aligned with origin/master, aligned model and mapping

.gitignore

@@ -1,6 +1,8 @@
 .DS_Store
 .idea
 *.iml
+*.ipr
+*.iws
 *~
 .classpath
 /*/.classpath

dhp-build/dhp-build-assembly-resources/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>eu.dnetlib.dhp</groupId>
         <artifactId>dhp-build</artifactId>
-        <version>1.0.5-SNAPSHOT</version>
+        <version>1.1.6-SNAPSHOT</version>
     </parent>
 
     <artifactId>dhp-build-assembly-resources</artifactId>

dhp-build/dhp-build-properties-maven-plugin/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>eu.dnetlib.dhp</groupId>
         <artifactId>dhp-build</artifactId>
-        <version>1.0.5-SNAPSHOT</version>
+        <version>1.1.6-SNAPSHOT</version>
     </parent>
 
     <artifactId>dhp-build-properties-maven-plugin</artifactId>

dhp-build/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>eu.dnetlib.dhp</groupId>
 		<artifactId>dhp</artifactId>
-		<version>1.0.5-SNAPSHOT</version>
+		<version>1.1.6-SNAPSHOT</version>
 	</parent>
 	<artifactId>dhp-build</artifactId>
 	<packaging>pom</packaging>

dhp-common/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>eu.dnetlib.dhp</groupId>
 		<artifactId>dhp</artifactId>
-		<version>1.0.5-SNAPSHOT</version>
+		<version>1.1.6-SNAPSHOT</version>
 		<relativePath>../</relativePath>
 	</parent>
 

dhp-schemas/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>eu.dnetlib.dhp</groupId>
         <artifactId>dhp</artifactId>
-        <version>1.0.5-SNAPSHOT</version>
+        <version>1.1.6-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
 

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Entity.java

@@ -1,118 +0,0 @@
-package eu.dnetlib.dhp.schema.dli;
-
-import java.io.Serializable;
-import java.util.List;
-
-public class Entity implements Serializable {
-
-    private String identifier;
-
-    private List<Pid> pid;
-
-    private List<String> title;
-
-    private List<String> date;
-
-    private String typology;
-
-    private List<String> authors;
-
-    private List<Subject> subject;
-
-    private String description;
-
-    private String completionStatus;
-
-    private List<Provenance> collectedFrom;
-
-    private List<String> publisher;
-
-
-    public String getIdentifier() {
-        return identifier;
-    }
-
-    public void setIdentifier(String identifier) {
-        this.identifier = identifier;
-    }
-
-    public List<Pid> getPid() {
-        return pid;
-    }
-
-    public void setPid(List<Pid> pid) {
-        this.pid = pid;
-    }
-
-    public List<String> getTitle() {
-        return title;
-    }
-
-    public void setTitle(List<String> title) {
-        this.title = title;
-    }
-
-    public List<String> getDate() {
-        return date;
-    }
-
-    public void setDate(List<String> date) {
-        this.date = date;
-    }
-
-    public String getTypology() {
-        return typology;
-    }
-
-    public void setTypology(String typology) {
-        this.typology = typology;
-    }
-
-    public List<String> getAuthors() {
-        return authors;
-    }
-
-    public void setAuthors(List<String> authors) {
-        this.authors = authors;
-    }
-
-    public List<Subject> getSubject() {
-        return subject;
-    }
-
-    public void setSubject(List<Subject> subject) {
-        this.subject = subject;
-    }
-
-    public String getDescription() {
-        return description;
-    }
-
-    public void setDescription(String description) {
-        this.description = description;
-    }
-
-    public List<Provenance> getCollectedFrom() {
-        return collectedFrom;
-    }
-
-    public void setCollectedFrom(List<Provenance> collectedFrom) {
-        this.collectedFrom = collectedFrom;
-    }
-
-    public List<String> getPublisher() {
-        return publisher;
-    }
-
-    public void setPublisher(List<String> publisher) {
-        this.publisher = publisher;
-    }
-
-    public String getCompletionStatus() {
-        return completionStatus;
-    }
-
-    public void setCompletionStatus(String completionStatus) {
-        this.completionStatus = completionStatus;
-    }
-}

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Pid.java

@@ -1,33 +0,0 @@
-package eu.dnetlib.dhp.schema.dli;
-
-import eu.dnetlib.dhp.utils.DHPUtils;
-import org.apache.commons.lang3.StringUtils;
-
-public class Pid {
-
-    private String pid;
-
-    private String pidType;
-
-    public String getPid() {
-        return pid;
-    }
-
-    public void setPid(String pid) {
-        this.pid = pid;
-    }
-
-    public String getPidType() {
-        return pidType;
-    }
-
-    public void setPidType(String pidType) {
-        this.pidType = pidType;
-    }
-
-    public String generateId() {
-        if(StringUtils.isEmpty(pid) || StringUtils.isEmpty(pidType))
-            return null;
-        return DHPUtils.md5(String.format("%s::%s", pid, pidType));
-    }
-}

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Provenance.java

@@ -1,35 +0,0 @@
-package eu.dnetlib.dhp.schema.dli;
-
-public class Provenance {
-
-    private String datasourceId;
-
-    private String datasourceName;
-
-    private String completionStatus;
-
-
-    public String getDatasourceId() {
-        return datasourceId;
-    }
-
-    public void setDatasourceId(String datasourceId) {
-        this.datasourceId = datasourceId;
-    }
-
-    public String getDatasourceName() {
-        return datasourceName;
-    }
-
-    public void setDatasourceName(String datasourceName) {
-        this.datasourceName = datasourceName;
-    }
-
-    public String getCompletionStatus() {
-        return completionStatus;
-    }
-
-    public void setCompletionStatus(String completionStatus) {
-        this.completionStatus = completionStatus;
-    }
-}

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Relation.java

@@ -1,52 +0,0 @@
-package eu.dnetlib.dhp.schema.dli;
-
-import java.io.Serializable;
-import java.util.List;
-
-public class Relation implements Serializable {
-
-	/**
-	 *
-	 */
-	private static final long serialVersionUID = -9103706796710618813L;
-
-	private String source;
-
-	private String target;
-
-	private List<Provenance> provenance;
-
-	private RelationSemantic semantic;
-
-	public String getSource() {
-		return source;
-	}
-
-	public void setSource(final String source) {
-		this.source = source;
-	}
-
-	public String getTarget() {
-		return target;
-	}
-
-	public void setTarget(final String target) {
-		this.target = target;
-	}
-
-	public List<Provenance> getProvenance() {
-		return provenance;
-	}
-
-	public void setProvenance(final List<Provenance> provenance) {
-		this.provenance = provenance;
-	}
-
-	public RelationSemantic getSemantic() {
-		return semantic;
-	}
-
-	public void setSemantic(final RelationSemantic semantic) {
-		this.semantic = semantic;
-	}
-}

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/RelationSemantic.java

@@ -1,16 +0,0 @@
-package eu.dnetlib.dhp.schema.dli;
-
-import java.io.Serializable;
-
-public class RelationSemantic extends Subject implements Serializable {
-
-    public String inverse;
-
-    public String getInverse() {
-        return inverse;
-    }
-
-    public void setInverse(String inverse) {
-        this.inverse = inverse;
-    }
-}

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Subject.java

@@ -1,35 +0,0 @@
-package eu.dnetlib.dhp.schema.dli;
-
-import java.io.Serializable;
-
-public class Subject implements Serializable {
-
-    private String schema;
-
-    private String value;
-
-    public Subject() {
-
-    }
-
-    public Subject(String schema, String value) {
-        this.schema = schema;
-        this.value = value;
-    }
-
-    public String getSchema() {
-        return schema;
-    }
-
-    public void setSchema(String schema) {
-        this.schema = schema;
-    }
-
-    public String getValue() {
-        return value;
-    }
-
-    public void setValue(String value) {
-        this.value = value;
-    }
-}

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java

@@ -0,0 +1,15 @@
+package eu.dnetlib.dhp.schema.oaf;
+
+public class Country extends Qualifier {
+
+    private DataInfo dataInfo;
+
+    public DataInfo getDataInfo() {
+        return dataInfo;
+    }
+
+    public void setDataInfo(DataInfo dataInfo) {
+        this.dataInfo = dataInfo;
+    }
+
+}

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java

@@ -1,6 +1,7 @@
 package eu.dnetlib.dhp.schema.oaf;
 
 import java.io.Serializable;
+import java.util.List;
 
 public class Instance implements Serializable {
 
@@ -12,7 +13,7 @@ public class Instance implements Serializable {
 
     private KeyValue hostedby;
 
-    private String url;
+    private List<String> url;
 
     // other research products specifc
     private  String distributionlocation;
@@ -21,6 +22,14 @@ public class Instance implements Serializable {
 
     private Field<String> dateofacceptance;
 
+    // ( article | book ) processing charges. Defined here to cope with possible wrongly typed results
+    private Field<String> processingchargeamount;
+
+    // currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly typed results
+    private Field<String> processingchargecurrency;
+
+    private Field<String> refereed; //peer-review status
+
     public Field<String> getLicense() {
         return license;
     }
@@ -53,11 +62,11 @@ public class Instance implements Serializable {
         this.hostedby = hostedby;
     }
 
-    public String getUrl() {
+    public List<String> getUrl() {
         return url;
     }
 
-    public void setUrl(String url) {
+    public void setUrl(List<String> url) {
         this.url = url;
     }
 
@@ -85,7 +94,29 @@ public class Instance implements Serializable {
         this.dateofacceptance = dateofacceptance;
     }
 
+    public Field<String> getProcessingchargeamount() {
+        return processingchargeamount;
+    }
 
+    public void setProcessingchargeamount(Field<String> processingchargeamount) {
+        this.processingchargeamount = processingchargeamount;
+    }
+
+    public Field<String> getProcessingchargecurrency() {
+        return processingchargecurrency;
+    }
+
+    public void setProcessingchargecurrency(Field<String> processingchargecurrency) {
+        this.processingchargecurrency = processingchargecurrency;
+    }
+
+    public Field<String> getRefereed() {
+        return refereed;
+    }
+
+    public void setRefereed(Field<String> refereed) {
+        this.refereed = refereed;
+    }
 
     public String toComparableString(){
         return String.format("%s::%s::%s::%s",

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java

@@ -1,10 +1,8 @@
 package eu.dnetlib.dhp.schema.oaf;
 
-import org.apache.commons.lang3.StringUtils;
-
 import java.io.Serializable;
-import java.util.*;
+import java.util.Comparator;
-import java.util.stream.Collectors;
+import java.util.List;
 
 public abstract class Result extends OafEntity implements Serializable {
 
@@ -16,7 +14,7 @@ public abstract class Result extends OafEntity implements Serializable {
     // common fields
     private Qualifier language;
 
-    private List<Qualifier> country;
+    private List<Country> country;
 
     private List<StructuredProperty> subject;
 
@@ -44,16 +42,10 @@ public abstract class Result extends OafEntity implements Serializable {
 
     private List<Field<String>> coverage;
 
-    private Field<String> refereed; //peer-review status
+    private Qualifier bestaccessright;
 
     private List<Context> context;
 
-    // ( article | book ) processing charges. Defined here to cope with possible wrongly typed results
-    private Field<String> processingchargeamount;
-
-    // currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly typed results
-    private Field<String> processingchargecurrency;
-
     private List<ExternalReference> externalReference;
 
     private List<Instance> instance;
@@ -82,11 +74,11 @@ public abstract class Result extends OafEntity implements Serializable {
         this.language = language;
     }
 
-    public List<Qualifier> getCountry() {
+    public List<Country> getCountry() {
         return country;
     }
 
-    public void setCountry(List<Qualifier> country) {
+    public void setCountry(List<Country> country) {
         this.country = country;
     }
 
@@ -194,12 +186,12 @@ public abstract class Result extends OafEntity implements Serializable {
         this.coverage = coverage;
     }
 
-    public Field<String> getRefereed() {
+    public Qualifier getBestaccessright() {
-        return refereed;
+        return bestaccessright;
     }
 
-    public void setRefereed(Field<String> refereed) {
+    public void setBestaccessright(Qualifier bestaccessright) {
-        this.refereed = refereed;
+        this.bestaccessright = bestaccessright;
     }
 
     public List<Context> getContext() {
@@ -226,24 +218,6 @@ public abstract class Result extends OafEntity implements Serializable {
         this.instance = instance;
     }
 
-    public Field<String> getProcessingchargeamount() {
-        return processingchargeamount;
-    }
-
-    public Result setProcessingchargeamount(Field<String> processingchargeamount) {
-        this.processingchargeamount = processingchargeamount;
-        return this;
-    }
-
-    public Field<String> getProcessingchargecurrency() {
-        return processingchargecurrency;
-    }
-
-    public Result setProcessingchargecurrency(Field<String> processingchargecurrency) {
-        this.processingchargecurrency = processingchargecurrency;
-        return this;
-    }
-
     @Override
     public void mergeFrom(OafEntity e) {
         super.mergeFrom(e);
@@ -287,19 +261,9 @@ public abstract class Result extends OafEntity implements Serializable {
 
         coverage = mergeLists(coverage, r.getCoverage());
 
-        if (r.getRefereed() != null && compareTrust(this, r) < 0)
-            refereed = r.getRefereed();
-
         context = mergeLists(context, r.getContext());
 
-        if (r.getProcessingchargeamount() != null && compareTrust(this, r) < 0)
-            processingchargeamount = r.getProcessingchargeamount();
-
-        if (r.getProcessingchargecurrency() != null && compareTrust(this, r) < 0)
-            processingchargecurrency = r.getProcessingchargecurrency();
-
         externalReference = mergeLists(externalReference, r.getExternalReference());
-
     }
 
 
@@ -314,5 +278,4 @@ public abstract class Result extends OafEntity implements Serializable {
         return a.size() > b.size() ? a : b;
     }
 
-
 }

dhp-workflows/dhp-aggregation/pom.xml

@@ -4,7 +4,7 @@
     <parent>
         <groupId>eu.dnetlib.dhp</groupId>
         <artifactId>dhp-workflows</artifactId>
-        <version>1.0.5-SNAPSHOT</version>
+        <version>1.1.6-SNAPSHOT</version>
     </parent>
     <artifactId>dhp-aggregation</artifactId>
     

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMongoExecutor.java

@@ -262,12 +262,9 @@ public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
 		r.setContributor(prepareContributors(doc, info));
 		r.setResourcetype(prepareResourceType(doc, info));
 		r.setCoverage(prepareCoverages(doc, info));
-		r.setRefereed(null); // NOT PRESENT IN MDSTORES
 		r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
 		r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
 		r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
-		r.setProcessingchargeamount(null); // NOT PRESENT IN MDSTORES
-		r.setProcessingchargecurrency(null); // NOT PRESENT IN MDSTORES
 	}
 
 	protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OafMigrationExecutor.java

@@ -104,7 +104,7 @@ public class OafMigrationExecutor extends AbstractMongoExecutor {
 			final String url = ((Node) o).getText().trim();
 			if (url.startsWith("http")) {
 				final Instance instance = new Instance();
-				instance.setUrl(url);
+				instance.setUrl(Arrays.asList(url));
 				instance.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", "dnet:publication_resource", "dnet:publication_resource"));
 				instance.setCollectedfrom(collectedfrom);
 				instance.setHostedby(hostedby);
@@ -112,6 +112,9 @@ public class OafMigrationExecutor extends AbstractMongoExecutor {
 				instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
 				instance.setAccessright(prepareQualifier(doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes"));
 				instance.setLicense(field(doc.valueOf("//oaf:license"), info));
+				instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
+				instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
+				instance.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
 				res.add(instance);
 			}
 		}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OdfMigrationExecutor.java

@@ -74,7 +74,7 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor {
 		final List<Instance> res = new ArrayList<>();
 		for (final Object o : doc.selectNodes("//dc:alternateIdentifier[@alternateIdentifierType='URL']")) {
 			final Instance instance = new Instance();
-			instance.setUrl(((Node) o).getText().trim());
+			instance.setUrl(Arrays.asList(((Node) o).getText().trim()));
 			instance.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", "dnet:publication_resource", "dnet:publication_resource"));
 			instance.setCollectedfrom(collectedfrom);
 			instance.setHostedby(hostedby);
@@ -82,6 +82,9 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor {
 			instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
 			instance.setAccessright(prepareQualifier(doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes"));
 			instance.setLicense(field(doc.valueOf("//oaf:license"), info));
+			instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
+			instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
+			instance.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
 			res.add(instance);
 		}
 		return res;

dhp-workflows/dhp-dedup/pom.xml

@@ -1,10 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.0.5-SNAPSHOT</version>
+        <version>1.1.6-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java

@@ -1,7 +1,6 @@
 package eu.dnetlib.dedup;
 
-import eu.dnetlib.dedup.graph.ConnectedComponent;
+import com.google.common.hash.Hashing;
-import eu.dnetlib.dedup.graph.GraphProcessor;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.pace.config.DedupConfig;
@@ -12,8 +11,6 @@ import org.apache.spark.api.java.JavaPairRDD;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.PairFunction;
-import org.apache.spark.graphx.Edge;
-import org.apache.spark.rdd.RDD;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
 import scala.Tuple2;
@@ -44,30 +41,23 @@ public class SparkCreateSimRels {
         final String inputPath = parser.get("sourcePath");
         final String entity = parser.get("entity");
         final String targetPath = parser.get("targetPath");
-//        final DedupConfig dedupConf = DedupConfig.load(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf2.json")));
+//        final DedupConfig dedupConf = DedupConfig.load(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
         final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf"));
 
-
         final long total = sc.textFile(inputPath + "/" + entity).count();
 
-        JavaPairRDD<Object, MapDocument> vertexes = sc.textFile(inputPath + "/" + entity)
+        JavaPairRDD<String, MapDocument> mapDocument = sc.textFile(inputPath + "/" + entity)
-                .map(s->{
+                .mapToPair(s->{
                     MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf,s);
-                    return new Tuple2<>(d.getIdentifier(), d);})
+                    return new Tuple2<>(d.getIdentifier(), d);});
-                .mapToPair((PairFunction<Tuple2<String, MapDocument>, Object, MapDocument>) t -> new Tuple2<Object, MapDocument>((long) t._1().hashCode(), t._2()));
-
-
-
-
-        JavaPairRDD<String, MapDocument> mapDocument = vertexes.mapToPair((PairFunction<Tuple2<Object, MapDocument>, String, MapDocument>) item -> new Tuple2<String, MapDocument>(item._2().getIdentifier(), item._2()));
 
         //create blocks for deduplication
-        JavaPairRDD<String, List<MapDocument>> blocks = Deduper.createsortedBlocks(sc,mapDocument, dedupConf);
+        JavaPairRDD<String, List<MapDocument>> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf);
-
+//        JavaPairRDD<String, Iterable<MapDocument>> blocks = Deduper.createBlocks(sc, mapDocument, dedupConf);
 
         //create relations by comparing only elements in the same group
         final JavaPairRDD<String,String> dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf);
-
+//        final JavaPairRDD<String,String> dedupRels = Deduper.computeRelations(sc, blocks, dedupConf);
 
         final JavaRDD<Relation> isSimilarToRDD = dedupRels.map(simRel -> {
             final Relation r = new Relation();
@@ -79,17 +69,5 @@ public class SparkCreateSimRels {
 
         spark.createDataset(isSimilarToRDD.rdd(), Encoders.bean(Relation.class)).write().mode("overwrite").save( DedupUtility.createSimRelPath(targetPath,entity));
 
-
-
-
-
-
-
-
-
-
     }
-
-
-
 }

dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/SparkCreateDedupTest.java

@@ -18,11 +18,11 @@ import java.util.List;
 public class SparkCreateDedupTest {
 
     String configuration;
-    String entity = "publication";
+    String entity = "organization";
 
     @Before
     public void setUp() throws IOException {
-        configuration = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dedup/conf/pub_dt.curr.conf.json"));
+        configuration = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dedup/conf/org.curr.conf.json"));
 
     }
 
@@ -31,7 +31,7 @@ public class SparkCreateDedupTest {
     public void createSimRelsTest() throws Exception {
         SparkCreateSimRels.main(new String[] {
                 "-mt", "local[*]",
-                "-s", "/home/sandro/betadump",
+                "-s", "/Users/miconis/dumps",
                 "-e", entity,
                 "-c", ArgumentApplicationParser.compressArgument(configuration),
                 "-t", "/tmp/dedup",
@@ -44,7 +44,7 @@ public class SparkCreateDedupTest {
 
         SparkCreateConnectedComponent.main(new String[] {
                 "-mt", "local[*]",
-                "-s", "/home/sandro/betadump",
+                "-s", "/Users/miconis/dumps",
                 "-e", entity,
                 "-c", ArgumentApplicationParser.compressArgument(configuration),
                 "-t", "/tmp/dedup",
@@ -56,7 +56,7 @@ public class SparkCreateDedupTest {
     public void dedupRecordTest() throws Exception {
         SparkCreateDedupRecord.main(new String[] {
                 "-mt", "local[*]",
-                "-s", "/home/sandro/betadump",
+                "-s", "/Users/miconis/dumps",
                 "-e", entity,
                 "-c", ArgumentApplicationParser.compressArgument(configuration),
                 "-d", "/tmp/dedup",
@@ -64,26 +64,10 @@ public class SparkCreateDedupTest {
     }
 
     @Test
-    public void printCC() throws Exception {
+    public void printConfiguration() throws Exception {
         System.out.println(ArgumentApplicationParser.compressArgument(configuration));
     }
 
-
-//            [20|grid________::6031f94bef015a37783268ec1e75f17f, 20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46]
-//            [20|grid________::672e1e5cef49e68f124d3da5225a7357, 20|grid________::7a402604c3853c7a0af14f88f56bf7e1]
-//            [20|grid________::2fc05b35e11d915b220a66356053eae2, 20|grid________::b02fb3176eb38f6c572722550c07e7ab]
-//            [20|grid________::bc86248ab2b8d7955dcaf592ba342262, 20|corda_______::45a8ec964029278fb938805182e247a8]
-//            [20|doajarticles::74551f800ad1c81a6cd31c5162887b7f, 20|rcuk________::86dc9a83df05a58917f38ca09f814617]
-//            [20|nsf_________::5e837d8e6444cc298db314ea54ad2f4a, 20|snsf________::7b54715f0ec5c6a0a44672f45d98be8d]
-//            [20|corda__h2020::7ee7e57bad06b92c1a568dd61e10ba8c, 20|snsf________::2d4a2695221a3ce0c749ee34e064c0b3]
-//            [20|corda_______::25220a523550176dac9e5432dac43596, 20|grid________::9782f16a46650cbbfaaa2315109507d1]
-//            [20|nih_________::88c3b664dcc7af9e827f94ac964cd66c, 20|grid________::238d3ac0a7d119d5c8342a647f5245f5]
-//            [20|rcuk________::0582c20fcfb270f9ec1b19b0f0dcd881, 20|nsf_________::9afa48ddf0bc2cd4f3c41dc41daabcdb]
-//            [20|rcuk________::fbc445f8d24e569bc8b640dba86ae978, 20|corda_______::5a8a4094f1b68a88fc56e65cea7ebfa0]
-//            [20|rcuk________::7485257cd5caaf6316ba8062feea801d, 20|grid________::dded811e5f5a4c9f7ca8f9955e52ade7]
-//            [20|nih_________::0576dd270d29d5b7c23dd15a827ccdb9, 20|corda_______::10ca69f6a4a121f75fdde1feee226ce0]
-//            [20|corda__h2020::0429f6addf10e9b2939d65c6fb097ffd, 20|grid________::6563ec73057624d5ccc0cd050b302181]
-
     @Test
     public void testHashCode() {
         final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f";

dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/org.curr.conf.json

@@ -7,9 +7,9 @@
     "queueMaxSize" : "2000",
     "groupMaxSize" : "50",
     "slidingWindowSize" : "200",
+    "idPath":"$.id",
     "rootBuilder" : [ "organization", "projectOrganization_participation_isParticipant", "datasourceOrganization_provision_isProvidedBy" ],
     "includeChildren" : "true",
-    "idPath": "$.id",
     "maxIterations": "20"
   },
   "pace" : {
@@ -31,7 +31,7 @@
           }
         ],
         "threshold": 1,
-        "aggregation": "SC",
+        "aggregation": "AVG",
         "positive": "MATCH",
         "negative": "NO_MATCH",
         "undefined": "layer2",
@@ -52,10 +52,24 @@
             "weight": 1,
             "countIfUndefined": "true",
             "params": {}
+          },
+          {
+            "field": "legalname",
+            "comparator": "numbersMatch",
+            "weight": 1,
+            "countIfUndefined": "true",
+            "params": {}
+          },
+          {
+            "field": "legalname",
+            "comparator": "romansMatch",
+            "weight": 1,
+            "countIfUndefined": "true",
+            "params": {}
           }
         ],
         "threshold": 1,
-        "aggregation": "NC",
+        "aggregation": "AND",
         "positive": "layer3",
         "negative": "NO_MATCH",
         "undefined": "layer3",
@@ -69,12 +83,11 @@
             "weight": 1.0,
             "countIfUndefined": "true",
             "params": {
-              "windowSize": "4",
+              "windowSize": "4"
-              "threshold": "0.0"
             }
           }
         ],
-        "threshold": 1.0,
+        "threshold": 0.7,
         "aggregation": "W_MEAN",
         "positive": "layer4",
         "negative": "NO_MATCH",
@@ -87,19 +100,18 @@
             "field": "legalname",
             "comparator": "keywordMatch",
             "weight": 1.0,
-            "countIfUndefined": "false",
+            "countIfUndefined": "true",
             "params": {
-              "windowSize": "4",
+              "windowSize": "4"
-              "threshold": "0.7"
             }
           }
         ],
-        "threshold": 1.0,
+        "threshold": 0.9,
-        "aggregation": "W_MEAN",
+        "aggregation": "AVG",
         "positive": "layer5",
         "negative": "NO_MATCH",
         "undefined": "layer5",
-        "ignoreUndefined": "false"
+        "ignoreUndefined": "true"
       },
       "layer5": {
         "fields": [
@@ -133,19 +145,20 @@
       { "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"},
       { "name" : "legalname", "type" : "String", "path" : "$.legalname.value" },
       { "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" },
-      { "name" : "gridid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid ==\"grid\")].value"}
+      { "name" : "gridid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='grid.ac')].value"},
+      { "name" : "originalId", "type" : "String", "path" : "$.id" }
     ],
     "blacklists" : {
       "legalname" : []
     },
     "synonyms": {
-      "key::1": ["university","università","università studi","universitario","universitaria","université","universitaire","universitaires","universidad","universitade","Universität","universitaet","Uniwersytet","университет","universiteit","πανεπιστήμιο","universitesi","universiteti", "universiti"],
+      "key::1": ["university","università","università studi","universitario","universitaria","université", "universite", "universitaire","universitaires","universidad","universitade","Universität","universitaet","Uniwersytet","университет","universiteit","πανεπιστήμιο","universitesi","universiteti", "universiti"],
       "key::2": ["studies","studi","études","estudios","estudos","Studien","studia","исследования","studies","σπουδές"],
       "key::3": ["advanced","superiore","supérieur","supérieure","supérieurs","supérieures","avancado","avancados","fortgeschrittene","fortgeschritten","zaawansowany","передовой","gevorderd","gevorderde","προχωρημένος","προχωρημένη","προχωρημένο","προχωρημένες","προχωρημένα","wyzsza"],
       "key::4": ["institute","istituto","institut","instituto","instituto","Institut","instytut","институт","instituut","ινστιτούτο"],
       "key::5": ["hospital","ospedale","hôpital","hospital","hospital","Krankenhaus","szpital","больница","ziekenhuis","νοσοκομείο"],
       "key::6": ["research","ricerca","recherche","investigacion","pesquisa","Forschung","badania","исследования","onderzoek","έρευνα","erevna","erevnas"],
-      "key::7": ["college","collegio","université","colegio","faculdade","Hochschule","Szkoła Wyższa","Высшая школа","universiteit","κολλέγιο"],
+      "key::7": ["college","collegio","colegio","faculdade","Hochschule","Szkoła Wyższa","Высшая школа","κολλέγιο"],
       "key::8": ["foundation","fondazione","fondation","fundación","fundação","Stiftung","Fundacja","фонд","stichting","ίδρυμα","idryma"],
       "key::9": ["center","centro","centre","centro","centro","zentrum","centrum","центр","centrum","κέντρο"],
       "key::10": ["national","nazionale","national","nationale","nationaux","nationales","nacional","nacional","national","krajowy","национальный","nationaal","nationale","εθνικό"],
@@ -233,7 +246,7 @@
       "key::92": ["automation","automazione","automatización","automação","Automatisierung","automatisering","αυτοματοποίηση","otomasyon","automatizálás","avtomatizacija","automatiseeritud",""],
       "key::93": ["pediatric","pediatria","pediatriche","pediatrico","pediátrico","pediatría","pediátrico","pediatria","pädiatrisch","pediatrische","παιδιατρική","pediatrik","gyermekgyógyászat","pediatrija","pediaatria",""],
       "key::94": ["photonics","fotonica","fotoniche","fotónica","fotônica","Photonik","fotonica","φωτονική","fotonik","fotonika","fotonika","fotoonika",""],
-      "key::95": ["mechanics","meccanica","meccaniche","mecánica","mecânica","Mechanik","Maschinenbau","mechanica","werktuigkunde","μηχανικής","mekanik","gépészet","mehanika","mehaanika",""],
+      "key::95": ["mechanics", "mechanical", "meccanica","meccaniche","mecánica","mecânica","Mechanik","Maschinenbau","mechanica","werktuigkunde","μηχανικής","mekanik","gépészet","mehanika","mehaanika",""],
       "key::96": ["psychiatrics","psichiatria","psichiatrica","psichiatriche","psiquiatría","psiquiatria","Psychiatrie","psychiatrie","ψυχιατρική","psikiyatrik","pszihiátria","psihiatrija","psühhaatria",""],
       "key::97": ["psychology","fisiologia","psicología","psicologia","Psychologie","psychologie","ψυχολογία","psikoloji","pszihológia","psihologija","psühholoogia",""],
       "key::98": ["automotive","industriaautomobilistica","industriadelautomóvil","automotriz","industriaautomotriz","automotivo","Automobilindustrie","autoindustrie","αυτοκίνητος","αυτοκίνητη","αυτοκίνητο","αυτοκινούμενος","αυτοκινούμενη","αυτοκινούμενο","αυτοκινητιστικός","αυτοκινητιστική","αυτοκινητιστικό","otomotiv","autóipari","samogiben","avtomobilskaindustrija","auto-",""],
@@ -243,7 +256,11 @@
       "key::102": ["informatics","informatica","informática","informática","informatica",""],
       "key::103": ["forschungsgemeinschaft","comunita ricerca","research community","research foundation","research association"],
       "key::104": ["commerce","ticaret","ticarət","commercio","trade","handel","comercio"],
-      "key::105" : ["state", "stato", "etade", "statale", "etat", "zustand", "estado"]
+      "key::105" : ["state", "stato", "etade", "estado", "statale", "etat", "zustand", "estado"],
+      "key::106" : ["seminary", "seminario", "seminaire", "seminar"],
+      "key::107" : ["agricultural forestry", "af", "a f"],
+      "key::108" : ["agricultural mechanical", "am", "a m"],
+      "key::109" : ["catholic", "catholique", "katholische", "catolica", "cattolica", "catolico"]
     }
   }
 }

dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/pub_dt.curr.conf.json

@@ -66,14 +66,13 @@
             "weight": 1.0,
             "countIfUndefined": "false",
             "params": {
-              "threshold": "0.5",
               "jpath_value": "$.value",
               "jpath_classid": "$.qualifier.classid"
             }
           }
         ],
-        "threshold": 1.0,
+        "threshold": 0.5,
-        "aggregation": "MAX",
+        "aggregation": "AVG",
         "positive": "MATCH",
         "negative": "layer2",
         "undefined": "layer2",
@@ -97,7 +96,7 @@
           }
         ],
         "threshold": 1.0,
-        "aggregation": "NC",
+        "aggregation": "AND",
         "positive": "layer3",
         "negative": "NO_MATCH",
         "undefined": "layer3",
@@ -114,7 +113,7 @@
           }
         ],
         "threshold": 0.99,
-        "aggregation": "SUM",
+        "aggregation": "AVG",
         "positive": "MATCH",
         "negative": "NO_MATCH",
         "undefined": "NO_MATCH",

dhp-workflows/dhp-distcp/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.0.5-SNAPSHOT</version>
+        <version>1.1.6-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

dhp-workflows/dhp-graph-mapper/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.0.5-SNAPSHOT</version>
+        <version>1.1.6-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

dhp-workflows/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>eu.dnetlib.dhp</groupId>
         <artifactId>dhp</artifactId>
-        <version>1.0.5-SNAPSHOT</version>
+        <version>1.1.6-SNAPSHOT</version>
         <relativePath>../</relativePath>
     </parent>
 

pom.xml

@@ -5,7 +5,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>eu.dnetlib.dhp</groupId>
 	<artifactId>dhp</artifactId>
-	<version>1.0.5-SNAPSHOT</version>
+	<version>1.1.6-SNAPSHOT</version>
 	<packaging>pom</packaging>
 
 	<url>http://www.d-net.research-infrastructures.eu</url>