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Master branch updates from beta September 2023 #337

Manually merged
claudio.atzori merged 1271 commits from beta into master 2023-09-06 11:31:09 +02:00
Conversation 0 Commits 1271 Files Changed 999 +134 -72
10 changed files with 134 additions and 72 deletions
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10
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java
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@ -6,6 +6,7 @@ import java.util.ArrayList;
import java.util.List;
import com.google.gson.Gson;
import org.apache.avro.generic.GenericData;
/** Created by miriam on 01/08/2018. */
public class Community implements Serializable {
@ -14,6 +15,7 @@ public class Community implements Serializable {
private List<String> subjects = new ArrayList<>();
private List<Provider> providers = new ArrayList<>();
private List<ZenodoCommunity> zenodoCommunities = new ArrayList<>();
private SelectionConstraints constraints = new SelectionConstraints();
public String toJson() {
final Gson g = new Gson();
@ -57,4 +59,12 @@ public class Community implements Serializable {
public void setZenodoCommunities(List<ZenodoCommunity> zenodoCommunities) {
this.zenodoCommunities = zenodoCommunities;
}
public SelectionConstraints getConstraints() {
return constraints;
}
public void setConstraints(SelectionConstraints constraints) {
this.constraints = constraints;
}
}

14
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java
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@ -24,6 +24,8 @@ public class CommunityConfiguration implements Serializable {
private Map<String, List<Pair<String, SelectionConstraints>>> datasourceMap = new HashMap<>();
// map zenodocommunityid -> communityid
private Map<String, List<Pair<String, SelectionConstraints>>> zenodocommunityMap = new HashMap<>();
// map communityid -> selectionconstraints
private Map<String, SelectionConstraints> selectionConstraintsMap = new HashMap<>();
public Map<String, List<Pair<String, SelectionConstraints>>> getSubjectMap() {
return subjectMap;
@ -51,6 +53,14 @@ public class CommunityConfiguration implements Serializable {
this.zenodocommunityMap = zenodocommunityMap;
}
public Map<String, SelectionConstraints> getSelectionConstraintsMap() {
return selectionConstraintsMap;
}
public void setSelectionConstraintsMap(Map<String, SelectionConstraints> selectionConstraintsMap) {
this.selectionConstraintsMap = selectionConstraintsMap;
}
CommunityConfiguration(final Map<String, Community> communities) {
this.communities = communities;
init();
@ -67,6 +77,9 @@ public class CommunityConfiguration implements Serializable {
if (zenodocommunityMap == null) {
zenodocommunityMap = Maps.newHashMap();
}
if(selectionConstraintsMap == null){
selectionConstraintsMap = Maps.newHashMap();
}
for (Community c : getCommunities().values()) {
// get subjects
@ -87,6 +100,7 @@ public class CommunityConfiguration implements Serializable {
new Pair<>(id, zc.getSelCriteria()),
zenodocommunityMap);
}
selectionConstraintsMap.put(id, c.getConstraints());
}
}

12
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java
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@ -85,9 +85,21 @@ public class CommunityConfigurationFactory {
c.setSubjects(parseSubjects(node));
c.setProviders(parseDatasources(node));
c.setZenodoCommunities(parseZenodoCommunities(node));
c.setConstraints(parseConstrains(node));
return c;
}
private static SelectionConstraints parseConstrains(Node node) {
Node aconstraints = node.selectSingleNode("./advancedConstraints");
if(aconstraints == null){
return null;
}
SelectionConstraints selectionConstraints = new Gson().fromJson(aconstraints.getText(), SelectionConstraints.class);
selectionConstraints.setSelection(resolver);
return selectionConstraints;
}
private static List<String> parseSubjects(final Node node) {
final List<String> subjects = Lists.newArrayList();

9
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java
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@ -11,6 +11,7 @@ public class Constraint implements Serializable {
private String verb;
private String field;
private String value;
// private String element;
private Selection selection;
public String getVerb() {
@ -50,4 +51,12 @@ public class Constraint implements Serializable {
public boolean verifyCriteria(String metadata) {
return selection.apply(metadata);
}
// public String getElement() {
// return element;
// }
//
// public void setElement(String element) {
// this.element = element;
// }
}

107
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
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@ -9,6 +9,9 @@ import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import org.apache.commons.lang3.StringUtils;
import com.google.gson.Gson;
@ -95,13 +98,6 @@ public class ResultTagger implements Serializable {
}
// result
// .getInstance()
// .stream()
// .map(i -> new Pair<>(i.getCollectedfrom().getKey(), i.getHostedby().getKey()))
// .flatMap(p -> Stream.of(p.getFst(), p.getSnd()))
// .map(s -> StringUtils.substringAfter(s, "|"))
// .collect(Collectors.toCollection(HashSet::new))
tmp
.forEach(
dsId -> datasources
@ -135,6 +131,19 @@ public class ResultTagger implements Serializable {
communities.addAll(czenodo);
/* Tagging for Advanced Constraints */
final Set<String> aconstraints = new HashSet<>();
conf.getSelectionConstraintsMap().keySet()
.forEach(communityId -> {
if(conf.getSelectionConstraintsMap().get(communityId) != null &&
conf.getSelectionConstraintsMap().get(communityId)
.getCriteria().stream().anyMatch(crit -> crit.verifyCriteria(param)))
aconstraints.add(communityId);
});
communities.addAll(aconstraints);
clearContext(result);
/* Verify if there is something to bulktag */
@ -152,30 +161,24 @@ public class ResultTagger implements Serializable {
dataInfoList = new ArrayList<>();
c.setDataInfo(dataInfoList);
}
if (subjects.contains(c.getId()))
if (subjects.contains(c))
dataInfoList
.add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
if (datasources.contains(c))
dataInfoList
.add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
if (czenodo.contains(c))
dataInfoList
.add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
if (aconstraints.contains(c))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_SUBJECT,
CLASS_NAME_BULKTAG_SUBJECT,
TAGGING_TRUST));
if (datasources.contains(c.getId()))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_DATASOURCE,
CLASS_NAME_BULKTAG_DATASOURCE,
TAGGING_TRUST));
if (czenodo.contains(c.getId()))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_CZENODO,
CLASS_NAME_BULKTAG_ZENODO,
TAGGING_TRUST));
OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_ADVANCED_CONSTRAINT, CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
}
});
@ -195,28 +198,22 @@ public class ResultTagger implements Serializable {
List<DataInfo> dataInfoList = new ArrayList<>();
if (subjects.contains(c))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_SUBJECT,
CLASS_NAME_BULKTAG_SUBJECT,
TAGGING_TRUST));
.add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
if (datasources.contains(c))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_DATASOURCE,
CLASS_NAME_BULKTAG_DATASOURCE,
TAGGING_TRUST));
.add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
if (czenodo.contains(c))
dataInfoList
.add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
if (aconstraints.contains(c))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_CZENODO,
CLASS_NAME_BULKTAG_ZENODO,
TAGGING_TRUST));
OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_ADVANCED_CONSTRAINT, CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
context.setDataInfo(dataInfoList);
return context;
})
@ -226,22 +223,4 @@ public class ResultTagger implements Serializable {
return result;
}
public static DataInfo getDataInfo(
String inference_provenance, String inference_class_id, String inference_class_name, String trust) {
DataInfo di = new DataInfo();
di.setInferred(true);
di.setInferenceprovenance(inference_provenance);
di.setProvenanceaction(getQualifier(inference_class_id, inference_class_name));
di.setTrust(trust);
return di;
}
public static Qualifier getQualifier(String inference_class_id, String inference_class_name) {
Qualifier pa = new Qualifier();
pa.setClassid(inference_class_id);
pa.setClassname(inference_class_name);
pa.setSchemeid(DNET_PROVENANCE_ACTIONS);
pa.setSchemename(DNET_PROVENANCE_ACTIONS);
return pa;
}
}

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java
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@ -11,12 +11,14 @@ public class TaggingConstants {
public static final String CLASS_ID_SUBJECT = "community:subject";
public static final String CLASS_ID_DATASOURCE = "community:datasource";
public static final String CLASS_ID_CZENODO = "community:zenodocommunity";
public static final String CLASS_ID_ADVANCED_CONSTRAINT = "community:advconstraint";
public static final String ZENODO_COMMUNITY_INDICATOR = "zenodo.org/communities/";
public static final String CLASS_NAME_BULKTAG_SUBJECT = "Bulktagging for Community - Subject";
public static final String CLASS_NAME_BULKTAG_DATASOURCE = "Bulktagging for Community - Datasource";
public static final String CLASS_NAME_BULKTAG_ZENODO = "Bulktagging for Community - Zenodo";
public static final String CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT = "Bulktagging for Community - Advanced Constraints";
public static final String TAGGING_TRUST = "0.8";
}

37
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java
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@ -6,7 +6,16 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import com.google.gson.Gson;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.bulktag.community.ProtoMap;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
@ -24,11 +33,6 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Software;
public class BulkTagJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
@ -39,7 +43,8 @@ public class BulkTagJobTest {
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}";
+ " \"description\" : \"$['description'][*]['value']\", "
+" \"subject\" :\"$['subject'][*]['value']\" }";
private static SparkSession spark;
@ -763,10 +768,28 @@ public class BulkTagJobTest {
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
idExplodeCommunity.show(false);
Assertions.assertEquals(3, idExplodeCommunity.count());
Assertions.assertEquals(4, idExplodeCommunity.count());
Assertions
.assertEquals(
3, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
Assertions
.assertEquals(
1, idExplodeCommunity.filter("provenance = 'community:advconstraint'").count());
}
// @Test
// void test1(){
// ProtoMap params = new Gson().fromJson(pathMap, ProtoMap.class);
// HashMap<String, String> param = new HashMap<>();
// for (String key : params.keySet()) {
// try {
// param.put(key, jsonContext.read(params.get(key)));
// } catch (com.jayway.jsonpath.PathNotFoundException e) {
// param.put(key, new ArrayList<>());
// }
// }
// return param;
// }
// }
}

5
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml
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@ -1193,6 +1193,9 @@
<organizations/>
</community>
<community id="science-innovation-policy">
<advancedConstraints>{"criteria":[{"constraint":[{"verb":"equals_ignorecase","field":"subject","value":"ciencias de la comunicación"},
{"verb":"equals","field":"subject","value":"Miriam"}]},
{"constraint":[{"verb":"equals","field":"subject","value":"miriam"}]}]}</advancedConstraints>
<subjects>
<subject>Sustainability-oriented science policy</subject>
<subject> STI policies</subject>
@ -1316,7 +1319,7 @@
<openaireId>opendoar____::358aee4cc897452c00244351e4d91f69</openaireId>
<selcriteria>{"criteria":[{"constraint":[{"verb":"contains_ignorecase","field":"title","value":"COVID-19"}]},
{"constraint":[{"verb":"contains_ignorecase","field":"title","value":"SARS-CoV-2"}]},
{"constraint":[{"verb":"contains_ignorecase","field":"title","value":"2019-nCoV"}]}]}
{"constraint":[{"verb":"contains_ignorecase","field":"title","value":"2019-nCoV"}}]}
</selcriteria>
</datasource>
<datasource>

10
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/dataset_10.json Normal file
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