forked from antonis.lempesis/dnet-hadoop
action migration workflow produces eu.dnetlib.dhp.schema.action.AtomicAction(s)
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@ -5,17 +5,14 @@ import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.common.base.Splitter;
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import com.google.common.collect.Lists;
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import com.google.protobuf.InvalidProtocolBufferException;
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import eu.dnetlib.actionmanager.actions.AtomicAction;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.data.proto.OafProtos;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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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 org.apache.commons.codec.binary.Base64;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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@ -84,59 +81,97 @@ public class TransformActions implements Serializable {
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log.info(String.format("transforming actions from '%s' to '%s'", sourcePath, targetDirectory));
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sc.sequenceFile(sourcePath, Text.class, Text.class)
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.mapToPair(a -> new Tuple2<>(a._1(), AtomicAction.fromJSON(a._2().toString())))
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.mapToPair(a -> new Tuple2<>(a._1(), eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON(a._2().toString())))
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.mapToPair(a -> new Tuple2<>(a._1(), transformAction(a._1().toString(), a._2())))
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.filter(t -> StringUtils.isNotBlank(t._2().toString()))
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.saveAsHadoopFile(targetDirectory.toString(), Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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}
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}
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}
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private Text transformAction(String atomicaActionId, AtomicAction aa) throws InvalidProtocolBufferException, JsonProcessingException {
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private Text transformAction(String atomicaActionId, eu.dnetlib.actionmanager.actions.AtomicAction aa) throws InvalidProtocolBufferException, JsonProcessingException {
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final Text out = new Text();
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final ObjectMapper mapper = new ObjectMapper();
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if (aa.getTargetValue() != null && aa.getTargetValue().length > 0) {
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Oaf oaf = ProtoConverter.convert(OafProtos.Oaf.parseFrom(aa.getTargetValue()));
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aa.setTargetValue(mapper.writeValueAsString(oaf).getBytes());
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out.set(mapper.writeValueAsString(doTransform(aa)));
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} else {
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if (atomicaActionId.contains("dedupSimilarity")) {
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final String[] splitId = atomicaActionId.split("@");
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String source = splitId[0];
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String target = splitId[2];
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String[] relSemantic = splitId[1].split("_");
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Relation rel = new Relation();
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rel.setSource(source);
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rel.setTarget(target);
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rel.setRelType(relSemantic[0]);
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rel.setSubRelType(relSemantic[1]);
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rel.setRelClass(relSemantic[2]);
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DataInfo d = new DataInfo();
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d.setDeletedbyinference(false);
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d.setInferenceprovenance("deduplication");
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d.setInferred(true);
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d.setInvisible(false);
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Qualifier provenanceaction = new Qualifier();
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provenanceaction.setClassid("deduplication");
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provenanceaction.setClassname("deduplication");
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provenanceaction.setSchemeid("dnet:provenanceActions");
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provenanceaction.setSchemename("dnet:provenanceActions");
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d.setProvenanceaction(provenanceaction);
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rel.setDataInfo(d);
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aa.setTargetValue(mapper.writeValueAsString(rel).getBytes());
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out.set(mapper.writeValueAsString(getRelationAtomicAction(atomicaActionId)));
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}
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}
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return new Text(mapper.writeValueAsString(aa));
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return out;
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}
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private AtomicAction<Relation> getRelationAtomicAction(String atomicaActionId) {
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final String[] splitId = atomicaActionId.split("@");
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String source = splitId[0];
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String target = splitId[2];
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String[] relSemantic = splitId[1].split("_");
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Relation rel = new Relation();
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rel.setSource(source);
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rel.setTarget(target);
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rel.setRelType(relSemantic[0]);
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rel.setSubRelType(relSemantic[1]);
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rel.setRelClass(relSemantic[2]);
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DataInfo d = new DataInfo();
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d.setDeletedbyinference(false);
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d.setInferenceprovenance("deduplication");
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d.setInferred(true);
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d.setInvisible(false);
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Qualifier provenanceaction = new Qualifier();
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provenanceaction.setClassid("deduplication");
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provenanceaction.setClassname("deduplication");
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provenanceaction.setSchemeid("dnet:provenanceActions");
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provenanceaction.setSchemename("dnet:provenanceActions");
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d.setProvenanceaction(provenanceaction);
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rel.setDataInfo(d);
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return new AtomicAction<>(Relation.class, rel);
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}
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private AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa) throws InvalidProtocolBufferException {
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final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue());
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final Oaf oaf = ProtoConverter.convert(proto_oaf);
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switch (proto_oaf.getKind()) {
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case entity:
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switch (proto_oaf.getEntity().getType()) {
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case datasource:
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return new AtomicAction<>(Datasource.class, (Datasource) oaf);
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case organization:
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return new AtomicAction<>(Organization.class, (Organization) oaf);
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case project:
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return new AtomicAction<>(Project.class, (Project) oaf);
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case result:
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final String resulttypeid = proto_oaf.getEntity().getResult().getMetadata().getResulttype().getClassid();
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switch (resulttypeid) {
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case "publication":
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return new AtomicAction<>(Publication.class, (Publication) oaf);
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case "software":
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return new AtomicAction<>(Software.class, (Software) oaf);
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case "other":
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return new AtomicAction<>(OtherResearchProduct.class, (OtherResearchProduct) oaf);
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case "dataset":
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return new AtomicAction<>(Dataset.class, (Dataset) oaf);
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default:
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// can be an update, where the resulttype is not specified
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return new AtomicAction<>(Result.class, (Result) oaf);
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}
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default:
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throw new IllegalArgumentException("invalid entity type: " + proto_oaf.getEntity().getType());
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}
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case relation:
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return new AtomicAction<>(Relation.class, (Relation) oaf);
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default:
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throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind());
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}
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}
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private String getTargetBaseDir(String isLookupUrl) throws ISLookUpException {
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@ -54,12 +54,25 @@
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</property>
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</parameters>
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</value>
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</property>
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</configuration>
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</global>
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<start to='migrate_actionsets' />
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<action name='migrate_actionsets'>
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.dhp.migration.actions.MigrateActionSet</main-class>
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<java-opt>-Dmapred.task.timeout=${distcp_task_timeout}</java-opt>
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<arg>-is</arg><arg>${isLookupUrl}</arg>
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@ -78,8 +91,6 @@
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<action name="transform_actions">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<master>yarn</master>
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<mode>cluster</mode>
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<name>transform_actions</name>
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