[WebCrawlAffiliation]remove from the creation of the action set the relations for pmc and pmid. Only doi are allowed
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@ -30,7 +30,6 @@ import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
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import eu.dnetlib.dhp.schema.oaf.utils.PidType;
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import io.netty.util.Constant;
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import scala.Tuple2;
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/**
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@ -105,8 +104,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
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final String ror = ROR_PREFIX
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+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
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ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
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// ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
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// ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
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return ret
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.iterator();
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@ -146,57 +144,22 @@ public class CreateActionSetFromWebEntries implements Serializable {
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"institution.country_code as country_code", "publication_year")
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.distinct();
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// .selectExpr(
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// "id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror",
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// "institution.country_code as country_code", "publication_year")
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// .distinct();
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}
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private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
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return spark
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.read()
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.option("header", true)
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.csv(inputPath)
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.json(inputPath)
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.select("OpenAlexId");
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}
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private static List<Relation> createAffiliationRelationPairPMCID(String pmcid, String ror) {
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if (pmcid == null)
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return new ArrayList<>();
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return createAffiliatioRelationPair(
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PMCID_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), removeResolver("PMC", pmcid))),
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ror);
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}
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private static List<Relation> createAffiliationRelationPairPMID(String pmid, String ror) {
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if (pmid == null)
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return new ArrayList<>();
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return createAffiliatioRelationPair(
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PMID_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), removeResolver("PMID", pmid))),
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ror);
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}
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private static String removeResolver(String pidType, String pid) {
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switch (pidType) {
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case "PMID":
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return pid.substring(33);
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case "PMC":
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return "PMC" + pid.substring(43);
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case "DOI":
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return pid.substring(16);
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}
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throw new RuntimeException();
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}
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if (pidType.equals("DOI")) {
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return pid.substring(16);
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}
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throw new IllegalArgumentException("DOI is the only supported PID type");
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}
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private static List<Relation> createAffiliationRelationPairDOI(String doi, String ror) {
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if (doi == null)
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