forked from D-Net/dnet-hadoop
This commit is contained in:
parent
8752d275fa
commit
0d8e496a63
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@ -2,7 +2,6 @@
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.List;
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@ -67,7 +66,6 @@ public class SparkOrcidToResultFromSemRelJob {
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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@ -0,0 +1,75 @@
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package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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import java.io.Serializable;
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import java.util.Objects;
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import java.util.Optional;
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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.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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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.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.bulktag.community.ResultTagger;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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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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/**
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* @author miriam.baglioni
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* @Date 09/12/23
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*/
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public class AppendNewRelations implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(AppendNewRelations.class);
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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AppendNewRelations.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_newrelation_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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runWithSparkHiveSession(
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conf,
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isSparkSessionManaged,
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spark -> appendNewRelation(spark, inputPath, outputPath));
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}
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private static void appendNewRelation(SparkSession spark, String inputPath, String outputPath) {
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readPath(spark, inputPath + "publication/relation", Relation.class)
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.union(readPath(spark, inputPath + "dataset/relation", Relation.class))
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.union(readPath(spark, inputPath + "otherresearchproduct/relation", Relation.class))
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.union(readPath(spark, inputPath + "software/relation", Relation.class))
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.write()
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.mode(SaveMode.Append)
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.option("compression", "gzip")
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.json(outputPath);
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}
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}
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@ -52,10 +52,13 @@ public class PrepareResultInstRepoAssociation {
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String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String datasourceOrganizationPath = parser.get("datasourceOrganizationPath");
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final String workingPath = parser.get("workingPath");
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log.info("workingPath : {}", workingPath);
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final String datasourceOrganizationPath = workingPath + "/preparedInfo/datasourceOrganization";
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log.info("datasourceOrganizationPath {}: ", datasourceOrganizationPath);
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final String alreadyLinkedPath = parser.get("alreadyLinkedPath");
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final String alreadyLinkedPath = workingPath + "/preparedInfo/alreadyLinked";
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log.info("alreadyLinkedPath {}: ", alreadyLinkedPath);
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List<String> blacklist = Optional
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@ -119,7 +119,7 @@ public class SparkResultToOrganizationFromIstRepoJob {
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"left_outer")
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.flatMap(createRelationFn(), Encoders.bean(Relation.class))
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.write()
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.mode(SaveMode.Append)
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath);
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}
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@ -11,16 +11,11 @@
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"paramDescription": "the hive metastore uris",
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"paramRequired": true
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},
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{
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"paramName":"dop",
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"paramLongName":"datasourceOrganizationPath",
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"paramDescription": "path where to store/find association from datasource and organization",
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"paramRequired": true
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},
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{
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"paramName":"alp",
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"paramLongName":"alreadyLinkedPath",
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"paramDescription": "path where to store/find already linked results and organizations",
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"paramName":"wp",
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"paramLongName":"workingPath",
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"paramDescription": "the working path",
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"paramRequired": true
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},
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{
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@ -1,5 +1,5 @@
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sourcePath=/tmp/beta_provision/graph/09_graph_dedup_enriched
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resumeFrom=OrcidPropagation
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resumeFrom=AffiliationInstitutionalRepository
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allowedsemrelsorcidprop=isSupplementedBy;isSupplementTo
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allowedsemrelsresultproject=isSupplementedBy;isSupplementTo
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allowedsemrelscommunitysemrel=isSupplementedBy;isSupplementTo
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@ -7,7 +7,20 @@ datasourceWhitelistForCountryPropagation=10|openaire____::3795d6478e30e2c9f787d4
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allowedtypes=pubsrepository::institutional
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outputPath=/tmp/miriam/enrichment_one_step
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organizationtoresultcommunitymap={"20|corda__h2020::3fb05a9524c3f790391261347852f638":["mes","euromarine"], "20|corda__h2020::e8dbe14cca9bf6fce09d468872f813f8":["mes","euromarine"], "20|snsf________::9b253f265e3bef5cae6d881fdf61aceb":["mes","euromarine"],"20|ukri________::e054eea0a47665af8c3656b5785ccf76":["mes","euromarine"],"20|corda__h2020::edc18d67c9b11fb616ca9f6e1db1b151":["mes","euromarine"],"20|ukri________::d5736d9da90521ddcdc7828a05a85e9a":["mes","euromarine"],"20|corda__h2020::f5d418d3aa1cf817ddefcc3fdc039f27":["mes","euromarine"],"20|snsf________::8fa091f8f25a846779acb4ea97b50aef":["mes","euromarine"],"20|corda__h2020::81e020977211c2c40fae2e1a50bffd71":["mes","euromarine"],"20|corda_______::81e020977211c2c40fae2e1a50bffd71":["mes","euromarine"],"20|snsf________::31d0a100e54e3cdb3c6f52d91e638c78":["mes","euromarine"],"20|corda__h2020::ea379ef91b8cc86f9ac5edc4169292db":["mes","euromarine"],"20|corda__h2020::f75ee2ee48e5cb0ec8c8d30aaa8fef70":["mes","euromarine"],"20|ukri________::e16010089551a1a9182a94604fc0ea59":["mes","euromarine"],"20|corda__h2020::38531a2cce7c5c347ffc439b07c1f43b":["mes","euromarine"],"20|corda_______::38531a2cce7c5c347ffc439b07c1f43b":["mes","euromarine"],"20|grid________::b2cbbf5eadbbf87d534b022bad3191d7":["mes","euromarine"],"20|snsf________::74730ef1439d7f7636a8be58a6b471b8":["mes","euromarine"],"20|nsf_________::ad72e19043a5a467e35f9b444d11563e":["mes","euromarine"],"20|ukri________::0fc3e92500290902a2d38ec2445e74c3":["mes","euromarine"],"20|grid________::ad2c29905da0eb3c06b3fa80cacd89ea":["mes","euromarine"],"20|corda__h2020::30b53e4d63d3724f00acb9cbaca40860":["mes","euromarine"],"20|corda__h2020::f60f84bee14ad93f0db0e49af1d5c317":["mes","euromarine"], "20|corda__h2020::7bf251ac3765b5e89d82270a1763d09f":["mes","euromarine"], "20|corda__h2020::65531bd11be9935948c7f2f4db1c1832":["mes","euromarine"], "20|corda__h2020::e0e98f86bbc76638bbb72a8fe2302946":["mes","euromarine"], "20|snsf________::3eb43582ac27601459a8d8b3e195724b":["mes","euromarine"], "20|corda__h2020::af2481dab65d06c8ea0ae02b5517b9b6":["mes","euromarine"], "20|corda__h2020::c19d05cfde69a50d3ebc89bd0ee49929":["mes","euromarine"], "20|corda__h2020::af0bfd9fc09f80d9488f56d71a9832f0":["mes","euromarine"], "20|ukri________::f33c02afb0dc66c49d0ed97ca5dd5cb0":["beopen"], "20|grid________::a867f78acdc5041b34acfe4f9a349157":["beopen"], "20|grid________::7bb116a1a9f95ab812bf9d2dea2be1ff":["beopen"], "20|corda__h2020::6ab0e0739dbe625b99a2ae45842164ad":["beopen"], "20|corda__h2020::8ba50792bc5f4d51d79fca47d860c602":["beopen"], "20|corda_______::8ba50792bc5f4d51d79fca47d860c602":["beopen"], "20|corda__h2020::e70e9114979e963eef24666657b807c3":["beopen"], "20|corda_______::e70e9114979e963eef24666657b807c3":["beopen"], "20|corda_______::15911e01e9744d57205825d77c218737":["beopen"], "20|opendoar____::056a41e24e2a9a67215e87bbee6a80ab":["beopen"], "20|opendoar____::7f67f2e6c6fbb0628f8160fcd3d92ae3":["beopen"], "20|grid________::a8ecfd7c084e561168bcbe6bf0daf3e3":["beopen"], "20|corda_______::7bbe6cc5d8ec1864739a04b0d020c9e9":["beopen"], "20|corda_______::3ff558e30c2e434d688539548300b050":["beopen"], "20|corda__h2020::5ffee5b3b83b33a8cf0e046877bd3a39":["beopen"], "20|corda__h2020::5187217e2e806a6df3579c46f82401bc":["beopen"], "20|grid________::5fa7e2709bcd945e26bfa18689adeec1":["beopen"], "20|corda_______::d8696683c53027438031a96ad27c3c07":["beopen"], "20|corda__h2020::d8696683c53027438031a96ad27c3c07":["beopen"], "20|ukri________::23a79ebdfa59790864e4a485881568c1":["beopen"], "20|corda__h2020::b76cf8fe49590a966953c37e18608af9":["beopen"], "20|grid________::d2f0204126ee709244a488a4cd3b91c2":["beopen"], "20|corda__h2020::05aba9d2ed17533d15221e5655ac11e6":["beopen"], "20|grid________::802401579481dc32062bdee69f5e6a34":["beopen"], "20|corda__h2020::3f6d9d54cac975a517ba6b252c81582d":["beopen"], "20|openorgs____::d11f981828c485cd23d93f7f24f24db1":["eut"], "20|openorgs____::e66fe5dd092752e1dd6fd29fc699933a":["eut"], "20|openorgs____::526468206bca24c1c90da6a312295cf4":["eut"], "20|openorgs____::08e311e656e65ccb32e07c66b15b6ff7":["eut"], "20|openorgs____::55a1f889758964b77682904218fdb298":["eut"], "20|openorgs____::530092b6970d60a5329beb9f39e8d7d4":["eut"], "20|openorgs____::aadafa39392b3e200102596a3a4aad9d":["eut"], "20|openorgs____::c3fe999c74fad308132b8a5971367dce":["eut"], "20|openorgs____::1624ff7c01bb641b91f4518539a0c28a":["aurora"], "20|openorgs____::cdda7cfe17c89eb50628ec2eb1f8acd2":["aurora"], "20|openorgs____::818b75030e0e40612d69e049843ede7e":["aurora"], "20|openorgs____::0b0102bae51f4f4ef5ba57fbe1523b92":["aurora"], "20|openorgs____::ed47496b44722f0e9d7b98898189be0d":["aurora"], "20|openorgs____::eb0669daa9efeb898a3090d8aac7c953":["aurora"], "20|openorgs____::eb391317ed0dc684aa81ac16265de041":["aurora"], "20|openorgs____::f7cfcc98245e22c7d6e321cde930e746":["aurora"], "20|openorgs____::f33179d3306ba2599f7a898b056b604f":["aurora"], "20|pending_org_::75c41e6dd18466709ef359323d96fa05":["aurora"]}
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pathMap={"author" : "$['author'][*]['fullname']", "title" : "$['title'][*]['value']", "orcid":"orcid":"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']", "contributor" : "$['contributor'][*]['value']", "description" : "$['description'][*]['value']"}
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pathMap ={"author":"$['author'][*]['fullname']", \
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"title":"$['title'][*]['value']",\
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"orcid":"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']" ,\
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"orcid_pending":"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']" ,\
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"contributor" : "$['contributor'][*]['value']",\
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"description" : "$['description'][*]['value']",\
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"subject" :"$['subject'][*]['value']" , \
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"fos" : "$['subject'][?(@['qualifier']['classid']=='FOS')].value" ,\
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"sdg" : "$['subject'][?(@['qualifier']['classid']=='SDG')].value",\
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"journal":"$['journal'].name",\
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"hostedby":"$['instance'][*]['hostedby']['key']",\
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"collectedfrom":"$['instance'][*]['collectedfrom']['key']",\
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"publisher":"$['publisher'].value",\
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"publicationyear":"$['dateofacceptance'].value"}
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blacklist=empty
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allowedpids=orcid;orcid_pending
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baseURL = https://services.openaire.eu/openaire/community/
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@ -47,6 +47,7 @@
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--workingPath</arg><arg>${workingDir}/affiliationInstRepo</arg>
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<arg>--blacklist</arg><arg>${blacklist}</arg>
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<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
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</spark>
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<ok to="fork_join_apply_resulttoorganization_propagation"/>
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<error to="Kill"/>
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@ -78,7 +79,7 @@
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--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
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<arg>--outputPath</arg><arg>${sourcePath}/relation</arg>
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<arg>--outputPath</arg><arg>${workingDir}/affiliationinstrepo/publication/relation</arg>
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<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/datasourceOrganization</arg>
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<arg>--alreadyLinkedPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/alreadyLinked</arg>
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<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
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@ -107,7 +108,7 @@
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--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
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<arg>--outputPath</arg><arg>${sourcePath}/relation</arg>
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<arg>--outputPath</arg><arg>${workingDir}/affiliationinstrepo/dataset/relation</arg>
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<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/datasourceOrganization</arg>
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<arg>--alreadyLinkedPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/alreadyLinked</arg>
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<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
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@ -136,7 +137,7 @@
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--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
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<arg>--outputPath</arg><arg>${sourcePath}/relation</arg>
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<arg>--outputPath</arg><arg>${workingDir}/affiliationinstrepo/otherresearchproduct/relation</arg>
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<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/datasourceOrganization</arg>
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<arg>--alreadyLinkedPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/alreadyLinked</arg>
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<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
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@ -165,7 +166,7 @@
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--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
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<arg>--outputPath</arg><arg>${sourcePath}/relation</arg>
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<arg>--outputPath</arg><arg>${workingDir}/affiliationinstrepo/software/relation</arg>
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<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/datasourceOrganization</arg>
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<arg>--alreadyLinkedPath</arg><arg>${workingDir}/affiliationInstRepo/preparedInfo/alreadyLinked</arg>
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<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
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@ -175,7 +176,32 @@
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<error to="Kill"/>
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</action>
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<join name="wait2" to="End"/>
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<join name="wait2" to="append_new_relations"/>
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<action name="append_new_relations">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>append new relations</name>
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<class>eu.dnetlib.dhp.resulttoorganizationfrominstrepo.AppendNewRelations</class>
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<jar>dhp-enrichment-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.dynamicAllocation.enabled=true
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--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
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</spark-opts>
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<arg>--outputPath</arg><arg>${sourcePath}/relation</arg>
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<arg>--sourcePath</arg><arg>${workingDir}/affiliationinstrepo/</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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