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extended the logic of the dump to consider the validation date in the relation (also in the dumped result for communities and funders at the level of the project), the extention on the instance for the APC, the pid, the alternate identifiers, and the extention of the AccessRight to store the OpenAccessRoute. Added new resourec for testing and extended the old class to verify the new dump. Fixed also issue on relation dump: only relation whose source and target are entities in the graph are dumped. The same hold for references to projects

This commit is contained in:
Miriam Baglioni 2021-08-06 18:56:18 +02:00
parent 6bd1eca7e0
commit c3931557e3
36 changed files with 820 additions and 294 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java
View File

@ -37,8 +37,8 @@ public class DumpProducts implements Serializable {
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
Utils.removeOutputDir(spark, outputPath); Utils.removeOutputDir(spark, outputPath);
execDump( execDump(
spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType);
}); });
} }

18
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java
View File

@ -29,15 +29,15 @@ public class QueryInformationSystem {
"</community>"; "</community>";
private static final String XQUERY_CI = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " private static final String XQUERY_CI = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
+ +
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
" and $x//CONFIGURATION/context[./@id=%s] " " and $x//CONFIGURATION/context[./@id=%s] "
+ +
" return " + " return " +
"<community> " + "<community> " +
"{$x//CONFIGURATION/context/@id}" + "{$x//CONFIGURATION/context/@id}" +
"{$x//CONFIGURATION/context/@label}" + "{$x//CONFIGURATION/context/@label}" +
"</community>"; "</community>";
public CommunityMap getCommunityMap(boolean singleCommunity, String community_id) public CommunityMap getCommunityMap(boolean singleCommunity, String community_id)
throws ISLookUpException, DocumentException { throws ISLookUpException, DocumentException {

133
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java
View File

@ -5,6 +5,10 @@ import java.io.Serializable;
import java.util.*; import java.util.*;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.*;
import eu.dnetlib.dhp.schema.dump.oaf.AccessRight; import eu.dnetlib.dhp.schema.dump.oaf.AccessRight;
import eu.dnetlib.dhp.schema.dump.oaf.Author; import eu.dnetlib.dhp.schema.dump.oaf.Author;
import eu.dnetlib.dhp.schema.dump.oaf.Country; import eu.dnetlib.dhp.schema.dump.oaf.Country;
@ -14,15 +18,13 @@ import eu.dnetlib.dhp.schema.dump.oaf.KeyValue;
import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
import eu.dnetlib.dhp.schema.dump.oaf.Qualifier; import eu.dnetlib.dhp.schema.dump.oaf.Qualifier;
import eu.dnetlib.dhp.schema.dump.oaf.Result; import eu.dnetlib.dhp.schema.dump.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.*;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.dump.oaf.community.Context; import eu.dnetlib.dhp.schema.dump.oaf.community.Context;
import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
public class ResultMapper implements Serializable { public class ResultMapper implements Serializable {
@ -137,9 +139,12 @@ public class ResultMapper implements Serializable {
} }
Optional<List<Measure>> mes = Optional.ofNullable(input.getMeasures()); Optional<List<Measure>> mes = Optional.ofNullable(input.getMeasures());
if(mes.isPresent()){ if (mes.isPresent()) {
List<KeyValue> measure = new ArrayList<>(); List<KeyValue> measure = new ArrayList<>();
mes.get().forEach(m -> m.getUnit().forEach(u -> measure.add(KeyValue.newInstance(u.getKey(), u.getValue())))); mes
.get()
.forEach(
m -> m.getUnit().forEach(u -> measure.add(KeyValue.newInstance(m.getId(), u.getValue()))));
out.setMeasures(measure); out.setMeasures(measure);
} }
@ -271,18 +276,17 @@ public class ResultMapper implements Serializable {
} }
List<ControlledField> pids = new ArrayList<>();
Optional Optional
.ofNullable(input.getPid()) .ofNullable(input.getPid())
.ifPresent( .ifPresent(
value -> value value -> out.setPid(value
.stream() .stream()
.forEach( .map(
p -> pids p ->
.add(
ControlledField ControlledField
.newInstance(p.getQualifier().getClassid(), p.getValue())))); .newInstance(p.getQualifier().getClassid(), p.getValue())).collect(Collectors.toList())));
out.setPid(pids);
oStr = Optional.ofNullable(input.getDateofacceptance()); oStr = Optional.ofNullable(input.getDateofacceptance());
if (oStr.isPresent()) { if (oStr.isPresent()) {
out.setPublicationdate(oStr.get().getValue()); out.setPublicationdate(oStr.get().getValue());
@ -292,10 +296,11 @@ public class ResultMapper implements Serializable {
out.setPublisher(oStr.get().getValue()); out.setPublisher(oStr.get().getValue());
} }
List<String> sourceList = new ArrayList<>();
Optional Optional
.ofNullable(input.getSource()) .ofNullable(input.getSource())
.ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); .ifPresent(value -> out.setSource(value.stream().map(s -> s.getValue()).collect(Collectors.toList()) ));
// value.stream().forEach(s -> sourceList.add(s.getValue())));
// out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList()));
List<Subject> subjectList = new ArrayList<>(); List<Subject> subjectList = new ArrayList<>();
Optional Optional
@ -421,8 +426,8 @@ public class ResultMapper implements Serializable {
code, code,
Constants.coarCodeLabelMap.get(code), Constants.coarCodeLabelMap.get(code),
Constants.COAR_ACCESS_RIGHT_SCHEMA)); Constants.COAR_ACCESS_RIGHT_SCHEMA));
if (opAr.get().getOpenAccessRoute() != null){ if (opAr.get().getOpenAccessRoute() != null) {
switch (opAr.get().getOpenAccessRoute()){ switch (opAr.get().getOpenAccessRoute()) {
case hybrid: case hybrid:
instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid);
break; break;
@ -441,14 +446,25 @@ public class ResultMapper implements Serializable {
} }
} }
Optional.ofNullable(i.getPid()) Optional
.ifPresent(pid -> instance.setPid( .ofNullable(i.getPid())
pid.stream().map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) .ifPresent(
.collect(Collectors.toList()))); pid -> instance
.setPid(
pid
.stream()
.map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
.collect(Collectors.toList())));
Optional.ofNullable(i.getAlternateIdentifier()) Optional
.ifPresent(ai -> instance.setAlternateIdentifier(ai.stream().map(p -> ControlledField. .ofNullable(i.getAlternateIdentifier())
newInstance(p.getQualifier().getClassid(), p.getValue())).collect(Collectors.toList()))); .ifPresent(
ai -> instance
.setAlternateIdentifier(
ai
.stream()
.map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
.collect(Collectors.toList())));
Optional Optional
.ofNullable(i.getLicense()) .ofNullable(i.getLicense())
@ -554,34 +570,55 @@ public class ResultMapper implements Serializable {
return a; return a;
} }
private static Pid getOrcid(List<StructuredProperty> p) { private static Pid getAuthorPid(StructuredProperty pid) {
for (StructuredProperty pid : p) { Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo());
if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) { if (di.isPresent()) {
Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo()); return Pid
if (di.isPresent()) { .newInstance(
return Pid
.newInstance(
ControlledField ControlledField
.newInstance( .newInstance(
pid.getQualifier().getClassid(), pid.getQualifier().getClassid(),
pid.getValue()), pid.getValue()),
Provenance Provenance
.newInstance( .newInstance(
di.get().getProvenanceaction().getClassname(), di.get().getProvenanceaction().getClassname(),
di.get().getTrust())); di.get().getTrust()));
} else { } else {
return Pid return Pid
.newInstance( .newInstance(
ControlledField ControlledField
.newInstance( .newInstance(
pid.getQualifier().getClassid(), pid.getQualifier().getClassid(),
pid.getValue()) pid.getValue())
); );
}
}
} }
}
private static Pid getOrcid(List<StructuredProperty> p) {
List<StructuredProperty> pid_list = p.stream().map(pid -> {
if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) ||
(pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))){
return pid;
}
return null;
}).filter(pid -> pid != null).collect(Collectors.toList());
if(pid_list.size() == 1){
return getAuthorPid(pid_list.get(0));
}
List<StructuredProperty> orcid = pid_list.stream().filter(ap -> ap.getQualifier().getClassid()
.equals(ModelConstants.ORCID)).collect(Collectors.toList());
if(orcid.size() == 1){
return getAuthorPid(orcid.get(0));
}
orcid = pid_list.stream().filter(ap -> ap.getQualifier().getClassid()
.equals(ModelConstants.ORCID_PENDING)).collect(Collectors.toList());
if(orcid.size() == 1){
return getAuthorPid(orcid.get(0));
}
return null; return null;
} }

23
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.oa.graph.dump; package eu.dnetlib.dhp.oa.graph.dump;
import java.io.BufferedWriter; import java.io.BufferedWriter;
@ -54,10 +55,10 @@ public class SaveCommunityMap implements Serializable {
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils String jsonConfiguration = IOUtils
.toString( .toString(
SaveCommunityMap.class SaveCommunityMap.class
.getResourceAsStream( .getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json")); "/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);
@ -71,8 +72,10 @@ public class SaveCommunityMap implements Serializable {
final String isLookUpUrl = parser.get("isLookUpUrl"); final String isLookUpUrl = parser.get("isLookUpUrl");
log.info("isLookUpUrl: {}", isLookUpUrl); log.info("isLookUpUrl: {}", isLookUpUrl);
final Boolean singleCommunity = Optional.ofNullable(parser.get("singleDeposition")) final Boolean singleCommunity = Optional
.map(Boolean::valueOf).orElse(false); .ofNullable(parser.get("singleDeposition"))
.map(Boolean::valueOf)
.orElse(false);
final String community_id = Optional.ofNullable(parser.get("communityId")).orElse(null); final String community_id = Optional.ofNullable(parser.get("communityId")).orElse(null);
@ -82,8 +85,12 @@ public class SaveCommunityMap implements Serializable {
} }
private void saveCommunityMap(boolean singleCommunity, String community_id) throws ISLookUpException, IOException, DocumentException { private void saveCommunityMap(boolean singleCommunity, String community_id)
writer.write(Utils.OBJECT_MAPPER.writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, community_id))); throws ISLookUpException, IOException, DocumentException {
writer
.write(
Utils.OBJECT_MAPPER
.writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, community_id)));
writer.close(); writer.close();
} }
} }

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java
View File

@ -48,14 +48,14 @@ public class SendToZenodoHDFS implements Serializable {
.orElse(false); .orElse(false);
final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null); final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null);
//final String communityMapPath = parser.get("communityMapPath"); // final String communityMapPath = parser.get("communityMapPath");
Configuration conf = new Configuration(); Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode); conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf); FileSystem fileSystem = FileSystem.get(conf);
//CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath); // CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath);
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
.listFiles( .listFiles(

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java
View File

@ -49,7 +49,7 @@ public class CommunitySplit implements Serializable {
.union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class));
communities communities
.keySet() .keySet()
.stream() .stream()
.forEach(c -> printResult(c, result, outputPath + "/" + communities.get(c).replace(" ", "_"))); .forEach(c -> printResult(c, result, outputPath + "/" + communities.get(c).replace(" ", "_")));

14
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java
View File

@ -8,6 +8,8 @@ import java.io.StringReader;
import java.util.*; import java.util.*;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.community.Validated;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
@ -76,7 +78,7 @@ public class SparkPrepareResultProject implements Serializable {
private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) { private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) {
Dataset<Relation> relation = Utils Dataset<Relation> relation = Utils
.readPath(spark, inputPath + "/relation", Relation.class) .readPath(spark, inputPath + "/relation", Relation.class)
.filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'"); .filter("dataInfo.deletedbyinference = false and lower(relClass) = '" + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'");
Dataset<eu.dnetlib.dhp.schema.oaf.Project> projects = Utils Dataset<eu.dnetlib.dhp.schema.oaf.Project> projects = Utils
.readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class);
@ -96,7 +98,7 @@ public class SparkPrepareResultProject implements Serializable {
rp.setResultId(s); rp.setResultId(s);
eu.dnetlib.dhp.schema.oaf.Project p = first._1(); eu.dnetlib.dhp.schema.oaf.Project p = first._1();
projectSet.add(p.getId()); projectSet.add(p.getId());
Project ps = getProject(p); Project ps = getProject(p, first._2);
List<Project> projList = new ArrayList<>(); List<Project> projList = new ArrayList<>();
projList.add(ps); projList.add(ps);
@ -105,7 +107,7 @@ public class SparkPrepareResultProject implements Serializable {
eu.dnetlib.dhp.schema.oaf.Project op = c._1(); eu.dnetlib.dhp.schema.oaf.Project op = c._1();
if (!projectSet.contains(op.getId())) { if (!projectSet.contains(op.getId())) {
projList projList
.add(getProject(op)); .add(getProject(op, c._2));
projectSet.add(op.getId()); projectSet.add(op.getId());
@ -120,7 +122,7 @@ public class SparkPrepareResultProject implements Serializable {
.json(outputPath); .json(outputPath);
} }
private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op) { private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op, Relation relation) {
Project p = Project Project p = Project
.newInstance( .newInstance(
op.getId(), op.getId(),
@ -155,7 +157,9 @@ public class SparkPrepareResultProject implements Serializable {
provenance.setTrust(di.get().getTrust()); provenance.setTrust(di.get().getTrust());
p.setProvenance(provenance); p.setProvenance(provenance);
} }
if (relation.getValidated()){
p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate()));
}
return p; return p;
} }

26
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java
View File

@ -1,6 +1,7 @@
package eu.dnetlib.dhp.oa.graph.dump.complete; package eu.dnetlib.dhp.oa.graph.dump.complete;
import static com.jayway.jsonpath.Filter.filter;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable; import java.io.Serializable;
@ -8,8 +9,12 @@ import java.io.StringReader;
import java.util.*; import java.util.*;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
@ -448,19 +453,18 @@ public class DumpGraphEntities implements Serializable {
private static <E extends OafEntity> void organizationMap(SparkSession spark, String inputPath, String outputPath, private static <E extends OafEntity> void organizationMap(SparkSession spark, String inputPath, String outputPath,
Class<E> inputClazz) { Class<E> inputClazz) {
Utils Utils.readPath(spark, inputPath, inputClazz)
.readPath(spark, inputPath, inputClazz) .map(
.map( (MapFunction<E, Organization>) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o),
(MapFunction<E, Organization>) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), Encoders.bean(Organization.class))
Encoders.bean(Organization.class)) .filter((FilterFunction<Organization>) o -> o!= null)
.filter(Objects::nonNull) .write()
.write() .mode(SaveMode.Overwrite)
.mode(SaveMode.Overwrite) .option("compression", "gzip")
.option("compression", "gzip") .json(outputPath);
.json(outputPath);
} }
private static Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) { private static eu.dnetlib.dhp.schema.dump.oaf.graph.Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) {
if (org.getDataInfo().getDeletedbyinference()) if (org.getDataInfo().getDeletedbyinference())
return null; return null;
Organization organization = new Organization(); Organization organization = new Organization();

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java
View File

@ -129,7 +129,7 @@ public class Extractor implements Serializable {
return relationList.iterator(); return relationList.iterator();
}, Encoders.bean(Relation.class)) }, Encoders.bean(Relation.class))
.write() .write()
.option("compression", "gzip") .option("compression", "gzip")
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.json(outputPath); .json(outputPath);

7
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java
View File

@ -5,6 +5,8 @@ import java.io.StringReader;
import java.util.*; import java.util.*;
import java.util.function.Consumer; import java.util.function.Consumer;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import org.dom4j.Document; import org.dom4j.Document;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
import org.dom4j.Element; import org.dom4j.Element;
@ -12,9 +14,9 @@ import org.dom4j.Node;
import org.dom4j.io.SAXReader; import org.dom4j.io.SAXReader;
import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.NotNull;
import eu.dnetlib.dhp.utils.DHPUtils;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.dhp.utils.DHPUtils;
public class QueryInformationSystem { public class QueryInformationSystem {
@ -136,6 +138,9 @@ public class QueryInformationSystem {
} }
private String makeOpenaireId(Node el, String prefix) { private String makeOpenaireId(Node el, String prefix) {
if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))){
return null;
}
String funder = null; String funder = null;
String grantId = null; String grantId = null;
String funding = null; String funding = null;

11
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java
View File

@ -107,13 +107,10 @@ public class SparkDumpRelationJob implements Serializable {
} }
} }
} }
// Optional if(relation.getValidated()){
// .ofNullable(relation.getDataInfo()) rel_new.setValidated(relation.getValidated());
// .ifPresent( rel_new.setValidationDate(relation.getValidationDate());
// datainfo -> rel_new }
// .setProvenance(
// Provenance
// .newInstance(datainfo.getProvenanceaction().getClassname(), datainfo.getTrust())));
return rel_new; return rel_new;

65
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java
View File

@ -44,9 +44,9 @@ public class SparkDumpFunderResults implements Serializable {
parser.parseArgument(args); parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional 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);
final String inputPath = parser.get("sourcePath"); final String inputPath = parser.get("sourcePath");
@ -55,40 +55,38 @@ public class SparkDumpFunderResults implements Serializable {
final String outputPath = parser.get("outputPath"); final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath); log.info("outputPath: {}", outputPath);
final String relationPath = parser.get("relationPath"); final String graphPath = parser.get("graphPath");
log.info("relationPath: {}", relationPath); log.info("relationPath: {}", graphPath);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
runWithSparkSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
Utils.removeOutputDir(spark, outputPath); Utils.removeOutputDir(spark, outputPath);
writeResultProjectList(spark, inputPath, outputPath, relationPath); writeResultProjectList(spark, inputPath, outputPath, graphPath);
}); });
} }
private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath,
String relationPath) { String graphPath) {
Dataset<Relation> relation = Utils Dataset<eu.dnetlib.dhp.schema.oaf.Project> project = Utils
.readPath(spark, relationPath + "/relation", Relation.class) .readPath(spark, graphPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class);
.filter(
"dataInfo.deletedbyinference = false and lower(relClass) = '"
+ ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'");
Dataset<CommunityResult> result = Utils Dataset<CommunityResult> result = Utils
.readPath(spark, inputPath + "/publication", CommunityResult.class) .readPath(spark, inputPath + "/publication", CommunityResult.class)
.union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class))
.union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class))
.union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class));
List<String> funderList = relation
.select("target") List<String> funderList = project
.map((MapFunction<Row, String>) value -> value.getString(0).substring(0, 15), Encoders.STRING()) .select("id")
.distinct() .map((MapFunction<Row, String>) value -> value.getString(0).substring(0, 15), Encoders.STRING())
.collectAsList(); .distinct()
.collectAsList();
funderList.forEach(funder -> { funderList.forEach(funder -> {
String fundernsp = funder.substring(3); String fundernsp = funder.substring(3);
@ -109,7 +107,7 @@ public class SparkDumpFunderResults implements Serializable {
} }
private static void dumpResults(String nsp, Dataset<CommunityResult> results, String outputPath, private static void dumpResults(String nsp, Dataset<CommunityResult> results, String outputPath,
String funderName) { String funderName) {
results.map((MapFunction<CommunityResult, CommunityResult>) r -> { results.map((MapFunction<CommunityResult, CommunityResult>) r -> {
if (!Optional.ofNullable(r.getProjects()).isPresent()) { if (!Optional.ofNullable(r.getProjects()).isPresent()) {
@ -117,7 +115,6 @@ public class SparkDumpFunderResults implements Serializable {
} }
for (Project p : r.getProjects()) { for (Project p : r.getProjects()) {
if (p.getId().startsWith(nsp)) { if (p.getId().startsWith(nsp)) {
if (nsp.startsWith("40|irb")) { if (nsp.startsWith("40|irb")) {
if (p.getFunder().getShortName().equals(funderName)) if (p.getFunder().getShortName().equals(funderName))
return r; return r;
@ -129,15 +126,15 @@ public class SparkDumpFunderResults implements Serializable {
} }
return null; return null;
}, Encoders.bean(CommunityResult.class)) }, Encoders.bean(CommunityResult.class))
.filter((FilterFunction<CommunityResult>) r -> r != null) .filter(Objects::nonNull)
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression", "gzip") .option("compression", "gzip")
.json(outputPath + "/" + funderName); .json(outputPath + "/" + funderName);
} }
private static void writeFunderResult(String funder, Dataset<CommunityResult> results, String outputPath, private static void writeFunderResult(String funder, Dataset<CommunityResult> results, String outputPath,
String funderDump) { String funderDump) {
if (funder.startsWith("40|irb")) { if (funder.startsWith("40|irb")) {
dumpResults(funder, results, outputPath, "HRZZ"); dumpResults(funder, results, outputPath, "HRZZ");

43
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java
View File

@ -10,6 +10,7 @@ import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SaveMode;
@ -21,14 +22,14 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.Constants;
import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
import scala.Tuple2; import scala.Tuple2;
import org.apache.spark.sql.*;
import eu.dnetlib.dhp.schema.oaf.Project;
/** /**
* Selects the results linked to projects. Only for these results the dump will be performed. * Selects the results linked to projects. Only for these results the dump will be performed.
* The code to perform the dump and to expend the dumped results with the informaiton related to projects * The code to perform the dump and to expend the dumped results with the information related to projects
* is the one used for the dump of the community products * is the one used for the dump of the community products
*/ */
public class SparkResultLinkedToProject implements Serializable { public class SparkResultLinkedToProject implements Serializable {
@ -78,6 +79,7 @@ public class SparkResultLinkedToProject implements Serializable {
private static <R extends Result> void writeResultsLinkedToProjects(SparkSession spark, Class<R> inputClazz, private static <R extends Result> void writeResultsLinkedToProjects(SparkSession spark, Class<R> inputClazz,
String inputPath, String outputPath, String graphPath) { String inputPath, String outputPath, String graphPath) {
Dataset<R> results = Utils Dataset<R> results = Utils
.readPath(spark, inputPath, inputClazz) .readPath(spark, inputPath, inputClazz)
.filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false");
@ -86,25 +88,32 @@ public class SparkResultLinkedToProject implements Serializable {
.filter( .filter(
"dataInfo.deletedbyinference = false and lower(relClass) = '" "dataInfo.deletedbyinference = false and lower(relClass) = '"
+ ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'");
Dataset<Project> project = Utils.readPath(spark, graphPath + "/project", Project.class);
spark results.createOrReplaceTempView("result");
.sql( relations.createOrReplaceTempView("relation");
"Select res.* " + project.createOrReplaceTempView("project");
"from relation rel " +
"join result res " + Dataset<R> tmp = spark
"on rel.source = res.id " + .sql(
"join project p " + "Select res.* " +
"on rel.target = p.id " + "from relation rel " +
"") "join result res " +
.as(Encoders.bean(inputClazz)) "on rel.source = res.id " +
.groupByKey( "join project p " +
(MapFunction< R, String>) value -> value "on rel.target = p.id " +
.getId(), "")
.as(Encoders.bean(inputClazz));
tmp
.groupByKey(
(MapFunction<R, String>) value -> value
.getId(),
Encoders.STRING()) Encoders.STRING())
.mapGroups((MapGroupsFunction<String, R, R>) (k, it) -> it.next(), Encoders.bean(inputClazz)) .mapGroups((MapGroupsFunction<String, R, R>) (k, it) -> it.next(), Encoders.bean(inputClazz))
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression", "gzip") .option("compression", "gzip")
.json(outputPath); .json(outputPath);
} }
} }

4
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json
View File

@ -18,8 +18,8 @@
"paramRequired": false "paramRequired": false
}, },
{ {
"paramName": "rp", "paramName": "gp",
"paramLongName": "relationPath", "paramLongName": "graphPath",
"paramDescription": "the relationPath", "paramDescription": "the relationPath",
"paramRequired": true "paramRequired": true
} }

4
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json
View File

@ -24,8 +24,8 @@
"paramRequired": true "paramRequired": true
}, },
{ {
"paramName":"rp", "paramName":"gp",
"paramLongName":"relationPath", "paramLongName":"graphPath",
"paramDescription": "the path to the relations", "paramDescription": "the path to the relations",
"paramRequired": true "paramRequired": true
} }

182
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java
View File

@ -7,7 +7,13 @@ import java.nio.file.Path;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.sun.xml.internal.ws.policy.AssertionSet;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.Instance;
import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.neethi.Assertion;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
@ -199,7 +205,7 @@ public class DumpJobTest {
Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90);
//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
} }
@ -302,6 +308,178 @@ public class DumpJobTest {
//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) //TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
}
@Test
public void testPublicationExtendedInstance(){
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<GraphResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
Assertions.assertEquals(1, verificationDataset.count());
verificationDataset.show(false);
GraphResult gr = verificationDataset.first();
Assertions.assertEquals(2, gr.getMeasures().size());
Assertions.assertTrue(gr.getMeasures().stream().anyMatch(m -> m.getKey().equals("influence")
&& m.getValue().equals("1.62759106106e-08")));
Assertions.assertTrue(gr.getMeasures().stream().anyMatch(m -> m.getKey().equals("popularity")
&& m.getValue().equals("0.22519296")));
Assertions.assertEquals(6, gr.getAuthor().size());
Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Nikolaidou,Charitini") &&
a.getName().equals("Charitini") && a.getSurname().equals("Nikolaidou")
&& a.getRank() == 1 && a.getPid() == null));
Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Votsi,Nefta") &&
a.getName().equals("Nefta") && a.getSurname().equals("Votsi")
&& a.getRank() == 2 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID)
&& a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null));
Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Sgardelis,Steanos") &&
a.getName().equals("Steanos") && a.getSurname().equals("Sgardelis")
&& a.getRank() == 3 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING)
&& a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null));
Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Halley,John") &&
a.getName().equals("John") && a.getSurname().equals("Halley")
&& a.getRank() == 4 && a.getPid() == null));
Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Pantis,John") &&
a.getName().equals("John") && a.getSurname().equals("Pantis")
&& a.getRank() == 5 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID)
&& a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null));
Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Tsiafouli,Maria") &&
a.getName().equals("Maria") && a.getSurname().equals("Tsiafouli")
&& a.getRank() == 6 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING)
&& a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null));
Assertions.assertEquals("publication", gr.getType());
Assertions.assertEquals("eng", gr.getLanguage().getCode());
Assertions.assertEquals("English", gr.getLanguage().getLabel());
Assertions.assertEquals(1, gr.getCountry().size());
Assertions.assertEquals("IT" , gr.getCountry().get(0).getCode());
Assertions.assertEquals("Italy" , gr.getCountry().get(0).getLabel());
Assertions.assertTrue( gr.getCountry().get(0).getProvenance() == null);
Assertions.assertEquals(12, gr.getSubjects().size());
Assertions.assertTrue(gr.getSubjects().stream().anyMatch(s -> s.getSubject().getValue().equals("Ecosystem Services hotspots")
&& s.getSubject().getScheme().equals("ACM") && s.getProvenance() != null &&
s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository")));
Assertions.assertTrue(gr.getSubjects().stream().anyMatch(s -> s.getSubject().getValue().equals("Natura 2000")
&& s.getSubject().getScheme().equals("") && s.getProvenance() != null &&
s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository")));
Assertions.assertEquals("Ecosystem Service capacity is higher in areas of multiple designation types",
gr.getMaintitle());
Assertions.assertEquals(null, gr.getSubtitle());
Assertions.assertEquals(1, gr.getDescription().size());
Assertions.assertTrue(gr.getDescription().get(0).startsWith("The implementation of the Ecosystem Service (ES) concept into practice"));
Assertions.assertTrue(gr.getDescription().get(0).endsWith("start complying with new standards and demands for nature conservation and environmental management."));
Assertions.assertEquals("2017-01-01", gr.getPublicationdate());
Assertions.assertEquals("Pensoft Publishers", gr.getPublisher());
Assertions.assertEquals(null, gr.getEmbargoenddate());
Assertions.assertEquals(1, gr.getSource().size());
Assertions.assertEquals("One Ecosystem 2: e13718", gr.getSource().get(0));
Assertions.assertEquals(1, gr.getFormat().size());
Assertions.assertEquals("text/html", gr.getFormat().get(0));
Assertions.assertEquals(0, gr.getContributor().size());
Assertions.assertEquals(0, gr.getCoverage().size());
Assertions.assertEquals(ModelConstants.ACCESS_RIGHT_OPEN, gr.getBestaccessright().getLabel());
Assertions.assertEquals(Constants.accessRightsCoarMap.get(ModelConstants.ACCESS_RIGHT_OPEN), gr.getBestaccessright().getCode());
Assertions.assertEquals(null, gr.getBestaccessright().getOpenAccessRoute());
Assertions.assertEquals("One Ecosystem", gr.getContainer().getName());
Assertions.assertEquals("2367-8194", gr.getContainer().getIssnOnline());
Assertions.assertEquals("", gr.getContainer().getIssnPrinted());
Assertions.assertEquals("", gr.getContainer().getIssnLinking());
Assertions.assertTrue(null == gr.getDocumentationUrl() || gr.getDocumentationUrl().size() == 0);
Assertions.assertTrue(null == gr.getCodeRepositoryUrl());
Assertions.assertEquals(null, gr.getProgrammingLanguage());
Assertions.assertTrue(null == gr.getContactperson() || gr.getContactperson().size() == 0);
Assertions.assertTrue(null == gr.getContactgroup() || gr.getContactgroup().size() == 0);
Assertions.assertTrue(null == gr.getTool() || gr.getTool().size() == 0);
Assertions.assertEquals(null, gr.getSize());
Assertions.assertEquals(null, gr.getVersion());
Assertions.assertTrue(null == gr.getGeolocation() || gr.getGeolocation().size() == 0);
Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId());
Assertions.assertEquals(2, gr.getOriginalId().size());
Assertions.assertTrue(gr.getOriginalId().contains("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2")
&& gr.getOriginalId().contains("10.3897/oneeco.2.e13718"));
Assertions.assertEquals(1, gr.getPid().size());
Assertions.assertTrue(gr.getPid().get(0).getScheme().equals("doi")
&& gr.getPid().get(0).getValue().equals("10.1016/j.triboint.2014.05.004"));
Assertions.assertEquals("2020-03-23T00:20:51.392Z", gr.getDateofcollection());
Assertions.assertEquals(1, gr.getInstance().size());
Instance instance = gr.getInstance().get(0);
Assertions.assertEquals(0, instance.getPid().size());
Assertions.assertEquals(1, instance.getAlternateIdentifier().size());
Assertions.assertTrue(instance.getAlternateIdentifier().get(0).getScheme().equals("doi")
&& instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718"));
Assertions.assertEquals(null, instance.getLicense());
Assertions.assertTrue(instance.getAccessright().getCode().equals(Constants.accessRightsCoarMap
.get(ModelConstants.ACCESS_RIGHT_OPEN)));
Assertions.assertTrue(instance.getAccessright().getLabel().equals(ModelConstants.ACCESS_RIGHT_OPEN));
Assertions.assertTrue(instance.getAccessright().getOpenAccessRoute().equals(OpenAccessRoute.green));
Assertions.assertEquals(2, instance.getUrl().size());
Assertions.assertTrue(instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718")
&& instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/"));
Assertions.assertEquals("2017-01-01",instance.getPublicationdate());
Assertions.assertEquals(null,instance.getArticleprocessingcharge());
Assertions.assertEquals("peerReviewed", instance.getRefereed());
} }
@Test @Test
@ -455,6 +633,8 @@ public class DumpJobTest {
Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1);
// verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset // verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset
// .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'") // .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'")
// .count() // .count()

109
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java
View File

@ -7,9 +7,11 @@ import java.nio.file.Path;
import java.util.HashMap; import java.util.HashMap;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.neethi.Assertion;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row; import org.apache.spark.sql.Row;
@ -236,4 +238,111 @@ public class PrepareResultProjectJobTest {
} }
@Test
public void testMatchValidated() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels")
.getPath();
SparkPrepareResultProject.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/preparedInfo",
"-sourcePath", sourcePath
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<ResultProject> tmp = sc
.textFile(workingDir.toString() + "/preparedInfo")
.map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class));
org.apache.spark.sql.Dataset<ResultProject> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(ResultProject.class));
Assertions.assertTrue(verificationDataset.count() == 2);
Assertions
.assertEquals(
1,
verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
Assertions
.assertEquals(
1,
verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
verificationDataset.createOrReplaceTempView("dataset");
String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " +
"MyT.validated.validatedByFunder, MyT.validated.validationDate "
+ "from dataset "
+ "lateral view explode(projectsList) p as MyT ";
org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
Assertions.assertEquals(3, resultExplodedProvenance.count());
Assertions.assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count());
Assertions
.assertEquals(
2,
resultExplodedProvenance
.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'")
.count());
Assertions
.assertEquals(
2,
resultExplodedProvenance
.filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter(
"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " +
"and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " +
"and validatedByFunder = true " +
"and validationDate = '2021-08-06'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter(
"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " +
"and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " +
"and validatedByFunder = true and validationDate = '2021-08-04'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter(
"project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " +
"and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " +
"and validatedByFunder = true and validationDate = '2021-08-05'")
.count());
Assertions
.assertEquals(
3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count());
}
} }

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java
View File

@ -24,7 +24,7 @@ public class QueryInformationSystemTest {
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
+ +
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
" and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') " " and ($x//context/param[./@name = 'status']/text() = 'all') "
+ +
" return " + " return " +
"<community> " + "<community> " +

8
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java
View File

@ -79,7 +79,7 @@ public class SplitForCommunityTest {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<CommunityResult> tmp = sc JavaRDD<CommunityResult> tmp = sc
.textFile(workingDir.toString() + "/split/dh-ch") .textFile(workingDir.toString() + "/split/Digital_Humanities_and_Cultural_Heritage")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
@ -92,7 +92,7 @@ public class SplitForCommunityTest {
1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); 1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
tmp = sc tmp = sc
.textFile(workingDir.toString() + "/split/egi") .textFile(workingDir.toString() + "/split/EGI_Federation")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
verificationDataset = spark verificationDataset = spark
@ -105,7 +105,7 @@ public class SplitForCommunityTest {
1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); 1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
tmp = sc tmp = sc
.textFile(workingDir.toString() + "/split/ni") .textFile(workingDir.toString() + "/split/Neuroinformatics")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
verificationDataset = spark verificationDataset = spark
@ -118,7 +118,7 @@ public class SplitForCommunityTest {
1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count()); 1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count());
tmp = sc tmp = sc
.textFile(workingDir.toString() + "/split/science-innovation-policy") .textFile(workingDir.toString() + "/split/Science_and_Innovation_Policy_Studies")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
verificationDataset = spark verificationDataset = spark

238
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java
View File

@ -1,8 +1,6 @@
package eu.dnetlib.dhp.oa.graph.dump.complete; package eu.dnetlib.dhp.oa.graph.dump.complete;
import eu.dnetlib.dhp.schema.oaf.Project;
import java.util.*; import java.util.*;
import java.util.function.Consumer; import java.util.function.Consumer;
import java.util.stream.Collectors; import java.util.stream.Collectors;
@ -16,6 +14,7 @@ import com.google.gson.Gson;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.dhp.utils.DHPUtils;
public class CreateRelationTest { public class CreateRelationTest {
@ -205,7 +204,7 @@ public class CreateRelationTest {
" <param name=\"suggestedAcknowledgement\"/>\n" + " <param name=\"suggestedAcknowledgement\"/>\n" +
" <param name=\"zenodoCommunity\">oac_ni</param>\n" + " <param name=\"zenodoCommunity\">oac_ni</param>\n" +
" <param name=\"creationdate\">2018-03-01T12:00:00</param>\n" + " <param name=\"creationdate\">2018-03-01T12:00:00</param>\n" +
" <category claim=\"false\" id=\"ni::projects\" label=\"NI Content providers\"/>\n" + " <category claim=\"false\" id=\"ni::projects\" label=\"NI Content providers\"/>\n" +
" <category claim=\"false\" id=\"ni::contentproviders\" label=\"NI Content providers\">\n" + " <category claim=\"false\" id=\"ni::contentproviders\" label=\"NI Content providers\">\n" +
" <concept claim=\"false\" id=\"ni::contentproviders::1\" label=\"OpenNeuro\">\n" + " <concept claim=\"false\" id=\"ni::contentproviders::1\" label=\"OpenNeuro\">\n" +
" <param name=\"openaireId\">re3data_____::5b9bf9171d92df854cf3c520692e9122</param>\n" + " <param name=\"openaireId\">re3data_____::5b9bf9171d92df854cf3c520692e9122</param>\n" +
@ -441,57 +440,65 @@ public class CreateRelationTest {
" <param name=\"zenodoCommunity\">oaa_elixir-gr</param>\n" + " <param name=\"zenodoCommunity\">oaa_elixir-gr</param>\n" +
" <param name=\"creationdate\">2018-03-01T12:00:00</param>\n" + " <param name=\"creationdate\">2018-03-01T12:00:00</param>\n" +
" <category claim=\"false\" id=\"elixir-gr::projects\" label=\"ELIXIR GR Projects\">\n" + " <category claim=\"false\" id=\"elixir-gr::projects\" label=\"ELIXIR GR Projects\">\n" +
" <concept claim=\"false\" id=\"ni::projects::12\" label=\"\">\n" + " <concept claim=\"false\" id=\"ni::projects::12\" label=\"\">\n" +
" <param name=\"projectfullname\">BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)</param>\n" + " <param name=\"projectfullname\">BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)</param>\n"
" <param name=\"acronym\"/>\n" + +
" <param name=\"CD_PROJECT_NUMBER\">1U24RR025736-01</param>\n" + " <param name=\"acronym\"/>\n" +
" <param name=\"funder\">NIH</param>\n" + " <param name=\"CD_PROJECT_NUMBER\">1U24RR025736-01</param>\n" +
" </concept>\n" + " <param name=\"funder\">NIH</param>\n" +
" <concept claim=\"false\" id=\"ni::projects::13\" label=\"\">\n" + " </concept>\n" +
" <param name=\"projectfullname\">COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning</param>\n" + " <concept claim=\"false\" id=\"ni::projects::13\" label=\"\">\n" +
" <param name=\"acronym\"/>\n" + " <param name=\"projectfullname\">COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning</param>\n"
" <param name=\"CD_PROJECT_NUMBER\">0223843</param>\n" + +
" <param name=\"funder\">NSF</param>\n" + " <param name=\"acronym\"/>\n" +
" </concept>\n" + " <param name=\"CD_PROJECT_NUMBER\">0223843</param>\n" +
" <concept claim=\"false\" id=\"ni::projects::14\" label=\"\">\n" + " <param name=\"funder\">NSF</param>\n" +
" <param name=\"projectfullname\">The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia</param>\n" + " </concept>\n" +
" <param name=\"acronym\"/>\n" + " <concept claim=\"false\" id=\"ni::projects::14\" label=\"\">\n" +
" <param name=\"CD_PROJECT_NUMBER\">5R01MH082795-05</param>\n" + " <param name=\"projectfullname\">The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia</param>\n"
" <param name=\"funder\">NIH</param>\n" + +
" </concept>\n" + " <param name=\"acronym\"/>\n" +
" <concept claim=\"false\" id=\"ni::projects::15\" label=\"\">\n" + " <param name=\"CD_PROJECT_NUMBER\">5R01MH082795-05</param>\n" +
" <param name=\"projectfullname\">Fragmented early life environmental and emotional / cognitive vulnerabilities</param>\n" + " <param name=\"funder\">NIH</param>\n" +
" <param name=\"acronym\"/>\n" + " </concept>\n" +
" <param name=\"CD_PROJECT_NUMBER\">1P50MH096889-01A1</param>\n" + " <concept claim=\"false\" id=\"ni::projects::15\" label=\"\">\n" +
" <param name=\"funder\">NIH</param>\n" + " <param name=\"projectfullname\">Fragmented early life environmental and emotional / cognitive vulnerabilities</param>\n"
" </concept>\n" + +
" <concept claim=\"false\" id=\"ni::projects::16\" label=\"\">\n" + " <param name=\"acronym\"/>\n" +
" <param name=\"projectfullname\">Enhancement of the 1000 Functional Connectome Project</param>\n" + " <param name=\"CD_PROJECT_NUMBER\">1P50MH096889-01A1</param>\n" +
" <param name=\"acronym\"/>\n" + " <param name=\"funder\">NIH</param>\n" +
" <param name=\"CD_PROJECT_NUMBER\">1R03MH096321-01A1</param>\n" + " </concept>\n" +
" <param name=\"funder\">TUBITAK</param>\n" + " <concept claim=\"false\" id=\"ni::projects::16\" label=\"\">\n" +
" </concept>\n" + " <param name=\"projectfullname\">Enhancement of the 1000 Functional Connectome Project</param>\n"
" <concept claim=\"false\" id=\"ni::projects::17\" label=\"\">\n" + +
" <param name=\"projectfullname\">CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project</param>\n" + " <param name=\"acronym\"/>\n" +
" <param name=\"acronym\"/>\n" + " <param name=\"CD_PROJECT_NUMBER\">1R03MH096321-01A1</param>\n" +
" <param name=\"CD_PROJECT_NUMBER\">1131441</param>\n" + " <param name=\"funder\">TUBITAK</param>\n" +
" <param name=\"funder\">NSF</param>\n" + " </concept>\n" +
" </concept>\n" + " <concept claim=\"false\" id=\"ni::projects::17\" label=\"\">\n" +
" <concept claim=\"false\" id=\"ni::projects::18\" label=\"\">\n" + " <param name=\"projectfullname\">CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project</param>\n"
" <param name=\"projectfullname\">Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI</param>\n" + +
" <param name=\"acronym\"/>\n" + " <param name=\"acronym\"/>\n" +
" <param name=\"CD_PROJECT_NUMBER\">0121950</param>\n" + " <param name=\"CD_PROJECT_NUMBER\">1131441</param>\n" +
" <param name=\"funder\">NSF</param>\n" + " <param name=\"funder\">NSF</param>\n" +
" </concept>\n" + " </concept>\n" +
" <concept claim=\"false\" id=\"ni::projects::18\" label=\"\">\n" + " <concept claim=\"false\" id=\"ni::projects::18\" label=\"\">\n" +
" <param name=\"projectfullname\">Transforming statistical methodology for neuroimaging meta-analysis.</param>\n" + " <param name=\"projectfullname\">Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI</param>\n"
" <param name=\"acronym\"/>\n" + +
" <param name=\"CD_PROJECT_NUMBER\">100309</param>\n" + " <param name=\"acronym\"/>\n" +
" <param name=\"funder\">WT</param>\n" + " <param name=\"CD_PROJECT_NUMBER\">0121950</param>\n" +
" </concept>\n" + " <param name=\"funder\">NSF</param>\n" +
" </category>" + " </concept>\n" +
" <concept claim=\"false\" id=\"ni::projects::18\" label=\"\">\n" +
" <param name=\"projectfullname\">Transforming statistical methodology for neuroimaging meta-analysis.</param>\n"
+
" <param name=\"acronym\"/>\n" +
" <param name=\"CD_PROJECT_NUMBER\">100309</param>\n" +
" <param name=\"funder\">WT</param>\n" +
" </concept>\n" +
" </category>" +
" <category claim=\"false\" id=\"elixir-gr::contentproviders\" label=\"Elixir-GR Content providers\">\n" " <category claim=\"false\" id=\"elixir-gr::contentproviders\" label=\"Elixir-GR Content providers\">\n"
+ +
" <concept claim=\"false\" id=\"elixir-gr::contentproviders::1\" label=\"bio.tools\">\n" + " <concept claim=\"false\" id=\"elixir-gr::contentproviders::1\" label=\"bio.tools\">\n" +
" <param name=\"openaireId\">rest________::b8e502674c3c3499d5374e9b2ea6d8d5</param>\n" + " <param name=\"openaireId\">rest________::b8e502674c3c3499d5374e9b2ea6d8d5</param>\n" +
@ -626,88 +633,87 @@ public class CreateRelationTest {
final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci); final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci);
queryInformationSystem queryInformationSystem
.getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class)); .getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class));
cInfoList.forEach(c -> System.out.println(new Gson().toJson(c))); cInfoList.forEach(c -> System.out.println(new Gson().toJson(c)));
List<Relation> rList = new ArrayList<>(); List<Relation> rList = new ArrayList<>();
cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add)); cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add));
Assertions.assertEquals(44 , rList.size()); Assertions.assertEquals(44, rList.size());
Assertions Assertions
.assertFalse( .assertFalse(
rList rList
.stream() .stream()
.map(r -> r.getSource().getId()) .map(r -> r.getSource().getId())
.collect(Collectors.toSet()) .collect(Collectors.toSet())
.contains( .contains(
String String
.format( .format(
"%s|%s::%s", Constants.CONTEXT_ID, "%s|%s::%s", Constants.CONTEXT_ID,
Constants.CONTEXT_NS_PREFIX, Constants.CONTEXT_NS_PREFIX,
DHPUtils.md5("dh-ch")))); DHPUtils.md5("dh-ch"))));
Assertions Assertions
.assertEquals( .assertEquals(
2, 2,
rList rList
.stream() .stream()
.filter( .filter(
r -> r r -> r
.getSource() .getSource()
.getId() .getId()
.equals( .equals(
String String
.format( .format(
"%s|%s::%s", Constants.CONTEXT_ID, "%s|%s::%s", Constants.CONTEXT_ID,
Constants.CONTEXT_NS_PREFIX, Constants.CONTEXT_NS_PREFIX,
DHPUtils.md5("clarin")))) DHPUtils.md5("clarin"))))
.collect(Collectors.toList()) .collect(Collectors.toList())
.size()); .size());
Assertions Assertions
.assertEquals( .assertEquals(
2, 2,
rList rList
.stream() .stream()
.filter( .filter(
r -> r r -> r
.getTarget() .getTarget()
.getId() .getId()
.equals( .equals(
String String
.format( .format(
"%s|%s::%s", Constants.CONTEXT_ID, "%s|%s::%s", Constants.CONTEXT_ID,
Constants.CONTEXT_NS_PREFIX, Constants.CONTEXT_NS_PREFIX,
DHPUtils.md5("clarin")))) DHPUtils.md5("clarin"))))
.collect(Collectors.toList()) .collect(Collectors.toList())
.size()); .size());
Set<String> tmp = rList Set<String> tmp = rList
.stream() .stream()
.filter( .filter(
r -> r r -> r
.getSource() .getSource()
.getId() .getId()
.equals( .equals(
String String
.format( .format(
"%s|%s::%s", Constants.CONTEXT_ID, "%s|%s::%s", Constants.CONTEXT_ID,
Constants.CONTEXT_NS_PREFIX, Constants.CONTEXT_NS_PREFIX,
DHPUtils.md5("clarin")))) DHPUtils.md5("clarin"))))
.map(r -> r.getTarget().getId()) .map(r -> r.getTarget().getId())
.collect(Collectors.toSet()); .collect(Collectors.toSet());
Assertions Assertions
.assertTrue( .assertTrue(
tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") && tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") &&
tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4") ); tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4"));
rList.forEach(rel -> { rList.forEach(rel -> {
if (rel.getSource().getId().startsWith("40|")){ if (rel.getSource().getId().startsWith("40|")) {
String proj = rel.getSource().getId().substring(3); String proj = rel.getSource().getId().substring(3);
Assertions.assertTrue(proj.substring(0, proj.indexOf("::")).length() == 12); Assertions.assertTrue(proj.substring(0, proj.indexOf("::")).length() == 12);
} }

76
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java
View File

@ -10,6 +10,7 @@ import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row; import org.apache.spark.sql.Row;
@ -71,7 +72,7 @@ public class DumpRelationTest {
public void test1() throws Exception { public void test1() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/relation") .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation")
.getPath(); .getPath();
SparkDumpRelationJob.main(new String[] { SparkDumpRelationJob.main(new String[] {
@ -93,6 +94,8 @@ public class DumpRelationTest {
verificationDataset.createOrReplaceTempView("table"); verificationDataset.createOrReplaceTempView("table");
verificationDataset.foreach((ForeachFunction<Relation>)r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
Dataset<Row> check = spark Dataset<Row> check = spark
.sql( .sql(
"SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance "
@ -127,4 +130,75 @@ public class DumpRelationTest {
.count()); .count());
} }
@Test
public void test2() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation_validated")
.getPath();
SparkDumpRelationJob.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/relation",
"-sourcePath", sourcePath
});
// dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset");
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
org.apache.spark.sql.Dataset<Relation> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
verificationDataset.createOrReplaceTempView("table");
verificationDataset.foreach((ForeachFunction<Relation>)r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
Dataset<Row> check = spark
.sql(
"SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance "
+
"from table ");
Assertions.assertEquals(20, check.filter("name = 'isProvidedBy'").count());
Assertions
.assertEquals(
20, check
.filter(
"name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " +
"provenance = 'Harvested'")
.count());
Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count());
Assertions
.assertEquals(
7, check
.filter(
"name = 'isParticipant' and stype = 'organization' and ttype = 'project' " +
"and provenance = 'Harvested'")
.count());
Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count());
Assertions
.assertEquals(
1, check
.filter(
"name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " +
"and provenance = 'Inferred by OpenAIRE'")
.count());
Assertions.assertEquals(2, check.filter("name = 'isProducedBy'").count());
Assertions
.assertEquals(
2, check
.filter(
"name = 'isProducedBy' and stype = 'project' and ttype = 'result' " +
"and provenance = 'Harvested' and validated = true " +
"and validationDate = '2021-08-06'")
.count());
}
} }

5
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java
View File

@ -6,6 +6,7 @@ import static org.mockito.Mockito.lenient;
import java.util.*; import java.util.*;
import java.util.function.Consumer; import java.util.function.Consumer;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
@ -528,7 +529,7 @@ public class QueryInformationSystemTest {
List<ContextInfo> cInfoList = new ArrayList<>(); List<ContextInfo> cInfoList = new ArrayList<>();
final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci); final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci);
queryInformationSystem.execContextRelationQuery(); queryInformationSystem.execContextRelationQuery();
queryInformationSystem.getContextRelation(consumer, "contentproviders", "10|"); queryInformationSystem.getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource"));
Assertions.assertEquals(5, cInfoList.size()); Assertions.assertEquals(5, cInfoList.size());
} }
@ -539,7 +540,7 @@ public class QueryInformationSystemTest {
List<ContextInfo> cInfoList = new ArrayList<>(); List<ContextInfo> cInfoList = new ArrayList<>();
final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci); final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci);
queryInformationSystem.execContextRelationQuery(); queryInformationSystem.execContextRelationQuery();
queryInformationSystem.getContextRelation(consumer, "contentproviders", "10"); queryInformationSystem.getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource"));
cInfoList.forEach(contextInfo -> { cInfoList.forEach(contextInfo -> {
switch (contextInfo.getId()) { switch (contextInfo.getId()) {

10
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java
View File

@ -75,8 +75,8 @@ public class ResultLinkedToProjectTest {
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json")
.getPath(); .getPath();
final String relationPath = getClass() final String graphPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json") .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch")
.getPath(); .getPath();
SparkResultLinkedToProject.main(new String[] { SparkResultLinkedToProject.main(new String[] {
@ -84,7 +84,7 @@ public class ResultLinkedToProjectTest {
"-outputPath", workingDir.toString() + "/preparedInfo", "-outputPath", workingDir.toString() + "/preparedInfo",
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
"-relationPath", relationPath "-graphPath", graphPath
}); });
@ -109,7 +109,7 @@ public class ResultLinkedToProjectTest {
.getPath(); .getPath();
final String relationPath = getClass() final String relationPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json") .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match")
.getPath(); .getPath();
SparkResultLinkedToProject.main(new String[] { SparkResultLinkedToProject.main(new String[] {
@ -117,7 +117,7 @@ public class ResultLinkedToProjectTest {
"-outputPath", workingDir.toString() + "/preparedInfo", "-outputPath", workingDir.toString() + "/preparedInfo",
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
"-relationPath", relationPath "-graphPath", relationPath
}); });

8
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java
View File

@ -75,7 +75,7 @@ public class SplitPerFunderTest {
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/split", "-outputPath", workingDir.toString() + "/split",
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-relationPath", sourcePath "-graphPath", sourcePath
}); });
@ -143,5 +143,11 @@ public class SplitPerFunderTest {
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
Assertions.assertEquals(1, tmp.count()); Assertions.assertEquals(1, tmp.count());
// CONICYT 0
tmp = sc
.textFile(workingDir.toString() + "/split/CONICYTF")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
Assertions.assertEquals(0, tmp.count());
} }
} }

12
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3
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9
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@ -1,9 +0,0 @@
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::2baa9032dc058d3c8ff780c426b0c19f","subRelType":"provision","target":"40|cihr________::1e5e62235d094afd01cd56e65112fc63"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::5ac587eb28411c351c2e357eb097fd3d","subRelType":"provision","target":"40|nwo_________::dc69ada721bf21ed51055b6421850d73"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::690b3aaf177a4c70b81bacd8d023cbdc","subRelType":"provision","target":"40|nih_________::031bb5f2f70239b3210eda38b2079f67"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::7a71f278237d1ab35088efda03fa007a","subRelType":"provision","target":"40|nsf_________::03748bcb5d754c951efec9700e18a56d"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::8b75543067b50076e70764917e188178","subRelType":"provision","target":"40|snsf________::50cb15ff7a6a3f8531f063770179e346"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::9f3ff882f023209d9ffb4dc32b77d376","subRelType":"provision","target":"40|corda_______::ffc1811633b3222e4764c7b0517f83e8"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::b566fa319c3923454e1e8eb886ab62d2","subRelType":"provision","target":"40|nhmrc_______::4e6c928fef9851b37ec73f4f6daca35b"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::e0554fb004a155bc23cfb43ee9fc8eae","subRelType":"provision","target":"40|corda__h2020::846b777af165fef7c904a81712a83b66"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::2baa9032dc058d3c8ff780c426b0c19f","subRelType":"provision","target":"40|irb_hr______::1e5e62235d094afd01cd56e65112fc63"}

12
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/project Normal file
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4
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json → dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relation
View File

@ -22,8 +22,8 @@
{"collectedfrom":[{"key":"10|openaire____::21f8a223b9925c2f87c404096080b046","value":"Registry of Research Data Repository"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|re3data_____::cafe7980294aa5f935f433e7c8aab844","subRelType":"provision","target":"20|dedup_wf_001::2806db65ba8029ee196679cad067eff2"} {"collectedfrom":[{"key":"10|openaire____::21f8a223b9925c2f87c404096080b046","value":"Registry of Research Data Repository"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|re3data_____::cafe7980294aa5f935f433e7c8aab844","subRelType":"provision","target":"20|dedup_wf_001::2806db65ba8029ee196679cad067eff2"}
{"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::0cd5965141113df5739f1ac7ac7f6d37","subRelType":"participation","target":"40|aka_________::1bc716a1763110da3eb1af867de718a8"} {"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::0cd5965141113df5739f1ac7ac7f6d37","subRelType":"participation","target":"40|aka_________::1bc716a1763110da3eb1af867de718a8"}
{"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::1e2df822bf0932ad0f77565789f22e17","subRelType":"participation","target":"40|aka_________::a6c805bcfd383bae043d8df38e79db78"} {"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::1e2df822bf0932ad0f77565789f22e17","subRelType":"participation","target":"40|aka_________::a6c805bcfd383bae043d8df38e79db78"}
{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_affiliations","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.8966"},"lastupdatetimestamp":1603564783812,"properties":[],"relClass":"isProducedBy","relType":"resultOrganization","target":"20|aka_________::2c3aab6bce7516338b4dbfb4f6f86db7","subRelType":"affiliation","source":"50|a89337edbe55::43e8b61e5e8d682545cb867be8118585"} {"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_affiliations","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.8966"},"lastupdatetimestamp":1603564783812,"properties":[],"relClass":"isProducedBy","relType":"resultOrganization","target":"40|aka_________::01bb7b48e29d732a1c7bc5150b9195c4","subRelType":"affiliation","source":"50|a89337edbe55::43e8b61e5e8d682545cb867be8118585"}
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12
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/project Normal file
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0
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json → dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relation
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dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/relation/relation_validated Normal file
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@ -0,0 +1,30 @@
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"40|doajarticles::2baa9032dc058d3c8ff780c426b0c19f","subRelType":"provision","target":"50|dedup_wf_001::2899e571609779168222fdeb59cb916d", "validated":true, "validationDate":"2021-08-06"}
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