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fixed mapping applied to ODF records. Added unit test to verify the mapping for OpenTrials

Browse Source
pull/115/head
Claudio Atzori 3 years ago
parent 50fc128ff7
commit 8c96a82a03
4 changed files with 206 additions and 30 deletions
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26
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
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@ -24,13 +24,7 @@ import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.oaiIProvenance;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.*;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document;
@ -38,6 +32,9 @@ import org.dom4j.DocumentFactory;
import org.dom4j.DocumentHelper;
import org.dom4j.Node;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.LicenseComparator;
import eu.dnetlib.dhp.schema.common.ModelConstants;
@ -330,7 +327,7 @@ public abstract class AbstractMdRecordToOafMapper {
r.setDataInfo(info);
r.setLastupdatetimestamp(lastUpdateTimestamp);
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
r.setOriginalId(Arrays.asList(findOriginalId(doc)));
r.setOriginalId(findOriginalId(doc));
r.setCollectedfrom(Arrays.asList(collectedFrom));
r.setPid(prepareResultPids(doc, info));
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection|//dri:dateOfCollection"));
@ -493,16 +490,23 @@ public abstract class AbstractMdRecordToOafMapper {
return null;
}
private String findOriginalId(final Document doc) {
private List<String> findOriginalId(final Document doc) {
final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
if (n != null) {
final String id = n.valueOf("./*[local-name()='identifier']");
if (StringUtils.isNotBlank(id)) {
return id;
return Lists.newArrayList(id);
}
}
return doc.valueOf("//*[local-name()='header']/*[local-name()='identifier']");
List<String> idList = doc
.selectNodes(
"normalize-space(//*[local-name()='header']/*[local-name()='identifier' or local-name()='recordIdentifier']/text())");
Set<String> originalIds = Sets.newHashSet(idList);
if (originalIds.isEmpty()) {
throw new IllegalStateException("missing originalID on " + doc.asXML());
}
return Lists.newArrayList(originalIds);
}
protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId) {

15
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
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@ -119,7 +119,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
instance.setCollectedfrom(collectedfrom);
instance.setHostedby(hostedby);
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
final String distributionlocation = doc.valueOf("//oaf:distributionlocation");
instance.setDistributionlocation(StringUtils.isNotBlank(distributionlocation) ? distributionlocation : null);
instance
.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
@ -200,12 +201,12 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@Override
protected List<Field<String>> prepareFormats(final Document doc, final DataInfo info) {
return prepareListFields(doc, "//*[local-name()=':format']", info);
return prepareListFields(doc, "//*[local-name()='format']", info);
}
@Override
protected Field<String> preparePublisher(final Document doc, final DataInfo info) {
return prepareField(doc, "//*[local-name()=':publisher']", info);
return prepareField(doc, "//*[local-name()='publisher']", info);
}
@Override
@ -220,7 +221,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@Override
protected Qualifier prepareLanguages(final Document doc) {
return prepareQualifier(doc, "//*[local-name()=':language']", DNET_LANGUAGES);
return prepareQualifier(doc, "//*[local-name()='language']", DNET_LANGUAGES);
}
@Override
@ -287,9 +288,9 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
for (final Object o : doc.selectNodes("//*[local-name()='geoLocation']")) {
final GeoLocation loc = new GeoLocation();
loc.setBox(((Node) o).valueOf("./*[local-name()=':geoLocationBox']"));
loc.setPlace(((Node) o).valueOf("./*[local-name()=':geoLocationPlace']"));
loc.setPoint(((Node) o).valueOf("./*[local-name()=':geoLocationPoint']"));
loc.setBox(((Node) o).valueOf("./*[local-name()='geoLocationBox']"));
loc.setPlace(((Node) o).valueOf("./*[local-name()='geoLocationPlace']"));
loc.setPoint(((Node) o).valueOf("./*[local-name()='geoLocationPoint']"));
res.add(loc);
}
return res;

120
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
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@ -1,10 +1,7 @@
package eu.dnetlib.dhp.oa.graph.raw;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.lenient;
import java.io.IOException;
@ -25,14 +22,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class)
@ -256,6 +246,112 @@ public class MappersTest {
assertEquals(r2.getValidationDate(), "2020-01-01");
}
@Test
void testOpentrial() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_opentrial.xml"));
final List<Oaf> list = new OdfToOafMapper(vocs, false).processMdRecord(xml);
assertEquals(1, list.size());
assertTrue(list.get(0) instanceof Dataset);
final Dataset d = (Dataset) list.get(0);
assertNotNull(d.getDateofcollection());
assertEquals("2019-03-27T15:15:22.22Z", d.getDateofcollection());
assertNotNull(d.getDateoftransformation());
assertEquals("2019-04-17T16:04:20.586Z", d.getDateoftransformation());
assertNotNull(d.getDataInfo());
assertFalse(d.getDataInfo().getInvisible());
assertFalse(d.getDataInfo().getDeletedbyinference());
assertEquals("0.9", d.getDataInfo().getTrust());
assertEquals("", d.getDataInfo().getInferenceprovenance());
assertEquals("sysimport:crosswalk:datasetarchive", d.getDataInfo().getProvenanceaction().getClassid());
assertEquals("sysimport:crosswalk:datasetarchive", d.getDataInfo().getProvenanceaction().getClassname());
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, d.getDataInfo().getProvenanceaction().getSchemeid());
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, d.getDataInfo().getProvenanceaction().getSchemename());
assertValidId(d.getId());
assertTrue(d.getOriginalId().size() == 1);
assertEquals("feabb67c-1fd1-423b-aec6-606d04ce53c6", d.getOriginalId().get(0));
assertValidId(d.getCollectedfrom().get(0).getKey());
assertNotNull(d.getTitle());
assertEquals(1, d.getTitle().size());
assertEquals(
"Validation of the Goodstrength System for Assessment of Abdominal Wall Strength in Patients With Incisional Hernia",
d.getTitle().get(0).getValue());
assertNotNull(d.getDescription());
assertEquals(1, d.getDescription().size());
assertTrue(StringUtils.isNotBlank(d.getDescription().get(0).getValue()));
assertTrue(d.getAuthor().size() == 1);
assertEquals("Jensen, Kristian K", d.getAuthor().get(0).getFullname());
assertEquals("Kristian K.", d.getAuthor().get(0).getName());
assertEquals("Jensen", d.getAuthor().get(0).getSurname());
assertNotNull(d.getAuthor().get(0).getPid());
assertTrue(d.getAuthor().get(0).getPid().isEmpty());
assertNotNull(d.getPid());
assertEquals(1, d.getPid().size());
assertEquals("NCT02321059", d.getPid().get(0).getValue());
assertEquals("nct", d.getPid().get(0).getQualifier().getClassid());
assertEquals("ClinicalTrials.gov Identifier", d.getPid().get(0).getQualifier().getClassname());
assertEquals(ModelConstants.DNET_PID_TYPES, d.getPid().get(0).getQualifier().getSchemeid());
assertEquals(ModelConstants.DNET_PID_TYPES, d.getPid().get(0).getQualifier().getSchemename());
assertNotNull(d.getPublisher());
assertEquals("nct", d.getPublisher().getValue());
assertTrue(d.getSubject().isEmpty());
assertTrue(d.getContext().isEmpty());
assertNotNull(d.getInstance());
assertTrue(d.getInstance().size() == 1);
Instance i = d.getInstance().get(0);
assertNotNull(i.getAccessright());
assertEquals(ModelConstants.DNET_ACCESS_MODES, i.getAccessright().getSchemeid());
assertEquals(ModelConstants.DNET_ACCESS_MODES, i.getAccessright().getSchemename());
assertEquals("OPEN", i.getAccessright().getClassid());
assertEquals("Open Access", i.getAccessright().getClassname());
assertNotNull(i.getCollectedfrom());
assertEquals("10|openaire____::b292fc2d7de505f78e3cae1b06ea8548", i.getCollectedfrom().getKey());
assertEquals("OpenTrials", i.getCollectedfrom().getValue());
assertNotNull(i.getHostedby());
assertEquals("10|openaire____::b292fc2d7de505f78e3cae1b06ea8548", i.getHostedby().getKey());
assertEquals("OpenTrials", i.getHostedby().getValue());
assertNotNull(i.getInstancetype());
assertEquals("0037", i.getInstancetype().getClassid());
assertEquals("Clinical Trial", i.getInstancetype().getClassname());
assertEquals(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getSchemeid());
assertEquals(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getSchemename());
assertNull(i.getLicense());
assertNotNull(i.getDateofacceptance());
assertEquals("2014-11-11", i.getDateofacceptance().getValue());
assertNull(i.getDistributionlocation());
assertNull(i.getProcessingchargeamount());
assertNull(i.getProcessingchargecurrency());
assertNotNull(i.getUrl());
assertEquals(2, i.getUrl().size());
assertTrue(i.getUrl().contains("http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT02321059"));
assertTrue(i.getUrl().contains("https://clinicaltrials.gov/ct2/show/NCT02321059"));
assertEquals("UNKNOWN", i.getRefereed().getClassid());
}
@Test
void testSoftware() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml"));

75
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_opentrial.xml
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@ -0,0 +1,75 @@
<?xml version="1.0" encoding="UTF-8"?>
<oai:record xmlns:dr="http://www.driver-repository.eu/namespace/dr"
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
xmlns:oaf="http://namespace.openaire.eu/oaf" xmlns:oai="http://www.openarchives.org/OAI/2.0/">
<oai:header>
<dri:objIdentifier>opentrials__::0000bf8e63d3d7e6b88421eabafae3f6</dri:objIdentifier>
<dri:recordIdentifier>feabb67c-1fd1-423b-aec6-606d04ce53c6</dri:recordIdentifier>
<dri:dateOfCollection>2019-03-27T15:15:22.22Z</dri:dateOfCollection>
<oaf:datasourceprefix>opentrials__</oaf:datasourceprefix>
<dr:dateOfTransformation>2019-04-17T16:04:20.586Z</dr:dateOfTransformation>
</oai:header>
<oai:metadata>
<resource xmlns="http://datacite.org/schema/kernel-3"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd">
<identifier identifierType="URL">https://clinicaltrials.gov/ct2/show/NCT02321059</identifier>
<alternateIdentifiers>
<alternateIdentifier alternateIdentifierType="URL">http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT02321059</alternateIdentifier>
<alternateIdentifier alternateIdentifierType="nct">NCT02321059</alternateIdentifier>
</alternateIdentifiers>
<creators>
<creator>
<creatorName>Jensen, Kristian K</creatorName>
</creator>
</creators>
<titles>
<title>Validation of the Goodstrength System for Assessment of Abdominal Wall Strength in Patients With Incisional Hernia</title>
</titles>
<publisher>nct</publisher>
<geoLocations>
<geoLocationPlace>Denmark</geoLocationPlace>
</geoLocations>
<resourceType resourceTypeGeneral="clinicalTrial">0037</resourceType>
<descriptions>
<description descriptionType="Abstract">Patients with an incisional hernia in the midline and controls with an intact abdominal wall are examined twice with one week apart, in order to establish the test-retest reliability and internal and external validity of the Goodstrength trunk dynamometer.</description>
</descriptions>
</resource>
<oaf:accessrights>OPEN</oaf:accessrights>
<dr:CobjCategory type="dataset">0037</dr:CobjCategory>
<oaf:dateAccepted>2014-11-11</oaf:dateAccepted>
<oaf:hostedBy id="openaire____::opentrials" name="OpenTrials"/>
<oaf:collectedFrom id="openaire____::opentrials" name="OpenTrials"/>
<oaf:about>
<oaf:datainfo>
<oaf:inferred>false</oaf:inferred>
<oaf:deletedbyinference>false</oaf:deletedbyinference>
<oaf:trust>0.9</oaf:trust>
<oaf:inferenceprovenance/>
<oaf:provenanceaction
classid="sysimport:crosswalk:datasetarchive"
classname="sysimport:crosswalk:datasetarchive"
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
</oaf:datainfo>
</oaf:about>
</oai:metadata>
<about xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">
<originDescription altered="true" harvestDate="2019-03-27T15:15:22.22Z">
<baseURL>file:///var/lib/dnet/data/opentrials/opentrials.csv</baseURL>
<identifier/>
<datestamp/>
<metadataNamespace/>
</originDescription>
</provenance>
<oaf:datainfo>
<oaf:inferred>false</oaf:inferred>
<oaf:deletedbyinference>false</oaf:deletedbyinference>
<oaf:trust>0.9</oaf:trust>
<oaf:inferenceprovenance/>
<oaf:provenanceaction classid="sysimport:crosswalk:datasetarchive"
classname="sysimport:crosswalk:datasetarchive"
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
</oaf:datainfo>
</about>
</oai:record>
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