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[Tagging Projects and Datasource] first extention of bulktagging to add the context to projects and datasource

This commit is contained in:
Miriam Baglioni 2024-02-13 16:37:14 +01:00
parent 3f7d262a4e
commit 6e1f383e4a
5 changed files with 161 additions and 17 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java
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@ -6,6 +6,7 @@ import java.io.IOException;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.URL;
import java.util.List;
import org.jetbrains.annotations.NotNull;
@ -77,4 +78,5 @@ public class QueryCommunityAPI {
return body;
}
}

53
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java
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@ -3,14 +3,13 @@ package eu.dnetlib.dhp.api;
import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.*;
import java.util.stream.Collectors;
import javax.management.Query;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Project;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -24,7 +23,6 @@ import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration;
import eu.dnetlib.dhp.bulktag.community.Provider;
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
import eu.dnetlib.dhp.bulktag.criteria.VerbResolverFactory;
import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob;
/**
* @author miriam.baglioni
@ -58,7 +56,7 @@ public class Utils implements Serializable {
if (d.getEnabled() == null || Boolean.FALSE.equals(d.getEnabled()))
return null;
Provider p = new Provider();
p.setOpenaireId("10|" + d.getOpenaireId());
p.setOpenaireId(ModelSupport.getIdPrefix(Datasource.class)+"|" + d.getOpenaireId());
p.setSelectionConstraints(d.getSelectioncriteria());
if (p.getSelectionConstraints() != null)
p.getSelectionConstraints().setSelection(resolver);
@ -113,6 +111,7 @@ public class Utils implements Serializable {
*/
public static CommunityEntityMap getCommunityOrganization(String baseURL) throws IOException {
CommunityEntityMap organizationMap = new CommunityEntityMap();
String entityPrefix = ModelSupport.getIdPrefix(Organization.class);
getValidCommunities(baseURL)
.forEach(community -> {
String id = community.getId();
@ -124,9 +123,9 @@ public class Utils implements Serializable {
if (!organizationMap
.keySet()
.contains(
"20|" + o))
organizationMap.put("20|" + o, new ArrayList<>());
organizationMap.get("20|" + o).add(community.getId());
entityPrefix + "|" + o))
organizationMap.put(entityPrefix + "|" + o, new ArrayList<>());
organizationMap.get(entityPrefix + "|" + o).add(community.getId());
});
} catch (IOException e) {
throw new RuntimeException(e);
@ -138,7 +137,7 @@ public class Utils implements Serializable {
public static CommunityEntityMap getCommunityProjects(String baseURL) throws IOException {
CommunityEntityMap projectMap = new CommunityEntityMap();
String entityPrefix = ModelSupport.getIdPrefix(Project.class);
getValidCommunities(baseURL)
.forEach(community -> {
int page = -1;
@ -155,9 +154,9 @@ public class Utils implements Serializable {
ContentModel.class);
if (cm.getContent().size() > 0) {
cm.getContent().forEach(p -> {
if (!projectMap.keySet().contains("40|" + p.getOpenaireId()))
projectMap.put("40|" + p.getOpenaireId(), new ArrayList<>());
projectMap.get("40|" + p.getOpenaireId()).add(community.getId());
if (!projectMap.keySet().contains(entityPrefix + "|" + p.getOpenaireId()))
projectMap.put(entityPrefix + "|" + p.getOpenaireId(), new ArrayList<>());
projectMap.get(entityPrefix + "|" + p.getOpenaireId()).add(community.getId());
});
}
} catch (IOException e) {
@ -174,4 +173,28 @@ public class Utils implements Serializable {
.map(community -> community.getId())
.collect(Collectors.toList());
}
public static List<EntityCommunities> getDatasourceCommunities(String baseURL)throws IOException{
List<CommunityModel> validCommunities = getValidCommunities(baseURL);
HashMap<String, Set<String>> map = new HashMap<>();
validCommunities.forEach(c -> {
try {
new ObjectMapper().readValue(QueryCommunityAPI.communityDatasource(c.getId(), baseURL), DatasourceList.class)
.forEach(d -> {
if (!map.keySet().contains(d.getOpenaireId()))
map.put(d.getOpenaireId(), new HashSet<>());
map.get(d.getOpenaireId()).add(c.getId());
});
} catch (IOException e) {
throw new RuntimeException(e);
}
});
return map.keySet().stream().map(k -> EntityCommunities.newInstance(k, map.get(k).stream().collect(Collectors.toList()))).collect(Collectors.toList());
}
}

39
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/EntityCommunities.java Normal file
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@ -0,0 +1,39 @@
package eu.dnetlib.dhp.api.model;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import java.io.Serializable;
import java.util.List;
/**
* @author miriam.baglioni
* @Date 13/02/24
*/
public class EntityCommunities implements Serializable {
private String entityId;
private List<String> communitiesId;
public String getEntityId() {
return entityId;
}
public void setEntityId(String entityId) {
this.entityId = entityId;
}
public List<String> getCommunitiesId() {
return communitiesId;
}
public void setCommunitiesId(List<String> communitiesId) {
this.communitiesId = communitiesId;
}
public static EntityCommunities newInstance(String dsid, List<String> csid){
EntityCommunities dsc = new EntityCommunities();
dsc.entityId = dsid;
dsc.communitiesId = csid;
return dsc;
}
}

82
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java
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@ -5,7 +5,14 @@ import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.*;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.api.model.CommunityEntityMap;
import eu.dnetlib.dhp.api.model.EntityCommunities;
import eu.dnetlib.dhp.api.model.DatasourceCommunitiesList;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.Project;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
@ -23,11 +30,11 @@ import com.google.gson.Gson;
import eu.dnetlib.dhp.api.Utils;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bulktag.community.*;
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;
import scala.Tuple2;
public class SparkBulkTagJob {
@ -89,9 +96,80 @@ public class SparkBulkTagJob {
spark -> {
extendCommunityConfigurationForEOSC(spark, inputPath, cc);
execBulkTag(spark, inputPath, outputPath, protoMappingParams, cc);
execDatasourceTag(spark, inputPath, outputPath, Utils.getDatasourceCommunities(baseURL));
execProjectTag(spark, inputPath, outputPath, Utils.getCommunityProjects(baseURL));
});
}
private static void execProjectTag(SparkSession spark, String inputPath, String outputPath, CommunityEntityMap communityProjects) {
Dataset<Project> projects = readPath(spark, inputPath + "project", Project.class);
Dataset<EntityCommunities> pc = spark.createDataset(communityProjects.keySet().stream().map(k -> EntityCommunities.newInstance(k, communityProjects.get(k))).collect(Collectors.toList()), Encoders.bean(EntityCommunities.class));
projects.joinWith(pc, projects.col("id").equalTo(pc.col("entityId")), "left")
.map((MapFunction<Tuple2<Project, EntityCommunities>, Project>) t2 -> {
Project ds = t2._1();
if (t2._2() != null){
List<String> context = ds.getContext().stream().map(c -> c.getId()).collect(Collectors.toList());
t2._2().getCommunitiesId().forEach(c -> {
if(!context.contains(c)){
Context con = new Context();
con.setId(c);
con.setDataInfo(Arrays.asList(OafMapperUtils.dataInfo(false,TaggingConstants.BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(TaggingConstants.CLASS_ID_DATASOURCE, TaggingConstants.CLASS_NAME_BULKTAG_DATASOURCE, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "1")));
ds.getContext().add(con)
}
});
}
return ds;
} ,Encoders.bean(Project.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(outputPath + "project");
readPath(spark, outputPath + "project", Datasource.class)
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(inputPath + "project");
}
private static void execDatasourceTag(SparkSession spark, String inputPath, String outputPath, List<EntityCommunities> datasourceCommunities) {
Dataset<Datasource> datasource = readPath(spark, inputPath + "datasource", Datasource.class);
Dataset<EntityCommunities> dc = spark.createDataset(datasourceCommunities, Encoders.bean(EntityCommunities.class));
datasource.joinWith(dc, datasource.col("id").equalTo(dc.col("entityId")), "left")
.map((MapFunction<Tuple2<Datasource, EntityCommunities>, Datasource>) t2 -> {
Datasource ds = t2._1();
if (t2._2() != null){
List<String> context = ds.getContext().stream().map(c -> c.getId()).collect(Collectors.toList());
t2._2().getCommunitiesId().forEach(c -> {
if(!context.contains(c)){
Context con = new Context();
con.setId(c);
con.setDataInfo(Arrays.asList(OafMapperUtils.dataInfo(false,TaggingConstants.BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(TaggingConstants.CLASS_ID_DATASOURCE, TaggingConstants.CLASS_NAME_BULKTAG_DATASOURCE, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "1")));
ds.getContext().add(con)
}
});
}
return ds;
} ,Encoders.bean(Datasource.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(outputPath + "datasource");
readPath(spark, outputPath + "datasource", Datasource.class)
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(inputPath + "datasource");
}
private static void extendCommunityConfigurationForEOSC(SparkSession spark, String inputPath,
CommunityConfiguration cc) {
@ -182,4 +260,6 @@ public class SparkBulkTagJob {
};
}
}

2
pom.xml
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@ -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>[4.17.3]</dhp-schemas.version>
<dhp-schemas.version>[5.17.3]</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>