forked from D-Net/dnet-hadoop
removed unuseful classes
This commit is contained in:
parent
edb00db86a
commit
0e447add66
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@ -1,690 +0,0 @@
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package eu.dnetlib.dhp.resulttocommunityfromsemrel;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.QueryInformationSystem;
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import eu.dnetlib.dhp.TypedRow;
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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 java.util.*;
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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.hadoop.fs.FileSystem;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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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.sql.Encoders;
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import org.apache.spark.sql.Row;
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import org.apache.spark.sql.SparkSession;
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import scala.Tuple2;
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public class SparkResultToCommunityThroughSemRelJob {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser =
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new ArgumentApplicationParser(
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IOUtils.toString(
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SparkResultToCommunityThroughSemRelJob.class.getResourceAsStream(
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"/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_communitytoresult_parameters.json")));
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parser.parseArgument(args);
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for (String key : parser.getObjectMap().keySet()) {
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System.out.println(key + " = " + parser.get(key));
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}
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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final SparkSession spark =
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SparkSession.builder()
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.appName(SparkResultToCommunityThroughSemRelJob.class.getSimpleName())
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.master(parser.get("master"))
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.config(conf)
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.enableHiveSupport()
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.getOrCreate();
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final String inputPath = parser.get("sourcePath");
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final String outputPath = "/tmp/provision/propagation/resulttocommunityfromsemrel";
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// final List<String> allowedsemrel =
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// Arrays.asList(parser.get("allowedsemrels").split(";"));
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final List<String> allowedsemrel = Arrays.asList("isSupplementedBy", "isSupplementTo");
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// final List<String> communityIdList =
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// QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
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final List<String> communityIdList =
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QueryInformationSystem.getCommunityList(
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"http://beta.services.openaire.eu:8280/is/services/isLookUp");
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createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
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JavaRDD<Publication> all_publication_rdd =
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sc.textFile(inputPath + "/publication")
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.map(item -> new ObjectMapper().readValue(item, Publication.class))
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.filter(p -> !p.getDataInfo().getDeletedbyinference())
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.cache();
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JavaRDD<Publication> publication_rdd =
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all_publication_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
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JavaRDD<Dataset> all_dataset_rdd =
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sc.textFile(inputPath + "/dataset")
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.map(item -> new ObjectMapper().readValue(item, Dataset.class))
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.filter(p -> !p.getDataInfo().getDeletedbyinference())
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.cache();
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JavaRDD<Dataset> dataset_rdd =
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all_dataset_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
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JavaRDD<OtherResearchProduct> all_orp_rdd =
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sc.textFile(inputPath + "/otherresearchproduct")
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.map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class))
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.filter(p -> !p.getDataInfo().getDeletedbyinference())
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.cache();
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JavaRDD<OtherResearchProduct> orp_rdd =
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all_orp_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
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JavaRDD<Software> all_software_rdd =
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sc.textFile(inputPath + "/software")
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.map(item -> new ObjectMapper().readValue(item, Software.class))
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.filter(p -> !p.getDataInfo().getDeletedbyinference())
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.cache();
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JavaRDD<Software> software_rdd =
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all_software_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
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JavaRDD<Relation> relation_rdd =
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sc.textFile(inputPath + "/relation")
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.map(item -> new ObjectMapper().readValue(item, Relation.class))
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.filter(r -> !r.getDataInfo().getDeletedbyinference())
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.filter(
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r ->
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allowedsemrel.contains(r.getRelClass())
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&& RELATION_RESULTRESULT_REL_TYPE.equals(
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r.getRelType()))
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.cache();
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org.apache.spark.sql.Dataset<Publication> publication =
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spark.createDataset(publication_rdd.rdd(), Encoders.bean(Publication.class));
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org.apache.spark.sql.Dataset<Dataset> dataset =
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spark.createDataset(dataset_rdd.rdd(), Encoders.bean(Dataset.class));
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org.apache.spark.sql.Dataset<OtherResearchProduct> other =
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spark.createDataset(orp_rdd.rdd(), Encoders.bean(OtherResearchProduct.class));
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org.apache.spark.sql.Dataset<Software> software =
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spark.createDataset(software_rdd.rdd(), Encoders.bean(Software.class));
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org.apache.spark.sql.Dataset<Relation> relation =
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spark.createDataset(relation_rdd.rdd(), Encoders.bean(Relation.class));
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publication.createOrReplaceTempView("publication");
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relation.createOrReplaceTempView("relation");
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dataset.createOrReplaceTempView("dataset");
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software.createOrReplaceTempView("software");
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other.createOrReplaceTempView("other");
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// org.apache.spark.sql.Dataset<Row> publication_context = getContext(spark,
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// "publication");
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// publication_context.createOrReplaceTempView("publication_context");
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org.apache.spark.sql.Dataset<Row> publication_context =
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spark.sql(
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"SELECT relation.source, "
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+ "publication.context , relation.target "
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+ "FROM publication "
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+ " JOIN relation "
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+ "ON id = source");
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org.apache.spark.sql.Dataset<Row> dataset_context = getContext(spark, "dataset");
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dataset_context.createOrReplaceTempView("dataset_context");
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org.apache.spark.sql.Dataset<Row> software_context = getContext(spark, "software");
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software_context.createOrReplaceTempView("software_context");
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org.apache.spark.sql.Dataset<Row> other_context = getContext(spark, "other");
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other_context.createOrReplaceTempView("other_context");
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publication =
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spark.createDataset(all_publication_rdd.rdd(), Encoders.bean(Publication.class));
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publication.createOrReplaceTempView("publication");
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dataset = spark.createDataset(all_dataset_rdd.rdd(), Encoders.bean(Dataset.class));
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dataset.createOrReplaceTempView("dataset");
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other = spark.createDataset(all_orp_rdd.rdd(), Encoders.bean(OtherResearchProduct.class));
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other.createOrReplaceTempView("other");
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software = spark.createDataset(all_software_rdd.rdd(), Encoders.bean(Software.class));
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software.createOrReplaceTempView("software");
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org.apache.spark.sql.Dataset<Row> toupdatesoftwareresult =
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getUpdateCommunitiesForTable(spark, "software");
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org.apache.spark.sql.Dataset<Row> toupdatedatasetresult =
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getUpdateCommunitiesForTable(spark, "dataset");
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org.apache.spark.sql.Dataset<Row> toupdatepublicationreresult =
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getUpdateCommunitiesForTable(spark, "publication");
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org.apache.spark.sql.Dataset<Row> toupdateotherresult =
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getUpdateCommunitiesForTable(spark, "other");
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createUpdateForResultDatasetWrite(
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toupdatesoftwareresult.toJavaRDD(),
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outputPath,
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"software_update",
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
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communityIdList);
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createUpdateForResultDatasetWrite(
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toupdatedatasetresult.toJavaRDD(),
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outputPath,
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"dataset_update",
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
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communityIdList);
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createUpdateForResultDatasetWrite(
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toupdatepublicationreresult.toJavaRDD(),
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outputPath,
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"publication_update",
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
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communityIdList);
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createUpdateForResultDatasetWrite(
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toupdateotherresult.toJavaRDD(),
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outputPath,
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"other_update",
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
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communityIdList);
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updateForDatasetDataset(
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toupdatedatasetresult.toJavaRDD(),
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dataset.toJavaRDD(),
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outputPath,
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"dataset",
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
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communityIdList);
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updateForOtherDataset(
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toupdateotherresult.toJavaRDD(),
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other.toJavaRDD(),
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outputPath,
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"otherresearchproduct",
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
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communityIdList);
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updateForSoftwareDataset(
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toupdatesoftwareresult.toJavaRDD(),
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software.toJavaRDD(),
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outputPath,
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"software",
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
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communityIdList);
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updateForPublicationDataset(
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toupdatepublicationreresult.toJavaRDD(),
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publication.toJavaRDD(),
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outputPath,
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"publication",
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
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PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
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communityIdList);
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/*
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JavaPairRDD<String, TypedRow> resultLinkedToCommunities = publication
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.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"publication"))
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.filter(p -> !(p == null))
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.mapToPair(toPair())
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.union(datasets
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.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"dataset"))
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.filter(p -> !(p == null))
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.mapToPair(toPair())
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)
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.union(software
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.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"software"))
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.filter(p -> !(p == null))
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.mapToPair(toPair())
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)
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.union(other
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.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"otherresearchproduct"))
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.filter(p -> !(p == null))
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.mapToPair(toPair())
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);
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JavaPairRDD<String, TypedRow> to_add_result_communities = resultLinkedToCommunities.join(result_result).map(r -> r._2()._1().setSourceId(r._2()._2().getTargetId()))
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.mapToPair(toPair());
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JavaPairRDD<String, Result> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
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JavaPairRDD<String, Result> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
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JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
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JavaPairRDD<String, Result> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
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updateResultForCommunity(pubs, to_add_result_communities, outputPath, "publication", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
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updateResultForCommunity(dss, to_add_result_communities, outputPath, "dataset", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
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updateResultForCommunity(sfw, to_add_result_communities, outputPath, "software", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
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updateResultForCommunity(orp, to_add_result_communities, outputPath, "otherresearchproduct", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
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//leftouterjoin result.to_add_result_communities (result = java pair rdd result) [left outer join perche' li voglio tutti anche quelli che non ho aggiornato]
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//per quelli che matchano cercare nel risultato se i context da aggiungere sono gia' presenti. Se non ci sono aggiungerli, altrimenti nulla
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*/
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}
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private static org.apache.spark.sql.Dataset<Row> getUpdateCommunitiesForTable(
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SparkSession spark, String table) {
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String query =
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"SELECT target_id, collect_set(co.id) context_id "
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+ " FROM (SELECT t.id target_id, s.context source_context "
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+ " FROM context_software s "
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+ " JOIN "
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+ table
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+ " t "
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+ " ON s.target = t.id "
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+ " UNION ALL "
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+ " SELECT t.id target_id, d.context source_context "
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+ " FROM dataset_context d "
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+ " JOIN "
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+ table
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+ " t"
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+ " ON s.target = t.id "
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+ " UNION ALL "
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+ " SELECT t.id target_id, p.context source_context "
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+ " FROM publication_context p"
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+ " JOIN "
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+ table
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+ " t "
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+ " on p.target = t.id "
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+ " UNION ALL "
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+ " SELECT t.id target_id, o.context source_context "
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+ " FROM other_context o "
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+ " JOIN "
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+ table
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+ " t "
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+ " ON o.target = t.id) TMP "
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+ " LATERAL VIEW EXPLODE(source_context) MyT as co "
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+ " GROUP BY target_id";
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return spark.sql(query);
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}
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private static JavaRDD<Result> createUpdateForResultDatasetWrite(
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JavaRDD<Row> toupdateresult,
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String outputPath,
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String type,
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String class_id,
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String class_name,
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List<String> communityIdList) {
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return toupdateresult
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.map(
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r -> {
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List<Context> contextList = new ArrayList();
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List<String> toAddContext = r.getList(1);
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for (String cId : toAddContext) {
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if (communityIdList.contains(cId)) {
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Context newContext = new Context();
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newContext.setId(cId);
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newContext.setDataInfo(
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Arrays.asList(
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getDataInfo(
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PROPAGATION_DATA_INFO_TYPE,
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class_id,
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class_name)));
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contextList.add(newContext);
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}
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}
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if (contextList.size() > 0) {
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Result ret = new Result();
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ret.setId(r.getString(0));
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ret.setContext(contextList);
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return ret;
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}
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return null;
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})
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.filter(r -> r != null);
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}
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private static void updateForSoftwareDataset(
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JavaRDD<Row> toupdateresult,
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JavaRDD<Software> result,
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String outputPath,
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String type,
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String class_id,
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String class_name,
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List<String> communityIdList) {
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JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
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getUpdateForResultDataset(
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toupdateresult,
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tmp,
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outputPath,
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type,
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class_id,
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class_name,
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communityIdList)
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.map(r -> (Software) r)
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.map(s -> new ObjectMapper().writeValueAsString(s))
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.saveAsTextFile(outputPath + "/" + type);
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}
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private static void updateForDatasetDataset(
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JavaRDD<Row> toupdateresult,
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JavaRDD<Dataset> result,
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String outputPath,
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String type,
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String class_id,
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String class_name,
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List<String> communityIdList) {
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JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
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getUpdateForResultDataset(
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toupdateresult,
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tmp,
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outputPath,
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type,
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class_id,
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class_name,
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communityIdList)
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.map(r -> (Dataset) r)
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.map(d -> new ObjectMapper().writeValueAsString(d))
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.saveAsTextFile(outputPath + "/" + type);
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}
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private static void updateForPublicationDataset(
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JavaRDD<Row> toupdateresult,
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JavaRDD<Publication> result,
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String outputPath,
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String type,
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String class_id,
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String class_name,
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List<String> communityIdList) {
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JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
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getUpdateForResultDataset(
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toupdateresult,
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tmp,
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outputPath,
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type,
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class_id,
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class_name,
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communityIdList)
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.map(r -> (Publication) r)
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.map(p -> new ObjectMapper().writeValueAsString(p))
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.saveAsTextFile(outputPath + "/" + type);
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}
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private static void updateForOtherDataset(
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JavaRDD<Row> toupdateresult,
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JavaRDD<OtherResearchProduct> result,
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String outputPath,
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String type,
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String class_id,
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String class_name,
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List<String> communityIdList) {
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JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
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getUpdateForResultDataset(
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toupdateresult,
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tmp,
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outputPath,
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type,
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class_id,
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||||
class_name,
|
||||
communityIdList)
|
||||
.map(r -> (OtherResearchProduct) r)
|
||||
.map(o -> new ObjectMapper().writeValueAsString(o))
|
||||
.saveAsTextFile(outputPath + "/" + type);
|
||||
}
|
||||
|
||||
private static JavaRDD<Result> getUpdateForResultDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
JavaPairRDD<String, Result> result,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
return result.leftOuterJoin(
|
||||
toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))))
|
||||
.map(
|
||||
c -> {
|
||||
if (!c._2()._2().isPresent()) {
|
||||
return c._2()._1();
|
||||
}
|
||||
|
||||
List<Object> toAddContext = c._2()._2().get();
|
||||
Set<String> context_set = new HashSet<>();
|
||||
for (Object cId : toAddContext) {
|
||||
String id = (String) cId;
|
||||
if (communityIdList.contains(id)) {
|
||||
context_set.add(id);
|
||||
}
|
||||
}
|
||||
for (Context context : c._2()._1().getContext()) {
|
||||
if (context_set.contains(context)) {
|
||||
context_set.remove(context);
|
||||
}
|
||||
}
|
||||
|
||||
List<Context> contextList =
|
||||
context_set.stream()
|
||||
.map(
|
||||
co -> {
|
||||
Context newContext = new Context();
|
||||
newContext.setId(co);
|
||||
newContext.setDataInfo(
|
||||
Arrays.asList(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
class_id,
|
||||
class_name)));
|
||||
return newContext;
|
||||
})
|
||||
.collect(Collectors.toList());
|
||||
|
||||
if (contextList.size() > 0) {
|
||||
Result r = new Result();
|
||||
r.setId(c._1());
|
||||
r.setContext(contextList);
|
||||
return r;
|
||||
}
|
||||
return null;
|
||||
})
|
||||
.filter(r -> r != null);
|
||||
|
||||
// return toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1)))
|
||||
// .join(result)
|
||||
// .map(c -> {
|
||||
// List<Object> toAddContext = c._2()._1();
|
||||
// Set<String> context_set = new HashSet<>();
|
||||
// for(Object cId: toAddContext){
|
||||
// String id = (String)cId;
|
||||
// if (communityIdList.contains(id)){
|
||||
// context_set.add(id);
|
||||
// }
|
||||
// }
|
||||
// for (Context context: c._2()._2().getContext()){
|
||||
// if(context_set.contains(context)){
|
||||
// context_set.remove(context);
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// List<Context> contextList = context_set.stream().map(co -> {
|
||||
// Context newContext = new Context();
|
||||
// newContext.setId(co);
|
||||
//
|
||||
// newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id,
|
||||
// class_name)));
|
||||
// return newContext;
|
||||
//
|
||||
// }).collect(Collectors.toList());
|
||||
//
|
||||
// if(contextList.size() > 0 ){
|
||||
// Result r = new Result();
|
||||
// r.setId(c._1());
|
||||
// r.setContext(contextList);
|
||||
// return r;
|
||||
// }
|
||||
// return null;
|
||||
// })
|
||||
// .filter(r -> r != null);
|
||||
}
|
||||
|
||||
private static JavaRDD<Software> createUpdateForSoftwareDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
List<String> communityList,
|
||||
JavaRDD<Software> result,
|
||||
String class_id,
|
||||
String class_name) {
|
||||
return result.mapToPair(s -> new Tuple2<>(s.getId(), s))
|
||||
.leftOuterJoin(getStringResultJavaPairRDD(toupdateresult, communityList))
|
||||
.map(
|
||||
c -> {
|
||||
Software oaf = c._2()._1();
|
||||
if (c._2()._2().isPresent()) {
|
||||
|
||||
HashSet<String> contexts = new HashSet<>(c._2()._2().get());
|
||||
|
||||
for (Context context : oaf.getContext()) {
|
||||
if (contexts.contains(context.getId())) {
|
||||
if (!context.getDataInfo().stream()
|
||||
.map(di -> di.getInferenceprovenance())
|
||||
.collect(Collectors.toSet())
|
||||
.contains(PROPAGATION_DATA_INFO_TYPE)) {
|
||||
context.getDataInfo()
|
||||
.add(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
class_id,
|
||||
class_name));
|
||||
// community id already in the context of the result.
|
||||
// Remove it from the set that has to be added
|
||||
contexts.remove(context.getId());
|
||||
}
|
||||
}
|
||||
}
|
||||
List<Context> cc = oaf.getContext();
|
||||
for (String cId : contexts) {
|
||||
Context context = new Context();
|
||||
context.setId(cId);
|
||||
context.setDataInfo(
|
||||
Arrays.asList(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
class_id,
|
||||
class_name)));
|
||||
cc.add(context);
|
||||
}
|
||||
oaf.setContext(cc);
|
||||
}
|
||||
return oaf;
|
||||
});
|
||||
}
|
||||
|
||||
private static JavaPairRDD<String, List<String>> getStringResultJavaPairRDD(
|
||||
JavaRDD<Row> toupdateresult, List<String> communityList) {
|
||||
return toupdateresult.mapToPair(
|
||||
c -> {
|
||||
List<String> contextList = new ArrayList<>();
|
||||
List<String> contexts = c.getList(1);
|
||||
for (String context : contexts) {
|
||||
if (communityList.contains(context)) {
|
||||
contextList.add(context);
|
||||
}
|
||||
}
|
||||
|
||||
return new Tuple2<>(c.getString(0), contextList);
|
||||
});
|
||||
}
|
||||
|
||||
private static org.apache.spark.sql.Dataset<Row> getContext(SparkSession spark, String table) {
|
||||
String query =
|
||||
"SELECT relation.source, "
|
||||
+ table
|
||||
+ ".context , relation.target "
|
||||
+ "FROM "
|
||||
+ table
|
||||
+ " JOIN relation "
|
||||
+ "ON id = source";
|
||||
|
||||
return spark.sql(query);
|
||||
}
|
||||
|
||||
private static Boolean relatedToCommunities(Result r, List<String> communityIdList) {
|
||||
Set<String> result_communities =
|
||||
r.getContext().stream().map(c -> c.getId()).collect(Collectors.toSet());
|
||||
for (String communityId : result_communities) {
|
||||
if (communityIdList.contains(communityId)) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
private static void updateResult(
|
||||
JavaPairRDD<String, Result> results,
|
||||
JavaPairRDD<String, TypedRow> toupdateresult,
|
||||
String outputPath,
|
||||
String type) {
|
||||
results.leftOuterJoin(toupdateresult)
|
||||
.map(
|
||||
p -> {
|
||||
Result r = p._2()._1();
|
||||
if (p._2()._2().isPresent()) {
|
||||
Set<String> communityList = p._2()._2().get().getAccumulator();
|
||||
for (Context c : r.getContext()) {
|
||||
if (communityList.contains(c.getId())) {
|
||||
// verify if the datainfo for this context contains
|
||||
// propagation
|
||||
if (!c.getDataInfo().stream()
|
||||
.map(di -> di.getInferenceprovenance())
|
||||
.collect(Collectors.toSet())
|
||||
.contains(PROPAGATION_DATA_INFO_TYPE)) {
|
||||
c.getDataInfo()
|
||||
.add(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME));
|
||||
// community id already in the context of the result.
|
||||
// Remove it from the set that has to be added
|
||||
communityList.remove(c.getId());
|
||||
}
|
||||
}
|
||||
}
|
||||
List<Context> cc = r.getContext();
|
||||
for (String cId : communityList) {
|
||||
Context context = new Context();
|
||||
context.setId(cId);
|
||||
context.setDataInfo(
|
||||
Arrays.asList(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME)));
|
||||
cc.add(context);
|
||||
}
|
||||
r.setContext(cc);
|
||||
}
|
||||
return r;
|
||||
})
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath + "/" + type);
|
||||
}
|
||||
|
||||
private static TypedRow getTypedRow(
|
||||
List<String> communityIdList, List<Context> context, String id, String type) {
|
||||
Set<String> result_communities =
|
||||
context.stream().map(c -> c.getId()).collect(Collectors.toSet());
|
||||
TypedRow tp = new TypedRow();
|
||||
tp.setSourceId(id);
|
||||
tp.setType(type);
|
||||
for (String communityId : result_communities) {
|
||||
if (communityIdList.contains(communityId)) {
|
||||
tp.add(communityId);
|
||||
}
|
||||
}
|
||||
if (tp.getAccumulator() != null) {
|
||||
return tp;
|
||||
}
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,682 +0,0 @@
|
|||
package eu.dnetlib.dhp.resulttocommunityfromsemrel;
|
||||
|
||||
import static eu.dnetlib.dhp.PropagationConstant.*;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.QueryInformationSystem;
|
||||
import eu.dnetlib.dhp.TypedRow;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaPairRDD;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class SparkResultToCommunityThroughSemRelJob2 {
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
final ArgumentApplicationParser parser =
|
||||
new ArgumentApplicationParser(
|
||||
IOUtils.toString(
|
||||
SparkResultToCommunityThroughSemRelJob2.class.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_communitytoresult_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
|
||||
final SparkSession spark =
|
||||
SparkSession.builder()
|
||||
.appName(SparkResultToCommunityThroughSemRelJob2.class.getSimpleName())
|
||||
.master(parser.get("master"))
|
||||
.config(conf)
|
||||
.enableHiveSupport()
|
||||
.getOrCreate();
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
final String inputPath = parser.get("sourcePath");
|
||||
final String outputPath = "/tmp/provision/propagation/resulttocommunityfromsemrel";
|
||||
|
||||
final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
|
||||
// final List<String> allowedsemrel = Arrays.asList("isSupplementedBy", "isSupplementTo");
|
||||
final List<String> communityIdList =
|
||||
QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
|
||||
// final List<String> communityIdList =
|
||||
// QueryInformationSystem.getCommunityList("http://beta.services.openaire.eu:8280/is/services/isLookUp");
|
||||
|
||||
createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
|
||||
|
||||
JavaRDD<Publication> publication_rdd =
|
||||
sc.textFile(inputPath + "/publication")
|
||||
.map(item -> new ObjectMapper().readValue(item, Publication.class));
|
||||
|
||||
System.out.println(publication_rdd.count());
|
||||
// JavaRDD<Dataset> dataset_rdd = sc.textFile(inputPath + "/dataset")
|
||||
// .map(item -> new ObjectMapper().readValue(item, Dataset.class));
|
||||
//
|
||||
// JavaRDD<OtherResearchProduct> orp_rdd = sc.textFile(inputPath +
|
||||
// "/otherresearchproduct")
|
||||
// .map(item -> new ObjectMapper().readValue(item,
|
||||
// OtherResearchProduct.class));
|
||||
//
|
||||
// JavaRDD<Software> software_rdd = sc.textFile(inputPath + "/software")
|
||||
// .map(item -> new ObjectMapper().readValue(item, Software.class));
|
||||
|
||||
JavaRDD<Relation> relation_rdd =
|
||||
sc.textFile(inputPath + "/relation")
|
||||
.map(item -> new ObjectMapper().readValue(item, Relation.class));
|
||||
|
||||
System.out.println(relation_rdd.count());
|
||||
|
||||
// .filter(r -> !r.getDataInfo().getDeletedbyinference())
|
||||
// .filter(r -> allowedsemrel.contains(r.getRelClass()) &&
|
||||
// RELATION_RESULTRESULT_REL_TYPE.equals(r.getRelType())).cache();
|
||||
|
||||
org.apache.spark.sql.Dataset<Publication> publication =
|
||||
spark.createDataset(publication_rdd.rdd(), Encoders.bean(Publication.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<Relation> relation =
|
||||
spark.createDataset(relation_rdd.rdd(), Encoders.bean(Relation.class));
|
||||
|
||||
// org.apache.spark.sql.Dataset<Dataset> dataset =
|
||||
// spark.createDataset(dataset_rdd.rdd(),
|
||||
// Encoders.bean(Dataset.class));
|
||||
//
|
||||
// org.apache.spark.sql.Dataset<OtherResearchProduct> other =
|
||||
// spark.createDataset(orp_rdd.rdd(),
|
||||
// Encoders.bean(OtherResearchProduct.class));
|
||||
//
|
||||
// org.apache.spark.sql.Dataset<Software> software =
|
||||
// spark.createDataset(software_rdd.rdd(),
|
||||
// Encoders.bean(Software.class));
|
||||
//
|
||||
// org.apache.spark.sql.Dataset<Relation> relation =
|
||||
// spark.createDataset(relation_rdd.rdd(),
|
||||
// Encoders.bean(Relation.class));
|
||||
|
||||
publication.createOrReplaceTempView("publication");
|
||||
relation.createOrReplaceTempView("relation");
|
||||
// relation.createOrReplaceTempView("relation");
|
||||
// dataset.createOrReplaceTempView("dataset");
|
||||
// software.createOrReplaceTempView("software");
|
||||
// other.createOrReplaceTempView("other");
|
||||
|
||||
String communitylist = getConstraintList(" co.id = '", communityIdList);
|
||||
|
||||
String semrellist = getConstraintList(" relClass = '", allowedsemrel);
|
||||
|
||||
String query =
|
||||
"Select source, community_context, target "
|
||||
+ "from (select id, collect_set(co.id) community_context "
|
||||
+ "from publication "
|
||||
+ "lateral view explode (context) c as co "
|
||||
+ "where datainfo.deletedbyinference = false "
|
||||
+ communitylist
|
||||
+ " group by id) p "
|
||||
+ "JOIN "
|
||||
+ "(select * "
|
||||
+ "from relation "
|
||||
+ "where datainfo.deletedbyinference = false and (relClass = 'isSupplementedBy' OR relClass = 'isSupplementTo')) r "
|
||||
+ "ON p.id = r.source";
|
||||
|
||||
org.apache.spark.sql.Dataset<Row> publication_context = spark.sql(query);
|
||||
publication_context.createOrReplaceTempView("publication_context");
|
||||
|
||||
// ( source, (mes, dh-ch-, ni), target )
|
||||
query =
|
||||
"select target , collect_set(co) "
|
||||
+ "from (select target, community_context "
|
||||
+ "from publication_context pc join publication p on "
|
||||
+ "p.id = pc.source) tmp "
|
||||
+ "lateral view explode (community_context) c as co "
|
||||
+ "group by target";
|
||||
|
||||
org.apache.spark.sql.Dataset<Row> toupdatepublicationreresult = spark.sql(query);
|
||||
|
||||
System.out.println(toupdatepublicationreresult.count());
|
||||
|
||||
toupdatepublicationreresult
|
||||
.toJavaRDD()
|
||||
.map(
|
||||
r -> {
|
||||
TypedRow tp = new TypedRow();
|
||||
tp.setSourceId(r.getString(0));
|
||||
r.getList(1).stream().forEach(c -> tp.add((String) c));
|
||||
return tp;
|
||||
})
|
||||
.map(tr -> new ObjectMapper().writeValueAsString(tr))
|
||||
.saveAsTextFile(outputPath + "/community2semrelonpublication");
|
||||
// toupdatepublicationreresult.toJavaRDD().flatMap(c -> {
|
||||
//
|
||||
// String source = c.getString(0);
|
||||
// List<Relation> relation_list = new ArrayList<>();
|
||||
// c.getList(1).stream()
|
||||
// .forEach(res -> {
|
||||
// Relation r = new Relation();
|
||||
// r.setSource(source);
|
||||
// r.setTarget((String)res);
|
||||
// r.setRelClass("produces");
|
||||
// relation_list.add(r);
|
||||
// r = new Relation();
|
||||
// r.setSource((String)res);
|
||||
// r.setTarget(source);
|
||||
// r.setRelClass("isProducedBy");
|
||||
// relation_list.add(r);
|
||||
// });
|
||||
// return relation_list.iterator();
|
||||
// }).map(tr -> new ObjectMapper().writeValueAsString(tr))
|
||||
// .saveAsTextFile(outputPath + "/community2semrel");
|
||||
//
|
||||
|
||||
// org.apache.spark.sql.Dataset<Row> toupdatesoftwareresult =
|
||||
// getUpdateCommunitiesForTable(spark, "software");
|
||||
// org.apache.spark.sql.Dataset<Row> toupdatedatasetresult =
|
||||
// getUpdateCommunitiesForTable(spark, "dataset");
|
||||
// org.apache.spark.sql.Dataset<Row> toupdatepublicationreresult =
|
||||
// getUpdateCommunitiesForTable(spark, "publication");
|
||||
// org.apache.spark.sql.Dataset<Row> toupdateotherresult =
|
||||
// getUpdateCommunitiesForTable(spark, "other");
|
||||
|
||||
// createUpdateForResultDatasetWrite(toupdatesoftwareresult.toJavaRDD(), outputPath,
|
||||
// "software_update",
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
|
||||
//
|
||||
// createUpdateForResultDatasetWrite(toupdatedatasetresult.toJavaRDD(), outputPath,
|
||||
// "dataset_update",
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
|
||||
|
||||
// createUpdateForResultDatasetWrite(toupdatepublicationreresult.toJavaRDD(),
|
||||
// outputPath, "publication_update",
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
|
||||
|
||||
// createUpdateForResultDatasetWrite(toupdateotherresult.toJavaRDD(), outputPath,
|
||||
// "other_update",
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
|
||||
//
|
||||
//
|
||||
// updateForDatasetDataset(toupdatedatasetresult.toJavaRDD(), dataset.toJavaRDD(),
|
||||
// outputPath, "dataset",
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
|
||||
//
|
||||
// updateForOtherDataset(toupdateotherresult.toJavaRDD(), other.toJavaRDD(),
|
||||
// outputPath, "otherresearchproduct",
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
|
||||
//
|
||||
// updateForSoftwareDataset(toupdatesoftwareresult.toJavaRDD(), software.toJavaRDD(),
|
||||
// outputPath, "software",
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
|
||||
//
|
||||
// updateForPublicationDataset(toupdatepublicationreresult.toJavaRDD(),
|
||||
// publication.toJavaRDD(), outputPath, "publication",
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
// PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
|
||||
//
|
||||
|
||||
/*
|
||||
JavaPairRDD<String, TypedRow> resultLinkedToCommunities = publication
|
||||
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"publication"))
|
||||
.filter(p -> !(p == null))
|
||||
.mapToPair(toPair())
|
||||
.union(datasets
|
||||
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"dataset"))
|
||||
.filter(p -> !(p == null))
|
||||
.mapToPair(toPair())
|
||||
)
|
||||
.union(software
|
||||
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"software"))
|
||||
.filter(p -> !(p == null))
|
||||
.mapToPair(toPair())
|
||||
)
|
||||
.union(other
|
||||
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"otherresearchproduct"))
|
||||
.filter(p -> !(p == null))
|
||||
.mapToPair(toPair())
|
||||
);
|
||||
|
||||
JavaPairRDD<String, TypedRow> to_add_result_communities = resultLinkedToCommunities.join(result_result).map(r -> r._2()._1().setSourceId(r._2()._2().getTargetId()))
|
||||
.mapToPair(toPair());
|
||||
|
||||
JavaPairRDD<String, Result> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
JavaPairRDD<String, Result> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
JavaPairRDD<String, Result> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
|
||||
updateResultForCommunity(pubs, to_add_result_communities, outputPath, "publication", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
|
||||
updateResultForCommunity(dss, to_add_result_communities, outputPath, "dataset", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
|
||||
updateResultForCommunity(sfw, to_add_result_communities, outputPath, "software", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
|
||||
updateResultForCommunity(orp, to_add_result_communities, outputPath, "otherresearchproduct", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
|
||||
//leftouterjoin result.to_add_result_communities (result = java pair rdd result) [left outer join perche' li voglio tutti anche quelli che non ho aggiornato]
|
||||
//per quelli che matchano cercare nel risultato se i context da aggiungere sono gia' presenti. Se non ci sono aggiungerli, altrimenti nulla
|
||||
*/
|
||||
}
|
||||
|
||||
private static org.apache.spark.sql.Dataset<Row> getUpdateCommunitiesForTable(
|
||||
SparkSession spark, String table) {
|
||||
String query =
|
||||
"SELECT target_id, collect_set(co.id) context_id "
|
||||
+ " FROM (SELECT t.id target_id, s.context source_context "
|
||||
+ " FROM context_software s "
|
||||
+ " JOIN "
|
||||
+ table
|
||||
+ " t "
|
||||
+ " ON s.target = t.id "
|
||||
+ " UNION ALL "
|
||||
+ " SELECT t.id target_id, d.context source_context "
|
||||
+ " FROM dataset_context d "
|
||||
+ " JOIN "
|
||||
+ table
|
||||
+ " t"
|
||||
+ " ON s.target = t.id "
|
||||
+ " UNION ALL "
|
||||
+ " SELECT t.id target_id, p.context source_context "
|
||||
+ " FROM publication_context p"
|
||||
+ " JOIN "
|
||||
+ table
|
||||
+ " t "
|
||||
+ " on p.target = t.id "
|
||||
+ " UNION ALL "
|
||||
+ " SELECT t.id target_id, o.context source_context "
|
||||
+ " FROM other_context o "
|
||||
+ " JOIN "
|
||||
+ table
|
||||
+ " t "
|
||||
+ " ON o.target = t.id) TMP "
|
||||
+ " LATERAL VIEW EXPLODE(source_context) MyT as co "
|
||||
+ " GROUP BY target_id";
|
||||
|
||||
return spark.sql(query);
|
||||
}
|
||||
|
||||
private static JavaRDD<Result> createUpdateForResultDatasetWrite(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
return toupdateresult
|
||||
.map(
|
||||
r -> {
|
||||
List<Context> contextList = new ArrayList();
|
||||
List<String> toAddContext = r.getList(1);
|
||||
for (String cId : toAddContext) {
|
||||
if (communityIdList.contains(cId)) {
|
||||
Context newContext = new Context();
|
||||
newContext.setId(cId);
|
||||
newContext.setDataInfo(
|
||||
Arrays.asList(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
class_id,
|
||||
class_name)));
|
||||
contextList.add(newContext);
|
||||
}
|
||||
}
|
||||
|
||||
if (contextList.size() > 0) {
|
||||
Result ret = new Result();
|
||||
ret.setId(r.getString(0));
|
||||
ret.setContext(contextList);
|
||||
return ret;
|
||||
}
|
||||
return null;
|
||||
})
|
||||
.filter(r -> r != null);
|
||||
}
|
||||
|
||||
private static void updateForSoftwareDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
JavaRDD<Software> result,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
|
||||
getUpdateForResultDataset(
|
||||
toupdateresult,
|
||||
tmp,
|
||||
outputPath,
|
||||
type,
|
||||
class_id,
|
||||
class_name,
|
||||
communityIdList)
|
||||
.map(r -> (Software) r)
|
||||
.map(s -> new ObjectMapper().writeValueAsString(s))
|
||||
.saveAsTextFile(outputPath + "/" + type);
|
||||
}
|
||||
|
||||
private static void updateForDatasetDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
JavaRDD<Dataset> result,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
|
||||
getUpdateForResultDataset(
|
||||
toupdateresult,
|
||||
tmp,
|
||||
outputPath,
|
||||
type,
|
||||
class_id,
|
||||
class_name,
|
||||
communityIdList)
|
||||
.map(r -> (Dataset) r)
|
||||
.map(d -> new ObjectMapper().writeValueAsString(d))
|
||||
.saveAsTextFile(outputPath + "/" + type);
|
||||
}
|
||||
|
||||
private static void updateForPublicationDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
JavaRDD<Publication> result,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
|
||||
getUpdateForResultDataset(
|
||||
toupdateresult,
|
||||
tmp,
|
||||
outputPath,
|
||||
type,
|
||||
class_id,
|
||||
class_name,
|
||||
communityIdList)
|
||||
.map(r -> (Publication) r)
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath + "/" + type);
|
||||
}
|
||||
|
||||
private static void updateForOtherDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
JavaRDD<OtherResearchProduct> result,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
|
||||
getUpdateForResultDataset(
|
||||
toupdateresult,
|
||||
tmp,
|
||||
outputPath,
|
||||
type,
|
||||
class_id,
|
||||
class_name,
|
||||
communityIdList)
|
||||
.map(r -> (OtherResearchProduct) r)
|
||||
.map(o -> new ObjectMapper().writeValueAsString(o))
|
||||
.saveAsTextFile(outputPath + "/" + type);
|
||||
}
|
||||
|
||||
private static JavaRDD<Result> getUpdateForResultDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
JavaPairRDD<String, Result> result,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
return result.leftOuterJoin(
|
||||
toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))))
|
||||
.map(
|
||||
c -> {
|
||||
if (!c._2()._2().isPresent()) {
|
||||
return c._2()._1();
|
||||
}
|
||||
|
||||
List<Object> toAddContext = c._2()._2().get();
|
||||
Set<String> context_set = new HashSet<>();
|
||||
for (Object cId : toAddContext) {
|
||||
String id = (String) cId;
|
||||
if (communityIdList.contains(id)) {
|
||||
context_set.add(id);
|
||||
}
|
||||
}
|
||||
for (Context context : c._2()._1().getContext()) {
|
||||
if (context_set.contains(context)) {
|
||||
context_set.remove(context);
|
||||
}
|
||||
}
|
||||
|
||||
List<Context> contextList =
|
||||
context_set.stream()
|
||||
.map(
|
||||
co -> {
|
||||
Context newContext = new Context();
|
||||
newContext.setId(co);
|
||||
newContext.setDataInfo(
|
||||
Arrays.asList(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
class_id,
|
||||
class_name)));
|
||||
return newContext;
|
||||
})
|
||||
.collect(Collectors.toList());
|
||||
|
||||
if (contextList.size() > 0) {
|
||||
Result r = new Result();
|
||||
r.setId(c._1());
|
||||
r.setContext(contextList);
|
||||
return r;
|
||||
}
|
||||
return null;
|
||||
})
|
||||
.filter(r -> r != null);
|
||||
|
||||
// return toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1)))
|
||||
// .join(result)
|
||||
// .map(c -> {
|
||||
// List<Object> toAddContext = c._2()._1();
|
||||
// Set<String> context_set = new HashSet<>();
|
||||
// for(Object cId: toAddContext){
|
||||
// String id = (String)cId;
|
||||
// if (communityIdList.contains(id)){
|
||||
// context_set.add(id);
|
||||
// }
|
||||
// }
|
||||
// for (Context context: c._2()._2().getContext()){
|
||||
// if(context_set.contains(context)){
|
||||
// context_set.remove(context);
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// List<Context> contextList = context_set.stream().map(co -> {
|
||||
// Context newContext = new Context();
|
||||
// newContext.setId(co);
|
||||
//
|
||||
// newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id,
|
||||
// class_name)));
|
||||
// return newContext;
|
||||
//
|
||||
// }).collect(Collectors.toList());
|
||||
//
|
||||
// if(contextList.size() > 0 ){
|
||||
// Result r = new Result();
|
||||
// r.setId(c._1());
|
||||
// r.setContext(contextList);
|
||||
// return r;
|
||||
// }
|
||||
// return null;
|
||||
// })
|
||||
// .filter(r -> r != null);
|
||||
}
|
||||
|
||||
private static JavaRDD<Software> createUpdateForSoftwareDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
List<String> communityList,
|
||||
JavaRDD<Software> result,
|
||||
String class_id,
|
||||
String class_name) {
|
||||
return result.mapToPair(s -> new Tuple2<>(s.getId(), s))
|
||||
.leftOuterJoin(getStringResultJavaPairRDD(toupdateresult, communityList))
|
||||
.map(
|
||||
c -> {
|
||||
Software oaf = c._2()._1();
|
||||
if (c._2()._2().isPresent()) {
|
||||
|
||||
HashSet<String> contexts = new HashSet<>(c._2()._2().get());
|
||||
|
||||
for (Context context : oaf.getContext()) {
|
||||
if (contexts.contains(context.getId())) {
|
||||
if (!context.getDataInfo().stream()
|
||||
.map(di -> di.getInferenceprovenance())
|
||||
.collect(Collectors.toSet())
|
||||
.contains(PROPAGATION_DATA_INFO_TYPE)) {
|
||||
context.getDataInfo()
|
||||
.add(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
class_id,
|
||||
class_name));
|
||||
// community id already in the context of the result.
|
||||
// Remove it from the set that has to be added
|
||||
contexts.remove(context.getId());
|
||||
}
|
||||
}
|
||||
}
|
||||
List<Context> cc = oaf.getContext();
|
||||
for (String cId : contexts) {
|
||||
Context context = new Context();
|
||||
context.setId(cId);
|
||||
context.setDataInfo(
|
||||
Arrays.asList(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
class_id,
|
||||
class_name)));
|
||||
cc.add(context);
|
||||
}
|
||||
oaf.setContext(cc);
|
||||
}
|
||||
return oaf;
|
||||
});
|
||||
}
|
||||
|
||||
private static JavaPairRDD<String, List<String>> getStringResultJavaPairRDD(
|
||||
JavaRDD<Row> toupdateresult, List<String> communityList) {
|
||||
return toupdateresult.mapToPair(
|
||||
c -> {
|
||||
List<String> contextList = new ArrayList<>();
|
||||
List<String> contexts = c.getList(1);
|
||||
for (String context : contexts) {
|
||||
if (communityList.contains(context)) {
|
||||
contextList.add(context);
|
||||
}
|
||||
}
|
||||
|
||||
return new Tuple2<>(c.getString(0), contextList);
|
||||
});
|
||||
}
|
||||
|
||||
private static org.apache.spark.sql.Dataset<Row> getContext(SparkSession spark, String table) {
|
||||
String query =
|
||||
"SELECT relation.source, "
|
||||
+ table
|
||||
+ ".context , relation.target "
|
||||
+ "FROM "
|
||||
+ table
|
||||
+ " JOIN relation "
|
||||
+ "ON id = source";
|
||||
|
||||
return spark.sql(query);
|
||||
}
|
||||
|
||||
private static Boolean relatedToCommunities(Result r, List<String> communityIdList) {
|
||||
Set<String> result_communities =
|
||||
r.getContext().stream().map(c -> c.getId()).collect(Collectors.toSet());
|
||||
for (String communityId : result_communities) {
|
||||
if (communityIdList.contains(communityId)) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
private static void updateResult(
|
||||
JavaPairRDD<String, Result> results,
|
||||
JavaPairRDD<String, TypedRow> toupdateresult,
|
||||
String outputPath,
|
||||
String type) {
|
||||
results.leftOuterJoin(toupdateresult)
|
||||
.map(
|
||||
p -> {
|
||||
Result r = p._2()._1();
|
||||
if (p._2()._2().isPresent()) {
|
||||
Set<String> communityList = p._2()._2().get().getAccumulator();
|
||||
for (Context c : r.getContext()) {
|
||||
if (communityList.contains(c.getId())) {
|
||||
// verify if the datainfo for this context contains
|
||||
// propagation
|
||||
if (!c.getDataInfo().stream()
|
||||
.map(di -> di.getInferenceprovenance())
|
||||
.collect(Collectors.toSet())
|
||||
.contains(PROPAGATION_DATA_INFO_TYPE)) {
|
||||
c.getDataInfo()
|
||||
.add(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME));
|
||||
// community id already in the context of the result.
|
||||
// Remove it from the set that has to be added
|
||||
communityList.remove(c.getId());
|
||||
}
|
||||
}
|
||||
}
|
||||
List<Context> cc = r.getContext();
|
||||
for (String cId : communityList) {
|
||||
Context context = new Context();
|
||||
context.setId(cId);
|
||||
context.setDataInfo(
|
||||
Arrays.asList(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME)));
|
||||
cc.add(context);
|
||||
}
|
||||
r.setContext(cc);
|
||||
}
|
||||
return r;
|
||||
})
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath + "/" + type);
|
||||
}
|
||||
|
||||
private static TypedRow getTypedRow(
|
||||
List<String> communityIdList, List<Context> context, String id, String type) {
|
||||
Set<String> result_communities =
|
||||
context.stream().map(c -> c.getId()).collect(Collectors.toSet());
|
||||
TypedRow tp = new TypedRow();
|
||||
tp.setSourceId(id);
|
||||
tp.setType(type);
|
||||
for (String communityId : result_communities) {
|
||||
if (communityIdList.contains(communityId)) {
|
||||
tp.add(communityId);
|
||||
}
|
||||
}
|
||||
if (tp.getAccumulator() != null) {
|
||||
return tp;
|
||||
}
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,660 +0,0 @@
|
|||
package eu.dnetlib.dhp.resulttocommunityfromsemrel;
|
||||
|
||||
import static eu.dnetlib.dhp.PropagationConstant.*;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.QueryInformationSystem;
|
||||
import eu.dnetlib.dhp.TypedRow;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaPairRDD;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class SparkResultToCommunityThroughSemRelJob3 {
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
final ArgumentApplicationParser parser =
|
||||
new ArgumentApplicationParser(
|
||||
IOUtils.toString(
|
||||
SparkResultToCommunityThroughSemRelJob3.class.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_communitytoresult_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
|
||||
final SparkSession spark =
|
||||
SparkSession.builder()
|
||||
.appName(SparkResultToCommunityThroughSemRelJob3.class.getSimpleName())
|
||||
.master(parser.get("master"))
|
||||
.config(conf)
|
||||
.enableHiveSupport()
|
||||
.getOrCreate();
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
final String inputPath = parser.get("sourcePath");
|
||||
final String outputPath = "/tmp/provision/propagation/resulttocommunityfromsemrel";
|
||||
|
||||
final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
|
||||
|
||||
final List<String> communityIdList =
|
||||
QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
|
||||
|
||||
createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
|
||||
|
||||
JavaRDD<Publication> publication_rdd =
|
||||
sc.textFile(inputPath + "/publication")
|
||||
.map(item -> new ObjectMapper().readValue(item, Publication.class));
|
||||
|
||||
JavaRDD<Dataset> dataset_rdd =
|
||||
sc.textFile(inputPath + "/dataset")
|
||||
.map(item -> new ObjectMapper().readValue(item, Dataset.class));
|
||||
|
||||
JavaRDD<OtherResearchProduct> orp_rdd =
|
||||
sc.textFile(inputPath + "/otherresearchproduct")
|
||||
.map(
|
||||
item ->
|
||||
new ObjectMapper()
|
||||
.readValue(item, OtherResearchProduct.class));
|
||||
|
||||
JavaRDD<Software> software_rdd =
|
||||
sc.textFile(inputPath + "/software")
|
||||
.map(item -> new ObjectMapper().readValue(item, Software.class));
|
||||
|
||||
JavaRDD<Relation> relation_rdd =
|
||||
sc.textFile(inputPath + "/relation")
|
||||
.map(item -> new ObjectMapper().readValue(item, Relation.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<Publication> publication =
|
||||
spark.createDataset(publication_rdd.rdd(), Encoders.bean(Publication.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<Relation> relation =
|
||||
spark.createDataset(relation_rdd.rdd(), Encoders.bean(Relation.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<Dataset> dataset =
|
||||
spark.createDataset(dataset_rdd.rdd(), Encoders.bean(Dataset.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<OtherResearchProduct> other =
|
||||
spark.createDataset(orp_rdd.rdd(), Encoders.bean(OtherResearchProduct.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<Software> software =
|
||||
spark.createDataset(software_rdd.rdd(), Encoders.bean(Software.class));
|
||||
|
||||
publication.createOrReplaceTempView("publication");
|
||||
relation.createOrReplaceTempView("relation");
|
||||
dataset.createOrReplaceTempView("dataset");
|
||||
software.createOrReplaceTempView("software");
|
||||
other.createOrReplaceTempView("other");
|
||||
|
||||
String communitylist = getConstraintList(" co.id = '", communityIdList);
|
||||
|
||||
String semrellist = getConstraintList(" relClass = '", allowedsemrel);
|
||||
|
||||
String query =
|
||||
"Select source, community_context, target "
|
||||
+ "from (select id, collect_set(co.id) community_context "
|
||||
+ "from publication "
|
||||
+ "lateral view explode (context) c as co "
|
||||
+ "where datainfo.deletedbyinference = false "
|
||||
+ communitylist
|
||||
+ " group by id) p "
|
||||
+ "JOIN "
|
||||
+ "(select * "
|
||||
+ "from relation "
|
||||
+ "where datainfo.deletedbyinference = false "
|
||||
+ semrellist
|
||||
+ ") r "
|
||||
+ "ON p.id = r.source";
|
||||
|
||||
org.apache.spark.sql.Dataset<Row> publication_context = spark.sql(query);
|
||||
publication_context.createOrReplaceTempView("publication_context");
|
||||
|
||||
// ( source, (mes, dh-ch-, ni), target )
|
||||
query =
|
||||
"select target , collect_set(co) "
|
||||
+ "from (select target, community_context "
|
||||
+ "from publication_context pc join publication p on "
|
||||
+ "p.id = pc.source) tmp "
|
||||
+ "lateral view explode (community_context) c as co "
|
||||
+ "group by target";
|
||||
|
||||
org.apache.spark.sql.Dataset<Row> toupdatepublicationreresult = spark.sql(query);
|
||||
org.apache.spark.sql.Dataset<Row> toupdatesoftwareresult =
|
||||
getUpdateCommunitiesForTable(spark, "software");
|
||||
org.apache.spark.sql.Dataset<Row> toupdatedatasetresult =
|
||||
getUpdateCommunitiesForTable(spark, "dataset");
|
||||
org.apache.spark.sql.Dataset<Row> toupdateotherresult =
|
||||
getUpdateCommunitiesForTable(spark, "other");
|
||||
|
||||
createUpdateForResultDatasetWrite(
|
||||
toupdatesoftwareresult.toJavaRDD(),
|
||||
outputPath,
|
||||
"software_update",
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
|
||||
communityIdList);
|
||||
|
||||
createUpdateForResultDatasetWrite(
|
||||
toupdatedatasetresult.toJavaRDD(),
|
||||
outputPath,
|
||||
"dataset_update",
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
|
||||
communityIdList);
|
||||
|
||||
createUpdateForResultDatasetWrite(
|
||||
toupdatepublicationreresult.toJavaRDD(),
|
||||
outputPath,
|
||||
"publication_update",
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
|
||||
communityIdList);
|
||||
|
||||
createUpdateForResultDatasetWrite(
|
||||
toupdateotherresult.toJavaRDD(),
|
||||
outputPath,
|
||||
"other_update",
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
|
||||
communityIdList);
|
||||
|
||||
updateForDatasetDataset(
|
||||
toupdatedatasetresult.toJavaRDD(),
|
||||
dataset.toJavaRDD(),
|
||||
outputPath,
|
||||
"dataset",
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
|
||||
communityIdList);
|
||||
|
||||
updateForOtherDataset(
|
||||
toupdateotherresult.toJavaRDD(),
|
||||
other.toJavaRDD(),
|
||||
outputPath,
|
||||
"otherresearchproduct",
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
|
||||
communityIdList);
|
||||
|
||||
updateForSoftwareDataset(
|
||||
toupdatesoftwareresult.toJavaRDD(),
|
||||
software.toJavaRDD(),
|
||||
outputPath,
|
||||
"software",
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
|
||||
communityIdList);
|
||||
|
||||
updateForPublicationDataset(
|
||||
toupdatepublicationreresult.toJavaRDD(),
|
||||
publication.toJavaRDD(),
|
||||
outputPath,
|
||||
"publication",
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
|
||||
communityIdList);
|
||||
//
|
||||
|
||||
/*
|
||||
JavaPairRDD<String, TypedRow> resultLinkedToCommunities = publication
|
||||
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"publication"))
|
||||
.filter(p -> !(p == null))
|
||||
.mapToPair(toPair())
|
||||
.union(datasets
|
||||
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"dataset"))
|
||||
.filter(p -> !(p == null))
|
||||
.mapToPair(toPair())
|
||||
)
|
||||
.union(software
|
||||
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"software"))
|
||||
.filter(p -> !(p == null))
|
||||
.mapToPair(toPair())
|
||||
)
|
||||
.union(other
|
||||
.map(p -> getTypedRow(communityIdList, p.getContext(), p.getId(),"otherresearchproduct"))
|
||||
.filter(p -> !(p == null))
|
||||
.mapToPair(toPair())
|
||||
);
|
||||
|
||||
JavaPairRDD<String, TypedRow> to_add_result_communities = resultLinkedToCommunities.join(result_result).map(r -> r._2()._1().setSourceId(r._2()._2().getTargetId()))
|
||||
.mapToPair(toPair());
|
||||
|
||||
JavaPairRDD<String, Result> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
JavaPairRDD<String, Result> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
JavaPairRDD<String, Result> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
|
||||
updateResultForCommunity(pubs, to_add_result_communities, outputPath, "publication", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
|
||||
updateResultForCommunity(dss, to_add_result_communities, outputPath, "dataset", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
|
||||
updateResultForCommunity(sfw, to_add_result_communities, outputPath, "software", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
|
||||
updateResultForCommunity(orp, to_add_result_communities, outputPath, "otherresearchproduct", PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME);
|
||||
//leftouterjoin result.to_add_result_communities (result = java pair rdd result) [left outer join perche' li voglio tutti anche quelli che non ho aggiornato]
|
||||
//per quelli che matchano cercare nel risultato se i context da aggiungere sono gia' presenti. Se non ci sono aggiungerli, altrimenti nulla
|
||||
*/
|
||||
}
|
||||
|
||||
private static org.apache.spark.sql.Dataset<Row> getUpdateCommunitiesForTable(
|
||||
SparkSession spark, String table) {
|
||||
String query =
|
||||
"SELECT target_id, collect_set(co.id) context_id "
|
||||
+ " FROM (SELECT t.id target_id, s.context source_context "
|
||||
+ " FROM context_software s "
|
||||
+ " JOIN "
|
||||
+ table
|
||||
+ " t "
|
||||
+ " ON s.target = t.id "
|
||||
+ " UNION ALL "
|
||||
+ " SELECT t.id target_id, d.context source_context "
|
||||
+ " FROM dataset_context d "
|
||||
+ " JOIN "
|
||||
+ table
|
||||
+ " t"
|
||||
+ " ON s.target = t.id "
|
||||
+ " UNION ALL "
|
||||
+ " SELECT t.id target_id, p.context source_context "
|
||||
+ " FROM publication_context p"
|
||||
+ " JOIN "
|
||||
+ table
|
||||
+ " t "
|
||||
+ " on p.target = t.id "
|
||||
+ " UNION ALL "
|
||||
+ " SELECT t.id target_id, o.context source_context "
|
||||
+ " FROM other_context o "
|
||||
+ " JOIN "
|
||||
+ table
|
||||
+ " t "
|
||||
+ " ON o.target = t.id) TMP "
|
||||
+ " LATERAL VIEW EXPLODE(source_context) MyT as co "
|
||||
+ " GROUP BY target_id";
|
||||
|
||||
return spark.sql(query);
|
||||
}
|
||||
|
||||
private static JavaRDD<Result> createUpdateForResultDatasetWrite(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
return toupdateresult
|
||||
.map(
|
||||
r -> {
|
||||
List<Context> contextList = new ArrayList();
|
||||
List<String> toAddContext = r.getList(1);
|
||||
for (String cId : toAddContext) {
|
||||
if (communityIdList.contains(cId)) {
|
||||
Context newContext = new Context();
|
||||
newContext.setId(cId);
|
||||
newContext.setDataInfo(
|
||||
Arrays.asList(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
class_id,
|
||||
class_name)));
|
||||
contextList.add(newContext);
|
||||
}
|
||||
}
|
||||
|
||||
if (contextList.size() > 0) {
|
||||
Result ret = new Result();
|
||||
ret.setId(r.getString(0));
|
||||
ret.setContext(contextList);
|
||||
return ret;
|
||||
}
|
||||
return null;
|
||||
})
|
||||
.filter(r -> r != null);
|
||||
}
|
||||
|
||||
private static void updateForSoftwareDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
JavaRDD<Software> result,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
|
||||
getUpdateForResultDataset(
|
||||
toupdateresult,
|
||||
tmp,
|
||||
outputPath,
|
||||
type,
|
||||
class_id,
|
||||
class_name,
|
||||
communityIdList)
|
||||
.map(r -> (Software) r)
|
||||
.map(s -> new ObjectMapper().writeValueAsString(s))
|
||||
.saveAsTextFile(outputPath + "/" + type);
|
||||
}
|
||||
|
||||
private static void updateForDatasetDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
JavaRDD<Dataset> result,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
|
||||
getUpdateForResultDataset(
|
||||
toupdateresult,
|
||||
tmp,
|
||||
outputPath,
|
||||
type,
|
||||
class_id,
|
||||
class_name,
|
||||
communityIdList)
|
||||
.map(r -> (Dataset) r)
|
||||
.map(d -> new ObjectMapper().writeValueAsString(d))
|
||||
.saveAsTextFile(outputPath + "/" + type);
|
||||
}
|
||||
|
||||
private static void updateForPublicationDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
JavaRDD<Publication> result,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
|
||||
getUpdateForResultDataset(
|
||||
toupdateresult,
|
||||
tmp,
|
||||
outputPath,
|
||||
type,
|
||||
class_id,
|
||||
class_name,
|
||||
communityIdList)
|
||||
.map(r -> (Publication) r)
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath + "/" + type);
|
||||
}
|
||||
|
||||
private static void updateForOtherDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
JavaRDD<OtherResearchProduct> result,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
|
||||
getUpdateForResultDataset(
|
||||
toupdateresult,
|
||||
tmp,
|
||||
outputPath,
|
||||
type,
|
||||
class_id,
|
||||
class_name,
|
||||
communityIdList)
|
||||
.map(r -> (OtherResearchProduct) r)
|
||||
.map(o -> new ObjectMapper().writeValueAsString(o))
|
||||
.saveAsTextFile(outputPath + "/" + type);
|
||||
}
|
||||
|
||||
private static JavaRDD<Result> getUpdateForResultDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
JavaPairRDD<String, Result> result,
|
||||
String outputPath,
|
||||
String type,
|
||||
String class_id,
|
||||
String class_name,
|
||||
List<String> communityIdList) {
|
||||
return result.leftOuterJoin(
|
||||
toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))))
|
||||
.map(
|
||||
c -> {
|
||||
if (!c._2()._2().isPresent()) {
|
||||
return c._2()._1();
|
||||
}
|
||||
|
||||
List<Object> toAddContext = c._2()._2().get();
|
||||
Set<String> context_set = new HashSet<>();
|
||||
for (Object cId : toAddContext) {
|
||||
String id = (String) cId;
|
||||
if (communityIdList.contains(id)) {
|
||||
context_set.add(id);
|
||||
}
|
||||
}
|
||||
for (Context context : c._2()._1().getContext()) {
|
||||
if (context_set.contains(context)) {
|
||||
context_set.remove(context);
|
||||
}
|
||||
}
|
||||
|
||||
List<Context> contextList =
|
||||
context_set.stream()
|
||||
.map(
|
||||
co -> {
|
||||
Context newContext = new Context();
|
||||
newContext.setId(co);
|
||||
newContext.setDataInfo(
|
||||
Arrays.asList(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
class_id,
|
||||
class_name)));
|
||||
return newContext;
|
||||
})
|
||||
.collect(Collectors.toList());
|
||||
|
||||
if (contextList.size() > 0) {
|
||||
Result r = new Result();
|
||||
r.setId(c._1());
|
||||
r.setContext(contextList);
|
||||
return r;
|
||||
}
|
||||
return null;
|
||||
})
|
||||
.filter(r -> r != null);
|
||||
|
||||
// return toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1)))
|
||||
// .join(result)
|
||||
// .map(c -> {
|
||||
// List<Object> toAddContext = c._2()._1();
|
||||
// Set<String> context_set = new HashSet<>();
|
||||
// for(Object cId: toAddContext){
|
||||
// String id = (String)cId;
|
||||
// if (communityIdList.contains(id)){
|
||||
// context_set.add(id);
|
||||
// }
|
||||
// }
|
||||
// for (Context context: c._2()._2().getContext()){
|
||||
// if(context_set.contains(context)){
|
||||
// context_set.remove(context);
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// List<Context> contextList = context_set.stream().map(co -> {
|
||||
// Context newContext = new Context();
|
||||
// newContext.setId(co);
|
||||
//
|
||||
// newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id,
|
||||
// class_name)));
|
||||
// return newContext;
|
||||
//
|
||||
// }).collect(Collectors.toList());
|
||||
//
|
||||
// if(contextList.size() > 0 ){
|
||||
// Result r = new Result();
|
||||
// r.setId(c._1());
|
||||
// r.setContext(contextList);
|
||||
// return r;
|
||||
// }
|
||||
// return null;
|
||||
// })
|
||||
// .filter(r -> r != null);
|
||||
}
|
||||
|
||||
private static JavaRDD<Software> createUpdateForSoftwareDataset(
|
||||
JavaRDD<Row> toupdateresult,
|
||||
List<String> communityList,
|
||||
JavaRDD<Software> result,
|
||||
String class_id,
|
||||
String class_name) {
|
||||
return result.mapToPair(s -> new Tuple2<>(s.getId(), s))
|
||||
.leftOuterJoin(getStringResultJavaPairRDD(toupdateresult, communityList))
|
||||
.map(
|
||||
c -> {
|
||||
Software oaf = c._2()._1();
|
||||
if (c._2()._2().isPresent()) {
|
||||
|
||||
HashSet<String> contexts = new HashSet<>(c._2()._2().get());
|
||||
|
||||
for (Context context : oaf.getContext()) {
|
||||
if (contexts.contains(context.getId())) {
|
||||
if (!context.getDataInfo().stream()
|
||||
.map(di -> di.getInferenceprovenance())
|
||||
.collect(Collectors.toSet())
|
||||
.contains(PROPAGATION_DATA_INFO_TYPE)) {
|
||||
context.getDataInfo()
|
||||
.add(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
class_id,
|
||||
class_name));
|
||||
// community id already in the context of the result.
|
||||
// Remove it from the set that has to be added
|
||||
contexts.remove(context.getId());
|
||||
}
|
||||
}
|
||||
}
|
||||
List<Context> cc = oaf.getContext();
|
||||
for (String cId : contexts) {
|
||||
Context context = new Context();
|
||||
context.setId(cId);
|
||||
context.setDataInfo(
|
||||
Arrays.asList(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
class_id,
|
||||
class_name)));
|
||||
cc.add(context);
|
||||
}
|
||||
oaf.setContext(cc);
|
||||
}
|
||||
return oaf;
|
||||
});
|
||||
}
|
||||
|
||||
private static JavaPairRDD<String, List<String>> getStringResultJavaPairRDD(
|
||||
JavaRDD<Row> toupdateresult, List<String> communityList) {
|
||||
return toupdateresult.mapToPair(
|
||||
c -> {
|
||||
List<String> contextList = new ArrayList<>();
|
||||
List<String> contexts = c.getList(1);
|
||||
for (String context : contexts) {
|
||||
if (communityList.contains(context)) {
|
||||
contextList.add(context);
|
||||
}
|
||||
}
|
||||
|
||||
return new Tuple2<>(c.getString(0), contextList);
|
||||
});
|
||||
}
|
||||
|
||||
private static org.apache.spark.sql.Dataset<Row> getContext(SparkSession spark, String table) {
|
||||
String query =
|
||||
"SELECT relation.source, "
|
||||
+ table
|
||||
+ ".context , relation.target "
|
||||
+ "FROM "
|
||||
+ table
|
||||
+ " JOIN relation "
|
||||
+ "ON id = source";
|
||||
|
||||
return spark.sql(query);
|
||||
}
|
||||
|
||||
private static Boolean relatedToCommunities(Result r, List<String> communityIdList) {
|
||||
Set<String> result_communities =
|
||||
r.getContext().stream().map(c -> c.getId()).collect(Collectors.toSet());
|
||||
for (String communityId : result_communities) {
|
||||
if (communityIdList.contains(communityId)) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
private static void updateResult(
|
||||
JavaPairRDD<String, Result> results,
|
||||
JavaPairRDD<String, TypedRow> toupdateresult,
|
||||
String outputPath,
|
||||
String type) {
|
||||
results.leftOuterJoin(toupdateresult)
|
||||
.map(
|
||||
p -> {
|
||||
Result r = p._2()._1();
|
||||
if (p._2()._2().isPresent()) {
|
||||
Set<String> communityList = p._2()._2().get().getAccumulator();
|
||||
for (Context c : r.getContext()) {
|
||||
if (communityList.contains(c.getId())) {
|
||||
// verify if the datainfo for this context contains
|
||||
// propagation
|
||||
if (!c.getDataInfo().stream()
|
||||
.map(di -> di.getInferenceprovenance())
|
||||
.collect(Collectors.toSet())
|
||||
.contains(PROPAGATION_DATA_INFO_TYPE)) {
|
||||
c.getDataInfo()
|
||||
.add(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME));
|
||||
// community id already in the context of the result.
|
||||
// Remove it from the set that has to be added
|
||||
communityList.remove(c.getId());
|
||||
}
|
||||
}
|
||||
}
|
||||
List<Context> cc = r.getContext();
|
||||
for (String cId : communityList) {
|
||||
Context context = new Context();
|
||||
context.setId(cId);
|
||||
context.setDataInfo(
|
||||
Arrays.asList(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME)));
|
||||
cc.add(context);
|
||||
}
|
||||
r.setContext(cc);
|
||||
}
|
||||
return r;
|
||||
})
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath + "/" + type);
|
||||
}
|
||||
|
||||
private static TypedRow getTypedRow(
|
||||
List<String> communityIdList, List<Context> context, String id, String type) {
|
||||
Set<String> result_communities =
|
||||
context.stream().map(c -> c.getId()).collect(Collectors.toSet());
|
||||
TypedRow tp = new TypedRow();
|
||||
tp.setSourceId(id);
|
||||
tp.setType(type);
|
||||
for (String communityId : result_communities) {
|
||||
if (communityIdList.contains(communityId)) {
|
||||
tp.add(communityId);
|
||||
}
|
||||
}
|
||||
if (tp.getAccumulator() != null) {
|
||||
return tp;
|
||||
}
|
||||
return null;
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue