diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index 18fecc6c2..1aed66dfd 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -531,12 +531,12 @@ public class PublicationToOaf implements Serializable { dataInfo.setInferred(false); dataInfo.setTrust("0.9"); dataInfo - .setProvenanceaction( - mapQualifier( - "sysimport:crosswalk:entityregistry", - "Harvested", - "dnet:provenanceActions", - "dnet:provenanceActions")); + .setProvenanceaction( + mapQualifier( + "sysimport:crosswalk:entityregistry", + "Harvested", + "dnet:provenanceActions", + "dnet:provenanceActions")); sp.setDataInfo(dataInfo); return sp; } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java index 360cf5ffa..692605b03 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java @@ -44,9 +44,6 @@ public class PropagationConstant { public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID = "authorpid:result"; public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME = "Propagation of authors pid to result through semantic relations"; - - - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final String cfHbforResultQuery = "select distinct r.id, inst.collectedfrom.key cf, inst.hostedby.key hb " diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java index 99ae1ee2d..dd8342980 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java @@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.Arrays; import java.util.List; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; @@ -23,6 +22,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.gson.Gson; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; @@ -104,7 +104,7 @@ public class PrepareResultOrcidAssociationStep1 { + " LATERAL VIEW EXPLODE (author) a AS MyT " + " LATERAL VIEW EXPLODE (MyT.pid) p AS MyP " + " WHERE lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID + "' or " - +" lower(MyP.qalifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp " + + " lower(MyP.qalifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp " + " GROUP BY id) r_t " + " JOIN (" + " SELECT source, target " diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index 55f18007d..9f08fe580 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.List; import java.util.Optional; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; @@ -24,6 +23,7 @@ import com.google.common.collect.Lists; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.PacePerson; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; @@ -203,7 +203,7 @@ public class SparkOrcidToResultFromSemRelJob { } for (StructuredProperty pid : pids.get()) { if (ModelConstants.ORCID_PENDING.equals(pid.getQualifier().getClassid().toLowerCase()) || - ModelConstants.ORCID.equals(pid.getQualifier().getClassid().toLowerCase())) { + ModelConstants.ORCID.equals(pid.getQualifier().getClassid().toLowerCase())) { return true; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java index 945f717bb..2a6fd3a1d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java @@ -191,11 +191,13 @@ public class CleaningFunctions { } final Set collectedFrom = Optional - .ofNullable(r.getCollectedfrom()) - .map(c -> c.stream() - .map(KeyValue::getKey) - .collect(Collectors.toCollection(HashSet::new))) - .orElse(new HashSet<>()); + .ofNullable(r.getCollectedfrom()) + .map( + c -> c + .stream() + .map(KeyValue::getKey) + .collect(Collectors.toCollection(HashSet::new))) + .orElse(new HashSet<>()); for (Author a : r.getAuthor()) { if (Objects.isNull(a.getPid())) { @@ -211,12 +213,13 @@ public class CleaningFunctions { .map(p -> { // hack to distinguish orcid from orcid_pending String pidProvenance = Optional - .ofNullable(p.getDataInfo()) - .map(d -> Optional - .ofNullable(d.getProvenanceaction()) - .map(Qualifier::getClassid) - .orElse("")) - .orElse(""); + .ofNullable(p.getDataInfo()) + .map( + d -> Optional + .ofNullable(d.getProvenanceaction()) + .map(Qualifier::getClassid) + .orElse("")) + .orElse(""); if (pidProvenance.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) { p.getQualifier().setClassid(ModelConstants.ORCID); } else { @@ -229,8 +232,8 @@ public class CleaningFunctions { Collectors .toMap( p -> p.getQualifier().getClassid() + p.getValue(), - Function.identity(), - (p1, p2) -> p1, + Function.identity(), + (p1, p2) -> p1, LinkedHashMap::new)) .values() .stream() diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 619df7716..e84f97836 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -7,11 +7,6 @@ import java.io.IOException; import java.io.StringReader; import java.util.List; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.OafMapperUtils; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; @@ -20,13 +15,18 @@ import org.dom4j.io.SAXReader; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; +import org.mockito.Mock; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; -import org.mockito.Mock; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.OafMapperUtils; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; //TODO to enable it we need to update the joined_entity.json test file //@Disabled @@ -44,34 +44,30 @@ public class XmlRecordFactoryTest { assertNotNull(je); Document doc = buildXml(je); - ////TODO specific test assertion on doc + //// TODO specific test assertion on doc } - - @Test void testBologna() throws IOException, DocumentException { final String json = IOUtils.toString(getClass().getResourceAsStream("oaf-bologna.json")); - Publication oaf = new ObjectMapper().readValue(json, Publication.class); + Publication oaf = new ObjectMapper().readValue(json, Publication.class); assertNotNull(oaf); JoinedEntity je = new JoinedEntity(); je.setEntity(oaf); assertNotNull(je); Document doc = buildXml(je); - //TODO specific test assertion on doc + // TODO specific test assertion on doc System.out.println(doc.asXML()); - - } private Document buildXml(JoinedEntity je) throws DocumentException { ContextMapper contextMapper = new ContextMapper(); XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, - otherDsTypeId); + otherDsTypeId); String xml = xmlRecordFactory.build(je);