forked from D-Net/dnet-hadoop
reimplementation of the author merging in deduprecord creation. implementation of the test class. minor changes
This commit is contained in:
commit
8b35e0e7f0
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@ -79,8 +79,6 @@ public class SparkRemoveBlacklistedRelationJob {
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Dataset<Relation> inputRelation = readRelations(spark, inputPath);
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Dataset<Relation> inputRelation = readRelations(spark, inputPath);
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Dataset<Relation> mergesRelation = readRelations(spark, mergesPath);
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Dataset<Relation> mergesRelation = readRelations(spark, mergesPath);
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log.info("InputRelationCount: {}", inputRelation.count());
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Dataset<Relation> dedupSource = blackListed
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Dataset<Relation> dedupSource = blackListed
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.joinWith(
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.joinWith(
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mergesRelation, blackListed.col("source").equalTo(mergesRelation.col("target")),
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mergesRelation, blackListed.col("source").equalTo(mergesRelation.col("target")),
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@ -103,11 +101,6 @@ public class SparkRemoveBlacklistedRelationJob {
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return c._1();
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return c._1();
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}, Encoders.bean(Relation.class));
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}, Encoders.bean(Relation.class));
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dedupBL
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.write()
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.mode(SaveMode.Overwrite)
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.json(blacklistPath + "/deduped");
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inputRelation
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inputRelation
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.joinWith(
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.joinWith(
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dedupBL, (inputRelation
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dedupBL, (inputRelation
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@ -4,31 +4,48 @@ package eu.dnetlib.dhp.broker.model;
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public enum Topic {
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public enum Topic {
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// ENRICHMENT MISSING
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// ENRICHMENT MISSING
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ENRICH_MISSING_OA_VERSION("ENRICH/MISSING/OPENACCESS_VERSION"), ENRICH_MISSING_ABSTRACT(
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ENRICH_MISSING_OA_VERSION("ENRICH/MISSING/OPENACCESS_VERSION"),
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"ENRICH/MISSING/ABSTRACT"), ENRICH_MISSING_PUBLICATION_DATE(
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ENRICH_MISSING_ABSTRACT("ENRICH/MISSING/ABSTRACT"),
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"ENRICH/MISSING/PUBLICATION_DATE"), ENRICH_MISSING_PID(
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ENRICH_MISSING_PUBLICATION_DATE("ENRICH/MISSING/PUBLICATION_DATE"),
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"ENRICH/MISSING/PID"), ENRICH_MISSING_PROJECT("ENRICH/MISSING/PROJECT"), ENRICH_MISSING_SOFTWARE(
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ENRICH_MISSING_PID("ENRICH/MISSING/PID"),
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"ENRICH/MISSING/SOFTWARE"), ENRICH_MISSING_SUBJECT_MESHEUROPMC(
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ENRICH_MISSING_PROJECT("ENRICH/MISSING/PROJECT"),
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"ENRICH/MISSING/SUBJECT/MESHEUROPMC"), ENRICH_MISSING_SUBJECT_ARXIV(
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ENRICH_MISSING_SOFTWARE("ENRICH/MISSING/SOFTWARE"),
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"ENRICH/MISSING/SUBJECT/ARXIV"), ENRICH_MISSING_SUBJECT_JEL(
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ENRICH_MISSING_SUBJECT_MESHEUROPMC("ENRICH/MISSING/SUBJECT/MESHEUROPMC"),
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"ENRICH/MISSING/SUBJECT/JEL"), ENRICH_MISSING_SUBJECT_DDC(
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ENRICH_MISSING_SUBJECT_ARXIV("ENRICH/MISSING/SUBJECT/ARXIV"),
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"ENRICH/MISSING/SUBJECT/DDC"), ENRICH_MISSING_SUBJECT_ACM(
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ENRICH_MISSING_SUBJECT_JEL("ENRICH/MISSING/SUBJECT/JEL"),
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"ENRICH/MISSING/SUBJECT/ACM"), ENRICH_MISSING_SUBJECT_RVK(
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ENRICH_MISSING_SUBJECT_DDC("ENRICH/MISSING/SUBJECT/DDC"),
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"ENRICH/MISSING/SUBJECT/RVK"), ENRICH_MISSING_AUTHOR_ORCID(
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ENRICH_MISSING_SUBJECT_ACM("ENRICH/MISSING/SUBJECT/ACM"),
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"ENRICH/MISSING/AUTHOR/ORCID"),
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ENRICH_MISSING_SUBJECT_RVK("ENRICH/MISSING/SUBJECT/RVK"),
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ENRICH_MISSING_AUTHOR_ORCID("ENRICH/MISSING/AUTHOR/ORCID"),
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// ENRICHMENT MORE
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// ENRICHMENT MORE
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ENRICH_MORE_PID("ENRICH/MORE/PID"), ENRICH_MORE_OA_VERSION("ENRICH/MORE/OPENACCESS_VERSION"), ENRICH_MORE_ABSTRACT(
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ENRICH_MORE_PID("ENRICH/MORE/PID"),
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"ENRICH/MORE/ABSTRACT"), ENRICH_MORE_PUBLICATION_DATE("ENRICH/MORE/PUBLICATION_DATE"), ENRICH_MORE_PROJECT(
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ENRICH_MORE_OA_VERSION("ENRICH/MORE/OPENACCESS_VERSION"),
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"ENRICH/MORE/PROJECT"), ENRICH_MORE_SUBJECT_MESHEUROPMC(
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ENRICH_MORE_ABSTRACT("ENRICH/MORE/ABSTRACT"),
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"ENRICH/MORE/SUBJECT/MESHEUROPMC"), ENRICH_MORE_SUBJECT_ARXIV(
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ENRICH_MORE_PUBLICATION_DATE("ENRICH/MORE/PUBLICATION_DATE"),
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"ENRICH/MORE/SUBJECT/ARXIV"), ENRICH_MORE_SUBJECT_JEL(
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ENRICH_MORE_PROJECT("ENRICH/MORE/PROJECT"),
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"ENRICH/MORE/SUBJECT/JEL"), ENRICH_MORE_SUBJECT_DDC(
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ENRICH_MORE_SUBJECT_MESHEUROPMC("ENRICH/MORE/SUBJECT/MESHEUROPMC"),
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"ENRICH/MORE/SUBJECT/DDC"), ENRICH_MORE_SUBJECT_ACM(
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ENRICH_MORE_SUBJECT_ARXIV("ENRICH/MORE/SUBJECT/ARXIV"),
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"ENRICH/MORE/SUBJECT/ACM"), ENRICH_MORE_SUBJECT_RVK("ENRICH/MORE/SUBJECT/RVK"),
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ENRICH_MORE_SUBJECT_JEL("ENRICH/MORE/SUBJECT/JEL"),
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ENRICH_MORE_SUBJECT_DDC("ENRICH/MORE/SUBJECT/DDC"),
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ENRICH_MORE_SUBJECT_ACM("ENRICH/MORE/SUBJECT/ACM"),
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ENRICH_MORE_SUBJECT_RVK("ENRICH/MORE/SUBJECT/RVK"),
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// ADDITION
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// ADDITION
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ADD_BY_PROJECT("ADD/BY_PROJECT");
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ADD_BY_PROJECT("ADD/BY_PROJECT"),
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// OTHER RELS
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ENRICH_MISSING_PUBLICATION_IS_RELATED_TO("ENRICH/MISSING/PUBLICATION/IS_RELATED_TO"),
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ENRICH_MISSING_PUBLICATION_REFERENCES("ENRICH/MISSING/PUBLICATION/REFERENCES"),
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ENRICH_MISSING_PUBLICATION_IS_REFERENCED_BY("ENRICH/MISSING/PUBLICATION/IS_REFERENCED_BY"),
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ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_TO("ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_TO"),
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ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_BY("ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_BY"),
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ENRICH_MISSING_DATASET_IS_RELATED_TO("ENRICH/MISSING/DATASET/IS_RELATED_TO"),
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ENRICH_MISSING_DATASET_REFERENCES("ENRICH/MISSING/DATASET/REFERENCES"),
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ENRICH_MISSING_DATASET_IS_REFERENCED_BY("ENRICH/MISSING/DATASET/IS_REFERENCED_BY"),
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ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_TO("ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_TO"),
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ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_BY("ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_BY");
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Topic(final String path) {
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Topic(final String path) {
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this.path = path;
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this.path = path;
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@ -42,9 +59,7 @@ public enum Topic {
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public static Topic fromPath(final String path) {
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public static Topic fromPath(final String path) {
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for (final Topic t : Topic.values()) {
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for (final Topic t : Topic.values()) {
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if (t.getPath().equals(path)) {
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if (t.getPath().equals(path)) { return t; }
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return t;
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}
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}
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}
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return null;
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return null;
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}
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}
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@ -9,28 +9,42 @@ import java.util.Optional;
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import java.util.stream.Collectors;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.io.IOUtils;
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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.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Column;
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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.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.broker.model.Event;
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import eu.dnetlib.dhp.broker.model.Event;
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import eu.dnetlib.dhp.broker.model.EventFactory;
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import eu.dnetlib.dhp.broker.model.EventFactory;
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import eu.dnetlib.dhp.broker.oa.util.EnrichMissingAbstract;
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import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingAbstract;
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import eu.dnetlib.dhp.broker.oa.util.EnrichMissingAuthorOrcid;
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import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingAuthorOrcid;
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import eu.dnetlib.dhp.broker.oa.util.EnrichMissingOpenAccess;
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import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingOpenAccess;
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import eu.dnetlib.dhp.broker.oa.util.EnrichMissingPid;
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import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPid;
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import eu.dnetlib.dhp.broker.oa.util.EnrichMissingProject;
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import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingProject;
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import eu.dnetlib.dhp.broker.oa.util.EnrichMissingPublicationDate;
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import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationDate;
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import eu.dnetlib.dhp.broker.oa.util.EnrichMissingSubject;
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import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingSubject;
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import eu.dnetlib.dhp.broker.oa.util.EnrichMoreOpenAccess;
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import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreOpenAccess;
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import eu.dnetlib.dhp.broker.oa.util.EnrichMorePid;
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import eu.dnetlib.dhp.broker.oa.matchers.EnrichMorePid;
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import eu.dnetlib.dhp.broker.oa.util.EnrichMoreSubject;
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import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreSubject;
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import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher;
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import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
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import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
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import eu.dnetlib.dhp.broker.oa.util.UpdateMatcher;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.Software;
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public class GenerateEventsApplication {
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public class GenerateEventsApplication {
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@ -47,12 +61,13 @@ public class GenerateEventsApplication {
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private static final UpdateMatcher<?> enrichMorePid = new EnrichMorePid();
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private static final UpdateMatcher<?> enrichMorePid = new EnrichMorePid();
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private static final UpdateMatcher<?> enrichMoreSubject = new EnrichMoreSubject();
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private static final UpdateMatcher<?> enrichMoreSubject = new EnrichMoreSubject();
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public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(final String[] args) throws Exception {
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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IOUtils
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.toString(
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.toString(GenerateEventsApplication.class
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GenerateEventsApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json")));
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json")));
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parser.parseArgument(args);
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parser.parseArgument(args);
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final Boolean isSparkSessionManaged = Optional
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final Boolean isSparkSessionManaged = Optional
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@ -67,10 +82,23 @@ public class GenerateEventsApplication {
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final String eventsPath = parser.get("eventsPath");
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final String eventsPath = parser.get("eventsPath");
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log.info("eventsPath: {}", eventsPath);
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log.info("eventsPath: {}", eventsPath);
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final SparkConf conf = new SparkConf();
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final SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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removeOutputDir(spark, eventsPath);
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removeOutputDir(spark, eventsPath);
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generateEvents(spark, graphPath, eventsPath);
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final JavaRDD<Event> eventsRdd = sc.emptyRDD();
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|
|
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eventsRdd.union(generateSimpleEvents(spark, graphPath, Publication.class));
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eventsRdd.union(generateSimpleEvents(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class));
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eventsRdd.union(generateSimpleEvents(spark, graphPath, Software.class));
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eventsRdd.union(generateSimpleEvents(spark, graphPath, OtherResearchProduct.class));
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|
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eventsRdd.saveAsTextFile(eventsPath, GzipCodec.class);
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});
|
});
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|
|
||||||
}
|
}
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@ -79,11 +107,34 @@ public class GenerateEventsApplication {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
|
}
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|
|
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private static void generateEvents(final SparkSession spark, final String graphPath, final String eventsPath) {
|
private static <R extends Result> JavaRDD<Event> generateSimpleEvents(final SparkSession spark,
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// TODO
|
final String graphPath,
|
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|
final Class<R> resultClazz) {
|
||||||
|
|
||||||
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final Dataset<R> results =
|
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readPath(spark, graphPath + "/" + resultClazz.getSimpleName().toLowerCase(), resultClazz)
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|
.filter(r -> r.getDataInfo().getDeletedbyinference());
|
||||||
|
|
||||||
|
final Dataset<Relation> rels =
|
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|
readPath(spark, graphPath + "/relation", Relation.class)
|
||||||
|
.filter(r -> r.getRelClass().equals("TODO")); // TODO mergedIN
|
||||||
|
|
||||||
|
final Column c = null; // TODO
|
||||||
|
|
||||||
|
final Dataset<Row> aa = results.joinWith(rels, results.col("id").equalTo(rels.col("source")), "inner")
|
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|
.groupBy(rels.col("target"))
|
||||||
|
.agg(c)
|
||||||
|
.filter(x -> x.size() > 1)
|
||||||
|
// generateSimpleEvents(...)
|
||||||
|
// flatMap()
|
||||||
|
// toRdd()
|
||||||
|
;
|
||||||
|
|
||||||
|
return null;
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
private List<Event> generateEvents(final Result... children) {
|
private List<Event> generateSimpleEvents(final Result... children) {
|
||||||
final List<UpdateInfo<?>> list = new ArrayList<>();
|
final List<UpdateInfo<?>> list = new ArrayList<>();
|
||||||
|
|
||||||
for (final Result target : children) {
|
for (final Result target : children) {
|
||||||
|
@ -102,4 +153,13 @@ public class GenerateEventsApplication {
|
||||||
return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
|
return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public static <R> Dataset<R> readPath(
|
||||||
|
final SparkSession spark,
|
||||||
|
final String inputPath,
|
||||||
|
final Class<R> clazz) {
|
||||||
|
return spark
|
||||||
|
.read()
|
||||||
|
.textFile(inputPath)
|
||||||
|
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
|
@ -1,11 +1,12 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.broker.oa.util;
|
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||||
|
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.broker.model.Topic;
|
import eu.dnetlib.dhp.broker.model.Topic;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
public class EnrichMissingAbstract extends UpdateMatcher<String> {
|
public class EnrichMissingAbstract extends UpdateMatcher<String> {
|
|
@ -1,5 +1,5 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.broker.oa.util;
|
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||||
|
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
@ -7,6 +7,7 @@ import java.util.List;
|
||||||
import org.apache.commons.lang3.tuple.Pair;
|
import org.apache.commons.lang3.tuple.Pair;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.broker.model.Topic;
|
import eu.dnetlib.dhp.broker.model.Topic;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
public class EnrichMissingAuthorOrcid extends UpdateMatcher<Pair<String, String>> {
|
public class EnrichMissingAuthorOrcid extends UpdateMatcher<Pair<String, String>> {
|
|
@ -0,0 +1,55 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||||
|
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
|
import eu.dnetlib.broker.objects.Instance;
|
||||||
|
import eu.dnetlib.dhp.broker.model.Topic;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.BrokerConstants;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
|
public class EnrichMissingOpenAccess extends UpdateMatcher<Instance> {
|
||||||
|
|
||||||
|
public EnrichMissingOpenAccess() {
|
||||||
|
super(true);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<UpdateInfo<Instance>> findUpdates(final Result source, final Result target) {
|
||||||
|
final long count = target
|
||||||
|
.getInstance()
|
||||||
|
.stream()
|
||||||
|
.map(i -> i.getAccessright().getClassid())
|
||||||
|
.filter(right -> right.equals(BrokerConstants.OPEN_ACCESS))
|
||||||
|
.count();
|
||||||
|
|
||||||
|
if (count > 0) {
|
||||||
|
return Arrays.asList();
|
||||||
|
}
|
||||||
|
|
||||||
|
return source
|
||||||
|
.getInstance()
|
||||||
|
.stream()
|
||||||
|
.filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS))
|
||||||
|
.map(ConversionUtils::oafInstanceToBrokerInstances)
|
||||||
|
.flatMap(s -> s)
|
||||||
|
.map(i -> generateUpdateInfo(i, source, target))
|
||||||
|
.collect(Collectors.toList());
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public UpdateInfo<Instance> generateUpdateInfo(final Instance highlightValue,
|
||||||
|
final Result source,
|
||||||
|
final Result target) {
|
||||||
|
return new UpdateInfo<>(
|
||||||
|
Topic.ENRICH_MISSING_OA_VERSION,
|
||||||
|
highlightValue, source, target,
|
||||||
|
(p, i) -> p.getInstances().add(i),
|
||||||
|
Instance::getUrl);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
|
@ -1,11 +1,14 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.broker.oa.util;
|
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||||
|
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import eu.dnetlib.broker.objects.Pid;
|
import eu.dnetlib.broker.objects.Pid;
|
||||||
import eu.dnetlib.dhp.broker.model.Topic;
|
import eu.dnetlib.dhp.broker.model.Topic;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
public class EnrichMissingPid extends UpdateMatcher<Pid> {
|
public class EnrichMissingPid extends UpdateMatcher<Pid> {
|
||||||
|
@ -16,8 +19,18 @@ public class EnrichMissingPid extends UpdateMatcher<Pid> {
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
protected List<UpdateInfo<Pid>> findUpdates(final Result source, final Result target) {
|
protected List<UpdateInfo<Pid>> findUpdates(final Result source, final Result target) {
|
||||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
final long count = target.getPid().size();
|
||||||
return Arrays.asList();
|
|
||||||
|
if (count > 0) {
|
||||||
|
return Arrays.asList();
|
||||||
|
}
|
||||||
|
|
||||||
|
return source
|
||||||
|
.getPid()
|
||||||
|
.stream()
|
||||||
|
.map(ConversionUtils::oafPidToBrokerPid)
|
||||||
|
.map(i -> generateUpdateInfo(i, source, target))
|
||||||
|
.collect(Collectors.toList());
|
||||||
}
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
|
@ -1,11 +1,12 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.broker.oa.util;
|
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||||
|
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import eu.dnetlib.broker.objects.Project;
|
import eu.dnetlib.broker.objects.Project;
|
||||||
import eu.dnetlib.dhp.broker.model.Topic;
|
import eu.dnetlib.dhp.broker.model.Topic;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
public class EnrichMissingProject extends UpdateMatcher<Project> {
|
public class EnrichMissingProject extends UpdateMatcher<Project> {
|
||||||
|
@ -21,7 +22,8 @@ public class EnrichMissingProject extends UpdateMatcher<Project> {
|
||||||
}
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public UpdateInfo<Project> generateUpdateInfo(final Project highlightValue, final Result source,
|
public UpdateInfo<Project> generateUpdateInfo(final Project highlightValue,
|
||||||
|
final Result source,
|
||||||
final Result target) {
|
final Result target) {
|
||||||
return new UpdateInfo<>(
|
return new UpdateInfo<>(
|
||||||
Topic.ENRICH_MISSING_PROJECT,
|
Topic.ENRICH_MISSING_PROJECT,
|
|
@ -1,10 +1,12 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.broker.oa.util;
|
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||||
|
|
||||||
|
import java.util.ArrayList;
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.broker.model.Topic;
|
import eu.dnetlib.dhp.broker.model.Topic;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
public class EnrichMissingPublicationDate extends UpdateMatcher<String> {
|
public class EnrichMissingPublicationDate extends UpdateMatcher<String> {
|
||||||
|
@ -15,12 +17,15 @@ public class EnrichMissingPublicationDate extends UpdateMatcher<String> {
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
protected List<UpdateInfo<String>> findUpdates(final Result source, final Result target) {
|
protected List<UpdateInfo<String>> findUpdates(final Result source, final Result target) {
|
||||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
if (isMissing(target.getDateofacceptance()) && !isMissing(source.getDateofacceptance())) {
|
||||||
return Arrays.asList();
|
return Arrays.asList(generateUpdateInfo(source.getDateofacceptance().getValue(), source, target));
|
||||||
|
}
|
||||||
|
return new ArrayList<>();
|
||||||
}
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public UpdateInfo<String> generateUpdateInfo(final String highlightValue, final Result source,
|
public UpdateInfo<String> generateUpdateInfo(final String highlightValue,
|
||||||
|
final Result source,
|
||||||
final Result target) {
|
final Result target) {
|
||||||
return new UpdateInfo<>(
|
return new UpdateInfo<>(
|
||||||
Topic.ENRICH_MISSING_PUBLICATION_DATE,
|
Topic.ENRICH_MISSING_PUBLICATION_DATE,
|
|
@ -0,0 +1,53 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||||
|
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Set;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
|
import org.apache.commons.lang3.tuple.Pair;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.broker.model.Topic;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
|
||||||
|
public class EnrichMissingSubject extends UpdateMatcher<Pair<String, String>> {
|
||||||
|
|
||||||
|
public EnrichMissingSubject() {
|
||||||
|
super(true);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<UpdateInfo<Pair<String, String>>> findUpdates(final Result source, final Result target) {
|
||||||
|
final Set<String> existingTypes = target
|
||||||
|
.getSubject()
|
||||||
|
.stream()
|
||||||
|
.map(StructuredProperty::getQualifier)
|
||||||
|
.map(Qualifier::getClassid)
|
||||||
|
.collect(Collectors.toSet());
|
||||||
|
|
||||||
|
return source
|
||||||
|
.getPid()
|
||||||
|
.stream()
|
||||||
|
.filter(pid -> !existingTypes.contains(pid.getQualifier().getClassid()))
|
||||||
|
.map(ConversionUtils::oafSubjectToPair)
|
||||||
|
.map(i -> generateUpdateInfo(i, source, target))
|
||||||
|
.collect(Collectors.toList());
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public UpdateInfo<Pair<String, String>> generateUpdateInfo(final Pair<String, String> highlightValue,
|
||||||
|
final Result source,
|
||||||
|
final Result target) {
|
||||||
|
|
||||||
|
return new UpdateInfo<>(
|
||||||
|
Topic.fromPath("ENRICH/MISSING/SUBJECT/" + highlightValue.getLeft()),
|
||||||
|
highlightValue, source, target,
|
||||||
|
(p, pair) -> p.getSubjects().add(pair.getRight()),
|
||||||
|
pair -> pair.getLeft() + "::" + pair.getRight());
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
|
@ -0,0 +1,53 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||||
|
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Set;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
|
import eu.dnetlib.broker.objects.Instance;
|
||||||
|
import eu.dnetlib.dhp.broker.model.Topic;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.BrokerConstants;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
|
public class EnrichMoreOpenAccess extends UpdateMatcher<Instance> {
|
||||||
|
|
||||||
|
public EnrichMoreOpenAccess() {
|
||||||
|
super(true);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<UpdateInfo<Instance>> findUpdates(final Result source, final Result target) {
|
||||||
|
final Set<String> urls = target
|
||||||
|
.getInstance()
|
||||||
|
.stream()
|
||||||
|
.filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS))
|
||||||
|
.map(i -> i.getUrl())
|
||||||
|
.flatMap(List::stream)
|
||||||
|
.collect(Collectors.toSet());
|
||||||
|
|
||||||
|
return source
|
||||||
|
.getInstance()
|
||||||
|
.stream()
|
||||||
|
.filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS))
|
||||||
|
.map(ConversionUtils::oafInstanceToBrokerInstances)
|
||||||
|
.flatMap(s -> s)
|
||||||
|
.filter(i -> !urls.contains(i.getUrl()))
|
||||||
|
.map(i -> generateUpdateInfo(i, source, target))
|
||||||
|
.collect(Collectors.toList());
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public UpdateInfo<Instance> generateUpdateInfo(final Instance highlightValue,
|
||||||
|
final Result source,
|
||||||
|
final Result target) {
|
||||||
|
return new UpdateInfo<>(
|
||||||
|
Topic.ENRICH_MORE_OA_VERSION,
|
||||||
|
highlightValue, source, target,
|
||||||
|
(p, i) -> p.getInstances().add(i),
|
||||||
|
Instance::getUrl);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
|
@ -1,11 +1,14 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.broker.oa.util;
|
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||||
|
|
||||||
import java.util.Arrays;
|
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
import java.util.Set;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import eu.dnetlib.broker.objects.Pid;
|
import eu.dnetlib.broker.objects.Pid;
|
||||||
import eu.dnetlib.dhp.broker.model.Topic;
|
import eu.dnetlib.dhp.broker.model.Topic;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
public class EnrichMorePid extends UpdateMatcher<Pid> {
|
public class EnrichMorePid extends UpdateMatcher<Pid> {
|
||||||
|
@ -16,8 +19,19 @@ public class EnrichMorePid extends UpdateMatcher<Pid> {
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
protected List<UpdateInfo<Pid>> findUpdates(final Result source, final Result target) {
|
protected List<UpdateInfo<Pid>> findUpdates(final Result source, final Result target) {
|
||||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
final Set<String> existingPids = target
|
||||||
return Arrays.asList();
|
.getPid()
|
||||||
|
.stream()
|
||||||
|
.map(pid -> pid.getQualifier().getClassid() + "::" + pid.getValue())
|
||||||
|
.collect(Collectors.toSet());
|
||||||
|
|
||||||
|
return source
|
||||||
|
.getPid()
|
||||||
|
.stream()
|
||||||
|
.filter(pid -> !existingPids.contains(pid.getQualifier().getClassid() + "::" + pid.getValue()))
|
||||||
|
.map(ConversionUtils::oafPidToBrokerPid)
|
||||||
|
.map(i -> generateUpdateInfo(i, source, target))
|
||||||
|
.collect(Collectors.toList());
|
||||||
}
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
|
@ -1,12 +1,15 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.broker.oa.util;
|
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||||
|
|
||||||
import java.util.Arrays;
|
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
import java.util.Set;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import org.apache.commons.lang3.tuple.Pair;
|
import org.apache.commons.lang3.tuple.Pair;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.broker.model.Topic;
|
import eu.dnetlib.dhp.broker.model.Topic;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
public class EnrichMoreSubject extends UpdateMatcher<Pair<String, String>> {
|
public class EnrichMoreSubject extends UpdateMatcher<Pair<String, String>> {
|
||||||
|
@ -17,18 +20,25 @@ public class EnrichMoreSubject extends UpdateMatcher<Pair<String, String>> {
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
protected List<UpdateInfo<Pair<String, String>>> findUpdates(final Result source, final Result target) {
|
protected List<UpdateInfo<Pair<String, String>>> findUpdates(final Result source, final Result target) {
|
||||||
// MESHEUROPMC
|
final Set<String> existingSubjects = target
|
||||||
// ARXIV
|
.getSubject()
|
||||||
// JEL
|
.stream()
|
||||||
// DDC
|
.map(pid -> pid.getQualifier().getClassid() + "::" + pid.getValue())
|
||||||
// ACM
|
.collect(Collectors.toSet());
|
||||||
|
|
||||||
return Arrays.asList();
|
return source
|
||||||
|
.getPid()
|
||||||
|
.stream()
|
||||||
|
.filter(pid -> !existingSubjects.contains(pid.getQualifier().getClassid() + "::" + pid.getValue()))
|
||||||
|
.map(ConversionUtils::oafSubjectToPair)
|
||||||
|
.map(i -> generateUpdateInfo(i, source, target))
|
||||||
|
.collect(Collectors.toList());
|
||||||
}
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public UpdateInfo<Pair<String, String>> generateUpdateInfo(final Pair<String, String> highlightValue,
|
public UpdateInfo<Pair<String, String>> generateUpdateInfo(final Pair<String, String> highlightValue,
|
||||||
final Result source, final Result target) {
|
final Result source,
|
||||||
|
final Result target) {
|
||||||
|
|
||||||
return new UpdateInfo<>(
|
return new UpdateInfo<>(
|
||||||
Topic.fromPath("ENRICH/MORE/SUBJECT/" + highlightValue.getLeft()),
|
Topic.fromPath("ENRICH/MORE/SUBJECT/" + highlightValue.getLeft()),
|
|
@ -1,5 +1,5 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.broker.oa.util;
|
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||||
|
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.Collection;
|
import java.util.Collection;
|
||||||
|
@ -10,6 +10,7 @@ import java.util.Map;
|
||||||
import org.apache.commons.codec.digest.DigestUtils;
|
import org.apache.commons.codec.digest.DigestUtils;
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Field;
|
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
|
@ -29,8 +30,7 @@ public abstract class UpdateMatcher<T> {
|
||||||
if (source != res) {
|
if (source != res) {
|
||||||
for (final UpdateInfo<T> info : findUpdates(source, res)) {
|
for (final UpdateInfo<T> info : findUpdates(source, res)) {
|
||||||
final String s = DigestUtils.md5Hex(info.getHighlightValueAsString());
|
final String s = DigestUtils.md5Hex(info.getHighlightValueAsString());
|
||||||
if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) {
|
if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) {} else {
|
||||||
} else {
|
|
||||||
infoMap.put(s, info);
|
infoMap.put(s, info);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
@ -53,11 +53,16 @@ public abstract class UpdateMatcher<T> {
|
||||||
|
|
||||||
protected abstract List<UpdateInfo<T>> findUpdates(Result source, Result target);
|
protected abstract List<UpdateInfo<T>> findUpdates(Result source, Result target);
|
||||||
|
|
||||||
protected abstract UpdateInfo<T> generateUpdateInfo(final T highlightValue, final Result source,
|
protected abstract UpdateInfo<T> generateUpdateInfo(final T highlightValue,
|
||||||
|
final Result source,
|
||||||
final Result target);
|
final Result target);
|
||||||
|
|
||||||
protected static boolean isMissing(final List<Field<String>> list) {
|
protected static boolean isMissing(final List<Field<String>> list) {
|
||||||
return list == null || list.isEmpty() || StringUtils.isBlank(list.get(0).getValue());
|
return list == null || list.isEmpty() || StringUtils.isBlank(list.get(0).getValue());
|
||||||
}
|
}
|
||||||
|
|
||||||
|
protected boolean isMissing(final Field<String> field) {
|
||||||
|
return field == null || StringUtils.isBlank(field.getValue());
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
|
@ -0,0 +1,7 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.broker.oa.util;
|
||||||
|
|
||||||
|
public class BrokerConstants {
|
||||||
|
|
||||||
|
public final static String OPEN_ACCESS = "OPEN";
|
||||||
|
}
|
|
@ -0,0 +1,36 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.broker.oa.util;
|
||||||
|
|
||||||
|
import java.util.stream.Stream;
|
||||||
|
|
||||||
|
import org.apache.commons.lang3.tuple.Pair;
|
||||||
|
|
||||||
|
import eu.dnetlib.broker.objects.Instance;
|
||||||
|
import eu.dnetlib.broker.objects.Pid;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
|
||||||
|
public class ConversionUtils {
|
||||||
|
|
||||||
|
public static Stream<Instance> oafInstanceToBrokerInstances(final eu.dnetlib.dhp.schema.oaf.Instance i) {
|
||||||
|
return i.getUrl().stream().map(url -> {
|
||||||
|
final Instance r = new Instance();
|
||||||
|
r.setUrl(url);
|
||||||
|
r.setInstancetype(i.getInstancetype().getClassid());
|
||||||
|
r.setLicense(BrokerConstants.OPEN_ACCESS);
|
||||||
|
r.setHostedby(i.getHostedby().getValue());
|
||||||
|
return r;
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Pid oafPidToBrokerPid(final StructuredProperty sp) {
|
||||||
|
final Pid pid = new Pid();
|
||||||
|
pid.setValue(sp.getValue());
|
||||||
|
pid.setType(sp.getQualifier().getClassid());
|
||||||
|
return pid;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static final Pair<String, String> oafSubjectToPair(final StructuredProperty sp) {
|
||||||
|
return Pair.of(sp.getQualifier().getClassid(), sp.getValue());
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
|
@ -1,33 +0,0 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.broker.oa.util;
|
|
||||||
|
|
||||||
import java.util.Arrays;
|
|
||||||
import java.util.List;
|
|
||||||
|
|
||||||
import eu.dnetlib.broker.objects.Instance;
|
|
||||||
import eu.dnetlib.dhp.broker.model.Topic;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
|
||||||
|
|
||||||
public class EnrichMissingOpenAccess extends UpdateMatcher<Instance> {
|
|
||||||
|
|
||||||
public EnrichMissingOpenAccess() {
|
|
||||||
super(true);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
protected List<UpdateInfo<Instance>> findUpdates(final Result source, final Result target) {
|
|
||||||
|
|
||||||
return Arrays.asList();
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public UpdateInfo<Instance> generateUpdateInfo(final Instance highlightValue, final Result source,
|
|
||||||
final Result target) {
|
|
||||||
return new UpdateInfo<>(
|
|
||||||
Topic.ENRICH_MISSING_OA_VERSION,
|
|
||||||
highlightValue, source, target,
|
|
||||||
(p, i) -> p.getInstances().add(i),
|
|
||||||
Instance::getUrl);
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
|
@ -1,40 +0,0 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.broker.oa.util;
|
|
||||||
|
|
||||||
import java.util.Arrays;
|
|
||||||
import java.util.List;
|
|
||||||
|
|
||||||
import org.apache.commons.lang3.tuple.Pair;
|
|
||||||
|
|
||||||
import eu.dnetlib.dhp.broker.model.Topic;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
|
||||||
|
|
||||||
public class EnrichMissingSubject extends UpdateMatcher<Pair<String, String>> {
|
|
||||||
|
|
||||||
public EnrichMissingSubject() {
|
|
||||||
super(true);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
protected List<UpdateInfo<Pair<String, String>>> findUpdates(final Result source, final Result target) {
|
|
||||||
// MESHEUROPMC
|
|
||||||
// ARXIV
|
|
||||||
// JEL
|
|
||||||
// DDC
|
|
||||||
// ACM
|
|
||||||
|
|
||||||
return Arrays.asList();
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public UpdateInfo<Pair<String, String>> generateUpdateInfo(final Pair<String, String> highlightValue,
|
|
||||||
final Result source, final Result target) {
|
|
||||||
|
|
||||||
return new UpdateInfo<>(
|
|
||||||
Topic.fromPath("ENRICH/MISSING/SUBJECT/" + highlightValue.getLeft()),
|
|
||||||
highlightValue, source, target,
|
|
||||||
(p, pair) -> p.getSubjects().add(pair.getRight()),
|
|
||||||
pair -> pair.getLeft() + "::" + pair.getRight());
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
|
@ -1,33 +0,0 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.broker.oa.util;
|
|
||||||
|
|
||||||
import java.util.Arrays;
|
|
||||||
import java.util.List;
|
|
||||||
|
|
||||||
import eu.dnetlib.broker.objects.Instance;
|
|
||||||
import eu.dnetlib.dhp.broker.model.Topic;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
|
||||||
|
|
||||||
public class EnrichMoreOpenAccess extends UpdateMatcher<Instance> {
|
|
||||||
|
|
||||||
public EnrichMoreOpenAccess() {
|
|
||||||
super(true);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
protected List<UpdateInfo<Instance>> findUpdates(final Result source, final Result target) {
|
|
||||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
|
||||||
return Arrays.asList();
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public UpdateInfo<Instance> generateUpdateInfo(final Instance highlightValue, final Result source,
|
|
||||||
final Result target) {
|
|
||||||
return new UpdateInfo<>(
|
|
||||||
Topic.ENRICH_MORE_OA_VERSION,
|
|
||||||
highlightValue, source, target,
|
|
||||||
(p, i) -> p.getInstances().add(i),
|
|
||||||
Instance::getUrl);
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
|
@ -25,7 +25,7 @@ public final class UpdateInfo<T> {
|
||||||
|
|
||||||
private final float trust;
|
private final float trust;
|
||||||
|
|
||||||
protected UpdateInfo(final Topic topic, final T highlightValue, final Result source, final Result target,
|
public UpdateInfo(final Topic topic, final T highlightValue, final Result source, final Result target,
|
||||||
final BiConsumer<Publication, T> compileHighlight,
|
final BiConsumer<Publication, T> compileHighlight,
|
||||||
final Function<T, String> highlightToString) {
|
final Function<T, String> highlightToString) {
|
||||||
this.topic = topic;
|
this.topic = topic;
|
||||||
|
|
|
@ -53,9 +53,7 @@ public class PrepareResultCommunitySetStep2 {
|
||||||
conf,
|
conf,
|
||||||
isSparkSessionManaged,
|
isSparkSessionManaged,
|
||||||
spark -> {
|
spark -> {
|
||||||
if (isTest(parser)) {
|
removeOutputDir(spark, outputPath);
|
||||||
removeOutputDir(spark, outputPath);
|
|
||||||
}
|
|
||||||
mergeInfo(spark, inputPath, outputPath);
|
mergeInfo(spark, inputPath, outputPath);
|
||||||
});
|
});
|
||||||
}
|
}
|
||||||
|
|
|
@ -84,7 +84,7 @@ public class SparkResultToOrganizationFromIstRepoJob {
|
||||||
conf,
|
conf,
|
||||||
isSparkSessionManaged,
|
isSparkSessionManaged,
|
||||||
spark -> {
|
spark -> {
|
||||||
removeOutputDir(spark, outputPath);
|
// removeOutputDir(spark, outputPath);
|
||||||
if (saveGraph) {
|
if (saveGraph) {
|
||||||
execPropagation(
|
execPropagation(
|
||||||
spark,
|
spark,
|
||||||
|
|
|
@ -1,8 +1,7 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.graph.raw;
|
package eu.dnetlib.dhp.oa.graph.raw;
|
||||||
|
|
||||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
|
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*;
|
||||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
|
|
||||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
|
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
|
||||||
|
|
||||||
import java.util.*;
|
import java.util.*;
|
||||||
|
@ -10,11 +9,13 @@ import java.util.stream.Collectors;
|
||||||
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
import org.dom4j.Document;
|
import org.dom4j.Document;
|
||||||
|
import org.dom4j.Element;
|
||||||
import org.dom4j.Node;
|
import org.dom4j.Node;
|
||||||
|
|
||||||
import com.google.common.collect.Lists;
|
import com.google.common.collect.Lists;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson;
|
import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
|
||||||
public class OafToOafMapper extends AbstractMdRecordToOafMapper {
|
public class OafToOafMapper extends AbstractMdRecordToOafMapper {
|
||||||
|
@ -28,15 +29,26 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
|
||||||
final List<Author> res = new ArrayList<>();
|
final List<Author> res = new ArrayList<>();
|
||||||
int pos = 1;
|
int pos = 1;
|
||||||
for (final Object o : doc.selectNodes("//dc:creator")) {
|
for (final Object o : doc.selectNodes("//dc:creator")) {
|
||||||
final Node n = (Node) o;
|
final Element e = (Element) o;
|
||||||
final Author author = new Author();
|
final Author author = new Author();
|
||||||
author.setFullname(n.getText());
|
author.setFullname(e.getText());
|
||||||
author.setRank(pos++);
|
author.setRank(pos++);
|
||||||
final PacePerson p = new PacePerson(n.getText(), false);
|
final PacePerson p = new PacePerson(e.getText(), false);
|
||||||
if (p.isAccurate()) {
|
if (p.isAccurate()) {
|
||||||
author.setName(p.getNormalisedFirstName());
|
author.setName(p.getNormalisedFirstName());
|
||||||
author.setSurname(p.getNormalisedSurname());
|
author.setSurname(p.getNormalisedSurname());
|
||||||
}
|
}
|
||||||
|
|
||||||
|
final String pid = e.attributeValue("nameIdentifier");
|
||||||
|
final String pidType = e.attributeValue("nameIdentifierScheme");
|
||||||
|
|
||||||
|
author.setPid(new ArrayList<>());
|
||||||
|
if (StringUtils.isNotBlank(pid) && StringUtils.isNotBlank(pidType)) {
|
||||||
|
author
|
||||||
|
.getPid()
|
||||||
|
.add(structuredProperty(pid, qualifier(pidType, pidType, DNET_PID_TYPES, DNET_PID_TYPES), info));
|
||||||
|
}
|
||||||
|
|
||||||
res.add(author);
|
res.add(author);
|
||||||
}
|
}
|
||||||
return res;
|
return res;
|
||||||
|
|
|
@ -63,17 +63,17 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
||||||
author.setSurname(surname);
|
author.setSurname(surname);
|
||||||
}
|
}
|
||||||
|
|
||||||
author.setAffiliation(prepareListFields(doc, "./datacite:affiliation", info));
|
author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info));
|
||||||
author.setPid(preparePids(doc, info));
|
author.setPid(preparePids(n, info));
|
||||||
author.setRank(pos++);
|
author.setRank(pos++);
|
||||||
res.add(author);
|
res.add(author);
|
||||||
}
|
}
|
||||||
return res;
|
return res;
|
||||||
}
|
}
|
||||||
|
|
||||||
private List<StructuredProperty> preparePids(final Document doc, final DataInfo info) {
|
private List<StructuredProperty> preparePids(final Node n, final DataInfo info) {
|
||||||
final List<StructuredProperty> res = new ArrayList<>();
|
final List<StructuredProperty> res = new ArrayList<>();
|
||||||
for (final Object o : doc.selectNodes("./datacite:nameIdentifier")) {
|
for (final Object o : n.selectNodes("./datacite:nameIdentifier")) {
|
||||||
res
|
res
|
||||||
.add(
|
.add(
|
||||||
structuredProperty(
|
structuredProperty(
|
||||||
|
|
|
@ -22,12 +22,13 @@ SELECT
|
||||||
'' AS inferenceprovenance,
|
'' AS inferenceprovenance,
|
||||||
d.id AS collectedfromid,
|
d.id AS collectedfromid,
|
||||||
d.officialname AS collectedfromname,
|
d.officialname AS collectedfromname,
|
||||||
o.country || '@@@' || o.country || '@@@dnet:countries@@@dnet:countries' AS country,
|
o.country || '@@@' || COALESCE(cntr.name,o.country) || '@@@dnet:countries@@@dnet:countries' AS country,
|
||||||
'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction,
|
'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction,
|
||||||
|
|
||||||
ARRAY[]::text[] AS pid
|
ARRAY[]::text[] AS pid
|
||||||
|
|
||||||
FROM dsm_organizations o
|
FROM dsm_organizations o
|
||||||
LEFT OUTER JOIN dsm_datasources d ON (d.id = o.collectedfrom)
|
LEFT OUTER JOIN dsm_datasources d ON (d.id = o.collectedfrom)
|
||||||
|
LEFT OUTER JOIN class cntr ON (cntr.code = o.country)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
|
@ -10,6 +10,7 @@ import static org.mockito.Mockito.when;
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
|
import java.util.Optional;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
@ -19,11 +20,8 @@ import org.junit.jupiter.api.extension.ExtendWith;
|
||||||
import org.mockito.Mock;
|
import org.mockito.Mock;
|
||||||
import org.mockito.junit.jupiter.MockitoExtension;
|
import org.mockito.junit.jupiter.MockitoExtension;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Software;
|
|
||||||
|
|
||||||
@ExtendWith(MockitoExtension.class)
|
@ExtendWith(MockitoExtension.class)
|
||||||
public class MappersTest {
|
public class MappersTest {
|
||||||
|
@ -54,7 +52,29 @@ public class MappersTest {
|
||||||
assertValidId(p.getId());
|
assertValidId(p.getId());
|
||||||
assertValidId(p.getCollectedfrom().get(0).getKey());
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
||||||
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
||||||
|
|
||||||
assertTrue(p.getAuthor().size() > 0);
|
assertTrue(p.getAuthor().size() > 0);
|
||||||
|
Optional<Author> author = p
|
||||||
|
.getAuthor()
|
||||||
|
.stream()
|
||||||
|
.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
|
||||||
|
.findFirst();
|
||||||
|
assertTrue(author.isPresent());
|
||||||
|
StructuredProperty pid = author
|
||||||
|
.get()
|
||||||
|
.getPid()
|
||||||
|
.stream()
|
||||||
|
.findFirst()
|
||||||
|
.get();
|
||||||
|
assertEquals("0000-0001-6651-1178", pid.getValue());
|
||||||
|
assertEquals("ORCID", pid.getQualifier().getClassid());
|
||||||
|
assertEquals("ORCID", pid.getQualifier().getClassname());
|
||||||
|
assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid());
|
||||||
|
assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename());
|
||||||
|
assertEquals("Votsi,Nefta", author.get().getFullname());
|
||||||
|
assertEquals("Votsi", author.get().getSurname());
|
||||||
|
assertEquals("Nefta", author.get().getName());
|
||||||
|
|
||||||
assertTrue(p.getSubject().size() > 0);
|
assertTrue(p.getSubject().size() > 0);
|
||||||
assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline()));
|
assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline()));
|
||||||
assertTrue(StringUtils.isNotBlank(p.getJournal().getName()));
|
assertTrue(StringUtils.isNotBlank(p.getJournal().getName()));
|
||||||
|
@ -100,6 +120,38 @@ public class MappersTest {
|
||||||
assertValidId(d.getCollectedfrom().get(0).getKey());
|
assertValidId(d.getCollectedfrom().get(0).getKey());
|
||||||
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
|
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
|
||||||
assertTrue(d.getAuthor().size() > 0);
|
assertTrue(d.getAuthor().size() > 0);
|
||||||
|
|
||||||
|
Optional<Author> author = d
|
||||||
|
.getAuthor()
|
||||||
|
.stream()
|
||||||
|
.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
|
||||||
|
.findFirst();
|
||||||
|
assertTrue(author.isPresent());
|
||||||
|
StructuredProperty pid = author
|
||||||
|
.get()
|
||||||
|
.getPid()
|
||||||
|
.stream()
|
||||||
|
.findFirst()
|
||||||
|
.get();
|
||||||
|
assertEquals("0000-0001-9074-1619", pid.getValue());
|
||||||
|
assertEquals("ORCID", pid.getQualifier().getClassid());
|
||||||
|
assertEquals("ORCID", pid.getQualifier().getClassname());
|
||||||
|
assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid());
|
||||||
|
assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename());
|
||||||
|
assertEquals("Baracchini, Theo", author.get().getFullname());
|
||||||
|
assertEquals("Baracchini", author.get().getSurname());
|
||||||
|
assertEquals("Theo", author.get().getName());
|
||||||
|
|
||||||
|
assertEquals(1, author.get().getAffiliation().size());
|
||||||
|
Optional<Field<String>> opAff = author
|
||||||
|
.get()
|
||||||
|
.getAffiliation()
|
||||||
|
.stream()
|
||||||
|
.findFirst();
|
||||||
|
assertTrue(opAff.isPresent());
|
||||||
|
Field<String> affiliation = opAff.get();
|
||||||
|
assertEquals("ISTI-CNR", affiliation.getValue());
|
||||||
|
|
||||||
assertTrue(d.getSubject().size() > 0);
|
assertTrue(d.getSubject().size() > 0);
|
||||||
assertTrue(d.getInstance().size() > 0);
|
assertTrue(d.getInstance().size() > 0);
|
||||||
assertTrue(d.getContext().size() > 0);
|
assertTrue(d.getContext().size() > 0);
|
||||||
|
|
|
@ -19,7 +19,7 @@
|
||||||
<metadata xmlns="http://namespace.openaire.eu/">
|
<metadata xmlns="http://namespace.openaire.eu/">
|
||||||
<dc:title>Ecosystem Service capacity is higher in areas of multiple designation types</dc:title>
|
<dc:title>Ecosystem Service capacity is higher in areas of multiple designation types</dc:title>
|
||||||
<dc:creator>Nikolaidou,Charitini</dc:creator>
|
<dc:creator>Nikolaidou,Charitini</dc:creator>
|
||||||
<dc:creator>Votsi,Nefta</dc:creator>
|
<dc:creator nameIdentifier="0000-0001-6651-1178" nameIdentifierScheme="ORCID">Votsi,Nefta</dc:creator>
|
||||||
<dc:creator>Sgardelis,Steanos</dc:creator>
|
<dc:creator>Sgardelis,Steanos</dc:creator>
|
||||||
<dc:creator>Halley,John</dc:creator>
|
<dc:creator>Halley,John</dc:creator>
|
||||||
<dc:creator>Pantis,John</dc:creator>
|
<dc:creator>Pantis,John</dc:creator>
|
||||||
|
|
|
@ -35,9 +35,10 @@
|
||||||
</creator>
|
</creator>
|
||||||
<creator>
|
<creator>
|
||||||
<creatorName>Baracchini, Theo</creatorName>
|
<creatorName>Baracchini, Theo</creatorName>
|
||||||
|
<nameIdentifier nameIdentifierScheme="ORCID">0000-0001-9074-1619</nameIdentifier>
|
||||||
<givenName>Theo</givenName>
|
<givenName>Theo</givenName>
|
||||||
<familyName>Baracchini</familyName>
|
<familyName>Baracchini</familyName>
|
||||||
<affiliation>Physics of Aquatic Systems Laboratory (APHYS) – Margaretha Kamprad Chair, ENAC, EPFL, Lausanne, 1015, Switzerland</affiliation>
|
<affiliation>ISTI-CNR</affiliation>
|
||||||
</creator>
|
</creator>
|
||||||
<creator>
|
<creator>
|
||||||
<creatorName>Wüest, Alfred</creatorName>
|
<creatorName>Wüest, Alfred</creatorName>
|
||||||
|
|
|
@ -521,6 +521,8 @@
|
||||||
<PARAM managedBy="system" name="params" required="true" type="string">
|
<PARAM managedBy="system" name="params" required="true" type="string">
|
||||||
{
|
{
|
||||||
'oozie.wf.application.path' : '/lib/dnet/oa/enrichment/country/oozie_app',
|
'oozie.wf.application.path' : '/lib/dnet/oa/enrichment/country/oozie_app',
|
||||||
|
'sparkExecutorCores' : '3',
|
||||||
|
'sparkExecutorMemory' : '10G',
|
||||||
'workingDir' : '/tmp/beta_provision/working_dir/country',
|
'workingDir' : '/tmp/beta_provision/working_dir/country',
|
||||||
'allowedtypes' : 'pubsrepository::institutional',
|
'allowedtypes' : 'pubsrepository::institutional',
|
||||||
'whitelist' : '10|opendoar____::300891a62162b960cf02ce3827bb363c',
|
'whitelist' : '10|opendoar____::300891a62162b960cf02ce3827bb363c',
|
||||||
|
|
Loading…
Reference in New Issue