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implemented DedupRecord factory for missing entities

This commit is contained in:
Sandro La Bruzzo 2019-12-13 09:40:02 +01:00
parent 545e940007
commit b4392f9f43
10 changed files with 143 additions and 37 deletions
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2
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Context.java
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@ -26,7 +26,7 @@ public class Context implements Serializable {
@Override
public int hashCode() {
return id.hashCode();
return id ==null? 0 : id.hashCode();
}
@Override

8
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java
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@ -25,8 +25,8 @@ public class Field<T> implements Serializable {
}
@Override
public int hashCode(){
return getValue().hashCode();
public int hashCode() {
return getValue() == null ? 0 : getValue().hashCode();
}
@Override
@ -37,11 +37,7 @@ public class Field<T> implements Serializable {
return false;
if (getClass() != obj.getClass())
return false;
Field<T> other = (Field<T>) obj;
return getValue().equals(other.getValue());
}
}

10
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java
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@ -1,5 +1,7 @@
package eu.dnetlib.dhp.schema.oaf;
import org.apache.commons.lang3.StringUtils;
import java.io.Serializable;
public class GeoLocation implements Serializable {
@ -35,8 +37,14 @@ public class GeoLocation implements Serializable {
}
public boolean isBlank() {
return StringUtils.isBlank(point) &&
StringUtils.isBlank(box) &&
StringUtils.isBlank(place);
}
public String toComparableString() {
return String.format("%s::%s%s", point != null ? point.toLowerCase() : "", box != null ? box.toLowerCase() : "",place != null ? place.toLowerCase() : "");
return isBlank()?"":String.format("%s::%s%s", point != null ? point.toLowerCase() : "", box != null ? box.toLowerCase() : "", place != null ? place.toLowerCase() : "");
}
@Override

3
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java
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@ -84,6 +84,9 @@ public class Instance implements Serializable {
public void setDateofacceptance(Field<String> dateofacceptance) {
this.dateofacceptance = dateofacceptance;
}
public String toComparableString(){
return String.format("%s::%s::%s::%s",
hostedby != null && hostedby.getKey()!= null ? hostedby.getKey().toLowerCase() : "",

8
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java
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@ -1,5 +1,7 @@
package eu.dnetlib.dhp.schema.oaf;
import org.apache.commons.lang3.StringUtils;
import java.io.Serializable;
public class KeyValue implements Serializable {
@ -35,7 +37,11 @@ public class KeyValue implements Serializable {
}
public String toComparableString() {
return String.format("%s::%s", key != null ? key.toLowerCase() : "", value != null ? value.toLowerCase() : "");
return isBlank()?"":String.format("%s::%s", key != null ? key.toLowerCase() : "", value != null ? value.toLowerCase() : "");
}
public boolean isBlank() {
return StringUtils.isBlank(key) && StringUtils.isBlank(value);
}
@Override

12
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java
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@ -34,4 +34,16 @@ public class OtherResearchProduct extends Result implements Serializable {
public void setTool(List<Field<String>> tool) {
this.tool = tool;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
OtherResearchProduct o = (OtherResearchProduct)e;
contactperson = mergeLists(contactperson, o.getContactperson());
contactgroup = mergeLists(contactgroup, o.getContactgroup());
tool = mergeLists(tool, o.getTool());
mergeOAFDataInfo(e);
}
}

11
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java
View File

@ -1,5 +1,7 @@
package eu.dnetlib.dhp.schema.oaf;
import org.apache.commons.lang3.StringUtils;
import java.io.Serializable;
public class Qualifier implements Serializable {
@ -42,13 +44,18 @@ public class Qualifier implements Serializable {
}
public String toComparableString() {
return String.format("%s::%s::%s::%s",
return isBlank()?"": String.format("%s::%s::%s::%s",
classid != null ? classid : "",
classname != null ? classname : "",
schemeid != null ? schemeid : "",
schemename != null ? schemename : "");
}
public boolean isBlank() {
return StringUtils.isBlank(classid) &&
StringUtils.isBlank(classname) &&
StringUtils.isBlank(schemeid) &&
StringUtils.isBlank(schemename);
}
@Override
public int hashCode() {
return toComparableString().hashCode();

25
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
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@ -252,10 +252,10 @@ public abstract class Result extends OafEntity implements Serializable {
instance = mergeLists(instance, r.getInstance());
if (r.getResulttype() != null && compareTrust(this, r)<0)
if (r.getResulttype() != null && compareTrust(this, r) < 0)
resulttype = r.getResulttype();
if (r.getLanguage() != null && compareTrust(this, r)<0)
if (r.getLanguage() != null && compareTrust(this, r) < 0)
language = r.getLanguage();
country = mergeLists(country, r.getCountry());
@ -268,10 +268,10 @@ public abstract class Result extends OafEntity implements Serializable {
description = longestLists(description, r.getDescription());
if (r.getPublisher() != null && compareTrust(this, r)<0)
if (r.getPublisher() != null && compareTrust(this, r) < 0)
publisher = r.getPublisher();
if (r.getEmbargoenddate() != null && compareTrust(this, r)<0)
if (r.getEmbargoenddate() != null && compareTrust(this, r) < 0)
embargoenddate = r.getEmbargoenddate();
source = mergeLists(source, r.getSource());
@ -287,15 +287,15 @@ public abstract class Result extends OafEntity implements Serializable {
coverage = mergeLists(coverage, r.getCoverage());
if (r.getRefereed() != null && compareTrust(this, r)<0)
if (r.getRefereed() != null && compareTrust(this, r) < 0)
refereed = r.getRefereed();
context = mergeLists(context, r.getContext());
if (r.getProcessingchargeamount() != null && compareTrust(this, r)<0)
if (r.getProcessingchargeamount() != null && compareTrust(this, r) < 0)
processingchargeamount = r.getProcessingchargeamount();
if (r.getProcessingchargecurrency() != null && compareTrust(this, r)<0)
if (r.getProcessingchargecurrency() != null && compareTrust(this, r) < 0)
processingchargecurrency = r.getProcessingchargecurrency();
externalReference = mergeLists(externalReference, r.getExternalReference());
@ -303,16 +303,15 @@ public abstract class Result extends OafEntity implements Serializable {
}
private List<Field<String>> longestLists(List<Field<String>> a, List<Field<String>> b) {
if(a == null || b == null)
return a==null?b:a;
if (a.size()== b.size()) {
if (a == null || b == null)
return a == null ? b : a;
if (a.size() == b.size()) {
int msa = a.stream().filter(i -> i.getValue() != null).map(i -> i.getValue().length()).max(Comparator.naturalOrder()).orElse(0);
int msb = b.stream().filter(i -> i.getValue() != null).map(i -> i.getValue().length()).max(Comparator.naturalOrder()).orElse(0);
return msa>msb?a:b;
return msa > msb ? a : b;
}
return a.size()> b.size()?a:b;
return a.size() > b.size() ? a : b;
}

15
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java
View File

@ -44,4 +44,19 @@ public class Software extends Result implements Serializable {
public void setProgrammingLanguage(Qualifier programmingLanguage) {
this.programmingLanguage = programmingLanguage;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
final Software s = (Software) e;
documentationUrl = mergeLists(documentationUrl, s.getDocumentationUrl());
license = mergeLists(license, s.getLicense());
codeRepositoryUrl = s.getCodeRepositoryUrl()!= null && compareTrust(this, s)<0?s.getCodeRepositoryUrl():codeRepositoryUrl;
programmingLanguage= s.getProgrammingLanguage()!= null && compareTrust(this, s)<0?s.getProgrammingLanguage():programmingLanguage;
mergeOAFDataInfo(e);
}
}

86
dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java
View File

@ -23,8 +23,6 @@ import static java.util.stream.Collectors.toMap;
public class DedupRecordFactory {
public static JavaRDD<OafEntity> createDedupRecord(final JavaSparkContext sc, final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, final OafEntityType entityType, final DedupConfig dedupConf) {
long ts = System.currentTimeMillis();
//<id, json_entity>
final JavaPairRDD<String, String> inputJsonEntities = sc.textFile(entitiesInputPath)
@ -49,20 +47,19 @@ public class DedupRecordFactory {
switch (entityType) {
case publication:
return sortedJoinResult.map(p->DedupRecordFactory.publicationMerger(p, ts));
return sortedJoinResult.map(p -> DedupRecordFactory.publicationMerger(p, ts));
case dataset:
return sortedJoinResult.map(d->DedupRecordFactory.datasetMerger(d,ts));
return sortedJoinResult.map(d -> DedupRecordFactory.datasetMerger(d, ts));
case project:
return sortedJoinResult.map(p->DedupRecordFactory.projectMerger(p,ts));
return sortedJoinResult.map(p -> DedupRecordFactory.projectMerger(p, ts));
case software:
return sortedJoinResult.map(s->DedupRecordFactory.softwareMerger(s,ts));
return sortedJoinResult.map(s -> DedupRecordFactory.softwareMerger(s, ts));
case datasource:
return sortedJoinResult.map(d->DedupRecordFactory.datasourceMerger(d,ts));
return sortedJoinResult.map(d -> DedupRecordFactory.datasourceMerger(d, ts));
case organization:
return sortedJoinResult.map(o->DedupRecordFactory.organizationMerger(o,ts));
return sortedJoinResult.map(o -> DedupRecordFactory.organizationMerger(o, ts));
case otherresearchproduct:
return sortedJoinResult.map(o->DedupRecordFactory.otherresearchproductMerger(o,ts));
return sortedJoinResult.map(o -> DedupRecordFactory.otherresearchproductMerger(o, ts));
default:
return null;
}
@ -153,12 +150,48 @@ public class DedupRecordFactory {
private static Software softwareMerger(Tuple2<String, Iterable<String>> e, final long ts) {
throw new NotImplementedException();
Software s = new Software(); //the result of the merge, to be returned at the end
s.setId(e._1());
final ObjectMapper mapper = new ObjectMapper();
final Collection<String> dateofacceptance = Lists.newArrayList();
if (e._2() != null)
e._2().forEach(soft -> {
try {
Software software = mapper.readValue(soft, Software.class);
s.mergeFrom(software);
s.setAuthor(DedupUtility.mergeAuthor(s.getAuthor(), software.getAuthor()));
//add to the list if they are not null
if (software.getDateofacceptance() != null)
dateofacceptance.add(software.getDateofacceptance().getValue());
} catch (Exception exc) {
throw new RuntimeException(exc);
}
});
s.setDateofacceptance(DatePicker.pick(dateofacceptance));
s.getDataInfo().setTrust("0.9");
s.setLastupdatetimestamp(ts);
return s;
}
private static Datasource datasourceMerger(Tuple2<String, Iterable<String>> e, final long ts) {
Datasource d = new Datasource(); //the result of the merge, to be returned at the end
d.setId(e._1());
final ObjectMapper mapper = new ObjectMapper();
if (e._2() != null)
e._2().forEach(dat -> {
try {
Datasource datasource = mapper.readValue(dat, Datasource.class);
throw new NotImplementedException();
d.mergeFrom(datasource);
} catch (Exception exc) {
throw new RuntimeException(exc);
}
});
d.getDataInfo().setTrust("0.9");
d.setLastupdatetimestamp(ts);
return d;
}
private static Organization organizationMerger(Tuple2<String, Iterable<String>> e, final long ts) {
@ -188,13 +221,40 @@ public class DedupRecordFactory {
throw new RuntimeException(exc);
}
});
o.getDataInfo().setTrust("0.9");
o.setLastupdatetimestamp(ts);
return o;
}
private static OtherResearchProduct otherresearchproductMerger(Tuple2<String, Iterable<String>> e, final long ts) {
throw new NotImplementedException();
OtherResearchProduct o = new OtherResearchProduct(); //the result of the merge, to be returned at the end
o.setId(e._1());
final ObjectMapper mapper = new ObjectMapper();
final Collection<String> dateofacceptance = Lists.newArrayList();
if (e._2() != null)
e._2().forEach(orp -> {
try {
OtherResearchProduct otherResearchProduct = mapper.readValue(orp, OtherResearchProduct.class);
o.mergeFrom(otherResearchProduct);
o.setAuthor(DedupUtility.mergeAuthor(o.getAuthor(), otherResearchProduct.getAuthor()));
//add to the list if they are not null
if (otherResearchProduct.getDateofacceptance() != null)
dateofacceptance.add(otherResearchProduct.getDateofacceptance().getValue());
} catch (Exception exc) {
throw new RuntimeException(exc);
}
});
o.setDateofacceptance(DatePicker.pick(dateofacceptance));
o.getDataInfo().setTrust("0.9");
o.setLastupdatetimestamp(ts);
return o;
}
}