Refactor PrepareAffiliationRelations.java to use OafMapperUtils common functions
This commit is contained in:
Serafeim Chatzopoulos
parent
bbc245696e
commit
12528ed2ef
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@ -1,19 +1,14 @@
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package eu.dnetlib.dhp.actionmanager.bipaffiliations;
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import static eu.dnetlib.dhp.actionmanager.Constants.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.Iterator;
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import java.util.List;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import eu.dnetlib.dhp.actionmanager.Constants;
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import eu.dnetlib.dhp.actionmanager.bipaffiliations.model.*;
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import eu.dnetlib.dhp.actionmanager.ror.GenerateRorActionSetJob;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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@ -25,7 +20,6 @@ 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.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.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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@ -33,16 +27,14 @@ import org.apache.spark.sql.Dataset;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import scala.Tuple2;
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/**
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* created the Atomic Action for each tipe of results
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* Creates action sets for Crossref affiliation relations inferred by BIP!
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*/
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public class PrepareAffiliationRelations implements Serializable {
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@ -50,19 +42,17 @@ public class PrepareAffiliationRelations implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelations.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String ID_PREFIX = "50|doi_________::";
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private static final String TRUST = "0.91";
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public static final String BIP_AFFILIATIONS_CLASSID = "sysimport:crosswalk:bipaffiliations";
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public static final String BIP_AFFILIATIONS_CLASSNAME = "Imported from BIP! Affiliations";
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public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
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public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by BIP!";
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public static final String BIP_INFERENCE_PROVENANCE = "bip_affiliation";
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public static <I extends Result> void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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PrepareAffiliationRelations.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json"));
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.toString(
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PrepareAffiliationRelations.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -91,14 +81,12 @@ public class PrepareAffiliationRelations implements Serializable {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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// load and parse affiliation relations from HDFS
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JavaRDD<AffiliationRelationDeserializer> affiliationRelationsDeserializeRDD = sc
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.textFile(inputPath)
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.map(item -> OBJECT_MAPPER.readValue(item, AffiliationRelationDeserializer.class));
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// for(AffiliationRelationDeserializer rel: bipDeserializeJavaRDD.collect()){
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// System.out.println(rel);
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// }
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// convert affiliation to an internal representation
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Dataset<AffiliationRelationModel> affiliationRelations =
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spark.createDataset(
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affiliationRelationsDeserializeRDD.flatMap(entry ->
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@ -112,15 +100,40 @@ public class PrepareAffiliationRelations implements Serializable {
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.rdd(),
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Encoders.bean(AffiliationRelationModel.class));
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// prepare action sets for affiliation relations
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affiliationRelations
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.map((MapFunction<AffiliationRelationModel, Relation>) affRel -> {
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String paperId = ID_PREFIX
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", affRel.getDoi()));
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final String affId = ID_PREFIX
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("ror", affRel.getRorId()));
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// DOI to OpenAIRE id
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final String paperId = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", affRel.getDoi()));
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return getRelation(paperId, affId, ModelConstants.HAS_AUTHOR_INSTITUTION);
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// ROR id to OpenAIRE id
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final String affId = GenerateRorActionSetJob.calculateOpenaireId(affRel.getRorId());
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Qualifier qualifier = OafMapperUtils.qualifier(
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BIP_AFFILIATIONS_CLASSID,
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BIP_AFFILIATIONS_CLASSNAME,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS);
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// format data info; setting `confidence` into relation's `trust`
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DataInfo dataInfo = OafMapperUtils.dataInfo(
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false,
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BIP_INFERENCE_PROVENANCE,
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true,
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false,
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qualifier,
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Double.toString(affRel.getConfidence()));
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return OafMapperUtils.getRelation(
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paperId,
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affId,
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ModelConstants.RESULT_ORGANIZATION,
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ModelConstants.AFFILIATION,
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ModelConstants.HAS_AUTHOR_INSTITUTION,
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null,
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dataInfo,
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null);
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}, Encoders.bean(Relation.class))
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.toJavaRDD()
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@ -131,50 +144,4 @@ public class PrepareAffiliationRelations implements Serializable {
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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}
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public static Relation getRelation(String source, String target, String relclass) {
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Relation r = new Relation();
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r.setCollectedfrom(getCollectedFrom());
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r.setSource(source);
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r.setTarget(target);
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r.setRelClass(relclass);
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r.setRelType(ModelConstants.RESULT_ORGANIZATION);
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r.setSubRelType(ModelConstants.AFFILIATION);
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r.setDataInfo(getDataInfo());
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return r;
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}
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public static List<KeyValue> getCollectedFrom() {
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KeyValue kv = new KeyValue();
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kv.setKey(ModelConstants.DNET_PROVENANCE_ACTIONS);
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kv.setValue(ModelConstants.DNET_PROVENANCE_ACTIONS);
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return Collections.singletonList(kv);
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}
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public static DataInfo getDataInfo() {
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DataInfo di = new DataInfo();
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di.setInferred(false);
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di.setDeletedbyinference(false);
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di.setTrust(TRUST);
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di.setProvenanceaction(
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getQualifier(
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BIP_AFFILIATIONS_CLASSID,
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BIP_AFFILIATIONS_CLASSNAME,
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ModelConstants.DNET_PROVENANCE_ACTIONS
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));
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return di;
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}
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public static Qualifier getQualifier(String class_id, String class_name,
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String qualifierSchema) {
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Qualifier pa = new Qualifier();
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pa.setClassid(class_id);
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pa.setClassname(class_name);
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pa.setSchemeid(qualifierSchema);
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pa.setSchemename(qualifierSchema);
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return pa;
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}
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}
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@ -168,7 +168,7 @@ public class GenerateRorActionSetJob {
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}
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private static String calculateOpenaireId(final String rorId) {
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public static String calculateOpenaireId(final String rorId) {
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return String.format("20|%s::%s", Constants.ROR_NS_PREFIX, DHPUtils.md5(rorId));
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}
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