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re-packaged graph dump workflow sources

This commit is contained in:
Claudio Atzori 2020-11-05 17:38:18 +01:00
parent 144216fb88
commit d10447e747
43 changed files with 50 additions and 77 deletions
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2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java
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@ -17,7 +17,7 @@ import com.google.gson.Gson;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.oa.graph.dump.graph.Constants; import eu.dnetlib.dhp.oa.graph.dump.complete.Constants;
import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.dhp.utils.DHPUtils;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Constants.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Constants.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.Serializable; import java.io.Serializable;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/ContextInfo.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/ContextInfo.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateContextEntities.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.IOException; import java.io.IOException;
@ -38,7 +38,7 @@ public class CreateContextEntities implements Serializable {
.toString( .toString(
CreateContextEntities.class CreateContextEntities.class
.getResourceAsStream( .getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump_whole/input_entity_parameter.json")); "/eu/dnetlib/dhp/oa/graph/dump/complete/input_entity_parameter.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateContextRelation.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.IOException; import java.io.IOException;
@ -44,7 +44,7 @@ public class CreateContextRelation implements Serializable {
.toString( .toString(
CreateContextRelation.class CreateContextRelation.class
.getResourceAsStream( .getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump_whole/input_entity_parameter.json")); "/eu/dnetlib/dhp/oa/graph/dump/complete/input_entity_parameter.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);

3
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpGraphEntities.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
@ -26,7 +26,6 @@ import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder; import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; import eu.dnetlib.dhp.schema.dump.oaf.graph.Project;
import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.H2020Programme;
import eu.dnetlib.dhp.schema.oaf.Journal; import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.OafEntity;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Extractor.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/MergedRels.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/MergedRels.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.Serializable; import java.io.Serializable;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/OrganizationMap.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/OrganizationMap.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.HashMap; import java.util.HashMap;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Process.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.Serializable; import java.io.Serializable;
import java.util.ArrayList; import java.util.ArrayList;

8
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/QueryInformationSystem.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java
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@ -1,13 +1,9 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.StringReader; import java.io.StringReader;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.*; import java.util.*;
import java.util.function.Consumer; import java.util.function.Consumer;
import java.util.stream.Collectors;
import org.dom4j.Document; import org.dom4j.Document;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
@ -16,8 +12,6 @@ import org.dom4j.Node;
import org.dom4j.io.SAXReader; import org.dom4j.io.SAXReader;
import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.NotNull;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkCollectAndSave.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
@ -31,7 +31,7 @@ public class SparkCollectAndSave implements Serializable {
.toString( .toString(
SparkCollectAndSave.class SparkCollectAndSave.class
.getResourceAsStream( .getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump_whole/input_collect_and_save.json")); "/eu/dnetlib/dhp/oa/graph/dump/complete/input_collect_and_save.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkDumpEntitiesJob.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.Serializable; import java.io.Serializable;
import java.util.Optional; import java.util.Optional;
@ -22,7 +22,7 @@ public class SparkDumpEntitiesJob implements Serializable {
.toString( .toString(
SparkDumpEntitiesJob.class SparkDumpEntitiesJob.class
.getResourceAsStream( .getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump_whole/input_parameters.json")); "/eu/dnetlib/dhp/oa/graph/dump/complete/input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);

7
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkDumpRelationJob.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
@ -7,7 +7,6 @@ import java.io.Serializable;
import java.util.Optional; import java.util.Optional;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
@ -17,8 +16,6 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
@ -40,7 +37,7 @@ public class SparkDumpRelationJob implements Serializable {
.toString( .toString(
SparkDumpRelationJob.class SparkDumpRelationJob.class
.getResourceAsStream( .getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump_whole/input_relationdump_parameters.json")); "/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);

5
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkExtractRelationFromEntities.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkExtractRelationFromEntities.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.Serializable; import java.io.Serializable;
import java.util.*; import java.util.*;
@ -9,9 +9,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.QueryInformationSystem;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
/** /**

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkOrganizationRelation.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
@ -39,7 +39,7 @@ public class SparkOrganizationRelation implements Serializable {
.toString( .toString(
SparkOrganizationRelation.class SparkOrganizationRelation.class
.getResourceAsStream( .getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump_whole/input_organization_parameters.json")); "/eu/dnetlib/dhp/oa/graph/dump/complete/input_organization_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/oozie_app/config-default.xml → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/config-default.xml
View File

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/oozie_app/workflow.xml → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/workflow.xml
View File

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_collect_and_save.json → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_collect_and_save.json
View File

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_entity_parameter.json → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_entity_parameter.json
View File

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_organization_parameters.json → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_organization_parameters.json
View File

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_parameters.json → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_parameters.json
View File

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_relationdump_parameters.json → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_parameters.json
View File

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/oozie_app/config-default.xml → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/config-default.xml
View File

32
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/oozie_app/workflow.xml → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml
View File

@ -156,7 +156,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Dump table publication </name> <name>Dump table publication </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -182,7 +182,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Dump table dataset </name> <name>Dump table dataset </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -208,7 +208,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Dump table ORP </name> <name>Dump table ORP </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -234,7 +234,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Dump table software </name> <name>Dump table software </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -260,7 +260,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Dump table organization </name> <name>Dump table organization </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -286,7 +286,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Dump table project </name> <name>Dump table project </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -312,7 +312,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Dump table datasource </name> <name>Dump table datasource </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -338,7 +338,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Dump table relation </name> <name>Dump table relation </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpRelationJob</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpRelationJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -367,7 +367,7 @@
<action name="create_entities_fromcontext"> <action name="create_entities_fromcontext">
<java> <java>
<main-class>eu.dnetlib.dhp.oa.graph.dump.graph.CreateContextEntities</main-class> <main-class>eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities</main-class>
<arg>--hdfsPath</arg><arg>${workingDir}/collect/communities_infrastructures</arg> <arg>--hdfsPath</arg><arg>${workingDir}/collect/communities_infrastructures</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg> <arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg> <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
@ -378,7 +378,7 @@
<action name="create_relation_fromcontext"> <action name="create_relation_fromcontext">
<java> <java>
<main-class>eu.dnetlib.dhp.oa.graph.dump.graph.CreateContextRelation</main-class> <main-class>eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextRelation</main-class>
<arg>--hdfsPath</arg><arg>${workingDir}/relation/context</arg> <arg>--hdfsPath</arg><arg>${workingDir}/relation/context</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg> <arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg> <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
@ -392,7 +392,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Dump table relation </name> <name>Dump table relation </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkOrganizationRelation</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkOrganizationRelation</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -427,7 +427,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Extract Relations from publication </name> <name>Extract Relations from publication </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkExtractRelationFromEntities</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -453,7 +453,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Dump table dataset </name> <name>Dump table dataset </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkExtractRelationFromEntities</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -479,7 +479,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Dump table ORP </name> <name>Dump table ORP </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkExtractRelationFromEntities</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -505,7 +505,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Dump table software </name> <name>Dump table software </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkExtractRelationFromEntities</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -533,7 +533,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Collect Results and Relations and put them in the right path </name> <name>Collect Results and Relations and put them in the right path </name>
<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkCollectAndSave</class> <class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkCollectAndSave</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/community_infrastructure_schema.json → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/community_infrastructure_schema.json
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0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/datasource_schema.json → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/datasource_schema.json
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0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/organization_schema.json → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/organization_schema.json
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0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/project_schema.json → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/project_schema.json
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0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/relation_schema.json → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/relation_schema.json
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0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/result_schema.json → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json
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3
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateEntityTest.java → dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import static org.mockito.Mockito.lenient; import static org.mockito.Mockito.lenient;
@ -7,7 +7,6 @@ import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;
import java.util.Map;
import java.util.function.Consumer; import java.util.function.Consumer;
import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Assertions;

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateRelationTest.java → dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.util.*; import java.util.*;
import java.util.function.Consumer; import java.util.function.Consumer;

8
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpOrganizationProjectDatasourceTest.java → dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.IOException; import java.io.IOException;
import java.nio.file.Files; import java.nio.file.Files;
@ -72,7 +72,7 @@ public class DumpOrganizationProjectDatasourceTest {
public void dumpOrganizationTest() throws Exception { public void dumpOrganizationTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/organization") .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/organization")
.getPath(); .getPath();
DumpGraphEntities dg = new DumpGraphEntities(); DumpGraphEntities dg = new DumpGraphEntities();
@ -101,7 +101,7 @@ public class DumpOrganizationProjectDatasourceTest {
public void dumpProjectTest() { public void dumpProjectTest() {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/project") .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/project")
.getPath(); .getPath();
DumpGraphEntities dg = new DumpGraphEntities(); DumpGraphEntities dg = new DumpGraphEntities();
@ -129,7 +129,7 @@ public class DumpOrganizationProjectDatasourceTest {
@Test @Test
public void dumpDatasourceTest() { public void dumpDatasourceTest() {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/datasource") .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/datasource")
.getPath(); .getPath();
DumpGraphEntities dg = new DumpGraphEntities(); DumpGraphEntities dg = new DumpGraphEntities();

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpRelationTest.java → dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.IOException; import java.io.IOException;
import java.nio.file.Files; import java.nio.file.Files;

10
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/ExtractRelationFromEntityTest.java → dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/ExtractRelationFromEntityTest.java
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@ -1,31 +1,23 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.IOException; import java.io.IOException;
import java.nio.file.Files; import java.nio.file.Files;
import java.nio.file.Path; import java.nio.file.Path;
import java.util.HashMap;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*; import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class ExtractRelationFromEntityTest { public class ExtractRelationFromEntityTest {

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/FunderParsingTest.java → dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/FunderParsingTest.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Assertions;

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/QueryInformationSystemTest.java → dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import static org.mockito.Mockito.lenient; import static org.mockito.Mockito.lenient;

9
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/RelationFromOrganizationTest.java → dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/RelationFromOrganizationTest.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.IOException; import java.io.IOException;
import java.nio.file.Files; import java.nio.file.Files;
@ -7,13 +7,10 @@ import java.nio.file.Path;
import java.util.HashMap; import java.util.HashMap;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.neethi.Assertion;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Assertions;
@ -24,9 +21,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
import eu.dnetlib.dhp.utils.DHPUtils;
public class RelationFromOrganizationTest { public class RelationFromOrganizationTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
@ -77,7 +72,7 @@ public class RelationFromOrganizationTest {
public void test1() throws Exception { public void test1() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/relation") .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation")
.getPath(); .getPath();
final String communityMapPath = getClass() final String communityMapPath = getClass()

0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/graph/datasource/datasource.json → dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/datasource/datasource.json
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0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/graph/organization/organization.json → dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/organization/organization.json
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0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/graph/project/project.json → dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/project/project.json
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0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/graph/relation/relation → dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/relation/relation
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