WIP: promote job implementation snapshot
This commit is contained in:
parent
69540f6f78
commit
cc63cdc9e6
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@ -1,7 +1,7 @@
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package eu.dnetlib.dhp.actionmanager;
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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 eu.dnetlib.data.proto.OafProtos;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.apache.commons.io.IOUtils;
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@ -10,15 +10,17 @@ import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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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.Dataset;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.types.*;
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import java.io.IOException;
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import java.util.Arrays;
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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.function.BiFunction;
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import java.util.function.Function;
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import static eu.dnetlib.dhp.actionmanager.PromoteActionSetFromHDFSFunctions.*;
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import static org.apache.spark.sql.functions.*;
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public class PromoteActionSetFromHDFSJob {
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@ -29,128 +31,132 @@ public class PromoteActionSetFromHDFSJob {
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.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/actionmanager_input_parameters.json")));
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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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String inputGraphPath = parser.get("inputGraphPath");
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List<String> inputActionSetPaths = Arrays.asList(parser.get("inputActionSetPaths").split(","));
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String inputActionSetPaths = parser.get("inputActionSetPaths");
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String graphTableName = parser.get("graphTableName");
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String outputGraphPath = parser.get("outputGraphPath");
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OafMergeAndGet.Strategy strategy = OafMergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy"));
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SparkConf conf = new SparkConf();
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conf.setMaster(parser.get("master"));
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(new Class[]{
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Author.class,
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Context.class,
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Country.class,
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DataInfo.class,
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eu.dnetlib.dhp.schema.oaf.Dataset.class,
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Datasource.class,
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ExternalReference.class,
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ExtraInfo.class,
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Field.class,
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GeoLocation.class,
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Instance.class,
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Journal.class,
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KeyValue.class,
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Oaf.class,
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OafEntity.class,
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OAIProvenance.class,
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Organization.class,
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OriginDescription.class,
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OtherResearchProduct.class,
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Project.class,
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Publication.class,
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Qualifier.class,
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Relation.class,
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Result.class,
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Software.class,
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StructuredProperty.class
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});
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try (SparkSession spark = SparkSession.builder().config(conf).getOrCreate()) {
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SparkSession spark = null;
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try {
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spark = SparkSession.builder().config(conf).getOrCreate();
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// ----- READ -----
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// dataset
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Dataset<eu.dnetlib.dhp.schema.oaf.Dataset> datasetDS = readGraphTable(
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spark, String.format("%s/dataset", inputGraphPath), eu.dnetlib.dhp.schema.oaf.Dataset.class)
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.cache();
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datasetDS.printSchema();
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datasetDS.show();
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// datasource
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Dataset<Datasource> datasourceDS =
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readGraphTable(spark, String.format("%s/datasource", inputGraphPath), Datasource.class)
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.cache();
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datasourceDS.printSchema();
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datasourceDS.show();
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// organization
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Dataset<Organization> organizationDS =
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readGraphTable(spark, String.format("%s/organization", inputGraphPath), Organization.class)
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.cache();
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organizationDS.printSchema();
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organizationDS.show();
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// otherresearchproduct
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Dataset<OtherResearchProduct> otherResearchProductDS =
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readGraphTable(spark, String.format("%s/otherresearchproduct", inputGraphPath), OtherResearchProduct.class)
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.cache();
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otherResearchProductDS.printSchema();
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otherResearchProductDS.show();
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// project
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Dataset<Project> projectDS =
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readGraphTable(spark, String.format("%s/project", inputGraphPath), Project.class)
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.cache();
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projectDS.printSchema();
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projectDS.show();
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// publication
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Dataset<Publication> publicationDS =
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readGraphTable(spark, String.format("%s/publication", inputGraphPath), Publication.class)
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.cache();
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publicationDS.printSchema();
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publicationDS.show();
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// relation
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Dataset<Relation> relationDS =
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readGraphTable(spark, String.format("%s/relation", inputGraphPath), Relation.class)
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.cache();
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relationDS.printSchema();
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relationDS.show();
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// software
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Dataset<Software> softwareDS =
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readGraphTable(spark, String.format("%s/software", inputGraphPath), Software.class)
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.cache();
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softwareDS.printSchema();
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softwareDS.show();
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// actions
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Dataset<String> actionPayloadDS = inputActionSetPaths.stream()
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.map(inputActionSetPath -> readActionSetPayload(spark, inputActionSetPath))
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.reduce(Dataset::union)
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.get()
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.cache();
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actionPayloadDS.printSchema();
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actionPayloadDS.show();
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System.out.println(String.join("\n", actionPayloadDS.takeAsList(20)));
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Dataset<String> relationActionPayloadDS = filterActionPayloadForRelations(actionPayloadDS)
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.cache();
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relationActionPayloadDS.printSchema();
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relationActionPayloadDS.show();
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Dataset<String> entityActionPayloadDS = filterActionPayloadForEntity(actionPayloadDS)
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.cache();
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entityActionPayloadDS.printSchema();
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entityActionPayloadDS.show();
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// ----- LOGIC -----
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Dataset<eu.dnetlib.dhp.schema.oaf.Dataset> processedDatasetDS =
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processEntityDS(datasetDS, entityActionPayloadDS, eu.dnetlib.dhp.schema.oaf.Dataset.class);
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Dataset<Datasource> processedDatasourceDS =
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processEntityDS(datasourceDS, entityActionPayloadDS, Datasource.class);
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Dataset<Organization> processedOrganizationDS =
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processEntityDS(organizationDS, entityActionPayloadDS, Organization.class);
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Dataset<OtherResearchProduct> processedOtherResearchProductDS =
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processEntityDS(otherResearchProductDS, entityActionPayloadDS, OtherResearchProduct.class);
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Dataset<Project> processedProjectDS =
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processEntityDS(projectDS, entityActionPayloadDS, Project.class);
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Dataset<Publication> processedPublicationDS =
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processEntityDS(publicationDS, entityActionPayloadDS, Publication.class);
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Dataset<Relation> processedRelationDS =
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processRelationDS(relationDS, relationActionPayloadDS);
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Dataset<Software> processedSoftwareDS =
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processEntityDS(softwareDS, entityActionPayloadDS, Software.class);
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// ----- SAVE -----
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processedDatasetDS.write()
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.save(String.format("%s/dataset", outputGraphPath));
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processedDatasourceDS.write()
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.save(String.format("%s/datasource", outputGraphPath));
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processedOrganizationDS.write()
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.save(String.format("%s/organization", outputGraphPath));
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processedOtherResearchProductDS.write()
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.save(String.format("%s/otherresearchproduct", outputGraphPath));
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processedProjectDS.write()
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.save(String.format("%s/project", outputGraphPath));
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processedPublicationDS.write()
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.save(String.format("%s/publication", outputGraphPath));
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processedRelationDS.write()
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.save(String.format("%s/relation", outputGraphPath));
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processedSoftwareDS.write()
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.save(String.format("%s/software", outputGraphPath));
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//TODO make graph table generic using enums
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switch (graphTableName) {
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case "dataset":
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processWith(spark,
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String.format("%s/%s", inputGraphPath, graphTableName),
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inputActionSetPaths,
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outputGraphPath,
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graphTableName,
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strategy,
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eu.dnetlib.dhp.schema.oaf.Dataset.class);
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break;
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case "datasource":
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processWith(spark,
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String.format("%s/%s", inputGraphPath, graphTableName),
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inputActionSetPaths,
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outputGraphPath,
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graphTableName,
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strategy,
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Datasource.class);
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break;
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case "organization":
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processWith(spark,
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String.format("%s/%s", inputGraphPath, graphTableName),
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inputActionSetPaths,
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outputGraphPath,
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graphTableName,
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strategy,
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Organization.class);
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break;
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case "otherresearchproduct":
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processWith(spark,
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String.format("%s/%s", inputGraphPath, graphTableName),
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inputActionSetPaths,
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outputGraphPath,
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graphTableName,
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strategy,
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OtherResearchProduct.class);
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break;
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case "project":
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processWith(spark,
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String.format("%s/%s", inputGraphPath, graphTableName),
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inputActionSetPaths,
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outputGraphPath,
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graphTableName,
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strategy,
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Project.class);
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break;
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case "publication":
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processWith(spark,
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String.format("%s/%s", inputGraphPath, graphTableName),
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inputActionSetPaths,
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outputGraphPath,
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graphTableName,
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strategy,
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Publication.class);
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break;
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case "relation":
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processWith(spark,
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String.format("%s/%s", inputGraphPath, graphTableName),
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inputActionSetPaths,
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outputGraphPath,
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graphTableName,
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strategy,
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Relation.class);
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break;
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case "software":
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processWith(spark,
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String.format("%s/%s", inputGraphPath, graphTableName),
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inputActionSetPaths,
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outputGraphPath,
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graphTableName,
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strategy,
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Software.class);
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break;
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default:
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throw new RuntimeException("error processing table: " + graphTableName);
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}
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} finally {
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if (Objects.nonNull(spark) && isSparkSessionManaged) {
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spark.stop();
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}
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}
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}
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@ -160,7 +166,7 @@ public class PromoteActionSetFromHDFSJob {
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StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty())
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));
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private static <T extends Oaf> Dataset<T> readGraphTable(SparkSession spark, String path, Class<T> clazz) {
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private static <T> Dataset<T> readGraphTable(SparkSession spark, String path, Class<T> clazz) {
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JavaRDD<Row> rows = JavaSparkContext
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.fromSparkContext(spark.sparkContext())
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.sequenceFile(path, Text.class, Text.class)
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@ -168,7 +174,15 @@ public class PromoteActionSetFromHDFSJob {
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return spark.createDataFrame(rows, KV_SCHEMA)
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.map((MapFunction<Row, T>) row -> new ObjectMapper().readValue(row.<String>getAs("value"), clazz),
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Encoders.bean(clazz));
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Encoders.kryo(clazz));
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}
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private static Dataset<String> readActionSetPayloads(SparkSession spark, String inputActionSetPaths) {
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return Arrays
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.stream(inputActionSetPaths.split(","))
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.map(inputActionSetPath -> readActionSetPayload(spark, inputActionSetPath))
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.reduce(Dataset::union)
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.get();
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}
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private static Dataset<String> readActionSetPayload(SparkSession spark, String inputActionSetPath) {
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@ -183,54 +197,99 @@ public class PromoteActionSetFromHDFSJob {
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.as(Encoders.STRING());
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}
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private static Dataset<String> filterActionPayloadForRelations(Dataset<String> actionPayloadDS) {
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return actionPayloadDS
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.where(get_json_object(col("target_value_json"), "$.kind").equalTo("relation"));
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private static <T extends Oaf> void processWith(SparkSession spark,
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String inputGraphTablePath,
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String inputActionSetPaths,
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String outputGraphPath,
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String graphTableName,
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OafMergeAndGet.Strategy strategy,
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Class<T> clazz) {
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// System.out.println("===== tableDS =====");
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Dataset<T> tableDS = readGraphTable(spark, inputGraphTablePath, clazz)
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.cache();
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// tableDS.printSchema();
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// tableDS.show();
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// tableDS.explain();
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// System.out.println("DEBUG: tableDS.partitions=" + tableDS.rdd().getNumPartitions());
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// System.out.println("===== actionPayloadDS =====");
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Dataset<String> actionPayloadDS = readActionSetPayloads(spark, inputActionSetPaths)
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.cache();
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// actionPayloadDS.printSchema();
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// actionPayloadDS.show();
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// actionPayloadDS.explain();
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// System.out.println("DEBUG: actionPayloadDS.partitions=" + actionPayloadDS.rdd().getNumPartitions());
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// System.out.println("===== processed =====");
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Dataset<T> processed = processGraphTable(tableDS, actionPayloadDS, strategy, clazz);
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// processed.printSchema();
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// processed.show();
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// processed.explain();
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// System.out.println("DEBUG: processed.partitions=" + processed.rdd().getNumPartitions());
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// System.out.println("===== result =====");
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Dataset<T> result = processed
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.map((MapFunction<T, T>) value -> value, Encoders.bean(clazz));
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// result.printSchema();
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// result.show();
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// result.explain();
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// System.out.println("DEBUG: result.partitions=" + result.rdd().getNumPartitions());
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String outputGraphTablePath = String.format("%s/%s", outputGraphPath, graphTableName);
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result.write()
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.format("parquet")
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.save(outputGraphTablePath);
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}
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private static Dataset<String> filterActionPayloadForEntity(Dataset<String> actionPayloadDS) {
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return actionPayloadDS
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.where(get_json_object(col("target_value_json"), "$.kind").equalTo("entity"));
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}
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private static <T extends OafEntity> Dataset<T> processEntityDS(Dataset<T> entityDS,
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Dataset<String> actionPayloadDS,
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Class<T> clazz) {
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Dataset<T> groupedAndMerged = groupEntitiesByIdAndMerge(entityDS, clazz);
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Dataset<T> joinedAndMerged = joinEntitiesWithActionPayloadAndMerge(groupedAndMerged,
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actionPayloadDS,
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PromoteActionSetFromHDFSJob::entityToActionPayloadJoinExpr,
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PromoteActionSetFromHDFSJob::actionPayloadToEntity,
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clazz);
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return groupEntitiesByIdAndMerge(joinedAndMerged, clazz);
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}
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private static <T extends OafEntity> Column entityToActionPayloadJoinExpr(Dataset<T> left,
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Dataset<String> right) {
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return left.col("id").equalTo(
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get_json_object(right.col("target_value_json"), "$.entity.id"));
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}
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public static <T extends OafEntity> T actionPayloadToEntity(String actionPayload,
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private static <T extends Oaf> Dataset<T> processGraphTable(Dataset<T> tableDS,
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Dataset<String> actionPayloadDS,
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OafMergeAndGet.Strategy strategy,
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Class<T> clazz) {
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try {
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OafProtos.Oaf oldEntity = new ObjectMapper().readValue(actionPayload, OafProtos.Oaf.class);
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return entityOldToNew(oldEntity, 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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SerializableSupplier<Function<T, String>> oafIdFn = () -> x -> {
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if (x instanceof Relation) {
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Relation r = (Relation) x;
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return Optional.ofNullable(r.getSource())
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.map(source -> Optional.ofNullable(r.getTarget())
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.map(target -> Optional.ofNullable(r.getRelType())
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.map(relType -> Optional.ofNullable(r.getSubRelType())
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.map(subRelType -> Optional.ofNullable(r.getRelClass())
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.map(relClass -> String.join(source, target, relType, subRelType, relClass))
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.orElse(String.join(source, target, relType, subRelType))
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)
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.orElse(String.join(source, target, relType))
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)
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.orElse(String.join(source, target))
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)
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.orElse(source)
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)
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.orElse(null);
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}
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return ((OafEntity) x).getId();
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};
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//TODO
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private static <T extends OafEntity> T entityOldToNew(OafProtos.Oaf old,
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Class<T> clazz) {
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return null;
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}
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SerializableSupplier<BiFunction<T, T, T>> mergeAndGetFn = OafMergeAndGet.functionFor(strategy);
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//TODO
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private static Dataset<Relation> processRelationDS(Dataset<Relation> relationDS,
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Dataset<String> actionPayloadDS) {
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return null;
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Dataset<T> joinedAndMerged = PromoteActionSetFromHDFSFunctions
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.joinOafEntityWithActionPayloadAndMerge(
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tableDS,
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actionPayloadDS,
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oafIdFn,
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() -> (json, c) -> {
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try {
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return new ObjectMapper().disable(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES).readValue(json, clazz);
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} catch (IOException e) {
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return null;
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}
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},
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mergeAndGetFn,
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clazz);
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return PromoteActionSetFromHDFSFunctions
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.groupOafByIdAndMerge(
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joinedAndMerged,
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oafIdFn,
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mergeAndGetFn,
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clazz
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);
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}
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}
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|
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@ -1,26 +1,38 @@
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[
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{
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"paramName": "mt",
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"paramLongName": "master",
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"paramDescription": "should be local or yarn",
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"paramRequired": true
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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||||
"paramDescription": "TODO",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "ig",
|
||||
"paramName": "igp",
|
||||
"paramLongName": "inputGraphPath",
|
||||
"paramDescription": "#TODO: input graph path",
|
||||
"paramDescription": "TODO: input graph path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "ia",
|
||||
"paramName": "iasp",
|
||||
"paramLongName": "inputActionSetPaths",
|
||||
"paramDescription": "#TODO: comma separated list of paths to input action sets",
|
||||
"paramDescription": "TODO: comma separated list of paths to input action sets",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "og",
|
||||
"paramName": "gtn",
|
||||
"paramLongName": "graphTableName",
|
||||
"paramDescription": "TODO",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "ogp",
|
||||
"paramLongName": "outputGraphPath",
|
||||
"paramDescription": "#TODO: the path of the result DataFrame on HDFS",
|
||||
"paramDescription": "TODO: the path of the result DataFrame on HDFS",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "mags",
|
||||
"paramLongName": "mergeAndGetStrategy",
|
||||
"paramDescription": "TODO",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
Loading…
Reference in New Issue