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added pdb to oaf class

This commit is contained in:
Sandro La Bruzzo 2021-06-21 09:36:40 +02:00
parent 4fe7b75644
commit 507e42102a
5 changed files with 2336 additions and 11 deletions
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14
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/aggregation/AbstractVocabularyTest.java
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@ -6,13 +6,13 @@ import static org.mockito.Mockito.lenient;
import java.io.IOException;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
import org.apache.commons.io.IOUtils;
import org.mockito.Mock;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.transformation.TransformationFactory;
import eu.dnetlib.dhp.transformation.TransformationJobTest;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -34,16 +34,22 @@ public abstract class AbstractVocabularyTest {
private static List<String> vocs() throws IOException {
return IOUtils
.readLines(TransformationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/terms.txt"));
.readLines(
Objects
.requireNonNull(
AbstractVocabularyTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/terms.txt")));
}
private static List<String> synonyms() throws IOException {
return IOUtils
.readLines(TransformationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/synonyms.txt"));
.readLines(
Objects
.requireNonNull(
AbstractVocabularyTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/synonyms.txt")));
}
protected void mockupTrasformationRule(final String trule, final String path) throws Exception {
final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path));
final String trValue = IOUtils.toString(Objects.requireNonNull(this.getClass().getResourceAsStream(path)));
lenient()
.when(isLookUpService.quickSearchProfile(String.format(TransformationFactory.TRULE_XQUERY, trule)))

2
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record.json
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1235
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt Normal file
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1080
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt Normal file
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16
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala
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@ -1,13 +1,14 @@
package eu.dnetlib.dhp.sx.bio
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
import eu.dnetlib.dhp.schema.oaf.{Dataset, Oaf}
import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Oaf}
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
import scala.collection.JavaConverters._
object PDBToOAF {
val dataInfo: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9")
def convert(input:String):List[Oaf]= {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
@ -18,13 +19,16 @@ object PDBToOAF {
val d = new Dataset
d.setPid(List(OafMapperUtils.structuredProperty()))
d.setPid(
List(
OafMapperUtils.structuredProperty(pdb, "pdb", "pdb", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES,dataInfo)
).asJava
)
List()
List(d)
}