → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttocommunityfromorganization/oozie_app/config-default.xml
View File

65
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttocommunityfromorganization/oozie_app/workflow.xml
View File

@ -36,55 +36,10 @@
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<ok to="prepare_result_communitylist"/>
<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">
<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">
<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">
<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">
<arg>${nameNode}/${sourcePath}/datasource</arg>
<arg>${nameNode}/${outputPath}/datasource</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<join name="copy_wait" to="prepare_result_communitylist"/>
<action name="prepare_result_communitylist">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -104,7 +59,7 @@
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
<arg>--outputPath</arg><arg>${workingDir}/communityorganization/preparedInfo/resultCommunityList</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--organizationtoresultcommunitymap</arg><arg>${organizationtoresultcommunitymap}</arg>
</spark>
@ -137,9 +92,9 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/communityorganization/preparedInfo/resultCommunityList</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/communityorganization/publication</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
@ -166,9 +121,9 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/communityorganization/preparedInfo/resultCommunityList</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/communityorganization/dataset</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
@ -195,9 +150,9 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/communityorganization/preparedInfo/resultCommunityList</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/communityorganization/otherresearchproduct</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
@ -224,9 +179,9 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/communityorganization/preparedInfo/resultCommunityList</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
<arg>--outputPath</arg><arg>${workingDir}/communityorganization/software</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_communitytoresult_parameters.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttocommunityfromsemrel/input_communitytoresult_parameters.json
View File

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_preparecommunitytoresult2_parameters.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttocommunityfromsemrel/input_preparecommunitytoresult2_parameters.json
View File

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_preparecommunitytoresult_parameters.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttocommunityfromsemrel/input_preparecommunitytoresult_parameters.json
View File

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/oozie_app/config-default.xml → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttocommunityfromsemrel/oozie_app/config-default.xml
View File

73
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/oozie_app/workflow.xml → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttocommunityfromsemrel/oozie_app/workflow.xml
View File

@ -29,62 +29,11 @@
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<ok to="fork_prepare_assoc_step1"/>
<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_prepare_assoc_step1"/>
<fork name="fork_prepare_assoc_step1">
<path start="join_prepare_publication"/>
@ -114,7 +63,7 @@
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetCommunityAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/communitysemrel/preparedInfo/targetCommunityAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
@ -143,7 +92,7 @@
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetCommunityAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/communitysemrel/preparedInfo/targetCommunityAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
@ -172,7 +121,7 @@
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetCommunityAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/communitysemrel/preparedInfo/targetCommunityAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
@ -201,7 +150,7 @@
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetCommunityAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/communitysemrel/preparedInfo/targetCommunityAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
@ -229,8 +178,8 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/preparedInfo/targetCommunityAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/mergedCommunityAssoc</arg>
<arg>--sourcePath</arg><arg>${workingDir}/communitysemrel/preparedInfo/targetCommunityAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/communitysemrel/preparedInfo/mergedCommunityAssoc</arg>
</spark>
<ok to="fork-join-exec-propagation"/>
<error to="Kill"/>
@ -261,7 +210,7 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/mergedCommunityAssoc</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/communitysemrel/preparedInfo/mergedCommunityAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
@ -290,7 +239,7 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/mergedCommunityAssoc</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/communitysemrel/preparedInfo/mergedCommunityAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
@ -319,7 +268,7 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/mergedCommunityAssoc</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/communitysemrel/preparedInfo/mergedCommunityAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
@ -348,7 +297,7 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/mergedCommunityAssoc</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/communitysemrel/preparedInfo/mergedCommunityAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>

20
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttoorganizationfrominstrepo/oozie_app/workflow.xml
View File

@ -46,8 +46,8 @@
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/datasourceOrganization</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/alreadyLinked</arg>
<arg>--blacklist</arg><arg>${blacklist}</arg>
</spark>
<ok to="fork_join_apply_resulttoorganization_propagation"/>
@ -81,8 +81,8 @@
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--outputPath</arg><arg>${outputPath}/relation</arg>
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/datasourceOrganization</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/alreadyLinked</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
</spark>
@ -110,8 +110,8 @@
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--outputPath</arg><arg>${outputPath}/relation</arg>
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/datasourceOrganization</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/alreadyLinked</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
</spark>
@ -139,8 +139,8 @@
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--outputPath</arg><arg>${outputPath}/relation</arg>
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/datasourceOrganization</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/alreadyLinked</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
</spark>
@ -168,8 +168,8 @@
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--outputPath</arg><arg>${outputPath}/relation</arg>
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/datasourceOrganization</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/alreadyLinked</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
</spark>

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/input_preparation_parameter.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttoorganizationfromsemrel/input_preparation_parameter.json
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0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/input_propagation_parameter.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttoorganizationfromsemrel/input_propagation_parameter.json
View File

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/config-default.xml → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttoorganizationfromsemrel/oozie_app/config-default.xml
View File

107
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/workflow.xml → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflow/resulttoorganizationfromsemrel/oozie_app/workflow.xml
View File

@ -39,95 +39,10 @@
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<ok to="prepare_info"/>
<error to="Kill"/>
</action>
<fork name="copy_entities">
<path start="copy_relation"/>
<path start="copy_publication"/>
<path start="copy_dataset"/>
<path start="copy_orp"/>
<path start="copy_software"/>
<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">
<arg>${nameNode}/${sourcePath}/relation</arg>
<arg>${nameNode}/${outputPath}/relation</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_publication">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/publication</arg>
<arg>${nameNode}/${outputPath}/publication</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_dataset">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/dataset</arg>
<arg>${nameNode}/${outputPath}/dataset</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_orp">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/otherresearchproduct</arg>
<arg>${nameNode}/${outputPath}/otherresearchproduct</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_software">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/software</arg>
<arg>${nameNode}/${outputPath}/software</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_organization">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/organization</arg>
<arg>${nameNode}/${outputPath}/organization</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_projects">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/project</arg>
<arg>${nameNode}/${outputPath}/project</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_datasources">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/datasource</arg>
<arg>${nameNode}/${outputPath}/datasource</arg>
</distcp>
<ok to="wait"/>
<error to="Kill"/>
</action>
<join name="wait" to="prepare_info"/>
<action name="prepare_info">
<spark xmlns="uri:oozie:spark-action:0.2">
@ -147,10 +62,10 @@
</spark-opts>
<arg>--graphPath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--leavesPath</arg><arg>${workingDir}/preparedInfo/leavesPath</arg>
<arg>--childParentPath</arg><arg>${workingDir}/preparedInfo/childParentPath</arg>
<arg>--resultOrgPath</arg><arg>${workingDir}/preparedInfo/resultOrgPath</arg>
<arg>--relationPath</arg><arg>${workingDir}/preparedInfo/relation</arg>
<arg>--leavesPath</arg><arg>${workingDir}/affiliationSemanticRelation/preparedInfo/leavesPath</arg>
<arg>--childParentPath</arg><arg>${workingDir}/affiliationSemanticRelation/preparedInfo/childParentPath</arg>
<arg>--resultOrgPath</arg><arg>${workingDir}/affiliationSemanticRelation/preparedInfo/resultOrgPath</arg>
<arg>--relationPath</arg><arg>${workingDir}/affiliationSemanticRelation/preparedInfo/relation</arg>
</spark>
<ok to="apply_resulttoorganization_propagation"/>
<error to="Kill"/>
@ -175,13 +90,13 @@
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--relationPath</arg><arg>${workingDir}/preparedInfo/relation</arg>
<arg>--outputPath</arg><arg>${outputPath}/relation</arg>
<arg>--leavesPath</arg><arg>${workingDir}/preparedInfo/leavesPath</arg>
<arg>--childParentPath</arg><arg>${workingDir}/preparedInfo/childParentPath</arg>
<arg>--resultOrgPath</arg><arg>${workingDir}/preparedInfo/resultOrgPath</arg>
<arg>--relationPath</arg><arg>${workingDir}/affiliationSemanticRelation/preparedInfo/relation</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--leavesPath</arg><arg>${workingDir}/affiliationSemanticRelation/preparedInfo/leavesPath</arg>
<arg>--childParentPath</arg><arg>${workingDir}/affiliationSemanticRelation/preparedInfo/childParentPath</arg>
<arg>--resultOrgPath</arg><arg>${workingDir}/affiliationSemanticRelation/preparedInfo/resultOrgPath</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--workingDir</arg><arg>${workingDir}/working</arg>
<arg>--workingDir</arg><arg>${workingDir}/affiliationSemanticRelation/working</arg>
<arg>--iterations</arg><arg>${iterations}</arg>
</spark>
<ok to="End"/>