Consistency graph workflow merges all the entities by ID
This commit is contained in:
parent
36173c13a5
commit
dfd6205b95
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@ -19,24 +19,24 @@ public class OafMapperUtils {
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public static Oaf merge(final Oaf o1, final Oaf o2) {
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if (ModelSupport.isSubClass(o1, OafEntity.class)) {
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if (ModelSupport.isSubClass(o1, Result.class)) {
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return mergeResults((Result) o1, (Result) o2);
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} else if (ModelSupport.isSubClass(o1, Datasource.class)) {
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((Datasource) o1).mergeFrom((Datasource) o2);
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} else if (ModelSupport.isSubClass(o1, Organization.class)) {
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((Organization) o1).mergeFrom((Organization) o2);
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} else if (ModelSupport.isSubClass(o1, Project.class)) {
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((Project) o1).mergeFrom((Project) o2);
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} else {
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throw new RuntimeException("invalid OafEntity subtype:" + o1.getClass().getCanonicalName());
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}
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return mergeEntities((OafEntity) o1, (OafEntity) o2);
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} else if (ModelSupport.isSubClass(o1, Relation.class)) {
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((Relation) o1).mergeFrom((Relation) o2);
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} else {
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throw new RuntimeException("invalid Oaf type:" + o1.getClass().getCanonicalName());
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}
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return o1;
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throw new RuntimeException("invalid Oaf type:" + o1.getClass().getCanonicalName());
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}
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public static OafEntity mergeEntities(OafEntity e1, OafEntity e2) {
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if (ModelSupport.isSubClass(e1, Result.class)) {
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return mergeResults((Result) e1, (Result) e2);
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} else if (ModelSupport.isSubClass(e1, Datasource.class)) {
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((Datasource) e1).mergeFrom((Datasource) e2);
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} else if (ModelSupport.isSubClass(e1, Organization.class)) {
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((Organization) e1).mergeFrom((Organization) e2);
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} else if (ModelSupport.isSubClass(e1, Project.class)) {
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((Project) e1).mergeFrom((Project) e2);
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}
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throw new RuntimeException("invalid OafEntity subtype:" + e1.getClass().getCanonicalName());
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}
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public static Result mergeResults(Result r1, Result r2) {
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@ -0,0 +1,93 @@
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package eu.dnetlib.dhp.oa.dedup;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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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.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.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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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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.toString(
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DispatchEntitiesSparkJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/dispatch_entities_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("inputPath");
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log.info("inputPath: {}", inputPath);
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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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Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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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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});
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}
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private static <T extends Oaf> 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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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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}
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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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@ -0,0 +1,202 @@
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package eu.dnetlib.dhp.oa.dedup;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;
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import java.io.IOException;
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import java.util.List;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.stream.Collectors;
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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.JavaSparkContext;
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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.*;
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import org.apache.spark.sql.expressions.Aggregator;
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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 com.jayway.jsonpath.Configuration;
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import com.jayway.jsonpath.DocumentContext;
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import com.jayway.jsonpath.JsonPath;
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import com.jayway.jsonpath.Option;
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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.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import scala.Tuple2;
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/**
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* Groups the graph content by entity identifier to ensure ID uniqueness
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*/
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public class GroupEntitiesSparkJob {
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private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class);
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private final static String ID_JPATH = "$.id";
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private final static String SOURCE_JPATH = "$.source";
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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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.toString(
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GroupEntitiesSparkJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/group_graph_entities_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String graphInputPath = parser.get("graphInputPath");
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log.info("graphInputPath: {}", graphInputPath);
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String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(ModelSupport.getOafModelClasses());
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
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groupEntities(spark, graphInputPath, outputPath);
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});
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}
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private static void groupEntities(
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SparkSession spark,
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String inputPath,
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String outputPath) {
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final TypedColumn<OafEntity, OafEntity> aggregator = new GroupingAggregator().toColumn();
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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spark
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.read()
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.textFile(toSeq(listPaths(inputPath, sc)))
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.map((MapFunction<String, OafEntity>) s -> parseOaf(s), Encoders.kryo(OafEntity.class))
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.filter((FilterFunction<OafEntity>) e -> StringUtils.isNotBlank(ModelSupport.idFn().apply(e)))
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.groupByKey((MapFunction<OafEntity, String>) oaf -> ModelSupport.idFn().apply(oaf), Encoders.STRING())
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.agg(aggregator)
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.map(
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(MapFunction<Tuple2<String, OafEntity>, String>) t -> t._2().getClass().getName() +
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"|" + OBJECT_MAPPER.writeValueAsString(t._2()),
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Encoders.STRING())
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.text(outputPath);
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}
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public static class GroupingAggregator extends Aggregator<OafEntity, OafEntity, OafEntity> {
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@Override
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public OafEntity zero() {
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return null;
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}
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@Override
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public OafEntity reduce(OafEntity b, OafEntity a) {
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return mergeAndGet(b, a);
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}
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private OafEntity mergeAndGet(OafEntity b, OafEntity a) {
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if (Objects.nonNull(a) && Objects.nonNull(b)) {
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return OafMapperUtils.mergeEntities(b, a);
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}
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return Objects.isNull(a) ? b : a;
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}
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@Override
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public OafEntity merge(OafEntity b, OafEntity a) {
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return mergeAndGet(b, a);
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}
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@Override
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public OafEntity finish(OafEntity j) {
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return j;
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}
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@Override
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public Encoder<OafEntity> bufferEncoder() {
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return Encoders.kryo(OafEntity.class);
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}
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@Override
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public Encoder<OafEntity> outputEncoder() {
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return Encoders.kryo(OafEntity.class);
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}
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}
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private static OafEntity parseOaf(String s) {
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DocumentContext dc = JsonPath
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.parse(s, Configuration.defaultConfiguration().addOptions(Option.SUPPRESS_EXCEPTIONS));
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final String id = dc.read(ID_JPATH);
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if (StringUtils.isNotBlank(id)) {
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String prefix = StringUtils.substringBefore(id, "|");
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switch (prefix) {
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case "10":
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return parse(s, Datasource.class);
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case "20":
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return parse(s, Organization.class);
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case "40":
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return parse(s, Project.class);
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case "50":
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String resultType = dc.read("$.resulttype.classid");
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switch (resultType) {
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case "publication":
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return parse(s, Publication.class);
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case "dataset":
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return parse(s, eu.dnetlib.dhp.schema.oaf.Dataset.class);
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case "software":
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return parse(s, Software.class);
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case "other":
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return parse(s, OtherResearchProduct.class);
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default:
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throw new IllegalArgumentException(String.format("invalid resultType: '%s'", resultType));
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}
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default:
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throw new IllegalArgumentException(String.format("invalid id prefix: '%s'", prefix));
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}
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} else {
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throw new IllegalArgumentException(String.format("invalid oaf: '%s'", s));
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}
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}
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private static <T extends OafEntity> OafEntity parse(String s, Class<T> clazz) {
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try {
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return OBJECT_MAPPER.readValue(s, clazz);
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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private static List<String> listPaths(String inputPath, JavaSparkContext sc) {
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return HdfsSupport
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.listFiles(inputPath, sc.hadoopConfiguration())
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.stream()
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.filter(f -> !f.equals("relation"))
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.collect(Collectors.toList());
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}
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}
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@ -3,6 +3,8 @@ package eu.dnetlib.dhp.oa.dedup;
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import static org.apache.spark.sql.functions.col;
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import java.util.Objects;
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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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@ -28,7 +30,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
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SOURCE, TARGET
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}
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public SparkPropagateRelation(ArgumentApplicationParser parser, SparkSession spark) throws Exception {
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public SparkPropagateRelation(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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}
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@ -55,13 +57,13 @@ public class SparkPropagateRelation extends AbstractSparkAction {
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final String graphBasePath = parser.get("graphBasePath");
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final String workingPath = parser.get("workingPath");
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final String dedupGraphPath = parser.get("dedupGraphPath");
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final String graphOutputPath = parser.get("graphOutputPath");
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log.info("graphBasePath: '{}'", graphBasePath);
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log.info("workingPath: '{}'", workingPath);
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log.info("dedupGraphPath: '{}'", dedupGraphPath);
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log.info("graphOutputPath: '{}'", graphOutputPath);
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final String outputRelationPath = DedupUtility.createEntityPath(dedupGraphPath, "relation");
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final String outputRelationPath = DedupUtility.createEntityPath(graphOutputPath, "relation");
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removeOutputDir(spark, outputRelationPath);
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Dataset<Relation> mergeRels = spark
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@ -101,7 +103,8 @@ public class SparkPropagateRelation extends AbstractSparkAction {
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newRels
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.union(updated)
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.union(mergeRels)
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.map((MapFunction<Relation, Relation>) r -> r, Encoders.kryo(Relation.class))),
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.map((MapFunction<Relation, Relation>) r -> r, Encoders.kryo(Relation.class)))
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.filter((FilterFunction<Relation>) r -> !Objects.equals(r.getSource(), r.getTarget())),
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outputRelationPath, SaveMode.Overwrite);
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}
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@ -2,15 +2,15 @@
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<parameters>
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<property>
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<name>graphBasePath</name>
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<description>the raw graph base path</description>
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<description>the input graph base path</description>
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</property>
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<property>
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<name>workingPath</name>
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<description>path of the working directory</description>
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</property>
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<property>
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<name>dedupGraphPath</name>
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<description>path of the dedup graph</description>
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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>sparkDriverMemory</name>
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@ -91,116 +91,224 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--i</arg><arg>${graphBasePath}</arg>
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<arg>--o</arg><arg>${dedupGraphPath}</arg>
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<arg>--w</arg><arg>${workingPath}</arg>
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<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
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<arg>--o</arg><arg>${graphOutputPath}</arg>
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<arg>--workingPath</arg><arg>${workingPath}</arg>
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</spark>
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<ok to="fork_copy_entities"/>
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<ok to="group_entities"/>
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<error to="Kill"/>
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</action>
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<fork name="fork_copy_entities">
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<path start="copy_datasource"/>
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<path start="copy_project"/>
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<path start="copy_organization"/>
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<path start="copy_publication"/>
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<path start="copy_dataset"/>
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<path start="copy_software"/>
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<path start="copy_otherresearchproduct"/>
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<action name="group_entities">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>group graph entities</name>
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<class>eu.dnetlib.dhp.oa.dedup.GroupEntitiesSparkJob</class>
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<jar>dhp-dedup-openaire-${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>--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"/>
|
||||
<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="copy_datasource">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/datasource"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/datasource</arg>
|
||||
<arg>${dedupGraphPath}/datasource</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<action name="dispatch_datasource">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch publications</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${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}/datasource</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_project">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/project"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/project</arg>
|
||||
<arg>${dedupGraphPath}/project</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<action name="dispatch_project">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch project</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${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="copy_organization">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/organization"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/organization</arg>
|
||||
<arg>${dedupGraphPath}/organization</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<action name="dispatch_organization">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch organization</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${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="copy_publication">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/publication"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/publication</arg>
|
||||
<arg>${dedupGraphPath}/publication</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<action name="dispatch_publication">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch publication</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${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="copy_dataset">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/dataset"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/dataset</arg>
|
||||
<arg>${dedupGraphPath}/dataset</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<action name="dispatch_dataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch dataset</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${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="copy_software">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/software"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/software</arg>
|
||||
<arg>${dedupGraphPath}/software</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<action name="dispatch_software">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch software</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${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="copy_otherresearchproduct">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/otherresearchproduct"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/otherresearchproduct</arg>
|
||||
<arg>${dedupGraphPath}/otherresearchproduct</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<action name="dispatch_otherresearchproduct">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch otherresearchproduct</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${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_copy" to="End"/>
|
||||
<join name="wait_dispatch" to="End"/>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "i",
|
||||
"paramLongName": "inputPath",
|
||||
"paramDescription": "the source path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "o",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "path of the output graph",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "c",
|
||||
"paramLongName": "graphTableClassName",
|
||||
"paramDescription": "the graph entity class name",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -13,7 +13,7 @@
|
|||
},
|
||||
{
|
||||
"paramName": "o",
|
||||
"paramLongName": "dedupGraphPath",
|
||||
"paramLongName": "graphOutputPath",
|
||||
"paramDescription": "the path of the dedup graph",
|
||||
"paramRequired": true
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue