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

Reviewed-on: #250

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

@@ -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;
+	}
 }

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

@@ -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());
 		}
 	}
 

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

@@ -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();

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java

@@ -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;
+//	}
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java

@@ -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)

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

@@ -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(
+							OafMapperUtils
-								BULKTAG_DATA_INFO_TYPE,
+								.dataInfo(
-								CLASS_ID_SUBJECT,
+									false, BULKTAG_DATA_INFO_TYPE, true, false,
-								CLASS_NAME_BULKTAG_SUBJECT,
+									OafMapperUtils
-								TAGGING_TRUST));
+										.qualifier(
-				if (datasources.contains(c.getId()))
+											CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS,
+											DNET_PROVENANCE_ACTIONS),
+									TAGGING_TRUST));
+				if (datasources.contains(c))
 					dataInfoList
 						.add(
-							getDataInfo(
+							OafMapperUtils
-								BULKTAG_DATA_INFO_TYPE,
+								.dataInfo(
-								CLASS_ID_DATASOURCE,
+									false, BULKTAG_DATA_INFO_TYPE, true, false,
-								CLASS_NAME_BULKTAG_DATASOURCE,
+									OafMapperUtils
-								TAGGING_TRUST));
+										.qualifier(
-				if (czenodo.contains(c.getId()))
+											CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS,
+											DNET_PROVENANCE_ACTIONS),
+									TAGGING_TRUST));
+				if (czenodo.contains(c))
 					dataInfoList
 						.add(
-							getDataInfo(
+							OafMapperUtils
-								BULKTAG_DATA_INFO_TYPE,
+								.dataInfo(
-								CLASS_ID_CZENODO,
+									false, BULKTAG_DATA_INFO_TYPE, true, false,
-								CLASS_NAME_BULKTAG_ZENODO,
+									OafMapperUtils
-								TAGGING_TRUST));
+										.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(
+								OafMapperUtils
-									BULKTAG_DATA_INFO_TYPE,
+									.dataInfo(
-									CLASS_ID_SUBJECT,
+										false, BULKTAG_DATA_INFO_TYPE, true, false,
-									CLASS_NAME_BULKTAG_SUBJECT,
+										OafMapperUtils
-									TAGGING_TRUST));
+											.qualifier(
+												CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS,
+												DNET_PROVENANCE_ACTIONS),
+										TAGGING_TRUST));
 					if (datasources.contains(c))
 						dataInfoList
 							.add(
-								getDataInfo(
+								OafMapperUtils
-									BULKTAG_DATA_INFO_TYPE,
+									.dataInfo(
-									CLASS_ID_DATASOURCE,
+										false, BULKTAG_DATA_INFO_TYPE, true, false,
-									CLASS_NAME_BULKTAG_DATASOURCE,
+										OafMapperUtils
-									TAGGING_TRUST));
+											.qualifier(
+												CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE,
+												DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS),
+										TAGGING_TRUST));
 					if (czenodo.contains(c))
 						dataInfoList
 							.add(
-								getDataInfo(
+								OafMapperUtils
-									BULKTAG_DATA_INFO_TYPE,
+									.dataInfo(
-									CLASS_ID_CZENODO,
+										false, BULKTAG_DATA_INFO_TYPE, true, false,
-									CLASS_NAME_BULKTAG_ZENODO,
+										OafMapperUtils
-									TAGGING_TRUST));
+											.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;
-	}
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java

@@ -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";
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java

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

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

@@ -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.bulktag.community.ProtoMap;
-import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
+import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.dhp.schema.oaf.Publication;
-import eu.dnetlib.dhp.schema.oaf.Software;
 
 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;
+//		}
+//	}
 }

dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml

@@ -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>

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java

@@ -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(

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java

@@ -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) {