small adjustments in the provisioning workflow
This commit is contained in:
parent
88fbb3a353
commit
0b55795d4d
|
|
@ -11,11 +11,13 @@ import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
|
|||
import eu.dnetlib.dhp.oa.provision.model.SortableRelation;
|
||||
import eu.dnetlib.dhp.schema.common.EntityType;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import java.util.List;
|
||||
import java.util.Objects;
|
||||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
|
|
@ -104,16 +106,12 @@ public class CreateRelatedEntitiesJob_phase1 {
|
|||
SparkSession spark,
|
||||
String inputRelationsPath,
|
||||
String inputEntityPath,
|
||||
Class<E> entityClazz,
|
||||
Class<E> clazz,
|
||||
String outputPath) {
|
||||
|
||||
Dataset<Tuple2<String, SortableRelation>> relsByTarget =
|
||||
readPathRelation(spark, inputRelationsPath)
|
||||
.filter(
|
||||
(FilterFunction<SortableRelation>)
|
||||
value ->
|
||||
value.getDataInfo().getDeletedbyinference()
|
||||
== false)
|
||||
.filter("dataInfo.deletedbyinference == false")
|
||||
.map(
|
||||
(MapFunction<SortableRelation, Tuple2<String, SortableRelation>>)
|
||||
r -> new Tuple2<>(r.getTarget(), r),
|
||||
|
|
@ -122,10 +120,11 @@ public class CreateRelatedEntitiesJob_phase1 {
|
|||
.cache();
|
||||
|
||||
Dataset<Tuple2<String, RelatedEntity>> entities =
|
||||
readPathEntity(spark, inputEntityPath, entityClazz)
|
||||
readPathEntity(spark, inputEntityPath, clazz)
|
||||
.filter("dataInfo.invisible == false")
|
||||
.map(
|
||||
(MapFunction<E, RelatedEntity>)
|
||||
value -> asRelatedEntity(value, entityClazz),
|
||||
value -> asRelatedEntity(value, clazz),
|
||||
Encoders.bean(RelatedEntity.class))
|
||||
.map(
|
||||
(MapFunction<RelatedEntity, Tuple2<String, RelatedEntity>>)
|
||||
|
|
@ -146,7 +145,7 @@ public class CreateRelatedEntitiesJob_phase1 {
|
|||
Encoders.bean(EntityRelEntity.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.parquet(outputPath + "/" + EntityType.fromClass(entityClazz));
|
||||
.parquet(outputPath + "/" + EntityType.fromClass(clazz));
|
||||
}
|
||||
|
||||
private static <E extends OafEntity> Dataset<E> readPathEntity(
|
||||
|
|
@ -161,6 +160,81 @@ public class CreateRelatedEntitiesJob_phase1 {
|
|||
Encoders.bean(entityClazz));
|
||||
}
|
||||
|
||||
public static <E extends OafEntity> RelatedEntity asRelatedEntity(E entity, Class<E> clazz) {
|
||||
|
||||
final RelatedEntity re = new RelatedEntity();
|
||||
re.setId(entity.getId());
|
||||
re.setType(EntityType.fromClass(clazz).name());
|
||||
|
||||
re.setPid(entity.getPid());
|
||||
re.setCollectedfrom(entity.getCollectedfrom());
|
||||
|
||||
switch (EntityType.fromClass(clazz)) {
|
||||
case publication:
|
||||
case dataset:
|
||||
case otherresearchproduct:
|
||||
case software:
|
||||
Result result = (Result) entity;
|
||||
|
||||
if (result.getTitle() != null && !result.getTitle().isEmpty()) {
|
||||
re.setTitle(result.getTitle().stream().findFirst().get());
|
||||
}
|
||||
|
||||
re.setDateofacceptance(getValue(result.getDateofacceptance()));
|
||||
re.setPublisher(getValue(result.getPublisher()));
|
||||
re.setResulttype(result.getResulttype());
|
||||
re.setInstances(result.getInstance());
|
||||
|
||||
// TODO still to be mapped
|
||||
// re.setCodeRepositoryUrl(j.read("$.coderepositoryurl"));
|
||||
|
||||
break;
|
||||
case datasource:
|
||||
Datasource d = (Datasource) entity;
|
||||
|
||||
re.setOfficialname(getValue(d.getOfficialname()));
|
||||
re.setWebsiteurl(getValue(d.getWebsiteurl()));
|
||||
re.setDatasourcetype(d.getDatasourcetype());
|
||||
re.setOpenairecompatibility(d.getOpenairecompatibility());
|
||||
|
||||
break;
|
||||
case organization:
|
||||
Organization o = (Organization) entity;
|
||||
|
||||
re.setLegalname(getValue(o.getLegalname()));
|
||||
re.setLegalshortname(getValue(o.getLegalshortname()));
|
||||
re.setCountry(o.getCountry());
|
||||
re.setWebsiteurl(getValue(o.getWebsiteurl()));
|
||||
break;
|
||||
case project:
|
||||
Project p = (Project) entity;
|
||||
|
||||
re.setProjectTitle(getValue(p.getTitle()));
|
||||
re.setCode(getValue(p.getCode()));
|
||||
re.setAcronym(getValue(p.getAcronym()));
|
||||
re.setContracttype(p.getContracttype());
|
||||
|
||||
List<Field<String>> f = p.getFundingtree();
|
||||
if (!f.isEmpty()) {
|
||||
re.setFundingtree(
|
||||
f.stream().map(s -> s.getValue()).collect(Collectors.toList()));
|
||||
}
|
||||
break;
|
||||
}
|
||||
return re;
|
||||
}
|
||||
|
||||
private static String getValue(Field<String> field) {
|
||||
return getFieldValueWithDefault(field, "");
|
||||
}
|
||||
|
||||
private static <T> T getFieldValueWithDefault(Field<T> f, T defaultValue) {
|
||||
return Optional.ofNullable(f)
|
||||
.filter(Objects::nonNull)
|
||||
.map(x -> x.getValue())
|
||||
.orElse(defaultValue);
|
||||
}
|
||||
|
||||
/**
|
||||
* Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline
|
||||
* delimited json text file,
|
||||
|
|
|
|||
|
|
@ -76,9 +76,6 @@ public class PrepareRelationsJob {
|
|||
String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
int numPartitions = Integer.parseInt(parser.get("relPartitions"));
|
||||
log.info("relPartitions: {}", numPartitions);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
|
|
@ -86,27 +83,14 @@ public class PrepareRelationsJob {
|
|||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
removeOutputDir(spark, outputPath);
|
||||
prepareRelationsFromPaths(spark, inputRelationsPath, outputPath, numPartitions);
|
||||
prepareRelationsFromPaths(spark, inputRelationsPath, outputPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static void prepareRelationsFromPaths(
|
||||
SparkSession spark, String inputRelationsPath, String outputPath, int numPartitions) {
|
||||
SparkSession spark, String inputRelationsPath, String outputPath) {
|
||||
readPathRelation(spark, inputRelationsPath)
|
||||
.filter(
|
||||
(FilterFunction<SortableRelation>)
|
||||
r -> {
|
||||
try {
|
||||
return r != null
|
||||
&& r.getDataInfo() != null
|
||||
&& !r.getDataInfo().getDeletedbyinference();
|
||||
} catch (NullPointerException e) {
|
||||
log.info(
|
||||
"invalid NPE '{}'",
|
||||
OBJECT_MAPPER.writeValueAsString(r));
|
||||
throw e;
|
||||
}
|
||||
})
|
||||
.filter("dataInfo.deletedbyinference == false")
|
||||
.groupByKey(
|
||||
(MapFunction<SortableRelation, String>) value -> value.getSource(),
|
||||
Encoders.STRING())
|
||||
|
|
@ -114,7 +98,6 @@ public class PrepareRelationsJob {
|
|||
(FlatMapGroupsFunction<String, SortableRelation, SortableRelation>)
|
||||
(key, values) -> Iterators.limit(values, MAX_RELS),
|
||||
Encoders.bean(SortableRelation.class))
|
||||
.repartition(numPartitions)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.parquet(outputPath);
|
||||
|
|
|
|||
|
|
@ -3,14 +3,8 @@ package eu.dnetlib.dhp.oa.provision.utils;
|
|||
import static org.apache.commons.lang3.StringUtils.substringAfter;
|
||||
|
||||
import com.google.common.collect.Sets;
|
||||
import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
|
||||
import eu.dnetlib.dhp.schema.common.EntityType;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import java.util.List;
|
||||
import java.util.Objects;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
public class GraphMappingUtils {
|
||||
|
||||
|
|
@ -18,81 +12,6 @@ public class GraphMappingUtils {
|
|||
|
||||
public static Set<String> authorPidTypes = Sets.newHashSet("orcid", "magidentifier");
|
||||
|
||||
public static <E extends OafEntity> RelatedEntity asRelatedEntity(E entity, Class<E> clazz) {
|
||||
|
||||
final RelatedEntity re = new RelatedEntity();
|
||||
re.setId(entity.getId());
|
||||
re.setType(EntityType.fromClass(clazz).name());
|
||||
|
||||
re.setPid(entity.getPid());
|
||||
re.setCollectedfrom(entity.getCollectedfrom());
|
||||
|
||||
switch (EntityType.fromClass(clazz)) {
|
||||
case publication:
|
||||
case dataset:
|
||||
case otherresearchproduct:
|
||||
case software:
|
||||
Result result = (Result) entity;
|
||||
|
||||
if (result.getTitle() == null && !result.getTitle().isEmpty()) {
|
||||
re.setTitle(result.getTitle().stream().findFirst().get());
|
||||
}
|
||||
|
||||
re.setDateofacceptance(getValue(result.getDateofacceptance()));
|
||||
re.setPublisher(getValue(result.getPublisher()));
|
||||
re.setResulttype(result.getResulttype());
|
||||
re.setInstances(result.getInstance());
|
||||
|
||||
// TODO still to be mapped
|
||||
// re.setCodeRepositoryUrl(j.read("$.coderepositoryurl"));
|
||||
|
||||
break;
|
||||
case datasource:
|
||||
Datasource d = (Datasource) entity;
|
||||
|
||||
re.setOfficialname(getValue(d.getOfficialname()));
|
||||
re.setWebsiteurl(getValue(d.getWebsiteurl()));
|
||||
re.setDatasourcetype(d.getDatasourcetype());
|
||||
re.setOpenairecompatibility(d.getOpenairecompatibility());
|
||||
|
||||
break;
|
||||
case organization:
|
||||
Organization o = (Organization) entity;
|
||||
|
||||
re.setLegalname(getValue(o.getLegalname()));
|
||||
re.setLegalshortname(getValue(o.getLegalshortname()));
|
||||
re.setCountry(o.getCountry());
|
||||
re.setWebsiteurl(getValue(o.getWebsiteurl()));
|
||||
break;
|
||||
case project:
|
||||
Project p = (Project) entity;
|
||||
|
||||
re.setProjectTitle(getValue(p.getTitle()));
|
||||
re.setCode(getValue(p.getCode()));
|
||||
re.setAcronym(getValue(p.getAcronym()));
|
||||
re.setContracttype(p.getContracttype());
|
||||
|
||||
List<Field<String>> f = p.getFundingtree();
|
||||
if (!f.isEmpty()) {
|
||||
re.setFundingtree(
|
||||
f.stream().map(s -> s.getValue()).collect(Collectors.toList()));
|
||||
}
|
||||
break;
|
||||
}
|
||||
return re;
|
||||
}
|
||||
|
||||
private static String getValue(Field<String> field) {
|
||||
return getFieldValueWithDefault(field, "");
|
||||
}
|
||||
|
||||
private static <T> T getFieldValueWithDefault(Field<T> f, T defaultValue) {
|
||||
return Optional.ofNullable(f)
|
||||
.filter(Objects::nonNull)
|
||||
.map(x -> x.getValue())
|
||||
.orElse(defaultValue);
|
||||
}
|
||||
|
||||
public static String removePrefix(final String s) {
|
||||
if (s.contains("|")) return substringAfter(s, "|");
|
||||
return s;
|
||||
|
|
|
|||
|
|
@ -98,6 +98,7 @@
|
|||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--inputRelationsPath</arg><arg>${inputGraphRootPath}/relation</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/relation</arg>
|
||||
|
|
|
|||
Loading…
Reference in New Issue