diff --git a/.gitignore b/.gitignore index 3f00d9729..4feeb36c3 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,8 @@ .DS_Store .idea *.iml +*.ipr +*.iws *~ .classpath /*/.classpath diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 834af77fa..0c4637def 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 7b50acd3d..308d78715 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index e0b20204c..e471af76d 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 43c2a3834..b736b22d8 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT ../ diff --git a/dhp-schemas/pom.xml b/dhp-schemas/pom.xml index 20896a61d..bea9489f9 100644 --- a/dhp-schemas/pom.xml +++ b/dhp-schemas/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT ../ diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Entity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Entity.java deleted file mode 100644 index 894d54eaf..000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Entity.java +++ /dev/null @@ -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; - - private List title; - - private List date; - - private String typology; - - private List authors; - - private List subject; - - private String description; - - private String completionStatus; - - private List collectedFrom; - - private List publisher; - - - public String getIdentifier() { - return identifier; - } - - public void setIdentifier(String identifier) { - this.identifier = identifier; - } - - public List getPid() { - return pid; - } - - public void setPid(List pid) { - this.pid = pid; - } - - public List getTitle() { - return title; - } - - public void setTitle(List title) { - this.title = title; - } - - public List getDate() { - return date; - } - - public void setDate(List date) { - this.date = date; - } - - public String getTypology() { - return typology; - } - - public void setTypology(String typology) { - this.typology = typology; - } - - public List getAuthors() { - return authors; - } - - public void setAuthors(List authors) { - this.authors = authors; - } - - public List getSubject() { - return subject; - } - - public void setSubject(List subject) { - this.subject = subject; - } - - public String getDescription() { - return description; - } - - public void setDescription(String description) { - this.description = description; - } - - public List getCollectedFrom() { - return collectedFrom; - } - - public void setCollectedFrom(List collectedFrom) { - this.collectedFrom = collectedFrom; - } - - public List getPublisher() { - return publisher; - } - - public void setPublisher(List publisher) { - this.publisher = publisher; - } - - public String getCompletionStatus() { - return completionStatus; - } - - public void setCompletionStatus(String completionStatus) { - this.completionStatus = completionStatus; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Pid.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Pid.java deleted file mode 100644 index 252245f45..000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Pid.java +++ /dev/null @@ -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)); - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Provenance.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Provenance.java deleted file mode 100644 index 300b1134b..000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Provenance.java +++ /dev/null @@ -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; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Relation.java deleted file mode 100644 index 66007e21d..000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Relation.java +++ /dev/null @@ -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; - - 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 getProvenance() { - return provenance; - } - - public void setProvenance(final List provenance) { - this.provenance = provenance; - } - - public RelationSemantic getSemantic() { - return semantic; - } - - public void setSemantic(final RelationSemantic semantic) { - this.semantic = semantic; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/RelationSemantic.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/RelationSemantic.java deleted file mode 100644 index ff871ef2d..000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/RelationSemantic.java +++ /dev/null @@ -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; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Subject.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Subject.java deleted file mode 100644 index bd89bc6dd..000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dli/Subject.java +++ /dev/null @@ -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; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java new file mode 100644 index 000000000..e81120e42 --- /dev/null +++ b/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; + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java index ceaaad6b0..f82296d8b 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java +++ b/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 url; // other research products specifc private String distributionlocation; @@ -21,6 +22,14 @@ public class Instance implements Serializable { private Field dateofacceptance; + // ( article | book ) processing charges. Defined here to cope with possible wrongly typed results + private Field processingchargeamount; + + // currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly typed results + private Field processingchargecurrency; + + private Field refereed; //peer-review status + public Field getLicense() { return license; } @@ -53,11 +62,11 @@ public class Instance implements Serializable { this.hostedby = hostedby; } - public String getUrl() { + public List getUrl() { return url; } - public void setUrl(String url) { + public void setUrl(List url) { this.url = url; } @@ -85,7 +94,29 @@ public class Instance implements Serializable { this.dateofacceptance = dateofacceptance; } + public Field getProcessingchargeamount() { + return processingchargeamount; + } + public void setProcessingchargeamount(Field processingchargeamount) { + this.processingchargeamount = processingchargeamount; + } + + public Field getProcessingchargecurrency() { + return processingchargecurrency; + } + + public void setProcessingchargecurrency(Field processingchargecurrency) { + this.processingchargecurrency = processingchargecurrency; + } + + public Field getRefereed() { + return refereed; + } + + public void setRefereed(Field refereed) { + this.refereed = refereed; + } public String toComparableString(){ return String.format("%s::%s::%s::%s", diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index eb5572ce1..5cb04da5e 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/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.stream.Collectors; +import java.util.Comparator; +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 country; + private List country; private List subject; @@ -44,16 +42,10 @@ public abstract class Result extends OafEntity implements Serializable { private List> coverage; - private Field refereed; //peer-review status + private Qualifier bestaccessright; private List context; - // ( article | book ) processing charges. Defined here to cope with possible wrongly typed results - private Field processingchargeamount; - - // currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly typed results - private Field processingchargecurrency; - private List externalReference; private List instance; @@ -82,11 +74,11 @@ public abstract class Result extends OafEntity implements Serializable { this.language = language; } - public List getCountry() { + public List getCountry() { return country; } - public void setCountry(List country) { + public void setCountry(List country) { this.country = country; } @@ -194,12 +186,12 @@ public abstract class Result extends OafEntity implements Serializable { this.coverage = coverage; } - public Field getRefereed() { - return refereed; + public Qualifier getBestaccessright() { + return bestaccessright; } - public void setRefereed(Field refereed) { - this.refereed = refereed; + public void setBestaccessright(Qualifier bestaccessright) { + this.bestaccessright = bestaccessright; } public List getContext() { @@ -226,24 +218,6 @@ public abstract class Result extends OafEntity implements Serializable { this.instance = instance; } - public Field getProcessingchargeamount() { - return processingchargeamount; - } - - public Result setProcessingchargeamount(Field processingchargeamount) { - this.processingchargeamount = processingchargeamount; - return this; - } - - public Field getProcessingchargecurrency() { - return processingchargecurrency; - } - - public Result setProcessingchargecurrency(Field 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; } - } diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index d523945ea..78831073f 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMongoExecutor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMongoExecutor.java index d1b618c7a..00d1aa60d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMongoExecutor.java +++ b/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); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OafMigrationExecutor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OafMigrationExecutor.java index 75360943c..c32568290 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OafMigrationExecutor.java +++ b/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); } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OdfMigrationExecutor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OdfMigrationExecutor.java index 54636b3bf..457534085 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OdfMigrationExecutor.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OdfMigrationExecutor.java @@ -74,7 +74,7 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor { final List 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; diff --git a/dhp-workflows/dhp-dedup/pom.xml b/dhp-workflows/dhp-dedup/pom.xml index 81ac94f01..0721af25d 100644 --- a/dhp-workflows/dhp-dedup/pom.xml +++ b/dhp-workflows/dhp-dedup/pom.xml @@ -1,10 +1,9 @@ - + dhp-workflows eu.dnetlib.dhp - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java index 48d442d04..831e45daf 100644 --- a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java +++ b/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 eu.dnetlib.dedup.graph.GraphProcessor; +import com.google.common.hash.Hashing; 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 vertexes = sc.textFile(inputPath + "/" + entity) - .map(s->{ + JavaPairRDD mapDocument = sc.textFile(inputPath + "/" + entity) + .mapToPair(s->{ MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf,s); - return new Tuple2<>(d.getIdentifier(), d);}) - .mapToPair((PairFunction, Object, MapDocument>) t -> new Tuple2((long) t._1().hashCode(), t._2())); - - - - - JavaPairRDD mapDocument = vertexes.mapToPair((PairFunction, String, MapDocument>) item -> new Tuple2(item._2().getIdentifier(), item._2())); + return new Tuple2<>(d.getIdentifier(), d);}); //create blocks for deduplication - JavaPairRDD> blocks = Deduper.createsortedBlocks(sc,mapDocument, dedupConf); - + JavaPairRDD> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf); +// JavaPairRDD> blocks = Deduper.createBlocks(sc, mapDocument, dedupConf); //create relations by comparing only elements in the same group final JavaPairRDD dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf); - +// final JavaPairRDD dedupRels = Deduper.computeRelations(sc, blocks, dedupConf); final JavaRDD 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)); - - - - - - - - - } - - - -} +} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/SparkCreateDedupTest.java b/dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/SparkCreateDedupTest.java index f294b10fe..f93703e37 100644 --- a/dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/SparkCreateDedupTest.java +++ b/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"; diff --git a/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/org.curr.conf.json b/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/org.curr.conf.json index 43003c2e0..2d0905562 100644 --- a/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/org.curr.conf.json +++ b/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", - "threshold": "0.0" + "windowSize": "4" } } ], - "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", - "threshold": "0.7" + "windowSize": "4" } } ], - "threshold": 1.0, - "aggregation": "W_MEAN", + "threshold": 0.9, + "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"] } } } \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/pub_dt.curr.conf.json b/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/pub_dt.curr.conf.json index 18b048e9e..6ca0ecd53 100644 --- a/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/pub_dt.curr.conf.json +++ b/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, - "aggregation": "MAX", + "threshold": 0.5, + "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", diff --git a/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/json/authors_merge.json b/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/json/authors_merge.json index 4e8b66d1b..090c94c26 100644 --- a/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/json/authors_merge.json +++ b/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/json/authors_merge.json @@ -1,3 +1,3 @@ -{"journal":{"name":"","issnPrinted":"","issnOnline":"","issnLinking":"","ep":"","iss":"","sp":"","vol":"","edition":"","conferenceplace":"","conferencedate":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"author":[{"fullname":"Nemkov, Pavel G.","name":"","surname":"","rank":1,"pid":[],"affiliation":[]},{"fullname":"Gayubo, Severiano F.","name":"","surname":"","rank":2,"pid":[{"value":"ORCID1","qualifier":{"classid":"orcid","classname":"orcid","schemeid":"dnet:pidType","schemename":"dnet:pidType"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"affiliation":[]},{"fullname":"Ciccio 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New Species Of Nysson Latreille (Hymenoptera: Crabronidae: Bembicinae) From Turkmenistan","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"relevantdate":[{"value":"2003-12-31","qualifier":{"classid":"dnet:date","classname":"dnet:date","schemeid":"dnet:date","schemename":"dnet:date"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"description":[{"value":"Nemkov, Pavel G., Gayubo, Severiano F. 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