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removed circular dependencies

This commit is contained in:
Sandro La Bruzzo 2019-10-25 09:24:18 +02:00
parent a10d071cf4
commit 09ffda03a2
9 changed files with 128 additions and 63 deletions
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10
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java
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@ -65,7 +65,7 @@ public class Datasource extends OafEntity implements Serializable {
private Field<String> databaseaccessrestriction;
// {feeRequired, registration, other}
private Field<String> datauploadrestriction9;
private Field<String> datauploadrestriction;
private Field<Boolean> versioning;
@ -298,12 +298,12 @@ public class Datasource extends OafEntity implements Serializable {
this.databaseaccessrestriction = databaseaccessrestriction;
}
public Field<String> getDatauploadrestriction9() {
return datauploadrestriction9;
public Field<String> getDatauploadrestriction() {
return datauploadrestriction;
}
public void setDatauploadrestriction9(Field<String> datauploadrestriction9) {
this.datauploadrestriction9 = datauploadrestriction9;
public void setDatauploadrestriction(Field<String> datauploadrestriction) {
this.datauploadrestriction = datauploadrestriction;
}
public Field<Boolean> getVersioning() {

36
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java
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@ -32,95 +32,107 @@ public class Journal implements Serializable {
return name;
}
public void setName(String name) {
public Journal setName(String name) {
this.name = name;
return this;
}
public String getIssnPrinted() {
return issnPrinted;
}
public void setIssnPrinted(String issnPrinted) {
public Journal setIssnPrinted(String issnPrinted) {
this.issnPrinted = issnPrinted;
return this;
}
public String getIssnOnline() {
return issnOnline;
}
public void setIssnOnline(String issnOnline) {
public Journal setIssnOnline(String issnOnline) {
this.issnOnline = issnOnline;
return this;
}
public String getIssnLinking() {
return issnLinking;
}
public void setIssnLinking(String issnLinking) {
public Journal setIssnLinking(String issnLinking) {
this.issnLinking = issnLinking;
return this;
}
public String getEp() {
return ep;
}
public void setEp(String ep) {
public Journal setEp(String ep) {
this.ep = ep;
return this;
}
public String getIss() {
return iss;
}
public void setIss(String iss) {
public Journal setIss(String iss) {
this.iss = iss;
return this;
}
public String getSp() {
return sp;
}
public void setSp(String sp) {
public Journal setSp(String sp) {
this.sp = sp;
return this;
}
public String getVol() {
return vol;
}
public void setVol(String vol) {
public Journal setVol(String vol) {
this.vol = vol;
return this;
}
public String getEdition() {
return edition;
}
public void setEdition(String edition) {
public Journal setEdition(String edition) {
this.edition = edition;
return this;
}
public String getConferenceplace() {
return conferenceplace;
}
public void setConferenceplace(String conferenceplace) {
public Journal setConferenceplace(String conferenceplace) {
this.conferenceplace = conferenceplace;
return this;
}
public String getConferencedate() {
return conferencedate;
}
public void setConferencedate(String conferencedate) {
public Journal setConferencedate(String conferencedate) {
this.conferencedate = conferencedate;
return this;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
public Journal setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
return this;
}
}

16
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java
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@ -18,7 +18,7 @@ public abstract class OafEntity extends Oaf implements Serializable {
private String dateoftransformation;
//TODO remove this field
private List<OafEntity> children;
// private List<OafEntity> children;
private List<ExtraInfo> extraInfo;
@ -73,13 +73,13 @@ public abstract class OafEntity extends Oaf implements Serializable {
this.dateoftransformation = dateoftransformation;
}
public List<OafEntity> getChildren() {
return children;
}
public void setChildren(List<OafEntity> children) {
this.children = children;
}
// public List<OafEntity> getChildren() {
// return children;
// }
//
// public void setChildren(List<OafEntity> children) {
// this.children = children;
// }
public List<ExtraInfo> getExtraInfo() {
return extraInfo;

18
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OriginDescription.java
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@ -16,7 +16,7 @@ public class OriginDescription implements Serializable {
private String metadataNamespace;
private OriginDescription originDescription;
//private OriginDescription originDescription;
public String getHarvestDate() {
return harvestDate;
@ -72,12 +72,12 @@ public class OriginDescription implements Serializable {
return this;
}
public OriginDescription getOriginDescription() {
return originDescription;
}
public OriginDescription setOriginDescription(OriginDescription originDescription) {
this.originDescription = originDescription;
return this;
}
// public OriginDescription getOriginDescription() {
// return originDescription;
// }
//
// public OriginDescription setOriginDescription(OriginDescription originDescription) {
// this.originDescription = originDescription;
// return this;
// }
}

18
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java
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@ -9,7 +9,7 @@ public class Qualifier implements Serializable {
private String schemeid;
private String schemename;
private DataInfo dataInfo;
// private DataInfo dataInfo;
public String getClassid() {
return classid;
@ -47,12 +47,12 @@ public class Qualifier implements Serializable {
return this;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public Qualifier setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
return this;
}
// public DataInfo getDataInfo() {
// return dataInfo;
// }
//
// public Qualifier setDataInfo(DataInfo dataInfo) {
// this.dataInfo = dataInfo;
// return this;
// }
}

38
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoConverter.java
View File

@ -20,7 +20,7 @@ public class ProtoConverter implements Serializable {
if (oaf.getKind() == KindProtos.Kind.entity)
return convertEntity(oaf);
else {
return convertRelation(oaf);
return convertRelation(oaf);
}
} catch (Throwable e) {
throw new RuntimeException(e);
@ -40,8 +40,8 @@ public class ProtoConverter implements Serializable {
.setRelClass(r.getRelClass())
.setCollectedFrom(r.getCollectedfromCount() > 0 ?
r.getCollectedfromList().stream()
.map(kv -> mapKV(kv))
.collect(Collectors.toList()) : null);
.map(kv -> mapKV(kv))
.collect(Collectors.toList()) : null);
}
private static OafEntity convertEntity(OafProtos.Oaf oaf) {
@ -151,6 +151,28 @@ public class ProtoConverter implements Serializable {
//TODO r3data fields
result.setReleasestartdate(mapStringField(datasource.getReleasestartdate()));
result.setReleaseenddate(mapStringField(datasource.getReleaseenddate()));
result.setMissionstatementurl(mapStringField(datasource.getMissionstatementurl()));
result.setDataprovider(mapBoolField(datasource.getDataprovider()));
result.setServiceprovider(mapBoolField(datasource.getServiceprovider()));
result.setDatabaseaccesstype(mapStringField(datasource.getDatabaseaccesstype()));
result.setDatauploadtype(mapStringField(datasource.getDatauploadtype()));
result.setDatabaseaccessrestriction(mapStringField(datasource.getDatabaseaccessrestriction()));
result.setDatauploadrestriction(mapStringField(datasource.getDatauploadrestriction()));
result.setVersioning(mapBoolField(datasource.getVersioning()));
result.setCitationguidelineurl(mapStringField(datasource.getCitationguidelineurl()));
result.setQualitymanagementkind(mapStringField(datasource.getQualitymanagementkind()));
result.setPidsystems(mapStringField(datasource.getPidsystems()));
result.setCertificates(mapStringField(datasource.getCertificates()));
result.setPolicies(datasource.getPoliciesList()
.stream()
.map(ProtoUtils::mapKV)
.collect(Collectors.toList())
);
result.setJournal(mapJournal(datasource.getJournal()));
return result;
}
@ -180,14 +202,14 @@ public class ProtoConverter implements Serializable {
.setKeywords(mapStringField(m.getKeywords()))
.setSubjects(m.getSubjectsCount() > 0 ?
m.getSubjectsList().stream()
.map(sp -> mapStructuredProperty(sp))
.collect(Collectors.toList()) : null)
.map(sp -> mapStructuredProperty(sp))
.collect(Collectors.toList()) : null)
.setTitle(mapStringField(m.getTitle()))
.setWebsiteurl(mapStringField(m.getWebsiteurl()))
.setFundingtree(m.getFundingtreeCount() > 0 ?
m.getFundingtreeList().stream()
.map(f -> mapStringField(f))
.collect(Collectors.toList()) : null)
.map(f -> mapStringField(f))
.collect(Collectors.toList()) : null)
.setJsonextrainfo(mapStringField(m.getJsonextrainfo()))
.setSummary(mapStringField(m.getSummary()))
.setOptional1(mapStringField(m.getOptional1()))
@ -206,7 +228,7 @@ public class ProtoConverter implements Serializable {
case "orp":
return createORP(oaf);
default:
throw new RuntimeException("received unknown type :"+oaf.getEntity().getResult().getMetadata().getResulttype().getClassid());
throw new RuntimeException("received unknown type :" + oaf.getEntity().getResult().getMetadata().getResulttype().getClassid());
}
}

28
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoUtils.java
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@ -34,8 +34,8 @@ public class ProtoUtils {
.setClassid(q.getClassid())
.setClassname(q.getClassname())
.setSchemeid(q.getSchemeid())
.setSchemename(q.getSchemename())
.setDataInfo(q.hasDataInfo() ? mapDataInfo(q.getDataInfo()) : null);
.setSchemename(q.getSchemename());
//.setDataInfo(q.hasDataInfo() ? mapDataInfo(q.getDataInfo()) : null);
}
public static StructuredProperty mapStructuredProperty(FieldTypeProtos.StructuredProperty sp) {
@ -68,10 +68,30 @@ public class ProtoUtils {
.setIdentifier(originDescription.getIdentifier())
.setDatestamp(originDescription.getDatestamp())
.setMetadataNamespace(originDescription.getMetadataNamespace());
if (originDescription.hasOriginDescription())
originDescriptionResult.setOriginDescription(mapOriginalDescription(originDescription.getOriginDescription()));
// if (originDescription.hasOriginDescription())
// originDescriptionResult.setOriginDescription(mapOriginalDescription(originDescription.getOriginDescription()));
return originDescriptionResult;
}
public static Journal mapJournal(FieldTypeProtos.Journal journal) {
return new Journal()
.setName(journal.getName())
.setIssnPrinted(journal.getIssnPrinted())
.setIssnOnline(journal.getIssnOnline())
.setIssnLinking(journal.getIssnLinking())
.setEp(journal.getEp())
.setIss(journal.getIss())
.setSp(journal.getSp())
.setVol(journal.getVol())
.setEdition(journal.getEdition())
.setConferenceplace(journal.getConferenceplace())
.setConferencedate(journal.getConferencedate())
.setDataInfo(mapDataInfo(journal.getDataInfo()))
;
}
public static Field<String> mapStringField(FieldTypeProtos.StringField s) {

23
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/SparkGraphImporterJob.java
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@ -1,15 +1,21 @@
package eu.dnetlib.dhp.graph;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Publication;
import org.apache.hadoop.io.Text;
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.sql.Dataset;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import scala.Tuple2;
import javax.xml.crypto.Data;
public class SparkGraphImporterJob {
@ -32,18 +38,19 @@ public class SparkGraphImporterJob {
final JavaRDD<Tuple2<String, String>> inputRDD = sc.sequenceFile("file:///home/sandro/part-m-00000", Text.class, Text.class).map(item -> new Tuple2<>(item._1.toString(), item._2.toString()));
Tuple2<String, String> item = inputRDD
final JavaRDD<Datasource> datasources = inputRDD
.filter(s -> s._1().split("@")[2].equalsIgnoreCase("body"))
.first();
System.out.println(item._1());
System.out.println(item._2());
.map(Tuple2::_2)
.map(ProtoConverter::convert)
.filter(s-> s instanceof Datasource)
.map(s->(Datasource)s);
final Encoder<Datasource> encoder = Encoders.bean(Datasource.class);
final Dataset<Datasource> mdstore = spark.createDataset(datasources.rdd(), encoder);
// .map(Tuple2::_2)
// .map(ProtoConverter::convert)
// .mapToPair((PairFunction<Oaf, String,Integer>) s-> new Tuple2<String, Integer>(s.getClass().getName(),1))
// .reduceByKey(Integer::sum).collect().forEach(System.out::println);
System.out.println(mdstore.count());
//
//
// .filter(s -> s instanceof Publication)

4
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/graph/ProtoConverterTest.java
View File

@ -1,5 +1,6 @@
package eu.dnetlib.dhp.graph;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import org.apache.commons.io.IOUtils;
@ -23,6 +24,9 @@ public class ProtoConverterTest {
System.out.println(ds.getId());
ObjectMapper mapper = new ObjectMapper();
System.out.println(mapper.writeValueAsString(result));
}