Merge pull request 'DispatchEntitiesSparkJob: manage all entity types together, support filtering by dataInfo.invisible flag' (#329) from dispatch_filter_invisible_entities into beta
Reviewed-on: #329
This commit is contained in:
commit
35b8deb2c6
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@ -11,25 +11,18 @@ 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.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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public class DispatchEntitiesSparkJob {
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private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesSparkJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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@ -54,11 +47,8 @@ public class DispatchEntitiesSparkJob {
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String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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String graphTableClassName = parser.get("graphTableClassName");
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log.info("graphTableClassName: {}", graphTableClassName);
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@SuppressWarnings("unchecked")
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Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
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boolean filterInvisible = Boolean.valueOf(parser.get("filterInvisible"));
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log.info("filterInvisible: {}", filterInvisible);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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@ -66,32 +56,43 @@ public class DispatchEntitiesSparkJob {
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isSparkSessionManaged,
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spark -> {
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HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
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dispatchEntities(spark, inputPath, entityClazz, outputPath);
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dispatchEntities(spark, inputPath, outputPath, filterInvisible);
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});
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}
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private static <T extends Oaf> void dispatchEntities(
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private static void dispatchEntities(
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SparkSession spark,
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String inputPath,
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Class<T> clazz,
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String outputPath) {
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String outputPath,
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boolean filterInvisible) {
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spark
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.read()
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.textFile(inputPath)
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.filter((FilterFunction<String>) s -> isEntityType(s, clazz))
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.map((MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"), Encoders.STRING())
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.map(
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(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz),
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Encoders.bean(clazz))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath);
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Dataset<String> df = spark.read().textFile(inputPath);
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ModelSupport.oafTypes.entrySet().parallelStream().forEach(entry -> {
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String entityType = entry.getKey();
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Class<?> clazz = entry.getValue();
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if (!entityType.equalsIgnoreCase("relation")) {
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Dataset<Row> entityDF = spark
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.read()
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.schema(Encoders.bean(clazz).schema())
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.json(
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df
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.filter((FilterFunction<String>) s -> s.startsWith(clazz.getName()))
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.map(
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(MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"),
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Encoders.STRING()));
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if (filterInvisible) {
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entityDF = entityDF.filter("dataInfo.invisible != true");
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}
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entityDF
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + "/" + entityType);
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}
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});
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}
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private static <T extends Oaf> boolean isEntityType(final String s, final Class<T> clazz) {
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return StringUtils.substringBefore(s, "|").equals(clazz.getName());
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}
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}
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@ -18,9 +18,9 @@
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"paramRequired": true
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},
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{
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"paramName": "c",
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"paramLongName": "graphTableClassName",
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"paramDescription": "the graph entity class name",
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"paramName": "fi",
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"paramLongName": "filterInvisible",
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"paramDescription": "if true filters out invisible entities",
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"paramRequired": true
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}
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]
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@ -12,6 +12,10 @@
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<name>graphOutputPath</name>
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<description>path of the output graph</description>
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</property>
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<property>
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<name>filterInvisible</name>
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<description>whether filter out invisible entities after merge</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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@ -24,7 +28,6 @@
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>oozieActionShareLibForSpark2</name>
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<description>oozie action sharelib for spark 2.*</description>
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@ -144,25 +147,15 @@
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<arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
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<arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
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</spark>
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<ok to="fork_dispatch_entities"/>
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<ok to="dispatch_entities"/>
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<error to="Kill"/>
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</action>
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<fork name="fork_dispatch_entities">
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<path start="dispatch_datasource"/>
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<path start="dispatch_project"/>
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<path start="dispatch_organization"/>
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<path start="dispatch_publication"/>
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<path start="dispatch_dataset"/>
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<path start="dispatch_software"/>
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<path start="dispatch_otherresearchproduct"/>
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</fork>
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<action name="dispatch_datasource">
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<action name="dispatch_entities">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dispatch publications</name>
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<name>Dispatch grouped entitities</name>
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<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
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<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
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<spark-opts>
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@ -176,164 +169,12 @@
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/datasource</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}</arg>
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<arg>--filterInvisible</arg><arg>${filterInvisible}</arg>
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</spark>
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<ok to="wait_dispatch"/>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<action name="dispatch_project">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dispatch project</name>
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<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
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<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/project</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
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</spark>
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<ok to="wait_dispatch"/>
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<error to="Kill"/>
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</action>
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<action name="dispatch_organization">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dispatch organization</name>
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<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
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<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/organization</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
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</spark>
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<ok to="wait_dispatch"/>
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<error to="Kill"/>
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</action>
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<action name="dispatch_publication">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dispatch publication</name>
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<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
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<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/publication</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
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</spark>
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<ok to="wait_dispatch"/>
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<error to="Kill"/>
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</action>
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<action name="dispatch_dataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dispatch dataset</name>
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<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
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<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/dataset</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
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</spark>
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<ok to="wait_dispatch"/>
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<error to="Kill"/>
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</action>
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<action name="dispatch_software">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dispatch software</name>
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<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
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<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/software</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
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</spark>
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<ok to="wait_dispatch"/>
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<error to="Kill"/>
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</action>
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<action name="dispatch_otherresearchproduct">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dispatch otherresearchproduct</name>
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<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
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<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
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</spark>
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<ok to="wait_dispatch"/>
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<error to="Kill"/>
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</action>
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<join name="wait_dispatch" to="End"/>
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<end name="End"/>
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</workflow-app>
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@ -1,15 +1,25 @@
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package eu.dnetlib.dhp.oa.dedup;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.common.collect.Sets;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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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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import eu.dnetlib.pace.util.MapDocumentUtil;
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import static java.nio.file.Files.createTempDirectory;
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||||
import static org.apache.spark.sql.functions.col;
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import static org.apache.spark.sql.functions.count;
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import static org.junit.jupiter.api.Assertions.*;
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||||
import static org.mockito.Mockito.lenient;
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||||
|
||||
import java.io.File;
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||||
import java.io.FileReader;
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import java.io.IOException;
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import java.io.Serializable;
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import java.net.URISyntaxException;
|
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import java.nio.file.Paths;
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import java.util.HashSet;
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||||
import java.util.List;
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||||
import java.util.Optional;
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||||
import java.util.Set;
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||||
import java.util.stream.Collectors;
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||||
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||||
import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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|
|
@ -26,26 +36,19 @@ import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.Mock;
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import org.mockito.Mockito;
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||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.google.common.collect.Sets;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||
import scala.Tuple2;
|
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|
||||
import java.io.File;
|
||||
import java.io.FileReader;
|
||||
import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Paths;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static java.nio.file.Files.createTempDirectory;
|
||||
import static org.apache.spark.sql.functions.col;
|
||||
import static org.apache.spark.sql.functions.count;
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
||||
public class SparkDedupTest implements Serializable {
|
||||
|
|
@ -723,26 +726,32 @@ public class SparkDedupTest implements Serializable {
|
|||
@Order(8)
|
||||
void testCleanBaseRelations() throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
|
||||
|
||||
// append dangling relations to be cleaned up
|
||||
Dataset<Row> df_before = spark.read().schema(Encoders.bean(Relation.class).schema()).json(testGraphBasePath + "/relation");
|
||||
Dataset<Row> df_input =df_before
|
||||
.unionByName(df_before.drop("source").withColumn("source", functions.lit("n/a")))
|
||||
.unionByName(df_before.drop("target").withColumn("target", functions.lit("n/a")));
|
||||
Dataset<Row> df_before = spark
|
||||
.read()
|
||||
.schema(Encoders.bean(Relation.class).schema())
|
||||
.json(testGraphBasePath + "/relation");
|
||||
Dataset<Row> df_input = df_before
|
||||
.unionByName(df_before.drop("source").withColumn("source", functions.lit("n/a")))
|
||||
.unionByName(df_before.drop("target").withColumn("target", functions.lit("n/a")));
|
||||
df_input.write().mode(SaveMode.Overwrite).json(testOutputBasePath + "_tmp");
|
||||
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[]{
|
||||
"--graphBasePath", testGraphBasePath,
|
||||
"--inputPath", testGraphBasePath + "/relation",
|
||||
"--outputPath", testDedupGraphBasePath + "/relation"
|
||||
});
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"--graphBasePath", testGraphBasePath,
|
||||
"--inputPath", testGraphBasePath + "/relation",
|
||||
"--outputPath", testDedupGraphBasePath + "/relation"
|
||||
});
|
||||
|
||||
new SparkCleanRelation(parser, spark).run(isLookUpService);
|
||||
|
||||
Dataset<Row> df_after = spark.read().schema(Encoders.bean(Relation.class).schema()).json(testDedupGraphBasePath + "/relation");
|
||||
Dataset<Row> df_after = spark
|
||||
.read()
|
||||
.schema(Encoders.bean(Relation.class).schema())
|
||||
.json(testDedupGraphBasePath + "/relation");
|
||||
|
||||
assertNotEquals(df_before.count(), df_input.count());
|
||||
assertNotEquals(df_input.count(), df_after.count());
|
||||
|
|
@ -753,7 +762,7 @@ public class SparkDedupTest implements Serializable {
|
|||
@Order(9)
|
||||
void testCleanDedupedRelations() throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
|
||||
|
||||
String inputRelPath = testDedupGraphBasePath + "/propagaterelation/relation";
|
||||
|
||||
|
|
@ -763,16 +772,19 @@ public class SparkDedupTest implements Serializable {
|
|||
df_before.filter(col("dataInfo.deletedbyinference").notEqual(true)).show(50, false);
|
||||
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[]{
|
||||
"--graphBasePath", testGraphBasePath,
|
||||
"--inputPath", inputRelPath,
|
||||
"--outputPath", testDedupGraphBasePath + "/relation"
|
||||
});
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"--graphBasePath", testGraphBasePath,
|
||||
"--inputPath", inputRelPath,
|
||||
"--outputPath", testDedupGraphBasePath + "/relation"
|
||||
});
|
||||
|
||||
new SparkCleanRelation(parser, spark).run(isLookUpService);
|
||||
|
||||
Dataset<Row> df_after = spark.read().schema(Encoders.bean(Relation.class).schema()).json(testDedupGraphBasePath + "/relation");
|
||||
Dataset<Row> df_after = spark
|
||||
.read()
|
||||
.schema(Encoders.bean(Relation.class).schema())
|
||||
.json(testDedupGraphBasePath + "/relation");
|
||||
|
||||
assertNotEquals(df_before.count(), df_after.count());
|
||||
assertEquals(0, df_after.count());
|
||||
|
|
|
|||
|
|
@ -12,6 +12,10 @@
|
|||
<name>graphOutputPath</name>
|
||||
<description>path of the output graph</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>filterInvisible</name>
|
||||
<description>whether filter out invisible entities after merge</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
|
|
@ -94,25 +98,15 @@
|
|||
<arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
</spark>
|
||||
<ok to="fork_dispatch_entities"/>
|
||||
<ok to="dispatch_entities"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<fork name="fork_dispatch_entities">
|
||||
<path start="dispatch_datasource"/>
|
||||
<path start="dispatch_project"/>
|
||||
<path start="dispatch_organization"/>
|
||||
<path start="dispatch_publication"/>
|
||||
<path start="dispatch_dataset"/>
|
||||
<path start="dispatch_software"/>
|
||||
<path start="dispatch_otherresearchproduct"/>
|
||||
</fork>
|
||||
|
||||
<action name="dispatch_datasource">
|
||||
<action name="dispatch_entities">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch publications</name>
|
||||
<name>Dispatch grouped entities</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
|
|
@ -126,165 +120,13 @@
|
|||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/datasource</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}</arg>
|
||||
<arg>--filterInvisible</arg><arg>${filterInvisible}</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<ok to="delete_target_relation"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_project">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch project</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/project</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_organization">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch organization</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/organization</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_publication">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch publication</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/publication</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_dataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch dataset</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/dataset</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_software">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch software</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/software</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_otherresearchproduct">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch otherresearchproduct</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="wait_dispatch" to="delete_target_relation"/>
|
||||
|
||||
<action name="delete_target_relation">
|
||||
<fs>
|
||||
<delete path="${nameNode}/${graphOutputPath}/relation"/>
|
||||
|
|
|
|||
|
|
@ -1,14 +1,14 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.group;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.nio.file.Paths;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
|
|
@ -19,17 +19,13 @@ import org.apache.spark.sql.Encoders;
|
|||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.*;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.google.common.collect.Lists;
|
||||
import java.io.IOException;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.nio.file.Paths;
|
||||
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
||||
public class GroupEntitiesSparkJobTest {
|
||||
|
|
@ -101,21 +97,16 @@ public class GroupEntitiesSparkJobTest {
|
|||
@Test
|
||||
@Order(2)
|
||||
void testDispatchEntities() throws Exception {
|
||||
for (String type : Lists
|
||||
.newArrayList(
|
||||
Publication.class.getCanonicalName(), eu.dnetlib.dhp.schema.oaf.Dataset.class.getCanonicalName())) {
|
||||
String directory = StringUtils.substringAfterLast(type, ".").toLowerCase();
|
||||
DispatchEntitiesSparkJob.main(new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-inputPath",
|
||||
groupEntityPath.toString(),
|
||||
"-outputPath",
|
||||
dispatchEntityPath.resolve(directory).toString(),
|
||||
"-graphTableClassName",
|
||||
type
|
||||
});
|
||||
}
|
||||
DispatchEntitiesSparkJob.main(new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-inputPath",
|
||||
groupEntityPath.toString(),
|
||||
"-outputPath",
|
||||
dispatchEntityPath.resolve(".").toString(),
|
||||
"-filterInvisible",
|
||||
Boolean.TRUE.toString()
|
||||
});
|
||||
|
||||
Dataset<Result> output = spark
|
||||
.read()
|
||||
|
|
@ -140,5 +131,4 @@ public class GroupEntitiesSparkJobTest {
|
|||
.filter((FilterFunction<String>) s -> s.equals("dataset"))
|
||||
.count());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue