Prepare actionsets for BIP affiliations
This commit is contained in:
Serafeim Chatzopoulos
parent
347a889b20
commit
bbc245696e
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@ -5,6 +5,8 @@ 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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@ -12,10 +14,16 @@ 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.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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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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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.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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@ -31,6 +39,7 @@ 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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@ -40,6 +49,12 @@ public class PrepareAffiliationRelations implements Serializable {
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private static final String DOI = "doi";
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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 <I extends Result> void main(String[] args) throws Exception {
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@ -76,93 +91,90 @@ public class PrepareAffiliationRelations implements Serializable {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<AffiliationRelationDeserializer> bipDeserializeJavaRDD = sc
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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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JavaRDD<AffiliationRelationModel> affiliationRelations =
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bipDeserializeJavaRDD.flatMap(entry ->
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entry.getMatchings().stream().flatMap(matching ->
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matching.getRorId().stream().map( rorId -> new AffiliationRelationModel(
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entry.getDoi(),
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rorId,
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matching.getConfidence()
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))).collect(Collectors.toList()).iterator());
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for(AffiliationRelationModel rel: affiliationRelations.collect()){
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System.out.println(rel);
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}
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// Dataset<AffiliationRelationModel> relations = spark
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// .createDataset(bipDeserializeJavaRDD.flatMap(entry -> {
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//// entry.keySet().stream().map(key -> {
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// AffiliationRelationModel rel = new AffiliationRelationModel(entry.getDoi())
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// System.out.println(entry);
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// return entry;
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//// BipScore bs = new BipScore();
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//// bs.setId(key);
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//// bs.setScoreList(entry.get(key));
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//// return bs;
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// }).collect(Collectors.toList()).iterator()).rdd(), Encoßders.bean(AffiliationRelationModel.class));
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Dataset<AffiliationRelationModel> affiliationRelations =
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spark.createDataset(
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affiliationRelationsDeserializeRDD.flatMap(entry ->
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entry.getMatchings().stream().flatMap(matching ->
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matching.getRorId().stream().map( rorId -> new AffiliationRelationModel(
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entry.getDoi(),
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rorId,
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matching.getConfidence()
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))).collect(Collectors.toList())
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.iterator())
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.rdd(),
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Encoders.bean(AffiliationRelationModel.class));
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// bipScores
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//
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// .map((MapFunction<BipScore, Result>) bs -> {
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// Result ret = new Result();
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//
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// ret.setId(bs.getId());
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//
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// ret.setMeasures(getMeasure(bs));
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//
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// return ret;
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// }, Encoders.bean(Result.class))
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// .toJavaRDD()
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// .map(p -> new AtomicAction(Result.class, p))
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// .mapToPair(
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// aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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// new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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// .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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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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return getRelation(paperId, affId, ModelConstants.HAS_AUTHOR_INSTITUTION);
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}, Encoders.bean(Relation.class))
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.toJavaRDD()
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.map(p -> new AtomicAction(Relation.class, p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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// }
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//
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// private static List<Measure> getMeasure(BipScore value) {
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// return value
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// .getScoreList()
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// .stream()
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// .map(score -> {
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// Measure m = new Measure();
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// m.setId(score.getId());
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// m
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// .setUnit(
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// score
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// .getUnit()
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// .stream()
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// .map(unit -> {
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// KeyValue kv = new KeyValue();
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// kv.setValue(unit.getValue());
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// kv.setKey(unit.getKey());
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// kv
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// .setDataInfo(
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// OafMapperUtils
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// .dataInfo(
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// false,
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// UPDATE_DATA_INFO_TYPE,
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// true,
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// false,
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// OafMapperUtils
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// .qualifier(
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// UPDATE_MEASURE_BIP_CLASS_ID,
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// UPDATE_CLASS_NAME,
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// ModelConstants.DNET_PROVENANCE_ACTIONS,
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// ModelConstants.DNET_PROVENANCE_ACTIONS),
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// ""));
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// return kv;
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// })
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// .collect(Collectors.toList()));
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// return m;
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// })
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// .collect(Collectors.toList());
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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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