forked from D-Net/dnet-hadoop
added new fields in xml
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9f1c7b8e17
commit
3e2a2d6e71
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@ -27,14 +27,20 @@ import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
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import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
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import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.Datasource;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Organization;
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import eu.dnetlib.dhp.schema.oaf.Project;
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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.StructuredProperty;
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import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits;
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import scala.Tuple2;
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/**
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* CreateRelatedEntitiesJob: (phase 1): prepare tuples [relation - target entity] (R - T): for each entity type
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* E_i map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information join
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* (R.target = T_i.id) save the tuples (R_i, T_i)
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* CreateRelatedEntitiesJob: (phase 1): prepare tuples [relation - target entity] (R - T): for each entity type E_i map E_i as RelatedEntity
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* T_i to simplify the model and extracting only the necessary information join (R.target = T_i.id) save the tuples (R_i, T_i)
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*/
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public class CreateRelatedEntitiesJob_phase1 {
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@ -42,68 +48,65 @@ public class CreateRelatedEntitiesJob_phase1 {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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public static void main(final String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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final String jsonConfiguration = IOUtils
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.toString(
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PrepareRelationsJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.json"));
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.getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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final Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputRelationsPath = parser.get("inputRelationsPath");
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final String inputRelationsPath = parser.get("inputRelationsPath");
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log.info("inputRelationsPath: {}", inputRelationsPath);
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String inputEntityPath = parser.get("inputEntityPath");
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final String inputEntityPath = parser.get("inputEntityPath");
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log.info("inputEntityPath: {}", inputEntityPath);
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String outputPath = parser.get("outputPath");
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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String graphTableClassName = parser.get("graphTableClassName");
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final String graphTableClassName = parser.get("graphTableClassName");
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log.info("graphTableClassName: {}", graphTableClassName);
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Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
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final Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
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SparkConf conf = new SparkConf();
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final SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(ProvisionModelSupport.getModelClasses());
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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removeOutputDir(spark, outputPath);
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joinRelationEntity(spark, inputRelationsPath, inputEntityPath, entityClazz, outputPath);
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});
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}
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private static <E extends OafEntity> void joinRelationEntity(
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SparkSession spark,
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String inputRelationsPath,
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String inputEntityPath,
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Class<E> clazz,
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String outputPath) {
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final SparkSession spark,
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final String inputRelationsPath,
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final String inputEntityPath,
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final Class<E> clazz,
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final String outputPath) {
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Dataset<Tuple2<String, Relation>> relsByTarget = readPathRelation(spark, inputRelationsPath)
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final Dataset<Tuple2<String, Relation>> relsByTarget = readPathRelation(spark, inputRelationsPath)
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.map(
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(MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(r.getTarget(),
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r),
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class)))
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.cache();
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Dataset<Tuple2<String, RelatedEntity>> entities = readPathEntity(spark, inputEntityPath, clazz)
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final Dataset<Tuple2<String, RelatedEntity>> entities = readPathEntity(spark, inputEntityPath, clazz)
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.filter("dataInfo.invisible == false")
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.map(
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(MapFunction<E, Tuple2<String, RelatedEntity>>) e -> new Tuple2<>(e.getId(), asRelatedEntity(e, clazz)),
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(RelatedEntity.class)))
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Encoders
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.tuple(Encoders.STRING(), Encoders.kryo(RelatedEntity.class)))
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.cache();
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relsByTarget
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@ -118,7 +121,9 @@ public class CreateRelatedEntitiesJob_phase1 {
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}
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private static <E extends OafEntity> Dataset<E> readPathEntity(
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SparkSession spark, String inputEntityPath, Class<E> entityClazz) {
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final SparkSession spark,
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final String inputEntityPath,
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final Class<E> entityClazz) {
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log.info("Reading Graph table from: {}", inputEntityPath);
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return spark
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@ -129,7 +134,7 @@ public class CreateRelatedEntitiesJob_phase1 {
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Encoders.bean(entityClazz));
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}
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public static <E extends OafEntity> RelatedEntity asRelatedEntity(E entity, Class<E> clazz) {
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public static <E extends OafEntity> RelatedEntity asRelatedEntity(final E entity, final Class<E> clazz) {
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final RelatedEntity re = new RelatedEntity();
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re.setId(entity.getId());
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@ -143,7 +148,7 @@ public class CreateRelatedEntitiesJob_phase1 {
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case dataset:
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case otherresearchproduct:
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case software:
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Result result = (Result) entity;
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final Result result = (Result) entity;
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if (result.getTitle() != null && !result.getTitle().isEmpty()) {
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final StructuredProperty title = result.getTitle().stream().findFirst().get();
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@ -170,16 +175,17 @@ public class CreateRelatedEntitiesJob_phase1 {
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break;
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case datasource:
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Datasource d = (Datasource) entity;
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final Datasource d = (Datasource) entity;
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re.setOfficialname(getValue(d.getOfficialname()));
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re.setWebsiteurl(getValue(d.getWebsiteurl()));
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re.setDatasourcetype(d.getDatasourcetype());
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re.setDatasourcetypeui(d.getDatasourcetypeui());
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re.setOpenairecompatibility(d.getOpenairecompatibility());
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break;
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case organization:
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Organization o = (Organization) entity;
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final Organization o = (Organization) entity;
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re.setLegalname(getValue(o.getLegalname()));
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re.setLegalshortname(getValue(o.getLegalshortname()));
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@ -187,14 +193,14 @@ public class CreateRelatedEntitiesJob_phase1 {
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re.setWebsiteurl(getValue(o.getWebsiteurl()));
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break;
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case project:
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Project p = (Project) entity;
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final Project p = (Project) entity;
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re.setProjectTitle(getValue(p.getTitle()));
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re.setCode(getValue(p.getCode()));
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re.setAcronym(getValue(p.getAcronym()));
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re.setContracttype(p.getContracttype());
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List<Field<String>> f = p.getFundingtree();
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final List<Field<String>> f = p.getFundingtree();
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if (!f.isEmpty()) {
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re.setFundingtree(f.stream().map(s -> s.getValue()).collect(Collectors.toList()));
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}
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@ -203,11 +209,11 @@ public class CreateRelatedEntitiesJob_phase1 {
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return re;
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}
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private static String getValue(Field<String> field) {
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private static String getValue(final Field<String> field) {
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return getFieldValueWithDefault(field, "");
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}
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private static <T> T getFieldValueWithDefault(Field<T> f, T defaultValue) {
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private static <T> T getFieldValueWithDefault(final Field<T> f, final T defaultValue) {
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return Optional
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.ofNullable(f)
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.filter(Objects::nonNull)
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@ -216,21 +222,21 @@ public class CreateRelatedEntitiesJob_phase1 {
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}
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/**
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* Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text
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* file,
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* Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text file,
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*
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* @param spark
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* @param relationPath
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* @return the Dataset<SortableRelation> containing all the relationships
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*/
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private static Dataset<Relation> readPathRelation(
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SparkSession spark, final String relationPath) {
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final SparkSession spark,
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final String relationPath) {
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log.info("Reading relations from: {}", relationPath);
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return spark.read().load(relationPath).as(Encoders.bean(Relation.class));
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}
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private static void removeOutputDir(SparkSession spark, String path) {
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private static void removeOutputDir(final SparkSession spark, final String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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}
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@ -735,6 +735,30 @@ public class XmlRecordFactory implements Serializable {
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.collect(Collectors.toList()));
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}
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if (ds.getJurisdiction() != null) {
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metadata.add(XmlSerializationUtils.mapQualifier("jurisdiction", ds.getJurisdiction()));
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}
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if (ds.getThematic() != null) {
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metadata.add(XmlSerializationUtils.asXmlElement("thematic", ds.getThematic().toString()));
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}
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if (ds.getKnowledgegraph() != null) {
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metadata
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.add(XmlSerializationUtils.asXmlElement("knowledgegraph", ds.getKnowledgegraph().toString()));
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}
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if (ds.getContentpolicies() != null) {
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metadata
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.addAll(
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ds
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.getContentpolicies()
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.stream()
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.filter(Objects::nonNull)
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.map(q -> XmlSerializationUtils.mapQualifier("contentpolicy", q))
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.collect(Collectors.toList()));
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}
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break;
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case organization:
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final Organization o = (Organization) entity;
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