implementation of the openorgs wfs, implementation of the raw_all wf to migrate openorgs db entities
miconis
3 years ago
parent
c7e2d5a59a
commit
4b2124a18e
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package eu.dnetlib.dhp.oa.dedup;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Optional;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.pace.config.DedupConfig;
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import org.apache.commons.io.IOUtils;
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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.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.dom4j.DocumentException;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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//copy simrels (verified) from relation to the workdir in order to make them available for the deduplication
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public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkCopyOpenorgsMergeRels.class);
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public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
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public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
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public SparkCopyOpenorgsMergeRels(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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}
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public static void main(String[] args) throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCopyOpenorgsMergeRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/copyOpenorgsMergeRels_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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new SparkCopyOpenorgsMergeRels(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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@Override
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public void run(ISLookUpService isLookUpService)
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throws DocumentException, IOException, ISLookUpException {
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// read oozie parameters
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final String graphBasePath = parser.get("graphBasePath");
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final String actionSetId = parser.get("actionSetId");
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final String workingPath = parser.get("workingPath");
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final int numPartitions = Optional
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.ofNullable(parser.get("numPartitions"))
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.map(Integer::valueOf)
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.orElse(NUM_PARTITIONS);
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log.info("numPartitions: '{}'", numPartitions);
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log.info("graphBasePath: '{}'", graphBasePath);
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log.info("actionSetId: '{}'", actionSetId);
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log.info("workingPath: '{}'", workingPath);
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log.info("Copying OpenOrgs Merge Rels");
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final String outputPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, "organization");
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removeOutputDir(spark, outputPath);
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final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation");
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DedupConfig dedupConf = getConfigurations(isLookUpService, actionSetId).get(0);
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JavaRDD<Relation> rawRels = spark
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.read()
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.textFile(relationPath)
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.map(patchRelFn(), Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(this::isOpenorgs) //takes only relations coming from openorgs
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.filter(this::filterOpenorgsRels) //takes only isSimilarTo relations between organizations from openorgs
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.filter(this::excludeOpenorgsMesh) //excludes relations between an organization and an openorgsmesh
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.filter(this::excludeNonOpenorgs); //excludes relations with no openorgs id involved
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//turn openorgs isSimilarTo relations into mergerels
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JavaRDD<Relation> mergeRels = rawRels.flatMap(rel -> {
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List<Relation> mergerels = new ArrayList<>();
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String openorgsId = rel.getSource().contains("openorgs____")? rel.getSource() : rel.getTarget();
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String mergedId = rel.getSource().contains("openorgs____")? rel.getTarget() : rel.getSource();
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mergerels.add(rel(openorgsId, mergedId, "merges", dedupConf));
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mergerels.add(rel(mergedId, openorgsId, "isMergedIn", dedupConf));
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return mergerels.iterator();
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});
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mergeRels.saveAsTextFile(outputPath);
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}
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private static MapFunction<String, Relation> patchRelFn() {
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return value -> {
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final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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return rel;
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};
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}
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private boolean filterOpenorgsRels(Relation rel) {
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if (rel.getRelClass().equals("isSimilarTo") && rel.getRelType().equals("organizationOrganization") && rel.getSubRelType().equals("dedup"))
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return true;
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return false;
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}
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private boolean isOpenorgs(Relation rel) {
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if (rel.getCollectedfrom() != null) {
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for (KeyValue k: rel.getCollectedfrom()) {
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if (k.getValue().equals("OpenOrgs Database")) {
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return true;
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}
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}
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}
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return false;
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}
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private boolean excludeOpenorgsMesh(Relation rel) {
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if (rel.getSource().equals("openorgsmesh") || rel.getTarget().equals("openorgsmesh")) {
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return false;
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}
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return true;
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}
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private boolean excludeNonOpenorgs(Relation rel) {
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if (rel.getSource().equals("openorgs____") || rel.getTarget().equals("openorgs____")) {
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return true;
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}
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return false;
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}
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private Relation rel(String source, String target, String relClass, DedupConfig dedupConf) {
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String entityType = dedupConf.getWf().getEntityType();
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Relation r = new Relation();
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r.setSource(source);
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r.setTarget(target);
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r.setRelClass(relClass);
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r.setRelType(entityType + entityType.substring(0, 1).toUpperCase() + entityType.substring(1));
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r.setSubRelType("dedup");
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DataInfo info = new DataInfo();
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info.setDeletedbyinference(false);
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info.setInferred(true);
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info.setInvisible(false);
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info.setInferenceprovenance(dedupConf.getWf().getConfigurationId());
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Qualifier provenanceAction = new Qualifier();
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provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
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provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
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provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
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provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
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info.setProvenanceaction(provenanceAction);
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// TODO calculate the trust value based on the similarity score of the elements in the CC
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// info.setTrust();
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r.setDataInfo(info);
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return r;
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}
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}
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@ -0,0 +1,110 @@
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package eu.dnetlib.dhp.oa.dedup;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.pace.util.MapDocumentUtil;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileStatus;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.io.compress.GzipCodec;
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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.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.PairFunction;
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import org.apache.spark.sql.Dataset;
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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 org.dom4j.DocumentException;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import scala.Tuple2;
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import java.io.IOException;
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import java.util.Optional;
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public class SparkCopyRelationsNoOpenorgs extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkUpdateEntity.class);
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private static final String IDJSONPATH = "$.id";
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public SparkCopyRelationsNoOpenorgs(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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}
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public static void main(String[] args) throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCopyRelationsNoOpenorgs.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(ModelSupport.getOafModelClasses());
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new SparkUpdateEntity(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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public void run(ISLookUpService isLookUpService) throws IOException {
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final String graphBasePath = parser.get("graphBasePath");
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final String workingPath = parser.get("workingPath");
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final String dedupGraphPath = parser.get("dedupGraphPath");
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log.info("graphBasePath: '{}'", graphBasePath);
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log.info("workingPath: '{}'", workingPath);
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log.info("dedupGraphPath: '{}'", dedupGraphPath);
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation");
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final String outputPath = DedupUtility.createEntityPath(dedupGraphPath, "relation");
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removeOutputDir(spark, outputPath);
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JavaRDD<Relation> simRels = spark
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.read()
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.textFile(relationPath)
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.map(patchRelFn(), Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(this::excludeOpenorgsRels);
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simRels.saveAsTextFile(outputPath);
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}
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private static MapFunction<String, Relation> patchRelFn() {
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return value -> {
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final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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return rel;
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};
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}
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private boolean excludeOpenorgsRels(Relation rel) {
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if (rel.getCollectedfrom() != null) {
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for (KeyValue k: rel.getCollectedfrom()) {
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if (k.getValue().equals("OpenOrgs Database")) {
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return false;
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}
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}
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}
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return true;
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}
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}
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@ -0,0 +1,9 @@
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package eu.dnetlib.dhp.oa.graph.raw.common;
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//enum to specify the different actions available for the MigrateDbEntitiesApplication job
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public enum MigrateAction {
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claims, // migrate claims to the raw graph
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openorgs, // migrate organizations from openorgs to the raw graph
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openaire // migrate openaire entities to the raw graph
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}
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@ -1,17 +1,47 @@
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SELECT local_id AS id1, oa_original_id AS id2 FROM openaire_simrels WHERE reltype = 'is_similar'
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-- relations approved by the user
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SELECT
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local_id AS id1,
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oa_original_id AS id2,
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'openaire____::openorgs' AS collectedfromid,
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'OpenOrgs Database' AS collectedfromname,
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false AS inferred,
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false AS deletedbyinference,
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0.99 AS trust,
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'' AS inferenceprovenance,
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'isSimilarTo' AS relclass
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FROM oa_duplicates WHERE reltype = 'is_similar'
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UNION ALL
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-- relations between openorgs and mesh (alternative names)
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SELECT
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o.id AS id1,
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'openorgsmesh'||substring(o.id, 13)||'-'||md5(a.acronym) AS id2
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FROM acronyms a
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LEFT OUTER JOIN organizations o ON (a.id = o.id)
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o.id AS id1,
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'openorgsmesh'||substring(o.id, 13)||'-'||md5(n.name) AS id2,
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'openaire____::openorgs' AS collectedfromid,
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'OpenOrgs Database' AS collectedfromname,
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false AS inferred,
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false AS deletedbyinference,
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0.99 AS trust,
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'' AS inferenceprovenance,
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'isSimilarTo' AS relclass
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FROM other_names n
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LEFT OUTER JOIN organizations o ON (n.id = o.id)
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UNION ALL
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-- diff relations approved by the user
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SELECT
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o.id AS id1,
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'openorgsmesh'||substring(o.id, 13)||'-'||md5(n.name) AS id2
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FROM other_names n
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LEFT OUTER JOIN organizations o ON (n.id = o.id)
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local_id AS id1,
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oa_original_id AS id2,
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'openaire____::openorgs' AS collectedfromid,
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'OpenOrgs Database' AS collectedfromname,
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false AS inferred,
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false AS deletedbyinference,
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0.99 AS trust,
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'' AS inferenceprovenance,
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'isDifferentFrom' AS relclass
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FROM oa_duplicates WHERE reltype = 'is_different'
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--TODO ???
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--Creare relazioni isDifferentFrom anche tra i suggerimenti: (A is_similar B) and (A is_different C) => (B is_different C)
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