lsmyrnaios
/
dnet-hadoop
forked from D-Net/dnet-hadoop
1
0
Fork 0
Code Pull Requests Activity

Merge pull request 'participant project contribution' (#223) from project_organization_contribution into beta 

Reviewed-on: D-Net/dnet-hadoop#223
This commit is contained in:
Claudio Atzori 2022-07-28 12:16:30 +02:00
parent ed98a6d9d0 1dd1e4fe3a
commit 37cfda0fc5
6 changed files with 170 additions and 175 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

58
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
View File

@ -419,4 +419,62 @@ public class OafMapperUtils {
m.setUnit(Arrays.asList(newKeyValueInstance(key, value, dataInfo)));
return m;
}
public static Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final OafEntity entity) {
return getRelation(source, target, relType, subRelType, relClass, entity, null);
}
public static Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final OafEntity entity,
final String validationDate) {
return getRelation(
source, target, relType, subRelType, relClass, entity.getCollectedfrom(), entity.getDataInfo(),
entity.getLastupdatetimestamp(), validationDate, null);
}
public static Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final List<KeyValue> collectedfrom,
final DataInfo dataInfo,
final Long lastupdatetimestamp) {
return getRelation(
source, target, relType, subRelType, relClass, collectedfrom, dataInfo, lastupdatetimestamp, null, null);
}
public static Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final List<KeyValue> collectedfrom,
final DataInfo dataInfo,
final Long lastupdatetimestamp,
final String validationDate,
final List<KeyValue> properties) {
final Relation rel = new Relation();
rel.setRelType(relType);
rel.setSubRelType(subRelType);
rel.setRelClass(relClass);
rel.setSource(source);
rel.setTarget(target);
rel.setCollectedfrom(collectedfrom);
rel.setDataInfo(dataInfo);
rel.setLastupdatetimestamp(lastupdatetimestamp);
rel.setValidated(StringUtils.isNotBlank(validationDate));
rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null);
rel.setProperties(properties);
return rel;
}
}

52
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -267,10 +267,13 @@ public abstract class AbstractMdRecordToOafMapper {
res
.add(
getRelation(
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate));
OafMapperUtils
.getRelation(
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate));
res
.add(getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate));
.add(
OafMapperUtils
.getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate));
}
}
@ -303,13 +306,16 @@ public abstract class AbstractMdRecordToOafMapper {
final String targetId = createOpenaireId(targetType, target, true);
rels
.add(
getRelation(
entity.getId(), targetId, relType, subRelType, relClass, entity, validationdDate));
OafMapperUtils
.getRelation(
entity.getId(), targetId, relType, subRelType, relClass, entity,
validationdDate));
rels
.add(
getRelation(
targetId, entity.getId(), relType, subRelType, relClassInverse, entity,
validationdDate));
OafMapperUtils
.getRelation(
targetId, entity.getId(), relType, subRelType, relClassInverse, entity,
validationdDate));
}
}
}
@ -317,36 +323,6 @@ public abstract class AbstractMdRecordToOafMapper {
return rels;
}
protected Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final OafEntity entity) {
return getRelation(source, target, relType, subRelType, relClass, entity, null);
}
protected Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final OafEntity entity,
final String validationDate) {
final Relation rel = new Relation();
rel.setRelType(relType);
rel.setSubRelType(subRelType);
rel.setRelClass(relClass);
rel.setSource(source);
rel.setTarget(target);
rel.setCollectedfrom(entity.getCollectedfrom());
rel.setDataInfo(entity.getDataInfo());
rel.setLastupdatetimestamp(entity.getLastupdatetimestamp());
rel.setValidated(StringUtils.isNotBlank(validationDate));
rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null);
return rel;
}
protected abstract List<Oaf> addOtherResultRels(
final Document doc,
final OafEntity entity);

155
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -1,32 +1,7 @@
package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASET_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASOURCE_ORGANIZATION;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS;
import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION;
import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTICIPANT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_MERGED_IN;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PARTICIPANT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PROVIDED_BY;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO;
import static eu.dnetlib.dhp.schema.common.ModelConstants.MERGES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.ORG_ORG_RELTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.ORP_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PARTICIPATION;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PROJECT_ORGANIZATION;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVIDES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVISION;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DATASET;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RELATIONSHIP;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*;
import java.io.Closeable;
@ -45,6 +20,8 @@ import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.DbClient;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
@ -68,6 +45,7 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable {
@ -437,25 +415,14 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final List<KeyValue> collectedFrom = listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
final Relation r1 = new Relation();
r1.setRelType(DATASOURCE_ORGANIZATION);
r1.setSubRelType(PROVISION);
r1.setRelClass(IS_PROVIDED_BY);
r1.setSource(dsId);
r1.setTarget(orgId);
r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r1 = OafMapperUtils
.getRelation(
dsId, orgId, DATASOURCE_ORGANIZATION, PRODUCES, IS_PROVIDED_BY, collectedFrom, info,
lastUpdateTimestamp);
final Relation r2 = new Relation();
r2.setRelType(DATASOURCE_ORGANIZATION);
r2.setSubRelType(PROVISION);
r2.setRelClass(PROVIDES);
r2.setSource(orgId);
r2.setTarget(dsId);
r2.setCollectedfrom(collectedFrom);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r2 = OafMapperUtils
.getRelation(
orgId, dsId, DATASOURCE_ORGANIZATION, PRODUCES, PROVIDES, collectedFrom, info, lastUpdateTimestamp);
return Arrays.asList(r1, r2);
} catch (final Exception e) {
@ -471,25 +438,20 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final List<KeyValue> collectedFrom = listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
final Relation r1 = new Relation();
r1.setRelType(PROJECT_ORGANIZATION);
r1.setSubRelType(PARTICIPATION);
r1.setRelClass(HAS_PARTICIPANT);
r1.setSource(projectId);
r1.setTarget(orgId);
r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
final List<KeyValue> properties = Lists
.newArrayList(
keyValue("contribution", String.valueOf(rs.getDouble("contribution"))),
keyValue("currency", rs.getString("currency")));
final Relation r2 = new Relation();
r2.setRelType(PROJECT_ORGANIZATION);
r2.setSubRelType(PARTICIPATION);
r2.setRelClass(IS_PARTICIPANT);
r2.setSource(orgId);
r2.setTarget(projectId);
r2.setCollectedfrom(collectedFrom);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r1 = OafMapperUtils
.getRelation(
projectId, orgId, PROJECT_ORGANIZATION, PARTICIPATION, HAS_PARTICIPANT, collectedFrom, info,
lastUpdateTimestamp, null, properties);
final Relation r2 = OafMapperUtils
.getRelation(
orgId, projectId, PROJECT_ORGANIZATION, PARTICIPATION, IS_PARTICIPANT, collectedFrom, info,
lastUpdateTimestamp, null, properties);
return Arrays.asList(r1, r2);
} catch (final Exception e) {
@ -703,25 +665,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final List<KeyValue> collectedFrom = listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
final Relation r1 = new Relation();
r1.setRelType(ORG_ORG_RELTYPE);
r1.setSubRelType(ModelConstants.DEDUP);
r1.setRelClass(MERGES);
r1.setSource(orgId1);
r1.setTarget(orgId2);
r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r1 = OafMapperUtils
.getRelation(orgId1, orgId2, ORG_ORG_RELTYPE, DEDUP, MERGES, collectedFrom, info, lastUpdateTimestamp);
final Relation r2 = new Relation();
r2.setRelType(ORG_ORG_RELTYPE);
r2.setSubRelType(ModelConstants.DEDUP);
r2.setRelClass(IS_MERGED_IN);
r2.setSource(orgId2);
r2.setTarget(orgId1);
r2.setCollectedfrom(collectedFrom);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r2 = OafMapperUtils
.getRelation(
orgId2, orgId1, ORG_ORG_RELTYPE, DEDUP, IS_MERGED_IN, collectedFrom, info, lastUpdateTimestamp);
return Arrays.asList(r1, r2);
} catch (final Exception e) {
throw new RuntimeException(e);
@ -738,17 +687,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final List<KeyValue> collectedFrom = listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
final Relation r = new Relation();
r.setRelType(ORG_ORG_RELTYPE);
r.setSubRelType(ModelConstants.RELATIONSHIP);
r.setRelClass(rs.getString("type"));
r.setSource(orgId1);
r.setTarget(orgId2);
r.setCollectedfrom(collectedFrom);
r.setDataInfo(info);
r.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(r);
return Arrays
.asList(
OafMapperUtils
.getRelation(
orgId1, orgId2, ORG_ORG_RELTYPE, RELATIONSHIP, rs.getString("type"), collectedFrom, info,
lastUpdateTimestamp));
} catch (final Exception e) {
throw new RuntimeException(e);
}
@ -765,29 +709,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final List<KeyValue> collectedFrom = listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
final Relation r1 = new Relation();
r1.setRelType(ORG_ORG_RELTYPE);
r1.setSubRelType(ModelConstants.DEDUP);
r1.setRelClass(relClass);
r1.setSource(orgId1);
r1.setTarget(orgId2);
r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
// removed because there's no difference between two sides //TODO
// final Relation r2 = new Relation();
// r2.setRelType(ORG_ORG_RELTYPE);
// r2.setSubRelType(ORG_ORG_SUBRELTYPE);
// r2.setRelClass(relClass);
// r2.setSource(orgId2);
// r2.setTarget(orgId1);
// r2.setCollectedfrom(collectedFrom);
// r2.setDataInfo(info);
// r2.setLastupdatetimestamp(lastUpdateTimestamp);
// return Arrays.asList(r1, r2);
return Arrays.asList(r1);
return Arrays
.asList(
OafMapperUtils
.getRelation(
orgId1, orgId2, ORG_ORG_RELTYPE, DEDUP, relClass, collectedFrom, info,
lastUpdateTimestamp));
} catch (final Exception e) {
throw new RuntimeException(e);
}

1
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql
View File

@ -3,6 +3,7 @@ SELECT
po.resporganization AS resporganization,
po.participantnumber AS participantnumber,
po.contribution AS contribution,
po.currency AS currency,
NULL AS startdate,
NULL AS enddate,
false AS inferred,

62
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java
View File

@ -1,9 +1,7 @@
package eu.dnetlib.dhp.oa.graph.raw;
import static org.junit.jupiter.api.Assertions.assertEquals;
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.ArgumentMatchers.anyString;
import static org.mockito.Mockito.lenient;
@ -31,11 +29,12 @@ import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
@ExtendWith(MockitoExtension.class)
public class MigrateDbEntitiesApplicationTest {
class MigrateDbEntitiesApplicationTest {
private MigrateDbEntitiesApplication app;
@ -61,7 +60,7 @@ public class MigrateDbEntitiesApplicationTest {
}
@Test
public void testProcessService() throws Exception {
void testProcessService() throws Exception {
final List<TypedField> fields = prepareMocks("services_resultset_entry.json");
final List<Oaf> list = app.processService(rs);
@ -74,7 +73,7 @@ public class MigrateDbEntitiesApplicationTest {
.getCollectedfrom()
.stream()
.map(KeyValue::getKey)
.forEach(dsId -> assertValidId(dsId));
.forEach(this::assertValidId);
assertEquals(1, ds.getPid().size());
assertEquals("r3d100010218", ds.getPid().get(0).getValue());
@ -163,14 +162,14 @@ public class MigrateDbEntitiesApplicationTest {
.stream()
.map(Qualifier::getSchemeid)
.collect(Collectors.toCollection(HashSet::new));
assertTrue(cpSchemeId.size() == 1);
assertEquals(1,cpSchemeId.size());
assertTrue(cpSchemeId.contains("eosc:contentpolicies"));
HashSet<String> cpSchemeName = ds
.getContentpolicies()
.stream()
.map(Qualifier::getSchemename)
.collect(Collectors.toCollection(HashSet::new));
assertTrue(cpSchemeName.size() == 1);
assertEquals(1, cpSchemeName.size());
assertTrue(cpSchemeName.contains("eosc:contentpolicies"));
assertEquals(2, ds.getContentpolicies().size());
assertEquals("Taxonomic classification", ds.getContentpolicies().get(0).getClassid());
@ -193,7 +192,7 @@ public class MigrateDbEntitiesApplicationTest {
}
@Test
public void testProcessProject() throws Exception {
void testProcessProject() throws Exception {
final List<TypedField> fields = prepareMocks("projects_resultset_entry.json");
final List<Oaf> list = app.processProject(rs);
@ -211,7 +210,7 @@ public class MigrateDbEntitiesApplicationTest {
}
@Test
public void testProcessOrganization() throws Exception {
void testProcessOrganization() throws Exception {
final List<TypedField> fields = prepareMocks("organizations_resultset_entry.json");
final List<Oaf> list = app.processOrganization(rs);
@ -238,7 +237,7 @@ public class MigrateDbEntitiesApplicationTest {
}
@Test
public void testProcessDatasourceOrganization() throws Exception {
void testProcessDatasourceOrganization() throws Exception {
final List<TypedField> fields = prepareMocks("datasourceorganization_resultset_entry.json");
final List<Oaf> list = app.processServiceOrganization(rs);
@ -255,7 +254,7 @@ public class MigrateDbEntitiesApplicationTest {
}
@Test
public void testProcessProjectOrganization() throws Exception {
void testProcessProjectOrganization() throws Exception {
final List<TypedField> fields = prepareMocks("projectorganization_resultset_entry.json");
final List<Oaf> list = app.processProjectOrganization(rs);
@ -271,6 +270,38 @@ public class MigrateDbEntitiesApplicationTest {
assertEquals(r2.getSource(), r1.getTarget());
assertValidId(r1.getCollectedfrom().get(0).getKey());
assertValidId(r2.getCollectedfrom().get(0).getKey());
assertEquals(ModelConstants.PROJECT_ORGANIZATION, r1.getRelType());
assertEquals(ModelConstants.PROJECT_ORGANIZATION, r2.getRelType());
assertEquals(ModelConstants.PARTICIPATION, r1.getSubRelType());
assertEquals(ModelConstants.PARTICIPATION, r2.getSubRelType());
if (r1.getSource().startsWith("40")) {
assertEquals(ModelConstants.HAS_PARTICIPANT, r1.getRelClass());
assertEquals(ModelConstants.IS_PARTICIPANT, r2.getRelClass());
} else if (r1.getSource().startsWith("20")) {
assertEquals(ModelConstants.IS_PARTICIPANT, r1.getRelClass());
assertEquals(ModelConstants.HAS_PARTICIPANT, r2.getRelClass());
}
assertNotNull(r1.getProperties());
checkProperty(r1, "contribution", "436754.0");
checkProperty(r2, "contribution", "436754.0");
checkProperty(r1, "currency","EUR");
checkProperty(r2, "currency", "EUR");
}
private void checkProperty(Relation r, String property, String value) {
final List<KeyValue> p = r
.getProperties()
.stream()
.filter(kv -> kv.getKey().equals(property))
.collect(Collectors.toList());
assertFalse(p.isEmpty());
assertEquals(1, p.size());
assertEquals(value, p.get(0).getValue());
}
@Test
@ -289,7 +320,7 @@ public class MigrateDbEntitiesApplicationTest {
}
@Test
public void testProcessClaims_rels() throws Exception {
void testProcessClaims_rels() throws Exception {
final List<TypedField> fields = prepareMocks("claimsrel_resultset_entry.json");
final List<Oaf> list = app.processClaims(rs);
@ -320,9 +351,6 @@ public class MigrateDbEntitiesApplicationTest {
assertValidId(r1.getCollectedfrom().get(0).getKey());
assertValidId(r2.getCollectedfrom().get(0).getKey());
// System.out.println(new ObjectMapper().writeValueAsString(r1));
// System.out.println(new ObjectMapper().writeValueAsString(r2));
}
private List<TypedField> prepareMocks(final String jsonFile) throws IOException, SQLException {
@ -385,7 +413,7 @@ public class MigrateDbEntitiesApplicationTest {
final String[] values = ((List<?>) tf.getValue())
.stream()
.filter(Objects::nonNull)
.map(o -> o.toString())
.map(Object::toString)
.toArray(String[]::new);
Mockito.when(arr.getArray()).thenReturn(values);

17
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json
View File

@ -2,12 +2,12 @@
{
"field": "project",
"type": "string",
"value": "nsf_________::1700003"
"value": "corda__h2020::824273"
},
{
"field": "resporganization",
"type": "string",
"value": "nsf_________::University_of_Notre_Dame"
"value": "corda__h2020::999945647"
},
{
"field": "participantnumber",
@ -16,8 +16,13 @@
},
{
"field": "contribution",
"type": "not_used",
"value": null
"type": "double",
"value": 436754
},
{
"field": "currency",
"type": "string",
"value": "EUR"
},
{
"field": "startdate",
@ -52,12 +57,12 @@
{
"field": "collectedfromid",
"type": "string",
"value": "openaire____::nsf"
"value": "openaire____::corda_h2020"
},
{
"field": "collectedfromname",
"type": "string",
"value": "NSF - National Science Foundation"
"value": "CORDA - COmmon Research DAta Warehouse - Horizon 2020"
},
{
"field": "semantics",