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Merge branch 'beta' into pid_cleaning

This commit is contained in:
Claudio Atzori 2023-06-12 13:32:22 +02:00
parent 1d33074fd1 fdbfb25614
commit d6a8b24711
40 changed files with 3035 additions and 453 deletions
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40
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java
View File

@ -57,7 +57,10 @@ public class PropagationConstant {
public static final String PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME = "Propagation of affiliation to result collected from datasources of type institutional repository";
public static final String PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_ID = "result:organization:semrel";
public static final String PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_NAME = "Propagation of affiliation to result through sematic relations";
public static final String PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_NAME = "Propagation of affiliation to result through semantic relations";
public static final String PROPAGATION_RELATION_PROJECT_ORGANIZATION_SEM_REL_CLASS_ID = "project:organization:semrel";
public static final String PROPAGATION_RELATION_PROJECT_ORGANIZATION_SEM_REL_CLASS_NAME = "Propagation of participation to project through semantic relations";
public static final String PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID = "result:project:semrel";
public static final String PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME = "Propagation of result to project through semantic relation";
@ -171,6 +174,41 @@ public class PropagationConstant {
return newRelations;
}
public static Relation getRelation(String source, String target, String rel_class) {
if (ModelConstants.HAS_PARTICIPANT.equals(rel_class)) {
return getParticipantRelation(source, target, rel_class);
} else
return getAffiliationRelation(source, target, rel_class);
}
public static Relation getParticipantRelation(
String source,
String target,
String rel_class) {
return getRelation(
source, target,
rel_class,
ModelConstants.PROJECT_ORGANIZATION,
ModelConstants.PARTICIPATION,
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_PROJECT_ORGANIZATION_SEM_REL_CLASS_ID,
PROPAGATION_RELATION_PROJECT_ORGANIZATION_SEM_REL_CLASS_NAME);
}
public static Relation getAffiliationRelation(
String source,
String target,
String rel_class) {
return getRelation(
source, target,
rel_class,
ModelConstants.RESULT_ORGANIZATION,
ModelConstants.AFFILIATION,
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_ID,
PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_NAME);
}
public static Relation getRelation(
String source,
String target,

9
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java
View File

@ -15,6 +15,7 @@ public class Community implements Serializable {
private List<Provider> providers = new ArrayList<>();
private List<ZenodoCommunity> zenodoCommunities = new ArrayList<>();
private SelectionConstraints constraints = new SelectionConstraints();
private SelectionConstraints removeConstraints = new SelectionConstraints();
public String toJson() {
final Gson g = new Gson();
@ -67,4 +68,12 @@ public class Community implements Serializable {
public void setConstraints(SelectionConstraints constraints) {
this.constraints = constraints;
}
public SelectionConstraints getRemoveConstraints() {
return removeConstraints;
}
public void setRemoveConstraints(SelectionConstraints removeConstraints) {
this.removeConstraints = removeConstraints;
}
}

15
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java
View File

@ -28,6 +28,8 @@ public class CommunityConfiguration implements Serializable {
private Map<String, SelectionConstraints> selectionConstraintsMap = new HashMap<>();
// map eosc datasource -> communityid
private Map<String, List<Pair<String, SelectionConstraints>>> eoscDatasourceMap = new HashMap<>();
// map communityid -> remove constraints
private Map<String, SelectionConstraints> removeConstraintsMap = new HashMap<>();
public Map<String, List<Pair<String, SelectionConstraints>>> getEoscDatasourceMap() {
return eoscDatasourceMap;
@ -71,6 +73,14 @@ public class CommunityConfiguration implements Serializable {
this.selectionConstraintsMap = selectionConstraintsMap;
}
public Map<String, SelectionConstraints> getRemoveConstraintsMap() {
return removeConstraintsMap;
}
public void setRemoveConstraintsMap(Map<String, SelectionConstraints> removeConstraintsMap) {
this.removeConstraintsMap = removeConstraintsMap;
}
CommunityConfiguration(final Map<String, Community> communities) {
this.communities = communities;
init();
@ -90,6 +100,9 @@ public class CommunityConfiguration implements Serializable {
if (selectionConstraintsMap == null) {
selectionConstraintsMap = Maps.newHashMap();
}
if (removeConstraintsMap == null) {
removeConstraintsMap = Maps.newHashMap();
}
for (Community c : getCommunities().values()) {
// get subjects
@ -111,6 +124,8 @@ public class CommunityConfiguration implements Serializable {
zenodocommunityMap);
}
selectionConstraintsMap.put(id, c.getConstraints());
removeConstraintsMap.put(id, c.getRemoveConstraints());
}
}

14
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java
View File

@ -86,6 +86,7 @@ public class CommunityConfigurationFactory {
c.setProviders(parseDatasources(node));
c.setZenodoCommunities(parseZenodoCommunities(node));
c.setConstraints(parseConstrains(node));
c.setRemoveConstraints(parseRemoveConstrains(node));
return c;
}
@ -102,6 +103,19 @@ public class CommunityConfigurationFactory {
return selectionConstraints;
}
private static SelectionConstraints parseRemoveConstrains(Node node) {
Node constsNode = node.selectSingleNode("./removeConstraints");
if (constsNode == null || StringUtils.isBlank(StringUtils.trim(constsNode.getText()))) {
return new SelectionConstraints();
}
SelectionConstraints selectionConstraints = new Gson()
.fromJson(constsNode.getText(), SelectionConstraints.class);
selectionConstraints.setSelection(resolver);
log.info("number of selection constraints set " + selectionConstraints.getCriteria().size());
return selectionConstraints;
}
private static List<String> parseSubjects(final Node node) {
final List<String> subjects = Lists.newArrayList();

23
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
View File

@ -79,6 +79,23 @@ public class ResultTagger implements Serializable {
break;
}
// communities contains all the communities to be not added to the context
final Set<String> removeCommunities = new HashSet<>();
conf
.getRemoveConstraintsMap()
.keySet()
.forEach(communityId -> {
if (conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null &&
conf
.getRemoveConstraintsMap()
.get(communityId)
.getCriteria()
.stream()
.anyMatch(crit -> crit.verifyCriteria(param)))
removeCommunities.add(communityId);
});
// communities contains all the communities to be added as context for the result
final Set<String> communities = new HashSet<>();
@ -164,7 +181,8 @@ public class ResultTagger implements Serializable {
.getSelectionConstraintsMap()
.keySet()
.forEach(communityId -> {
if (conf.getSelectionConstraintsMap().get(communityId).getCriteria() != null &&
if (!removeCommunities.contains(communityId) &&
conf.getSelectionConstraintsMap().get(communityId).getCriteria() != null &&
conf
.getSelectionConstraintsMap()
.get(communityId)
@ -175,6 +193,9 @@ public class ResultTagger implements Serializable {
});
communities.addAll(aconstraints);
communities.removeAll(removeCommunities);
if (aconstraints.size() > 0)
log.info("Found {} for advancedConstraints ", aconstraints.size());

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/Leaves.java → dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/entitytoorganizationfromsemrel/Leaves.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.resulttoorganizationfromsemrel;
package eu.dnetlib.dhp.entitytoorganizationfromsemrel;
import java.io.Serializable;

37
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/PrepareInfo.java → dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/entitytoorganizationfromsemrel/PrepareInfo.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.resulttoorganizationfromsemrel;
package eu.dnetlib.dhp.entitytoorganizationfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
@ -47,13 +47,20 @@ public class PrepareInfo implements Serializable {
"' and datainfo.deletedbyinference = false " +
"GROUP BY source";
// associate projects to all the participant orgs
private static final String PROJECT_ORGANIZATION_QUERY = "SELECT source key, collect_set(target) as valueSet " +
"FROM relation " +
"WHERE lower(relclass) = '" + ModelConstants.HAS_PARTICIPANT.toLowerCase() +
"' and datainfo.deletedbyinference = false " +
"GROUP BY source";
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkResultToOrganizationFromIstRepoJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/input_preparation_parameter.json"));
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/input_preparation_parameter.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
@ -74,6 +81,9 @@ public class PrepareInfo implements Serializable {
final String resultOrganizationPath = parser.get("resultOrgPath");
log.info("resultOrganizationPath: {}", resultOrganizationPath);
final String projectOrgPath = parser.get("projectOrganizationPath");
log.info("projectOrgPath: {}", projectOrgPath);
final String relationPath = parser.get("relationPath");
log.info("relationPath: {}", relationPath);
@ -89,11 +99,13 @@ public class PrepareInfo implements Serializable {
childParentPath,
leavesPath,
resultOrganizationPath,
projectOrgPath,
relationPath));
}
private static void prepareInfo(SparkSession spark, String inputPath, String childParentOrganizationPath,
String currentIterationPath, String resultOrganizationPath, String relationPath) {
String currentIterationPath, String resultOrganizationPath, String projectOrganizationPath,
String relationPath) {
Dataset<Relation> relation = readPath(spark, inputPath + "/relation", Relation.class);
relation.createOrReplaceTempView("relation");
@ -113,6 +125,14 @@ public class PrepareInfo implements Serializable {
.option("compression", "gzip")
.json(resultOrganizationPath);
spark
.sql(PROJECT_ORGANIZATION_QUERY)
.as(Encoders.bean(KeyValueSet.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(projectOrganizationPath);
relation
.filter(
(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
@ -120,7 +140,16 @@ public class PrepareInfo implements Serializable {
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(relationPath);
.json(relationPath + "/result");
relation
.filter(
(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
r.getRelClass().equals(ModelConstants.HAS_PARTICIPANT))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(relationPath + "/project");
Dataset<String> children = spark
.sql(

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/PropagationCounter.java → dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/entitytoorganizationfromsemrel/PropagationCounter.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.resulttoorganizationfromsemrel;
package eu.dnetlib.dhp.entitytoorganizationfromsemrel;
import java.io.Serializable;

99
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/SparkResultToOrganizationFromSemRel.java → dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/entitytoorganizationfromsemrel/SparkResultToOrganizationFromSemRel.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.resulttoorganizationfromsemrel;
package eu.dnetlib.dhp.entitytoorganizationfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
@ -30,7 +30,8 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
public class SparkResultToOrganizationFromSemRel implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkResultToOrganizationFromSemRel.class);
private static final int MAX_ITERATION = 5;
public static final String NEW_RELATION_PATH = "/newRelation";
public static final String NEW_RESULT_RELATION_PATH = "/newResultRelation";
public static final String NEW_PROJECT_RELATION_PATH = "/newProjectRelation";
public static void main(String[] args) throws Exception {
@ -38,7 +39,7 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
.toString(
SparkResultToOrganizationFromIstRepoJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/input_propagation_parameter.json"));
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/input_propagation_parameter.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
@ -62,6 +63,9 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
final String resultOrganizationPath = parser.get("resultOrgPath");
log.info("resultOrganizationPath: {}", resultOrganizationPath);
final String projectOrganizationPath = parser.get("projectOrganizationPath");
log.info("projectOrganizationPath: {}", projectOrganizationPath);
final String workingPath = parser.get("workingDir");
log.info("workingPath: {}", workingPath);
@ -88,6 +92,7 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
leavesPath,
childParentPath,
resultOrganizationPath,
projectOrganizationPath,
relationPath,
workingPath,
outputPath,
@ -98,13 +103,14 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
String leavesPath,
String childParentPath,
String resultOrganizationPath,
String projectOrganizationPath,
String graphPath,
String workingPath,
String outputPath,
int iterations) {
if (iterations == 1) {
doPropagateOnce(
spark, leavesPath, childParentPath, resultOrganizationPath, graphPath,
spark, leavesPath, childParentPath, resultOrganizationPath, projectOrganizationPath, graphPath,
workingPath, outputPath);
} else {
@ -123,26 +129,34 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
notReachedFirstParent);
doPropagate(
spark, leavesPath, childParentPath, resultOrganizationPath, graphPath,
spark, leavesPath, childParentPath, resultOrganizationPath, projectOrganizationPath, graphPath,
workingPath, outputPath, propagationCounter);
}
}
private static void doPropagateOnce(SparkSession spark, String leavesPath, String childParentPath,
String resultOrganizationPath, String graphPath, String workingPath,
String resultOrganizationPath, String projectOrganizationPath, String graphPath, String workingPath,
String outputPath) {
StepActions
.execStep(
spark, graphPath, workingPath + NEW_RELATION_PATH,
leavesPath, childParentPath, resultOrganizationPath);
spark, graphPath + "/result", workingPath + NEW_RESULT_RELATION_PATH,
leavesPath, childParentPath, resultOrganizationPath, ModelConstants.HAS_AUTHOR_INSTITUTION);
addNewRelations(spark, workingPath + NEW_RELATION_PATH, outputPath);
addNewRelations(spark, workingPath + NEW_RESULT_RELATION_PATH, outputPath);
StepActions
.execStep(
spark, graphPath + "/project", workingPath + NEW_PROJECT_RELATION_PATH,
leavesPath, childParentPath, projectOrganizationPath, ModelConstants.HAS_PARTICIPANT);
addNewRelations(spark, workingPath + NEW_PROJECT_RELATION_PATH, outputPath);
}
private static void doPropagate(SparkSession spark, String leavesPath, String childParentPath,
String resultOrganizationPath, String graphPath, String workingPath, String outputPath,
String resultOrganizationPath, String projectOrganizationPath, String graphPath, String workingPath,
String outputPath,
PropagationCounter propagationCounter) {
int iteration = 0;
long leavesCount;
@ -151,13 +165,18 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
iteration++;
StepActions
.execStep(
spark, graphPath, workingPath + NEW_RELATION_PATH,
leavesPath, childParentPath, resultOrganizationPath);
spark, graphPath + "/result", workingPath + NEW_RESULT_RELATION_PATH,
leavesPath, childParentPath, resultOrganizationPath, ModelConstants.HAS_AUTHOR_INSTITUTION);
StepActions
.execStep(
spark, graphPath + "/project", workingPath + NEW_PROJECT_RELATION_PATH,
leavesPath, childParentPath, projectOrganizationPath, ModelConstants.HAS_PARTICIPANT);
StepActions
.prepareForNextStep(
spark, workingPath + NEW_RELATION_PATH, resultOrganizationPath, leavesPath,
childParentPath, workingPath + "/leaves", workingPath + "/resOrg");
moveOutput(spark, workingPath, leavesPath, resultOrganizationPath);
spark, workingPath, resultOrganizationPath, projectOrganizationPath, leavesPath,
childParentPath, workingPath + "/leaves", workingPath + "/resOrg", workingPath + "/projOrg");
moveOutput(spark, workingPath, leavesPath, resultOrganizationPath, projectOrganizationPath);
leavesCount = readPath(spark, leavesPath, Leaves.class).count();
} while (leavesCount > 0 && iteration < MAX_ITERATION);
@ -185,7 +204,8 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
propagationCounter.getNotReachedFirstParent().add(1);
}
addNewRelations(spark, workingPath + NEW_RELATION_PATH, outputPath);
addNewRelations(spark, workingPath + NEW_RESULT_RELATION_PATH, outputPath);
addNewRelations(spark, workingPath + NEW_PROJECT_RELATION_PATH, outputPath);
}
private static void moveOutput(SparkSession spark, String workingPath, String leavesPath,
@ -204,6 +224,28 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
}
private static void moveOutput(SparkSession spark, String workingPath, String leavesPath,
String resultOrganizationPath, String projectOrganizationPath) {
readPath(spark, workingPath + "/leaves", Leaves.class)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(leavesPath);
readPath(spark, workingPath + "/resOrg", KeyValueSet.class)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(resultOrganizationPath);
readPath(spark, workingPath + "/projOrg", KeyValueSet.class)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(projectOrganizationPath);
}
private static void addNewRelations(SparkSession spark, String newRelationPath, String outputPath) {
Dataset<Relation> relation = readPath(spark, newRelationPath, Relation.class);
@ -212,16 +254,21 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
.mapGroups(
(MapGroupsFunction<String, Relation, Relation>) (k, it) -> it.next(), Encoders.bean(Relation.class))
.flatMap(
(FlatMapFunction<Relation, Relation>) r -> Arrays
.asList(
r, getRelation(
r.getTarget(), r.getSource(), ModelConstants.IS_AUTHOR_INSTITUTION_OF,
ModelConstants.RESULT_ORGANIZATION,
ModelConstants.AFFILIATION,
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_ID,
PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_NAME))
.iterator()
(FlatMapFunction<Relation, Relation>) r -> {
if (r.getSource().startsWith("50|")) {
return Arrays
.asList(
r, getAffiliationRelation(
r.getTarget(), r.getSource(), ModelConstants.IS_AUTHOR_INSTITUTION_OF))
.iterator();
} else {
return Arrays
.asList(
r, getParticipantRelation(
r.getTarget(), r.getSource(), ModelConstants.IS_PARTICIPANT))
.iterator();
}
}
, Encoders.bean(Relation.class))
.write()

69
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/StepActions.java → dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/entitytoorganizationfromsemrel/StepActions.java
View File

@ -1,8 +1,10 @@
package eu.dnetlib.dhp.resulttoorganizationfromsemrel;
package eu.dnetlib.dhp.entitytoorganizationfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.PropagationConstant.readPath;
import static eu.dnetlib.dhp.entitytoorganizationfromsemrel.SparkResultToOrganizationFromSemRel.NEW_PROJECT_RELATION_PATH;
import static eu.dnetlib.dhp.entitytoorganizationfromsemrel.SparkResultToOrganizationFromSemRel.NEW_RESULT_RELATION_PATH;
import java.io.Serializable;
import java.util.*;
@ -14,8 +16,6 @@ import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
@ -28,13 +28,14 @@ public class StepActions implements Serializable {
public static void execStep(SparkSession spark,
String graphPath, String newRelationPath,
String leavesPath, String chldParentOrgPath, String resultOrgPath) {
String leavesPath, String chldParentOrgPath, String entityOrgPath, String rel_class) {
Dataset<Relation> relationGraph = readPath(spark, graphPath, Relation.class);
// select only the relation source target among those proposed by propagation that are not already existent
getNewRels(
newRelationPath, relationGraph,
getPropagationRelation(spark, leavesPath, chldParentOrgPath, resultOrgPath));
getPropagationRelation(spark, leavesPath, chldParentOrgPath, entityOrgPath, rel_class));
}
@ -45,16 +46,33 @@ public class StepActions implements Serializable {
changeLeavesSet(spark, leavesPath, chldParentOrgPath, leavesOutputPath);
// add the new relations obtained from propagation to the keyvalueset result organization
updateResultOrganization(
updateEntityOrganization(
spark, resultOrgPath, readPath(spark, selectedRelsPath, Relation.class), orgOutputPath);
}
private static void updateResultOrganization(SparkSession spark, String resultOrgPath,
public static void prepareForNextStep(SparkSession spark, String selectedRelsPath, String resultOrgPath,
String projectOrgPath,
String leavesPath, String chldParentOrgPath, String leavesOutputPath,
String orgOutputPath, String outputProjectPath) {
// use of the parents as new leaves set
changeLeavesSet(spark, leavesPath, chldParentOrgPath, leavesOutputPath);
// add the new relations obtained from propagation to the keyvalueset result organization
updateEntityOrganization(
spark, resultOrgPath, readPath(spark, selectedRelsPath + NEW_RESULT_RELATION_PATH, Relation.class),
orgOutputPath);
updateEntityOrganization(
spark, projectOrgPath, readPath(spark, selectedRelsPath + NEW_PROJECT_RELATION_PATH, Relation.class),
outputProjectPath);
}
private static void updateEntityOrganization(SparkSession spark, String entityOrgPath,
Dataset<Relation> selectedRels, String outputPath) {
Dataset<KeyValueSet> resultOrg = readPath(spark, resultOrgPath, KeyValueSet.class);
resultOrg
Dataset<KeyValueSet> entityOrg = readPath(spark, entityOrgPath, KeyValueSet.class);
entityOrg
.joinWith(
selectedRels, resultOrg
selectedRels, entityOrg
.col("key")
.equalTo(selectedRels.col("source")),
"left")
@ -129,7 +147,12 @@ public class StepActions implements Serializable {
.getDataInfo()
.getProvenanceaction()
.getClassid()
.equals(PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_ID))
.equals(PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_ID)
&& !rel
.getDataInfo()
.getProvenanceaction()
.getClassid()
.equals(PROPAGATION_RELATION_PROJECT_ORGANIZATION_SEM_REL_CLASS_ID))
.count() > 0) {
return null;
}
@ -152,19 +175,20 @@ public class StepActions implements Serializable {
private static Dataset<Relation> getPropagationRelation(SparkSession spark,
String leavesPath,
String chldParentOrgPath,
String resultOrgPath) {
String entityOrgPath,
String semantics) {
Dataset<KeyValueSet> childParent = readPath(spark, chldParentOrgPath, KeyValueSet.class);
Dataset<KeyValueSet> resultOrg = readPath(spark, resultOrgPath, KeyValueSet.class);
Dataset<KeyValueSet> entityOrg = readPath(spark, entityOrgPath, KeyValueSet.class);
Dataset<Leaves> leaves = readPath(spark, leavesPath, Leaves.class);
childParent.createOrReplaceTempView("childParent");
resultOrg.createOrReplaceTempView("resultOrg");
entityOrg.createOrReplaceTempView("entityOrg");
leaves.createOrReplaceTempView("leaves");
Dataset<KeyValueSet> resultParent = spark
.sql(
"SELECT resId as key, " +
"SELECT entityId as key, " +
"collect_set(parent) valueSet " +
"FROM (SELECT key as child, parent " +
" FROM childParent " +
@ -172,14 +196,14 @@ public class StepActions implements Serializable {
"JOIN leaves " +
"ON leaves.value = cp.child " +
"JOIN (" +
"SELECT key as resId, org " +
"FROM resultOrg " +
"SELECT key as entityId, org " +
"FROM entityOrg " +
"LATERAL VIEW explode (valueSet) ks as org ) as ro " +
"ON leaves.value = ro.org " +
"GROUP BY resId")
"GROUP BY entityId")
.as(Encoders.bean(KeyValueSet.class));
// create new relations from result to organization for each result linked to a leaf
// create new relations from entity to organization for each entity linked to a leaf
return resultParent
.flatMap(
(FlatMapFunction<KeyValueSet, Relation>) v -> v
@ -189,12 +213,7 @@ public class StepActions implements Serializable {
orgId -> getRelation(
v.getKey(),
orgId,
ModelConstants.HAS_AUTHOR_INSTITUTION,
ModelConstants.RESULT_ORGANIZATION,
ModelConstants.AFFILIATION,
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_ID,
PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_NAME))
semantics))
.collect(Collectors.toList())
.iterator(),
Encoders.bean(Relation.class));

3
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq
View File

@ -10,6 +10,9 @@ where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] and $x//con
return
<community>
{ $x//CONFIGURATION/context/@id}
<removeConstraints>
{$x//CONFIGURATION/context/param[./@name='removeConstraints']/text() }
</removeConstraints>
<advancedConstraints>
{$x//CONFIGURATION/context/param[./@name='advancedConstraints']/text() }
</advancedConstraints>

6
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/input_preparation_parameter.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/input_preparation_parameter.json
View File

@ -40,5 +40,11 @@
"paramLongName": "relationPath",
"paramDescription": "the path where to store the selected subset of relations",
"paramRequired": false
},
{
"paramName": "pop",
"paramLongName": "projectOrganizationPath",
"paramDescription": "the number of iterations to be computed",
"paramRequired": true
}
]

7
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/input_propagation_parameter.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/input_propagation_parameter.json
View File

@ -52,5 +52,10 @@
"paramLongName": "iterations",
"paramDescription": "the number of iterations to be computed",
"paramRequired": false
}
},{
"paramName": "pop",
"paramLongName": "projectOrganizationPath",
"paramDescription": "the number of iterations to be computed",
"paramRequired": true
}
]

0
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/config-default.xml → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/oozie_app/config-default.xml
View File

5
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/workflow.xml → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/oozie_app/workflow.xml
View File

@ -134,7 +134,7 @@
<master>yarn</master>
<mode>cluster</mode>
<name>PrepareResultOrganizationAssociation</name>
<class>eu.dnetlib.dhp.resulttoorganizationfromsemrel.PrepareInfo</class>
<class>eu.dnetlib.dhp.entitytoorganizationfromsemrel.PrepareInfo</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
@ -150,6 +150,7 @@
<arg>--leavesPath</arg><arg>${workingDir}/preparedInfo/leavesPath</arg>
<arg>--childParentPath</arg><arg>${workingDir}/preparedInfo/childParentPath</arg>
<arg>--resultOrgPath</arg><arg>${workingDir}/preparedInfo/resultOrgPath</arg>
<arg>--projectOrganizationPath</arg><arg>${workingDir}/preparedInfo/projectOrganizationPath</arg>
<arg>--relationPath</arg><arg>${workingDir}/preparedInfo/relation</arg>
</spark>
<ok to="apply_resulttoorganization_propagation"/>
@ -161,7 +162,7 @@
<master>yarn</master>
<mode>cluster</mode>
<name>resultToOrganizationFromSemRel</name>
<class>eu.dnetlib.dhp.resulttoorganizationfromsemrel.SparkResultToOrganizationFromSemRel</class>
<class>eu.dnetlib.dhp.entitytoorganizationfromsemrel.SparkResultToOrganizationFromSemRel</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}

49
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java
View File

@ -39,8 +39,10 @@ public class BulkTagJobTest {
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\", "
+ " \"subject\" :\"$['subject'][*]['value']\" , " +
"\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"" +
"} ";
"\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"," +
"\"sdg\" : \"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"," +
"\"hostedby\" : \"$['instance'][*]['hostedby']['key']\" , " +
"\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"} ";
private static SparkSession spark;
@ -56,7 +58,7 @@ public class BulkTagJobTest {
.toString(
BulkTagJobTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_dth.xml"));
"/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_remove.xml"));
} catch (IOException e) {
e.printStackTrace();
}
@ -1525,4 +1527,45 @@ public class BulkTagJobTest {
.count());
}
@Test
void removeTest() throws Exception {
final String pathMap = BulkTagJobTest.pathMap;
SparkBulkTagJob
.main(
new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints")
.getPath(),
"-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath", workingDir.toString() + "/dataset",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(12, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+ "from dataset "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyD.inferenceprovenance = 'bulktagging'";
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'dth'").count());
}
}

194
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/PrepareInfoJobTest.java → dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/entitytoorganizationfromsemrel/PrepareInfoJobTest.java
View File

@ -1,22 +1,17 @@
package eu.dnetlib.dhp.resulttoorganizationfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.readPath;
package eu.dnetlib.dhp.entitytoorganizationfromsemrel;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
@ -28,7 +23,6 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.KeyValueSet;
import eu.dnetlib.dhp.projecttoresult.SparkResultToProjectThroughSemRelJob;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class PrepareInfoJobTest {
@ -78,11 +72,12 @@ public class PrepareInfoJobTest {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-graphPath", getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/childparenttest1")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/childparenttest1")
.getPath(),
"-hive_metastore_uris", "",
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-projectOrganizationPath", workingDir.toString() + "/projectOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
@ -223,11 +218,12 @@ public class PrepareInfoJobTest {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-graphPath", getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/childparenttest2")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/childparenttest2")
.getPath(),
"-hive_metastore_uris", "",
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-projectOrganizationPath", workingDir.toString() + "/projectOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
@ -343,11 +339,12 @@ public class PrepareInfoJobTest {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-graphPath", getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/resultorganizationtest")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/resultorganizationtest")
.getPath(),
"-hive_metastore_uris", "",
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-projectOrganizationPath", workingDir.toString() + "/projectOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
@ -355,7 +352,38 @@ public class PrepareInfoJobTest {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.textFile(workingDir.toString() + "/relation")
.textFile(workingDir.toString() + "/relation/result")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
Assertions.assertEquals(7, verificationDs.count());
}
@Test
public void relationProjectTest() throws Exception {
PrepareInfo
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-graphPath", getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/projectorganizationtest")
.getPath(),
"-hive_metastore_uris", "",
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-projectOrganizationPath", workingDir.toString() + "/projectOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.textFile(workingDir.toString() + "/relation/project")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
@ -373,11 +401,12 @@ public class PrepareInfoJobTest {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-graphPath", getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/resultorganizationtest")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/resultorganizationtest")
.getPath(),
"-hive_metastore_uris", "",
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-projectOrganizationPath", workingDir.toString() + "/projectOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
@ -498,6 +527,141 @@ public class PrepareInfoJobTest {
}
@Test
public void projectOrganizationTest1() throws Exception {
PrepareInfo
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-graphPath", getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/projectorganizationtest")
.getPath(),
"-hive_metastore_uris", "",
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-projectOrganizationPath", workingDir.toString() + "/projectOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<KeyValueSet> tmp = sc
.textFile(workingDir.toString() + "/projectOrganization/")
.map(item -> OBJECT_MAPPER.readValue(item, KeyValueSet.class));
Dataset<KeyValueSet> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(KeyValueSet.class));
Assertions.assertEquals(5, verificationDs.count());
Assertions
.assertEquals(
2, verificationDs
.filter("key = '40|doajarticles::2baa9032dc058d3c8ff780c426b0c19f'")
.collectAsList()
.get(0)
.getValueSet()
.size());
Assertions
.assertTrue(
verificationDs
.filter("key = '40|doajarticles::2baa9032dc058d3c8ff780c426b0c19f'")
.collectAsList()
.get(0)
.getValueSet()
.contains("20|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
verificationDs
.filter("key = '40|doajarticles::2baa9032dc058d3c8ff780c426b0c19f'")
.collectAsList()
.get(0)
.getValueSet()
.contains("20|pippo_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertEquals(
2, verificationDs
.filter("key = '40|dedup_wf_001::2899e571609779168222fdeb59cb916d'")
.collectAsList()
.get(0)
.getValueSet()
.size());
Assertions
.assertTrue(
verificationDs
.filter("key = '40|dedup_wf_001::2899e571609779168222fdeb59cb916d'")
.collectAsList()
.get(0)
.getValueSet()
.contains("20|doajarticles::396262ee936f3d3e26ff0e60bea6cae0"));
Assertions
.assertTrue(
verificationDs
.filter("key = '40|dedup_wf_001::2899e571609779168222fdeb59cb916d'")
.collectAsList()
.get(0)
.getValueSet()
.contains("20|pippo_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertEquals(
1, verificationDs
.filter("key = '40|doajarticles::03748bcb5d754c951efec9700e18a56d'")
.collectAsList()
.get(0)
.getValueSet()
.size());
Assertions
.assertTrue(
verificationDs
.filter("key = '40|doajarticles::03748bcb5d754c951efec9700e18a56d'")
.collectAsList()
.get(0)
.getValueSet()
.contains("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertEquals(
1, verificationDs
.filter("key = '40|openaire____::ec653e804967133b9436fdd30d3ff51d'")
.collectAsList()
.get(0)
.getValueSet()
.size());
Assertions
.assertTrue(
verificationDs
.filter("key = '40|openaire____::ec653e804967133b9436fdd30d3ff51d'")
.collectAsList()
.get(0)
.getValueSet()
.contains("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
Assertions
.assertEquals(
1, verificationDs
.filter("key = '40|doajarticles::1cae0b82b56ccd97c2db1f698def7074'")
.collectAsList()
.get(0)
.getValueSet()
.size());
Assertions
.assertTrue(
verificationDs
.filter("key = '40|doajarticles::1cae0b82b56ccd97c2db1f698def7074'")
.collectAsList()
.get(0)
.getValueSet()
.contains("20|opendoar____::a5fcb8eb25ebd6f7cd219e0fa1e6ddc1"));
verificationDs
.foreach((ForeachFunction<KeyValueSet>) v -> System.out.println(OBJECT_MAPPER.writeValueAsString(v)));
}
@Test
public void foundLeavesTest1() throws Exception {
@ -507,11 +671,12 @@ public class PrepareInfoJobTest {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-graphPath", getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/resultorganizationtest")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/resultorganizationtest")
.getPath(),
"-hive_metastore_uris", "",
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-projectOrganizationPath", workingDir.toString() + "/projectOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"
@ -534,11 +699,12 @@ public class PrepareInfoJobTest {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-graphPath", getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/childparenttest1")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/childparenttest1")
.getPath(),
"-hive_metastore_uris", "",
"-leavesPath", workingDir.toString() + "/currentIteration/",
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
"-projectOrganizationPath", workingDir.toString() + "/projectOrganization/",
"-childParentPath", workingDir.toString() + "/childParentOrg/",
"-relationPath", workingDir.toString() + "/relation"

900
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/entitytoorganizationfromsemrel/SparkJobTest.java Normal file
View File

@ -0,0 +1,900 @@
package eu.dnetlib.dhp.entitytoorganizationfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.readPath;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.KeyValueSet;
import eu.dnetlib.dhp.PropagationConstant;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class SparkJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(SparkJobTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(StepActionsTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(PrepareInfoJobTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(PrepareInfoJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public void completeResultExecution() throws Exception {
final String graphPath = getClass()
.getResource("/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/graph")
.getPath();
final String leavesPath = getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/currentIteration/")
.getPath();
final String childParentPath = getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/childParentOrg/")
.getPath();
final String resultOrgPath = getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/resultOrganization/")
.getPath();
final String projectOrgPath = getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/projectOrganization/")
.getPath();
readPath(spark, leavesPath, Leaves.class)
.write()
.option("compression", "gzip")
.json(workingDir.toString() + "/leavesInput");
readPath(spark, resultOrgPath, KeyValueSet.class)
.write()
.option("compression", "gzip")
.json(workingDir.toString() + "/orgsInput");
readPath(spark, projectOrgPath, KeyValueSet.class)
.write()
.option("compression", "gzip")
.json(workingDir.toString() + "/projectInput");
SparkResultToOrganizationFromSemRel
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-relationPath", graphPath,
"-hive_metastore_uris", "",
"-outputPath", workingDir.toString() + "/finalrelation",
"-leavesPath", workingDir.toString() + "/leavesInput",
"-resultOrgPath", workingDir.toString() + "/orgsInput",
"-projectOrganizationPath", workingDir.toString() + "/projectInput",
"-childParentPath", childParentPath,
"-workingDir", workingDir.toString()
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Relation> temp = sc
.textFile(workingDir.toString() + "/finalrelation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Assertions.assertEquals(36, temp.count());
JavaRDD<Relation> result = temp.filter(r -> r.getSource().startsWith("50|") || r.getTarget().startsWith("50|"));
Assertions.assertEquals(18, result.count());
result.foreach(r -> Assertions.assertEquals(ModelConstants.AFFILIATION, r.getSubRelType()));
result.foreach(r -> Assertions.assertEquals(ModelConstants.RESULT_ORGANIZATION, r.getRelType()));
result
.foreach(
r -> Assertions
.assertEquals(
PropagationConstant.PROPAGATION_DATA_INFO_TYPE, r.getDataInfo().getInferenceprovenance()));
result
.foreach(
r -> Assertions
.assertEquals(
PropagationConstant.PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_ID,
r.getDataInfo().getProvenanceaction().getClassid()));
result
.foreach(
r -> Assertions
.assertEquals(
PropagationConstant.PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_NAME,
r.getDataInfo().getProvenanceaction().getClassname()));
result
.foreach(
r -> Assertions
.assertEquals(
"0.85",
r.getDataInfo().getTrust()));
Assertions.assertEquals(9, result.filter(r -> r.getSource().substring(0, 3).equals("50|")).count());
result
.filter(r -> r.getSource().substring(0, 3).equals("50|"))
.foreach(r -> Assertions.assertEquals(ModelConstants.HAS_AUTHOR_INSTITUTION, r.getRelClass()));
Assertions
.assertEquals(
2,
result.filter(r -> r.getSource().equals("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074")).count());
Assertions
.assertEquals(
3,
result.filter(r -> r.getSource().equals("50|dedup_wf_001::2899e571609779168222fdeb59cb916d")).count());
Assertions
.assertEquals(
2,
result.filter(r -> r.getSource().equals("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f")).count());
Assertions
.assertEquals(
1,
result.filter(r -> r.getSource().equals("50|openaire____::ec653e804967133b9436fdd30d3ff51d")).count());
Assertions
.assertEquals(
1,
result.filter(r -> r.getSource().equals("50|doajarticles::03748bcb5d754c951efec9700e18a56d")).count());
Assertions.assertEquals(9, result.filter(r -> r.getSource().substring(0, 3).equals("20|")).count());
result
.filter(r -> r.getSource().substring(0, 3).equals("20|"))
.foreach(r -> Assertions.assertEquals(ModelConstants.IS_AUTHOR_INSTITUTION_OF, r.getRelClass()));
Assertions
.assertEquals(
1,
result.filter(r -> r.getSource().equals("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074")).count());
Assertions
.assertEquals(
1,
result.filter(r -> r.getSource().equals("20|dedup_wf_001::2899e571609779168222fdeb59cb916d")).count());
Assertions
.assertEquals(
2,
result.filter(r -> r.getSource().equals("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f")).count());
Assertions
.assertEquals(
2,
result.filter(r -> r.getSource().equals("20|openaire____::ec653e804967133b9436fdd30d3ff51d")).count());
Assertions
.assertEquals(
3,
result.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d")).count());
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074"))
.map(r -> r.getTarget())
.collect()
.contains("20|openaire____::ec653e804967133b9436fdd30d3ff51d"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::03748bcb5d754c951efec9700e18a56d"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
.map(r -> r.getTarget())
.collect()
.contains("20|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::03748bcb5d754c951efec9700e18a56d"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("50|openaire____::ec653e804967133b9436fdd30d3ff51d"))
.map(r -> r.getTarget())
.collect()
.contains("20|openaire____::ec653e804967133b9436fdd30d3ff51d"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("50|doajarticles::03748bcb5d754c951efec9700e18a56d"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::03748bcb5d754c951efec9700e18a56d"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("20|openaire____::ec653e804967133b9436fdd30d3ff51d"))
.map(r -> r.getTarget())
.collect()
.contains("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("20|openaire____::ec653e804967133b9436fdd30d3ff51d"))
.map(r -> r.getTarget())
.collect()
.contains("50|openaire____::ec653e804967133b9436fdd30d3ff51d"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
.map(r -> r.getTarget())
.collect()
.contains("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
.map(r -> r.getTarget())
.collect()
.contains("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d"))
.map(r -> r.getTarget())
.collect()
.contains("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d"))
.map(r -> r.getTarget())
.collect()
.contains("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d"))
.map(r -> r.getTarget())
.collect()
.contains("50|doajarticles::03748bcb5d754c951efec9700e18a56d"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("20|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
.map(r -> r.getTarget())
.collect()
.contains("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
result
.filter(r -> r.getSource().equals("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074"))
.map(r -> r.getTarget())
.collect()
.contains("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
}
@Test
public void completeProjectExecution() throws Exception {
final String graphPath = getClass()
.getResource("/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/graph")
.getPath();
final String leavesPath = getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/currentIteration/")
.getPath();
final String childParentPath = getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/childParentOrg/")
.getPath();
final String resultOrgPath = getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/resultOrganization/")
.getPath();
final String projectOrgPath = getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/projectOrganization/")
.getPath();
readPath(spark, leavesPath, Leaves.class)
.write()
.option("compression", "gzip")
.json(workingDir.toString() + "/leavesInput");
readPath(spark, resultOrgPath, KeyValueSet.class)
.write()
.option("compression", "gzip")
.json(workingDir.toString() + "/orgsInput");
readPath(spark, projectOrgPath, KeyValueSet.class)
.write()
.option("compression", "gzip")
.json(workingDir.toString() + "/projectInput");
SparkResultToOrganizationFromSemRel
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-relationPath", graphPath,
"-hive_metastore_uris", "",
"-outputPath", workingDir.toString() + "/finalrelation",
"-leavesPath", workingDir.toString() + "/leavesInput",
"-resultOrgPath", workingDir.toString() + "/orgsInput",
"-projectOrganizationPath", workingDir.toString() + "/projectInput",
"-childParentPath", childParentPath,
"-workingDir", workingDir.toString()
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Relation> temp = sc
.textFile(workingDir.toString() + "/finalrelation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Assertions.assertEquals(36, temp.count());
JavaRDD<Relation> project = temp
.filter(r -> r.getSource().startsWith("40|") || r.getTarget().startsWith("40|"));
Assertions.assertEquals(18, project.count());
project.foreach(r -> Assertions.assertEquals(ModelConstants.PARTICIPATION, r.getSubRelType()));
project.foreach(r -> Assertions.assertEquals(ModelConstants.PROJECT_ORGANIZATION, r.getRelType()));
project
.foreach(
r -> Assertions
.assertEquals(
PropagationConstant.PROPAGATION_DATA_INFO_TYPE, r.getDataInfo().getInferenceprovenance()));
project
.foreach(
r -> Assertions
.assertEquals(
PropagationConstant.PROPAGATION_RELATION_PROJECT_ORGANIZATION_SEM_REL_CLASS_ID,
r.getDataInfo().getProvenanceaction().getClassid()));
project
.foreach(
r -> Assertions
.assertEquals(
PropagationConstant.PROPAGATION_RELATION_PROJECT_ORGANIZATION_SEM_REL_CLASS_NAME,
r.getDataInfo().getProvenanceaction().getClassname()));
project
.foreach(
r -> Assertions
.assertEquals(
"0.85",
r.getDataInfo().getTrust()));
Assertions.assertEquals(9, project.filter(r -> r.getSource().substring(0, 3).equals("40|")).count());
project
.filter(r -> r.getSource().substring(0, 3).equals("40|"))
.foreach(r -> Assertions.assertEquals(ModelConstants.HAS_PARTICIPANT, r.getRelClass()));
Assertions
.assertEquals(
2,
project.filter(r -> r.getSource().equals("40|doajarticles::1cae0b82b56ccd97c2db1f698def7074")).count());
Assertions
.assertEquals(
3,
project.filter(r -> r.getSource().equals("40|dedup_wf_001::2899e571609779168222fdeb59cb916d")).count());
Assertions
.assertEquals(
2,
project.filter(r -> r.getSource().equals("40|doajarticles::2baa9032dc058d3c8ff780c426b0c19f")).count());
Assertions
.assertEquals(
1,
project.filter(r -> r.getSource().equals("40|openaire____::ec653e804967133b9436fdd30d3ff51d")).count());
Assertions
.assertEquals(
1,
project.filter(r -> r.getSource().equals("40|doajarticles::03748bcb5d754c951efec9700e18a56d")).count());
Assertions.assertEquals(9, project.filter(r -> r.getSource().substring(0, 3).equals("20|")).count());
project
.filter(r -> r.getSource().substring(0, 3).equals("20|"))
.foreach(r -> Assertions.assertEquals(ModelConstants.IS_PARTICIPANT, r.getRelClass()));
Assertions
.assertEquals(
1,
project.filter(r -> r.getSource().equals("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074")).count());
Assertions
.assertEquals(
1,
project.filter(r -> r.getSource().equals("20|dedup_wf_001::2899e571609779168222fdeb59cb916d")).count());
Assertions
.assertEquals(
2,
project.filter(r -> r.getSource().equals("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f")).count());
Assertions
.assertEquals(
2,
project.filter(r -> r.getSource().equals("20|openaire____::ec653e804967133b9436fdd30d3ff51d")).count());
Assertions
.assertEquals(
3,
project.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d")).count());
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("40|doajarticles::1cae0b82b56ccd97c2db1f698def7074"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("40|doajarticles::1cae0b82b56ccd97c2db1f698def7074"))
.map(r -> r.getTarget())
.collect()
.contains("20|openaire____::ec653e804967133b9436fdd30d3ff51d"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("40|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("40|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::03748bcb5d754c951efec9700e18a56d"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("40|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
.map(r -> r.getTarget())
.collect()
.contains("20|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("40|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("40|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::03748bcb5d754c951efec9700e18a56d"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("40|openaire____::ec653e804967133b9436fdd30d3ff51d"))
.map(r -> r.getTarget())
.collect()
.contains("20|openaire____::ec653e804967133b9436fdd30d3ff51d"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("40|doajarticles::03748bcb5d754c951efec9700e18a56d"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::03748bcb5d754c951efec9700e18a56d"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("20|openaire____::ec653e804967133b9436fdd30d3ff51d"))
.map(r -> r.getTarget())
.collect()
.contains("40|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("20|openaire____::ec653e804967133b9436fdd30d3ff51d"))
.map(r -> r.getTarget())
.collect()
.contains("40|openaire____::ec653e804967133b9436fdd30d3ff51d"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
.map(r -> r.getTarget())
.collect()
.contains("40|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
.map(r -> r.getTarget())
.collect()
.contains("40|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d"))
.map(r -> r.getTarget())
.collect()
.contains("40|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d"))
.map(r -> r.getTarget())
.collect()
.contains("40|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d"))
.map(r -> r.getTarget())
.collect()
.contains("40|doajarticles::03748bcb5d754c951efec9700e18a56d"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("20|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
.map(r -> r.getTarget())
.collect()
.contains("40|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
project
.filter(r -> r.getSource().equals("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074"))
.map(r -> r.getTarget())
.collect()
.contains("40|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
}
@Test
public void singleIterationExecution() throws Exception {
final String graphPath = getClass()
.getResource("/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/graph")
.getPath();
final String leavesPath = getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/currentIteration/")
.getPath();
final String childParentPath = getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/childParentOrg/")
.getPath();
final String resultOrgPath = getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/resultOrganization/")
.getPath();
final String projectOrgPath = getClass()
.getResource(
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/projectOrganization/")
.getPath();
readPath(spark, leavesPath, Leaves.class)
.write()
.option("compression", "gzip")
.json(workingDir.toString() + "/leavesInput");
readPath(spark, resultOrgPath, KeyValueSet.class)
.write()
.option("compression", "gzip")
.json(workingDir.toString() + "/orgsInput");
readPath(spark, projectOrgPath, KeyValueSet.class)
.write()
.option("compression", "gzip")
.json(workingDir.toString() + "/projectInput");
SparkResultToOrganizationFromSemRel
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-relationPath", graphPath,
"-hive_metastore_uris", "",
"-outputPath", workingDir.toString() + "/finalrelation",
"-leavesPath", workingDir.toString() + "/leavesInput",
"-resultOrgPath", workingDir.toString() + "/orgsInput",
"-projectOrganizationPath", workingDir.toString() + "/projectInput",
"-childParentPath", childParentPath,
"-workingDir", workingDir.toString(),
"-iterations", "1"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Relation> temp = sc
.textFile(workingDir.toString() + "/finalrelation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Assertions.assertEquals(16, temp.count());
Assertions.assertEquals(4, temp.filter(r -> r.getSource().startsWith("50|")).count());
Assertions.assertEquals(4, temp.filter(r -> r.getTarget().startsWith("50|")).count());
Assertions.assertEquals(4, temp.filter(r -> r.getSource().startsWith("40|")).count());
Assertions.assertEquals(4, temp.filter(r -> r.getTarget().startsWith("40|")).count());
Assertions.assertEquals(8, temp.filter(r -> r.getSource().startsWith("20|")).count());
Assertions.assertEquals(8, temp.filter(r -> r.getSource().startsWith("20|")).count());
// JavaRDD<Relation> result = temp.filter(r -> r.getSource().startsWith("50|") || r.getTarget().startsWith("50|"));
// Assertions.assertEquals(18, result.count());
// result.foreach(r -> Assertions.assertEquals(ModelConstants.AFFILIATION, r.getSubRelType()));
// result.foreach(r -> Assertions.assertEquals(ModelConstants.RESULT_ORGANIZATION, r.getRelType()));
// result
// .foreach(
// r -> Assertions
// .assertEquals(
// PropagationConstant.PROPAGATION_DATA_INFO_TYPE, r.getDataInfo().getInferenceprovenance()));
// result
// .foreach(
// r -> Assertions
// .assertEquals(
// PropagationConstant.PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_ID,
// r.getDataInfo().getProvenanceaction().getClassid()));
// result
// .foreach(
// r -> Assertions
// .assertEquals(
// PropagationConstant.PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_NAME,
// r.getDataInfo().getProvenanceaction().getClassname()));
// result
// .foreach(
// r -> Assertions
// .assertEquals(
// "0.85",
// r.getDataInfo().getTrust()));
//
// Assertions.assertEquals(9, result.filter(r -> r.getSource().substring(0, 3).equals("50|")).count());
// result
// .filter(r -> r.getSource().substring(0, 3).equals("50|"))
// .foreach(r -> Assertions.assertEquals(ModelConstants.HAS_AUTHOR_INSTITUTION, r.getRelClass()));
// Assertions
// .assertEquals(
// 2, result.filter(r -> r.getSource().equals("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074")).count());
// Assertions
// .assertEquals(
// 3, result.filter(r -> r.getSource().equals("50|dedup_wf_001::2899e571609779168222fdeb59cb916d")).count());
// Assertions
// .assertEquals(
// 2, result.filter(r -> r.getSource().equals("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f")).count());
// Assertions
// .assertEquals(
// 1, result.filter(r -> r.getSource().equals("50|openaire____::ec653e804967133b9436fdd30d3ff51d")).count());
// Assertions
// .assertEquals(
// 1, result.filter(r -> r.getSource().equals("50|doajarticles::03748bcb5d754c951efec9700e18a56d")).count());
//
// Assertions.assertEquals(9, result.filter(r -> r.getSource().substring(0, 3).equals("20|")).count());
// result
// .filter(r -> r.getSource().substring(0, 3).equals("20|"))
// .foreach(r -> Assertions.assertEquals(ModelConstants.IS_AUTHOR_INSTITUTION_OF, r.getRelClass()));
// Assertions
// .assertEquals(
// 1, result.filter(r -> r.getSource().equals("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074")).count());
// Assertions
// .assertEquals(
// 1, result.filter(r -> r.getSource().equals("20|dedup_wf_001::2899e571609779168222fdeb59cb916d")).count());
// Assertions
// .assertEquals(
// 2, result.filter(r -> r.getSource().equals("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f")).count());
// Assertions
// .assertEquals(
// 2, result.filter(r -> r.getSource().equals("20|openaire____::ec653e804967133b9436fdd30d3ff51d")).count());
// Assertions
// .assertEquals(
// 3, result.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d")).count());
//
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074"))
// .map(r -> r.getTarget())
// .collect()
// .contains("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074"))
// .map(r -> r.getTarget())
// .collect()
// .contains("20|openaire____::ec653e804967133b9436fdd30d3ff51d"));
//
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
// .map(r -> r.getTarget())
// .collect()
// .contains("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
// .map(r -> r.getTarget())
// .collect()
// .contains("20|doajarticles::03748bcb5d754c951efec9700e18a56d"));
//
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
// .map(r -> r.getTarget())
// .collect()
// .contains("20|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
// .map(r -> r.getTarget())
// .collect()
// .contains("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
// .map(r -> r.getTarget())
// .collect()
// .contains("20|doajarticles::03748bcb5d754c951efec9700e18a56d"));
//
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("50|openaire____::ec653e804967133b9436fdd30d3ff51d"))
// .map(r -> r.getTarget())
// .collect()
// .contains("20|openaire____::ec653e804967133b9436fdd30d3ff51d"));
//
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("50|doajarticles::03748bcb5d754c951efec9700e18a56d"))
// .map(r -> r.getTarget())
// .collect()
// .contains("20|doajarticles::03748bcb5d754c951efec9700e18a56d"));
//
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("20|openaire____::ec653e804967133b9436fdd30d3ff51d"))
// .map(r -> r.getTarget())
// .collect()
// .contains("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("20|openaire____::ec653e804967133b9436fdd30d3ff51d"))
// .map(r -> r.getTarget())
// .collect()
// .contains("50|openaire____::ec653e804967133b9436fdd30d3ff51d"));
//
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
// .map(r -> r.getTarget())
// .collect()
// .contains("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
// .map(r -> r.getTarget())
// .collect()
// .contains("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
//
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d"))
// .map(r -> r.getTarget())
// .collect()
// .contains("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d"))
// .map(r -> r.getTarget())
// .collect()
// .contains("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d"))
// .map(r -> r.getTarget())
// .collect()
// .contains("50|doajarticles::03748bcb5d754c951efec9700e18a56d"));
//
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("20|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
// .map(r -> r.getTarget())
// .collect()
// .contains("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
//
// Assertions
// .assertTrue(
// result
// .filter(r -> r.getSource().equals("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074"))
// .map(r -> r.getTarget())
// .collect()
// .contains("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
}
}

29
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/StepActionsTest.java → dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/entitytoorganizationfromsemrel/StepActionsTest.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.resulttoorganizationfromsemrel;
package eu.dnetlib.dhp.entitytoorganizationfromsemrel;
import java.io.IOException;
import java.nio.file.Files;
@ -73,21 +73,22 @@ public class StepActionsTest {
.execStep(
spark, getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/graph/result")
.getPath(),
workingDir.toString() + "/newRelationPath",
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/currentIteration/")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/currentIteration/")
.getPath(),
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/childParentOrg/")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/childParentOrg/")
.getPath(),
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/resultOrganization/")
.getPath());
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/resultOrganization/")
.getPath(),
ModelConstants.HAS_AUTHOR_INSTITUTION);
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -203,19 +204,19 @@ public class StepActionsTest {
spark,
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/relsforiteration1/")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/relsforiteration1/")
.getPath(),
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/resultOrganization/")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/resultOrganization/")
.getPath(),
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/currentIteration/")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/currentIteration/")
.getPath(),
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/childParentOrg/")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/childParentOrg/")
.getPath(),
workingDir.toString() + "/tempLeaves", workingDir.toString() + "/tempOrgs");
@ -248,19 +249,19 @@ public class StepActionsTest {
spark,
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/relsforiteration1/")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/relsforiteration1/")
.getPath(),
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/resultOrganization/")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/resultOrganization/")
.getPath(),
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/currentIteration/")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/currentIteration/")
.getPath(),
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/childParentOrg/")
"/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/childParentOrg/")
.getPath(),
workingDir.toString() + "/tempLeaves", workingDir.toString() + "/tempOrgs");

325
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/SparkJobTest.java
View File

@ -1,325 +0,0 @@
package eu.dnetlib.dhp.resulttoorganizationfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged;
import static eu.dnetlib.dhp.PropagationConstant.readPath;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.KeyValueSet;
import eu.dnetlib.dhp.PropagationConstant;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class SparkJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(SparkJobTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(StepActionsTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(PrepareInfoJobTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(PrepareInfoJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public void completeExecution() throws Exception {
final String graphPath = getClass()
.getResource("/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep")
.getPath();
final String leavesPath = getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/currentIteration/")
.getPath();
final String childParentPath = getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/childParentOrg/")
.getPath();
final String resultOrgPath = getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/resultOrganization/")
.getPath();
readPath(spark, leavesPath, Leaves.class)
.write()
.option("compression", "gzip")
.json(workingDir.toString() + "/leavesInput");
readPath(spark, resultOrgPath, KeyValueSet.class)
.write()
.option("compression", "gzip")
.json(workingDir.toString() + "/orgsInput");
SparkResultToOrganizationFromSemRel
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-relationPath", graphPath,
"-hive_metastore_uris", "",
"-outputPath", workingDir.toString() + "/finalrelation",
"-leavesPath", workingDir.toString() + "/leavesInput",
"-resultOrgPath", workingDir.toString() + "/orgsInput",
"-childParentPath", childParentPath,
"-workingDir", workingDir.toString()
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.textFile(workingDir.toString() + "/finalrelation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
Assertions.assertEquals(18, tmp.count());
tmp.foreach(r -> Assertions.assertEquals(ModelConstants.AFFILIATION, r.getSubRelType()));
tmp.foreach(r -> Assertions.assertEquals(ModelConstants.RESULT_ORGANIZATION, r.getRelType()));
tmp
.foreach(
r -> Assertions
.assertEquals(
PropagationConstant.PROPAGATION_DATA_INFO_TYPE, r.getDataInfo().getInferenceprovenance()));
tmp
.foreach(
r -> Assertions
.assertEquals(
PropagationConstant.PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_ID,
r.getDataInfo().getProvenanceaction().getClassid()));
tmp
.foreach(
r -> Assertions
.assertEquals(
PropagationConstant.PROPAGATION_RELATION_RESULT_ORGANIZATION_SEM_REL_CLASS_NAME,
r.getDataInfo().getProvenanceaction().getClassname()));
tmp
.foreach(
r -> Assertions
.assertEquals(
"0.85",
r.getDataInfo().getTrust()));
Assertions.assertEquals(9, tmp.filter(r -> r.getSource().substring(0, 3).equals("50|")).count());
tmp
.filter(r -> r.getSource().substring(0, 3).equals("50|"))
.foreach(r -> Assertions.assertEquals(ModelConstants.HAS_AUTHOR_INSTITUTION, r.getRelClass()));
Assertions
.assertEquals(
2, tmp.filter(r -> r.getSource().equals("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074")).count());
Assertions
.assertEquals(
3, tmp.filter(r -> r.getSource().equals("50|dedup_wf_001::2899e571609779168222fdeb59cb916d")).count());
Assertions
.assertEquals(
2, tmp.filter(r -> r.getSource().equals("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f")).count());
Assertions
.assertEquals(
1, tmp.filter(r -> r.getSource().equals("50|openaire____::ec653e804967133b9436fdd30d3ff51d")).count());
Assertions
.assertEquals(
1, tmp.filter(r -> r.getSource().equals("50|doajarticles::03748bcb5d754c951efec9700e18a56d")).count());
Assertions.assertEquals(9, tmp.filter(r -> r.getSource().substring(0, 3).equals("20|")).count());
tmp
.filter(r -> r.getSource().substring(0, 3).equals("20|"))
.foreach(r -> Assertions.assertEquals(ModelConstants.IS_AUTHOR_INSTITUTION_OF, r.getRelClass()));
Assertions
.assertEquals(
1, tmp.filter(r -> r.getSource().equals("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074")).count());
Assertions
.assertEquals(
1, tmp.filter(r -> r.getSource().equals("20|dedup_wf_001::2899e571609779168222fdeb59cb916d")).count());
Assertions
.assertEquals(
2, tmp.filter(r -> r.getSource().equals("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f")).count());
Assertions
.assertEquals(
2, tmp.filter(r -> r.getSource().equals("20|openaire____::ec653e804967133b9436fdd30d3ff51d")).count());
Assertions
.assertEquals(
3, tmp.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d")).count());
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074"))
.map(r -> r.getTarget())
.collect()
.contains("20|openaire____::ec653e804967133b9436fdd30d3ff51d"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::03748bcb5d754c951efec9700e18a56d"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
.map(r -> r.getTarget())
.collect()
.contains("20|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::03748bcb5d754c951efec9700e18a56d"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("50|openaire____::ec653e804967133b9436fdd30d3ff51d"))
.map(r -> r.getTarget())
.collect()
.contains("20|openaire____::ec653e804967133b9436fdd30d3ff51d"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("50|doajarticles::03748bcb5d754c951efec9700e18a56d"))
.map(r -> r.getTarget())
.collect()
.contains("20|doajarticles::03748bcb5d754c951efec9700e18a56d"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("20|openaire____::ec653e804967133b9436fdd30d3ff51d"))
.map(r -> r.getTarget())
.collect()
.contains("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("20|openaire____::ec653e804967133b9436fdd30d3ff51d"))
.map(r -> r.getTarget())
.collect()
.contains("50|openaire____::ec653e804967133b9436fdd30d3ff51d"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
.map(r -> r.getTarget())
.collect()
.contains("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"))
.map(r -> r.getTarget())
.collect()
.contains("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d"))
.map(r -> r.getTarget())
.collect()
.contains("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d"))
.map(r -> r.getTarget())
.collect()
.contains("50|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("20|doajarticles::03748bcb5d754c951efec9700e18a56d"))
.map(r -> r.getTarget())
.collect()
.contains("50|doajarticles::03748bcb5d754c951efec9700e18a56d"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("20|dedup_wf_001::2899e571609779168222fdeb59cb916d"))
.map(r -> r.getTarget())
.collect()
.contains("50|dedup_wf_001::2899e571609779168222fdeb59cb916d"));
Assertions
.assertTrue(
tmp
.filter(r -> r.getSource().equals("20|doajarticles::1cae0b82b56ccd97c2db1f698def7074"))
.map(r -> r.getTarget())
.collect()
.contains("50|doajarticles::1cae0b82b56ccd97c2db1f698def7074"));
}
}

1555
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_remove.xml Normal file
View File

File diff suppressed because it is too large Load Diff

4
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/dataset_10.json
View File

File diff suppressed because one or more lines are too long

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/childparenttest1/relation → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/childparenttest1/relation
View File

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/childparenttest2/relation → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/childparenttest2/relation
View File

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/childParentOrg/childparent → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/childParentOrg/childparent
View File

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/currentIteration/leaves → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/currentIteration/leaves
View File

7
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/graph/project Normal file
View File

@ -0,0 +1,7 @@
{"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":"hasParticipant","relType":"datasourceOrganization","source":"40|doajarticles::2baa9032dc058d3c8ff780c426b0c19f","subRelType":"provision","target":"20|dedup_wf_001::2899e571609779168222fdeb59cb916d","validated":false}
{"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":"hasParticipant","relType":"datasourceOrganization","source":"40|doajarticles::2baa9032dc058d3c8ff780c426b0c19f","subRelType":"provision","target":"20|pippo_wf_001::2899e571609779168222fdeb59cb916d","validated":false}
{"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":"hasParticipant","relType":"datasourceOrganization","source":"40|dedup_wf_001::2899e571609779168222fdeb59cb916d","subRelType":"provision","target":"20|pippo_wf_001::2899e571609779168222fdeb59cb916d","validated":false}
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0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/resultorganizationtest/relation → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/graph/result
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dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/relsforiteration1/relation → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/relsforiteration1/relation
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0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/execstep/resultOrganization/resultorganization → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/execstep/resultOrganization/resultorganization
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{"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":"hasAuthorInstitution","relType":"datasourceOrganization","source":"50|doajarticles::03748bcb5d754c951efec9700e18a56d","subRelType":"provision","target":"20|doajarticles::2baa9032dc058d3c8ff780c426b0c19f"}
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{"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":"hasAuthorInstitution","relType":"datasourceOrganization","source":"50|doajarticles::1cae0b82b56ccd97c2db1f698def7074","subRelType":"provision","target":"20|opendoar____::a5fcb8eb25ebd6f7cd219e0fa1e6ddc1"}

20
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -5,8 +5,6 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.createOpenaireId;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.*;
import java.util.stream.Collectors;
@ -17,7 +15,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.common.Constants;
@ -27,12 +24,13 @@ import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
public abstract class AbstractMdRecordToOafMapper {
protected final VocabularyGroup vocs;
protected static final UrlValidator URL_VALIDATOR = UrlValidator.getInstance();
private final boolean invisible;
private final boolean shouldHashId;
@ -393,7 +391,7 @@ public abstract class AbstractMdRecordToOafMapper {
r.setPublisher(preparePublisher(doc, info));
r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info));
r.setSource(prepareSources(doc, info));
r.setFulltext(prepareListFields(doc, "//oaf:fulltext", info));
r.setFulltext(prepareListURL(doc, "//oaf:fulltext", info));
r.setFormat(prepareFormats(doc, info));
r.setContributor(prepareContributors(doc, info));
r.setResourcetype(prepareResourceType(doc, info));
@ -672,6 +670,14 @@ public abstract class AbstractMdRecordToOafMapper {
qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
}
protected List<Field<String>> prepareListURL(final Node node, final String xpath, final DataInfo info) {
return listFields(
info, prepareListString(node, xpath)
.stream()
.filter(URL_VALIDATOR::isValid)
.collect(Collectors.toList()));
}
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
return field(node.valueOf(xpath), info);
}
@ -695,13 +701,13 @@ public abstract class AbstractMdRecordToOafMapper {
}
protected Set<String> validateUrl(Collection<String> url) {
UrlValidator urlValidator = UrlValidator.getInstance();
if (Objects.isNull(url)) {
return new HashSet<>();
}
return url
.stream()
.filter(u -> urlValidator.isValid(u))
.filter(URL_VALIDATOR::isValid)
.collect(Collectors.toCollection(HashSet::new));
}

8
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
View File

@ -140,7 +140,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
final List<StructuredProperty> alternateIdentifier = prepareResultPids(doc, info);
final List<StructuredProperty> pid = IdentifierFactory.getPids(alternateIdentifier, collectedfrom);
final Set<StructuredProperty> pids = pid.stream().collect(Collectors.toCollection(HashSet::new));
final Set<StructuredProperty> pids = new HashSet<>(pid);
instance
.setAlternateIdentifier(
@ -158,6 +158,12 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
instance
.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
prepareListURL(doc, "//oaf:fulltext", info)
.stream()
.findFirst()
.map(Field::getValue)
.ifPresent(instance::setFulltext);
final List<Node> nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier"));
final List<String> url = nodes
.stream()

7
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
View File

@ -144,7 +144,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
final List<StructuredProperty> alternateIdentifier = prepareResultPids(doc, info);
final List<StructuredProperty> pid = IdentifierFactory.getPids(alternateIdentifier, collectedfrom);
final Set<StructuredProperty> pids = pid.stream().collect(Collectors.toCollection(HashSet::new));
final Set<StructuredProperty> pids = new HashSet<>(pid);
instance
.setAlternateIdentifier(
@ -161,6 +161,11 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
instance
.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
prepareListURL(doc, "//oaf:fulltext", info)
.stream()
.findFirst()
.map(Field::getValue)
.ifPresent(instance::setFulltext);
final Set<String> url = new HashSet<>();
for (final Object o : doc

5
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOpenOrgsForProvision.sql
View File

@ -15,7 +15,10 @@ SELECT
'OpenOrgs Database' AS collectedfromname,
o.country || '@@@dnet:countries' AS country,
'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction,
array_remove(array_cat(array_agg(DISTINCT i.otherid || '###' || i.type || '@@@dnet:pid_types'), array_agg(DISTINCT idup.otherid || '###' || idup.type || '@@@dnet:pid_types')), NULL) AS pid,
ARRAY(SELECT DISTINCT pid FROM unnest(array_cat(
array_agg(DISTINCT i.otherid || '###' || i.type || '@@@dnet:pid_types'),
array_agg(DISTINCT idup.otherid || '###' || idup.type || '@@@dnet:pid_types')
)) as t(pid) where pid IS NOT NULL),
(array_remove(array_cat(ARRAY[o.ec_legalbody], array_agg(od.ec_legalbody)), NULL))[1] AS eclegalbody,
(array_remove(array_cat(ARRAY[o.ec_legalperson], array_agg(od.ec_legalperson)), NULL))[1] AS eclegalperson,
(array_remove(array_cat(ARRAY[o.ec_nonprofit], array_agg(od.ec_nonprofit)), NULL))[1] AS ecnonprofit,

19
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -27,7 +27,6 @@ import eu.dnetlib.dhp.common.Constants;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -52,7 +51,7 @@ class MappersTest {
}
@Test
void testPublication() throws IOException, DocumentException {
void testPublication() throws IOException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_record.xml")));
@ -112,13 +111,17 @@ class MappersTest {
assertNotNull(i.getAccessright());
assertEquals("OPEN", i.getAccessright().getClassid());
});
assertEquals("0001", p.getInstance().get(0).getRefereed().getClassid());
assertNotNull(p.getInstance().get(0).getPid());
assertTrue(p.getInstance().get(0).getPid().isEmpty());
final Instance instance = p.getInstance().get(0);
assertEquals("0001", instance.getRefereed().getClassid());
assertNotNull(instance.getPid());
assertTrue(instance.getPid().isEmpty());
assertTrue(!p.getInstance().get(0).getAlternateIdentifier().isEmpty());
assertEquals("doi", p.getInstance().get(0).getAlternateIdentifier().get(0).getQualifier().getClassid());
assertEquals("10.3897/oneeco.2.e13718", p.getInstance().get(0).getAlternateIdentifier().get(0).getValue());
assertFalse(instance.getAlternateIdentifier().isEmpty());
assertEquals("doi", instance.getAlternateIdentifier().get(0).getQualifier().getClassid());
assertEquals("10.3897/oneeco.2.e13718", instance.getAlternateIdentifier().get(0).getValue());
assertNotNull(instance.getFulltext());
assertEquals("https://oneecosystem.pensoft.net/article/13718/", instance.getFulltext());
assertNotNull(p.getBestaccessright());
assertEquals("OPEN", p.getBestaccessright().getClassid());

2
pom.xml
View File

@ -807,7 +807,7 @@
<mockito-core.version>3.3.3</mockito-core.version>
<mongodb.driver.version>3.4.2</mongodb.driver.version>
<vtd.version>[2.12,3.0)</vtd.version>
<dhp-schemas.version>[3.16.0]</dhp-schemas.version>
<dhp-schemas.version>[3.17.1-SNAPSHOT]</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>