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towards EOSC datasource profiles #130

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alessia.bardi merged 7 commits from datasource_model_eosc_beta into beta 2021-08-23 11:58:35 +02:00
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2 changed files with 73 additions and 43 deletions
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86
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java
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@ -27,14 +27,20 @@ import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits;
import scala.Tuple2; import scala.Tuple2;
/** /**
* CreateRelatedEntitiesJob: (phase 1): prepare tuples [relation - target entity] (R - T): for each entity type * CreateRelatedEntitiesJob: (phase 1): prepare tuples [relation - target entity] (R - T): for each entity type E_i map E_i as RelatedEntity
* E_i map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information join * 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)
* (R.target = T_i.id) save the tuples (R_i, T_i)
*/ */
public class CreateRelatedEntitiesJob_phase1 { public class CreateRelatedEntitiesJob_phase1 {
@ -42,68 +48,65 @@ public class CreateRelatedEntitiesJob_phase1 {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception { public static void main(final String[] args) throws Exception {
String jsonConfiguration = IOUtils final String jsonConfiguration = IOUtils
.toString( .toString(
PrepareRelationsJob.class PrepareRelationsJob.class
.getResourceAsStream( .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.json"));
"/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional final Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged")) .ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf) .map(Boolean::valueOf)
.orElse(Boolean.TRUE); .orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputRelationsPath = parser.get("inputRelationsPath"); final String inputRelationsPath = parser.get("inputRelationsPath");
log.info("inputRelationsPath: {}", inputRelationsPath); log.info("inputRelationsPath: {}", inputRelationsPath);
String inputEntityPath = parser.get("inputEntityPath"); final String inputEntityPath = parser.get("inputEntityPath");
log.info("inputEntityPath: {}", inputEntityPath); log.info("inputEntityPath: {}", inputEntityPath);
String outputPath = parser.get("outputPath"); final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath); log.info("outputPath: {}", outputPath);
String graphTableClassName = parser.get("graphTableClassName"); final String graphTableClassName = parser.get("graphTableClassName");
log.info("graphTableClassName: {}", graphTableClassName); log.info("graphTableClassName: {}", graphTableClassName);
Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName); final Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(ProvisionModelSupport.getModelClasses()); conf.registerKryoClasses(ProvisionModelSupport.getModelClasses());
runWithSparkSession( runWithSparkSession(conf, isSparkSessionManaged, spark -> {
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath); removeOutputDir(spark, outputPath);
joinRelationEntity(spark, inputRelationsPath, inputEntityPath, entityClazz, outputPath); joinRelationEntity(spark, inputRelationsPath, inputEntityPath, entityClazz, outputPath);
}); });
} }
private static <E extends OafEntity> void joinRelationEntity( private static <E extends OafEntity> void joinRelationEntity(
SparkSession spark, final SparkSession spark,
String inputRelationsPath, final String inputRelationsPath,
String inputEntityPath, final String inputEntityPath,
Class<E> clazz, final Class<E> clazz,
String outputPath) { final String outputPath) {
Dataset<Tuple2<String, Relation>> relsByTarget = readPathRelation(spark, inputRelationsPath) final Dataset<Tuple2<String, Relation>> relsByTarget = readPathRelation(spark, inputRelationsPath)
.map( .map(
(MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(r.getTarget(), (MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(r.getTarget(),
r), r),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class))) Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class)))
.cache(); .cache();
Dataset<Tuple2<String, RelatedEntity>> entities = readPathEntity(spark, inputEntityPath, clazz) final Dataset<Tuple2<String, RelatedEntity>> entities = readPathEntity(spark, inputEntityPath, clazz)
.filter("dataInfo.invisible == false") .filter("dataInfo.invisible == false")
.map( .map(
(MapFunction<E, Tuple2<String, RelatedEntity>>) e -> new Tuple2<>(e.getId(), asRelatedEntity(e, clazz)), (MapFunction<E, Tuple2<String, RelatedEntity>>) e -> new Tuple2<>(e.getId(), asRelatedEntity(e, clazz)),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(RelatedEntity.class))) Encoders
.tuple(Encoders.STRING(), Encoders.kryo(RelatedEntity.class)))
.cache(); .cache();
relsByTarget relsByTarget
@ -118,7 +121,9 @@ public class CreateRelatedEntitiesJob_phase1 {
} }
private static <E extends OafEntity> Dataset<E> readPathEntity( private static <E extends OafEntity> Dataset<E> readPathEntity(
SparkSession spark, String inputEntityPath, Class<E> entityClazz) { final SparkSession spark,
final String inputEntityPath,
final Class<E> entityClazz) {
log.info("Reading Graph table from: {}", inputEntityPath); log.info("Reading Graph table from: {}", inputEntityPath);
return spark return spark
@ -129,7 +134,7 @@ public class CreateRelatedEntitiesJob_phase1 {
Encoders.bean(entityClazz)); Encoders.bean(entityClazz));
} }
public static <E extends OafEntity> RelatedEntity asRelatedEntity(E entity, Class<E> clazz) { public static <E extends OafEntity> RelatedEntity asRelatedEntity(final E entity, final Class<E> clazz) {
final RelatedEntity re = new RelatedEntity(); final RelatedEntity re = new RelatedEntity();
re.setId(entity.getId()); re.setId(entity.getId());
@ -143,7 +148,7 @@ public class CreateRelatedEntitiesJob_phase1 {
case dataset: case dataset:
case otherresearchproduct: case otherresearchproduct:
case software: case software:
Result result = (Result) entity; final Result result = (Result) entity;
if (result.getTitle() != null && !result.getTitle().isEmpty()) { if (result.getTitle() != null && !result.getTitle().isEmpty()) {
final StructuredProperty title = result.getTitle().stream().findFirst().get(); final StructuredProperty title = result.getTitle().stream().findFirst().get();
@ -170,16 +175,17 @@ public class CreateRelatedEntitiesJob_phase1 {
break; break;
case datasource: case datasource:
Datasource d = (Datasource) entity; final Datasource d = (Datasource) entity;
re.setOfficialname(getValue(d.getOfficialname())); re.setOfficialname(getValue(d.getOfficialname()));
re.setWebsiteurl(getValue(d.getWebsiteurl())); re.setWebsiteurl(getValue(d.getWebsiteurl()));
re.setDatasourcetype(d.getDatasourcetype()); re.setDatasourcetype(d.getDatasourcetype());
re.setDatasourcetypeui(d.getDatasourcetypeui());
re.setOpenairecompatibility(d.getOpenairecompatibility()); re.setOpenairecompatibility(d.getOpenairecompatibility());
break; break;
case organization: case organization:
Organization o = (Organization) entity; final Organization o = (Organization) entity;
re.setLegalname(getValue(o.getLegalname())); re.setLegalname(getValue(o.getLegalname()));
re.setLegalshortname(getValue(o.getLegalshortname())); re.setLegalshortname(getValue(o.getLegalshortname()));
@ -187,14 +193,14 @@ public class CreateRelatedEntitiesJob_phase1 {
re.setWebsiteurl(getValue(o.getWebsiteurl())); re.setWebsiteurl(getValue(o.getWebsiteurl()));
break; break;
case project: case project:
Project p = (Project) entity; final Project p = (Project) entity;
re.setProjectTitle(getValue(p.getTitle())); re.setProjectTitle(getValue(p.getTitle()));
re.setCode(getValue(p.getCode())); re.setCode(getValue(p.getCode()));
re.setAcronym(getValue(p.getAcronym())); re.setAcronym(getValue(p.getAcronym()));
re.setContracttype(p.getContracttype()); re.setContracttype(p.getContracttype());
List<Field<String>> f = p.getFundingtree(); final List<Field<String>> f = p.getFundingtree();
if (!f.isEmpty()) { if (!f.isEmpty()) {
re.setFundingtree(f.stream().map(s -> s.getValue()).collect(Collectors.toList())); re.setFundingtree(f.stream().map(s -> s.getValue()).collect(Collectors.toList()));
} }
@ -203,11 +209,11 @@ public class CreateRelatedEntitiesJob_phase1 {
return re; return re;
} }
private static String getValue(Field<String> field) { private static String getValue(final Field<String> field) {
return getFieldValueWithDefault(field, ""); return getFieldValueWithDefault(field, "");
} }
private static <T> T getFieldValueWithDefault(Field<T> f, T defaultValue) { private static <T> T getFieldValueWithDefault(final Field<T> f, final T defaultValue) {
return Optional return Optional
.ofNullable(f) .ofNullable(f)
.filter(Objects::nonNull) .filter(Objects::nonNull)
@ -216,21 +222,21 @@ public class CreateRelatedEntitiesJob_phase1 {
} }
/** /**
* Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text * Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text file,
* file,
* *
* @param spark * @param spark
* @param relationPath * @param relationPath
* @return the Dataset<SortableRelation> containing all the relationships * @return the Dataset<SortableRelation> containing all the relationships
*/ */
private static Dataset<Relation> readPathRelation( private static Dataset<Relation> readPathRelation(
SparkSession spark, final String relationPath) { final SparkSession spark,
final String relationPath) {
log.info("Reading relations from: {}", relationPath); log.info("Reading relations from: {}", relationPath);
return spark.read().load(relationPath).as(Encoders.bean(Relation.class)); return spark.read().load(relationPath).as(Encoders.bean(Relation.class));
} }
private static void removeOutputDir(SparkSession spark, String path) { private static void removeOutputDir(final SparkSession spark, final String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
} }
} }

24
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
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@ -735,6 +735,30 @@ public class XmlRecordFactory implements Serializable {
.collect(Collectors.toList())); .collect(Collectors.toList()));
} }
if (ds.getJurisdiction() != null) {
metadata.add(XmlSerializationUtils.mapQualifier("jurisdiction", ds.getJurisdiction()));
}
if (ds.getThematic() != null) {
metadata.add(XmlSerializationUtils.asXmlElement("thematic", ds.getThematic().toString()));
}
if (ds.getKnowledgegraph() != null) {
metadata
.add(XmlSerializationUtils.asXmlElement("knowledgegraph", ds.getKnowledgegraph().toString()));
}
if (ds.getContentpolicies() != null) {
metadata
.addAll(
ds
.getContentpolicies()
.stream()
.filter(Objects::nonNull)
.map(q -> XmlSerializationUtils.mapQualifier("contentpolicy", q))
.collect(Collectors.toList()));
}
break; break;
case organization: case organization:
final Organization o = (Organization) entity; final Organization o = (Organization) entity;