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Merge branch 'beta' into invisible_relations

This commit is contained in:
Claudio Atzori 2023-09-04 16:13:06 +02:00
parent 5b06c9d06f 15666e86a8
commit adec6692ca
4 changed files with 22 additions and 19 deletions
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16
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
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@ -80,16 +80,15 @@ public class PrepareAffiliationRelations implements Serializable {
// load and parse affiliation relations from HDFS // load and parse affiliation relations from HDFS
Dataset<Row> df = spark Dataset<Row> df = spark
.read() .read()
.schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:ARRAY<STRING>,`Confidence`:DOUBLE>>") .schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
.json(inputPath); .json(inputPath);
// unroll nested arrays // unroll nested arrays
df = df df = df
.withColumn("matching", functions.explode(new Column("Matchings"))) .withColumn("matching", functions.explode(new Column("Matchings")))
.withColumn("rorid", functions.explode(new Column("matching.RORid")))
.select( .select(
new Column("DOI").as("doi"), new Column("DOI").as("doi"),
new Column("rorid"), new Column("matching.RORid").as("rorid"),
new Column("matching.Confidence").as("confidence")); new Column("matching.Confidence").as("confidence"));
// prepare action sets for affiliation relations // prepare action sets for affiliation relations
@ -121,8 +120,10 @@ public class PrepareAffiliationRelations implements Serializable {
qualifier, qualifier,
Double.toString(row.getAs("confidence"))); Double.toString(row.getAs("confidence")));
List<KeyValue> collectedfrom = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
// return bi-directional relations // return bi-directional relations
return getAffiliationRelationPair(paperId, affId, dataInfo).iterator(); return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
}) })
.map(p -> new AtomicAction(Relation.class, p)) .map(p -> new AtomicAction(Relation.class, p))
@ -133,7 +134,8 @@ public class PrepareAffiliationRelations implements Serializable {
} }
private static List<Relation> getAffiliationRelationPair(String paperId, String affId, DataInfo dataInfo) { private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,
DataInfo dataInfo) {
return Arrays return Arrays
.asList( .asList(
OafMapperUtils OafMapperUtils
@ -143,7 +145,7 @@ public class PrepareAffiliationRelations implements Serializable {
ModelConstants.RESULT_ORGANIZATION, ModelConstants.RESULT_ORGANIZATION,
ModelConstants.AFFILIATION, ModelConstants.AFFILIATION,
ModelConstants.HAS_AUTHOR_INSTITUTION, ModelConstants.HAS_AUTHOR_INSTITUTION,
null, collectedfrom,
dataInfo, dataInfo,
null), null),
OafMapperUtils OafMapperUtils
@ -153,7 +155,7 @@ public class PrepareAffiliationRelations implements Serializable {
ModelConstants.RESULT_ORGANIZATION, ModelConstants.RESULT_ORGANIZATION,
ModelConstants.AFFILIATION, ModelConstants.AFFILIATION,
ModelConstants.IS_AUTHOR_INSTITUTION_OF, ModelConstants.IS_AUTHOR_INSTITUTION_OF,
null, collectedfrom,
dataInfo, dataInfo,
null)); null));
} }

4
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties
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@ -31,5 +31,5 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
# The following is needed as a property of a workflow # The following is needed as a property of a workflow
oozie.wf.application.path=${oozieTopWfApplicationPath} oozie.wf.application.path=${oozieTopWfApplicationPath}
inputPath=/user/schatz/affiliations/data-v3.1.json inputPath=/data/bip-affiliations/data.json
outputPath=/tmp/crossref-affiliations-output-v3.1 outputPath=/tmp/crossref-affiliations-output-v5

8
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
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@ -101,7 +101,7 @@ public class PrepareAffiliationRelationsTest {
// ); // );
// } // }
// count the number of relations // count the number of relations
assertEquals(16, tmp.count()); assertEquals(20, tmp.count());
Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class)); Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
dataset.createOrReplaceTempView("result"); dataset.createOrReplaceTempView("result");
@ -112,7 +112,7 @@ public class PrepareAffiliationRelationsTest {
// verify that we have equal number of bi-directional relations // verify that we have equal number of bi-directional relations
Assertions Assertions
.assertEquals( .assertEquals(
8, execVerification 10, execVerification
.filter( .filter(
"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'") "relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
.collectAsList() .collectAsList()
@ -120,14 +120,14 @@ public class PrepareAffiliationRelationsTest {
Assertions Assertions
.assertEquals( .assertEquals(
8, execVerification 10, execVerification
.filter( .filter(
"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'") "relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
.collectAsList() .collectAsList()
.size()); .size());
// check confidence value of a specific relation // check confidence value of a specific relation
String sourceDOI = "10.1105/tpc.8.3.343"; String sourceDOI = "10.1061/(asce)0733-9399(2002)128:7(759)";
final String sourceOpenaireId = ID_PREFIX final String sourceOpenaireId = ID_PREFIX
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", sourceDOI)); + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", sourceDOI));

13
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json
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@ -1,6 +1,7 @@
{"DOI":"10.1061\/(asce)0733-9399(2002)128:7(759)","Matchings":[{"RORid":["https:\/\/ror.org\/01teme464"],"Confidence":0.73},{"RORid":["https:\/\/ror.org\/03yxnpp24"],"Confidence":0.7071067812}]} {"DOI":"10.1061\/(asce)0733-9399(2002)128:7(759)","Matchings":[{"RORid":"https:\/\/ror.org\/03yxnpp24","Confidence":0.7071067812},{"RORid":"https:\/\/ror.org\/01teme464","Confidence":0.89}]}
{"DOI":"10.1105\/tpc.8.3.343","Matchings":[{"RORid":["https:\/\/ror.org\/02k40bc56"],"Confidence":0.7071067812}]} {"DOI":"10.1105\/tpc.8.3.343","Matchings":[{"RORid":"https:\/\/ror.org\/02k40bc56","Confidence":0.7071067812}]}
{"DOI":"10.1161\/01.cir.0000013305.01850.37","Matchings":[{"RORid":["https:\/\/ror.org\/00qjgza05"],"Confidence":1}]} {"DOI":"10.1161\/01.cir.0000013305.01850.37","Matchings":[{"RORid":"https:\/\/ror.org\/00qjgza05","Confidence":1}]}
{"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":["https:\/\/ror.org\/05apxxy63"],"Confidence":1},{"RORid":["https:\/\/ror.org\/035xkbk20"],"Confidence":1}]} {"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":"https:\/\/ror.org\/035xkbk20","Confidence":1},{"RORid":"https:\/\/ror.org\/05apxxy63","Confidence":1}]}
{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":["https:\/\/ror.org\/04j198w64"],"Confidence":0.58}]} {"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":"https:\/\/ror.org\/04j198w64","Confidence":0.82}]}
{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":["https:\/\/ror.org\/057xtrt18"],"Confidence":0.7071067812}]} {"DOI":"10.1061\/(asce)0733-9372(2002)128:7(588)","Matchings":[{"RORid":"https:\/\/ror.org\/03m8km719","Confidence":0.8660254038},{"RORid":"https:\/\/ror.org\/02aze4h65","Confidence":0.87}]}
{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":"https:\/\/ror.org\/057xtrt18","Confidence":0.7071067812}]}