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mergin with branch beta

This commit is contained in:
Miriam Baglioni 2023-10-31 14:36:03 +01:00
parent a4214ced1e a870aa2b09
commit e9a20fc8f6
5 changed files with 72 additions and 11 deletions
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10
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
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@ -286,6 +286,12 @@ public class GraphCleaningFunctions extends CleaningFunctions {
public static <T extends Oaf> T cleanup(T value, VocabularyGroup vocs) {
if (Objects.isNull(value.getDataInfo())) {
final DataInfo d = new DataInfo();
d.setDeletedbyinference(false);
value.setDataInfo(d);
}
if (value instanceof OafEntity) {
OafEntity e = (OafEntity) value;
@ -305,6 +311,10 @@ public class GraphCleaningFunctions extends CleaningFunctions {
} else if (value instanceof Result) {
Result r = (Result) value;
if (Objects.isNull(r.getContext())) {
r.setContext(new ArrayList<>());
}
if (Objects.nonNull(r.getFulltext())
&& (ModelConstants.SOFTWARE_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()) ||
ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) {

7
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java
View File

@ -27,6 +27,7 @@ import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
public class SparkBulkTagJob {
@ -165,10 +166,12 @@ public class SparkBulkTagJob {
// TODO remove this hack as soon as the values fixed by this method will be provided as NON null
private static <R extends Result> MapFunction<R, R> patchResult() {
return r -> {
if (r.getDataInfo().getDeletedbyinference() == null) {
if (Objects.isNull(r.getDataInfo())) {
r.setDataInfo(OafMapperUtils.dataInfo(false, "", false, false, OafMapperUtils.unknown("", ""), ""));
} else if (r.getDataInfo().getDeletedbyinference() == null) {
r.getDataInfo().setDeletedbyinference(false);
}
if (r.getContext() == null) {
if (Objects.isNull(r.getContext())) {
r.setContext(new ArrayList<>());
}
return r;

32
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java
View File

@ -5,10 +5,7 @@ import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
@ -88,14 +85,33 @@ public class PrepareResultCountrySet {
// selects all the results non deleted by inference and non invisible
Dataset<R> result = readPath(spark, inputPath, resultClazz)
.filter(
(FilterFunction<R>) r -> !r.getDataInfo().getDeletedbyinference() &&
!r.getDataInfo().getInvisible());
(FilterFunction<R>) r -> Optional
.ofNullable(r.getDataInfo())
.map(dataInfo -> !dataInfo.getDeletedbyinference() && !dataInfo.getInvisible())
.orElse(true));
// of the results collects the distinct keys for collected from (at the level of the result) and hosted by
// and produces pairs resultId, key for each distinct key associated to the result
result.flatMap((FlatMapFunction<R, EntityEntityRel>) r -> {
Set<String> cfhb = r.getCollectedfrom().stream().map(cf -> cf.getKey()).collect(Collectors.toSet());
cfhb.addAll(r.getInstance().stream().map(i -> i.getHostedby().getKey()).collect(Collectors.toSet()));
Set<String> cfhb = Optional
.ofNullable(r.getCollectedfrom())
.map(cf -> cf.stream().map(KeyValue::getKey).collect(Collectors.toSet()))
.orElse(new HashSet<>());
cfhb
.addAll(
Optional
.ofNullable(r.getInstance())
.map(
i -> i
.stream()
.map(
ii -> Optional
.ofNullable(ii.getHostedby())
.map(KeyValue::getKey)
.orElse(null))
.filter(Objects::nonNull)
.collect(Collectors.toSet()))
.orElse(new HashSet<>()));
return cfhb
.stream()
.map(value -> EntityEntityRel.newInstance(r.getId(), value))

32
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/config-default.xml
View File

@ -1,4 +1,12 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
@ -7,4 +15,28 @@
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
</property>
<property>
<name>sparkExecutorNumber</name>
<value>4</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
</configuration>

2
pom.xml
View File

@ -888,7 +888,7 @@
<mockito-core.version>3.3.3</mockito-core.version>
<mongodb.driver.version>3.4.2</mongodb.driver.version>
<vtd.version>[2.12,3.0)</vtd.version>
<dhp-schemas.version>[3.17.1]</dhp-schemas.version>
<dhp-schemas.version>[3.17.2]</dhp-schemas.version>
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>