Merge pull request 'BulkTagging extension' (#250) from horizontalConstraints into beta

Reviewed-on: D-Net/dnet-hadoop#250
This commit is contained in:
Claudio Atzori 2022-09-27 14:56:31 +02:00
commit b4b6a4457c
14 changed files with 209 additions and 70 deletions

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@ -5,6 +5,8 @@ import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import org.apache.avro.generic.GenericData;
import com.google.gson.Gson;
/** Created by miriam on 01/08/2018. */
@ -14,6 +16,7 @@ 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 +60,12 @@ 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;
}
}

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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());
}
}

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@ -85,9 +85,22 @@ 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();

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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;
// }
}

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@ -18,6 +18,8 @@ public class QueryInformationSystem {
+ " let $datasources := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::contentproviders')]/concept "
+ " let $organizations := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::resultorganizations')]/concept "
+ " let $communities := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::zenodocommunities')]/concept "
+ " let $fos := $x//CONFIGURATION/context/param[./@name='fos']/text() "
+ " let $sdg := $x//CONFIGURATION/context/param[./@name='sdg']/text() "
+
"let $zenodo := $x//param[./@name='zenodoCommunity']/text() "
+ " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] and $x//context/param[./@name = 'status']/text() != 'hidden' "
@ -28,6 +30,12 @@ public class QueryInformationSystem {
+ " {for $y in tokenize($subj,',') "
+ " return "
+ " <subject>{$y}</subject>} "
+ " {for $y in tokenize($fos,',') "
+ " return "
+ " <subject>{$y}</subject>} "
+ " {for $y in tokenize($sdg,',') "
+ " return "
+ " <subject>{$y}</subject>} "
+ " </subjects> "
+ " <datasources> "
+ " {for $d in $datasources "
@ -61,6 +69,9 @@ public class QueryInformationSystem {
+ " </selcriteria> "
+ " </zenodocommunity>} "
+ " </zenodocommunities> "
+ "<advancedConstraint>"
+ "{$x//CONFIGURATION/context/param[./@name='advancedConstraint']/text()} "
+ "</advancedConstraint>"
+ " </community>";
public static CommunityConfiguration getCommunityConfiguration(final String isLookupUrl)

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@ -15,7 +15,10 @@ import com.google.gson.Gson;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
/** Created by miriam on 02/08/2018. */
public class ResultTagger implements Serializable {
@ -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 +131,25 @@ 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 +167,51 @@ public class ResultTagger implements Serializable {
dataInfoList = new ArrayList<>();
c.setDataInfo(dataInfoList);
}
if (subjects.contains(c.getId()))
if (subjects.contains(c))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_SUBJECT,
CLASS_NAME_BULKTAG_SUBJECT,
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.getId()))
if (datasources.contains(c))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_DATASOURCE,
CLASS_NAME_BULKTAG_DATASOURCE,
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.getId()))
if (czenodo.contains(c))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_CZENODO,
CLASS_NAME_BULKTAG_ZENODO,
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(
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));
}
});
@ -196,27 +232,48 @@ public class ResultTagger implements Serializable {
if (subjects.contains(c))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_SUBJECT,
CLASS_NAME_BULKTAG_SUBJECT,
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,
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(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_CZENODO,
CLASS_NAME_BULKTAG_ZENODO,
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(
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 +283,4 @@ 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;
}
}

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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";
}

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@ -121,8 +121,7 @@ public class SparkEoscBulkTag implements Serializable {
.getInstance()
.stream()
.anyMatch(
i -> (hostedByList.contains(i.getHostedby().getKey())) ||
(value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0))
i -> (hostedByList.contains(i.getHostedby().getKey())))
&&
!value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) {
Context context = new Context();

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@ -6,6 +6,10 @@ 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 org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
@ -23,11 +27,12 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
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;
import eu.dnetlib.dhp.bulktag.community.ProtoMap;
import eu.dnetlib.dhp.schema.oaf.*;
public class BulkTagJobTest {
@ -39,7 +44,8 @@ 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 +769,28 @@ 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;
// }
// }
}

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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>

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@ -10,7 +10,6 @@ import java.util.stream.Collectors;
import javax.swing.text.html.Option;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
@ -33,6 +32,7 @@ import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob;
import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
public class CleanCountrySparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class);
@ -113,7 +113,10 @@ public class CleanCountrySparkJob implements Serializable {
if (r
.getPid()
.stream()
.anyMatch(p -> p.getQualifier().getClassid()
.anyMatch(
p -> p
.getQualifier()
.getClassid()
.equals(PidType.doi) && pidInParam(p.getValue(), verifyParam))) {
r
.setCountry(

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@ -422,7 +422,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final Relation r2 = OafMapperUtils
.getRelation(
orgId, dsId, DATASOURCE_ORGANIZATION, PROVISION, PROVIDES, collectedFrom, info, lastUpdateTimestamp);
orgId, dsId, DATASOURCE_ORGANIZATION, PROVISION, PROVIDES, collectedFrom, info,
lastUpdateTimestamp);
return Arrays.asList(r1, r2);
} catch (final Exception e) {