forked from D-Net/dnet-hadoop
re-packaged graph dump workflow sources
This commit is contained in:
parent
144216fb88
commit
d10447e747
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@ -17,7 +17,7 @@ import com.google.gson.Gson;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.oa.graph.dump.graph.Constants;
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import eu.dnetlib.dhp.oa.graph.dump.complete.Constants;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import java.io.Serializable;
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import java.io.Serializable;
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import java.util.List;
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import java.io.BufferedWriter;
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import java.io.IOException;
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@ -38,7 +38,7 @@ public class CreateContextEntities implements Serializable {
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.toString(
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CreateContextEntities.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump_whole/input_entity_parameter.json"));
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"/eu/dnetlib/dhp/oa/graph/dump/complete/input_entity_parameter.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import java.io.BufferedWriter;
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import java.io.IOException;
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@ -44,7 +44,7 @@ public class CreateContextRelation implements Serializable {
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.toString(
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CreateContextRelation.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump_whole/input_entity_parameter.json"));
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"/eu/dnetlib/dhp/oa/graph/dump/complete/input_entity_parameter.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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@ -26,7 +26,6 @@ import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.Project;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.H2020Programme;
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import eu.dnetlib.dhp.schema.oaf.Journal;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import java.io.Serializable;
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import java.util.ArrayList;
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import java.util.HashMap;
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import java.io.Serializable;
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import java.util.ArrayList;
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@ -1,13 +1,9 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import java.io.StringReader;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.sql.Statement;
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import java.util.*;
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import java.util.function.Consumer;
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import java.util.stream.Collectors;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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@ -16,8 +12,6 @@ import org.dom4j.Node;
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import org.dom4j.io.SAXReader;
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import org.jetbrains.annotations.NotNull;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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@ -31,7 +31,7 @@ public class SparkCollectAndSave implements Serializable {
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.toString(
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SparkCollectAndSave.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump_whole/input_collect_and_save.json"));
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"/eu/dnetlib/dhp/oa/graph/dump/complete/input_collect_and_save.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import java.io.Serializable;
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import java.util.Optional;
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@ -22,7 +22,7 @@ public class SparkDumpEntitiesJob implements Serializable {
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.toString(
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SparkDumpEntitiesJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump_whole/input_parameters.json"));
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"/eu/dnetlib/dhp/oa/graph/dump/complete/input_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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@ -7,7 +7,6 @@ import java.io.Serializable;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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@ -17,8 +16,6 @@ import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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@ -40,7 +37,7 @@ public class SparkDumpRelationJob implements Serializable {
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.toString(
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SparkDumpRelationJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump_whole/input_relationdump_parameters.json"));
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"/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import java.io.Serializable;
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import java.util.*;
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@ -9,9 +9,6 @@ import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.QueryInformationSystem;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.schema.oaf.Result;
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/**
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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@ -39,7 +39,7 @@ public class SparkOrganizationRelation implements Serializable {
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.toString(
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SparkOrganizationRelation.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump_whole/input_organization_parameters.json"));
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"/eu/dnetlib/dhp/oa/graph/dump/complete/input_organization_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -156,7 +156,7 @@
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table publication </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -182,7 +182,7 @@
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table dataset </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table ORP </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table software </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -260,7 +260,7 @@
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table organization </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table project </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -312,7 +312,7 @@
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table datasource </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -338,7 +338,7 @@
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table relation </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpRelationJob</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpRelationJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -367,7 +367,7 @@
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<action name="create_entities_fromcontext">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.graph.CreateContextEntities</main-class>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities</main-class>
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<arg>--hdfsPath</arg><arg>${workingDir}/collect/communities_infrastructures</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
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@ -378,7 +378,7 @@
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<action name="create_relation_fromcontext">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.graph.CreateContextRelation</main-class>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextRelation</main-class>
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<arg>--hdfsPath</arg><arg>${workingDir}/relation/context</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
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@ -392,7 +392,7 @@
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table relation </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkOrganizationRelation</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkOrganizationRelation</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -427,7 +427,7 @@
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Extract Relations from publication </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkExtractRelationFromEntities</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -453,7 +453,7 @@
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table dataset </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkExtractRelationFromEntities</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -479,7 +479,7 @@
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table ORP </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkExtractRelationFromEntities</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -505,7 +505,7 @@
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table software </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkExtractRelationFromEntities</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -533,7 +533,7 @@
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Collect Results and Relations and put them in the right path </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.graph.SparkCollectAndSave</class>
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<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkCollectAndSave</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import static org.mockito.Mockito.lenient;
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@ -7,7 +7,6 @@ import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Map;
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import java.util.function.Consumer;
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import org.junit.jupiter.api.Assertions;
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import java.util.*;
|
||||
import java.util.function.Consumer;
|
|
@ -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.nio.file.Files;
|
||||
|
@ -72,7 +72,7 @@ public class DumpOrganizationProjectDatasourceTest {
|
|||
public void dumpOrganizationTest() throws Exception {
|
||||
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/organization")
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/organization")
|
||||
.getPath();
|
||||
|
||||
DumpGraphEntities dg = new DumpGraphEntities();
|
||||
|
@ -101,7 +101,7 @@ public class DumpOrganizationProjectDatasourceTest {
|
|||
public void dumpProjectTest() {
|
||||
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/project")
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/project")
|
||||
.getPath();
|
||||
|
||||
DumpGraphEntities dg = new DumpGraphEntities();
|
||||
|
@ -129,7 +129,7 @@ public class DumpOrganizationProjectDatasourceTest {
|
|||
@Test
|
||||
public void dumpDatasourceTest() {
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/datasource")
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/datasource")
|
||||
.getPath();
|
||||
|
||||
DumpGraphEntities dg = new DumpGraphEntities();
|
|
@ -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.nio.file.Files;
|
|
@ -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.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.util.HashMap;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
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.LoggerFactory;
|
||||
|
||||
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.enabling.is.lookup.rmi.ISLookUpService;
|
||||
|
||||
public class ExtractRelationFromEntityTest {
|
||||
|
|
@ -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.junit.jupiter.api.Assertions;
|
|
@ -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;
|
||||
|
|
@ -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.nio.file.Files;
|
||||
|
@ -7,13 +7,10 @@ import java.nio.file.Path;
|
|||
import java.util.HashMap;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.neethi.Assertion;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.AfterAll;
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
|
@ -24,9 +21,7 @@ import org.slf4j.LoggerFactory;
|
|||
|
||||
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.utils.DHPUtils;
|
||||
|
||||
public class RelationFromOrganizationTest {
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
@ -77,7 +72,7 @@ public class RelationFromOrganizationTest {
|
|||
public void test1() throws Exception {
|
||||
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/relation")
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/relation")
|
||||
.getPath();
|
||||
|
||||
final String communityMapPath = getClass()
|
Loading…
Reference in New Issue