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graph cleaning, suggestions from ticket 8898 - round 2 #356

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claudio.atzori merged 3 commits from cleaning_8898 into beta 2023-11-22 14:00:38 +01:00
Conversation 1 Commits 3 Files Changed 3 +138 -26
8 changed files with 138 additions and 26 deletions
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40
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
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@ -12,6 +12,7 @@ import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec; import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.sql.*; import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
@ -57,11 +58,14 @@ public class PrepareAffiliationRelations implements Serializable {
Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser); Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath"); final String crossrefInputPath = parser.get("crossrefInputPath");
log.info("inputPath {}: ", inputPath); log.info("crossrefInputPath: {}", crossrefInputPath);
final String pubmedInputPath = parser.get("pubmedInputPath");
log.info("pubmedInputPath: {}", pubmedInputPath);
final String outputPath = parser.get("outputPath"); final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath); log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
@ -70,12 +74,28 @@ public class PrepareAffiliationRelations implements Serializable {
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
Constants.removeOutputDir(spark, outputPath); Constants.removeOutputDir(spark, outputPath);
prepareAffiliationRelations(spark, inputPath, outputPath);
List<KeyValue> collectedFromCrossref = OafMapperUtils
.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
spark, crossrefInputPath, collectedFromCrossref);
List<KeyValue> collectedFromPubmed = OafMapperUtils
.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
spark, pubmedInputPath, collectedFromPubmed);
crossrefRelations
.union(pubmedRelations)
.saveAsHadoopFile(
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
}); });
} }
private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath, private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
String outputPath) { String inputPath,
List<KeyValue> collectedfrom) {
// load and parse affiliation relations from HDFS // load and parse affiliation relations from HDFS
Dataset<Row> df = spark Dataset<Row> df = spark
@ -92,7 +112,7 @@ public class PrepareAffiliationRelations implements Serializable {
new Column("matching.Confidence").as("confidence")); new Column("matching.Confidence").as("confidence"));
// prepare action sets for affiliation relations // prepare action sets for affiliation relations
df return df
.toJavaRDD() .toJavaRDD()
.flatMap((FlatMapFunction<Row, Relation>) row -> { .flatMap((FlatMapFunction<Row, Relation>) row -> {
@ -120,8 +140,6 @@ 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, collectedfrom, dataInfo).iterator(); return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
@ -129,9 +147,7 @@ public class PrepareAffiliationRelations implements Serializable {
.map(p -> new AtomicAction(Relation.class, p)) .map(p -> new AtomicAction(Relation.class, p))
.mapToPair( .mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa)))) new Text(OBJECT_MAPPER.writeValueAsString(aa))));
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
} }
private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom, private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,

12
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json
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@ -6,9 +6,15 @@
"paramRequired": false "paramRequired": false
}, },
{ {
"paramName": "ip", "paramName": "cip",
"paramLongName": "inputPath", "paramLongName": "crossrefInputPath",
"paramDescription": "the URL from where to get the programme file", "paramDescription": "the path to get the input data from Crossref",
"paramRequired": true
},
{
"paramName": "pip",
"paramLongName": "pubmedInputPath",
"paramDescription": "the path to get the input data from Pubmed",
"paramRequired": true "paramRequired": true
}, },
{ {

3
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties
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@ -31,5 +31,6 @@ 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=/data/bip-affiliations/data.json crossrefInputPath=/data/bip-affiliations/data.json
pubmedInputPath=/data/bip-affiliations/pubmed-data.json
outputPath=/tmp/crossref-affiliations-output-v5 outputPath=/tmp/crossref-affiliations-output-v5

13
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml
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@ -2,8 +2,12 @@
<parameters> <parameters>
<property> <property>
<name>inputPath</name> <name>crossrefInputPath</name>
<description>the path where to find the inferred affiliation relations</description> <description>the path where to find the inferred affiliation relations from Crossref</description>
</property>
<property>
<name>pubmedInputPath</name>
<description>the path where to find the inferred affiliation relations from Pubmed</description>
</property> </property>
<property> <property>
<name>outputPath</name> <name>outputPath</name>
@ -83,7 +87,7 @@
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Produces the atomic action with the inferred by BIP! affiliation relations from Crossref</name> <name>Produces the atomic action with the inferred by BIP! affiliation relations (from Crossref and Pubmed)</name>
<class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations</class> <class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar> <jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
@ -96,7 +100,8 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts> </spark-opts>
<arg>--inputPath</arg><arg>${inputPath}</arg> <arg>--crossrefInputPath</arg><arg>${crossrefInputPath}</arg>
<arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg> <arg>--outputPath</arg><arg>${outputPath}</arg>
</spark> </spark>
<ok to="End"/> <ok to="End"/>

15
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
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@ -74,7 +74,11 @@ public class PrepareAffiliationRelationsTest {
@Test @Test
void testMatch() throws Exception { void testMatch() throws Exception {
String affiliationRelationsPath = getClass() String crossrefAffiliationRelationPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
.getPath();
String pubmedAffiliationRelationsPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json") .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
.getPath(); .getPath();
@ -84,7 +88,8 @@ public class PrepareAffiliationRelationsTest {
.main( .main(
new String[] { new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-inputPath", affiliationRelationsPath, "-crossrefInputPath", crossrefAffiliationRelationPath,
"-pubmedInputPath", pubmedAffiliationRelationsPath,
"-outputPath", outputPath "-outputPath", outputPath
}); });
@ -101,7 +106,7 @@ public class PrepareAffiliationRelationsTest {
// ); // );
// } // }
// count the number of relations // count the number of relations
assertEquals(20, tmp.count()); assertEquals(40, 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 +117,7 @@ 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(
10, execVerification 20, execVerification
.filter( .filter(
"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'") "relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
.collectAsList() .collectAsList()
@ -120,7 +125,7 @@ public class PrepareAffiliationRelationsTest {
Assertions Assertions
.assertEquals( .assertEquals(
10, execVerification 20, execVerification
.filter( .filter(
"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'") "relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
.collectAsList() .collectAsList()

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
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@ -29,7 +29,7 @@ public abstract class AbstractMdRecordToOafMapper {
protected final VocabularyGroup vocs; protected final VocabularyGroup vocs;
protected static final UrlValidator URL_VALIDATOR = UrlValidator.getInstance(); protected static final UrlValidator URL_VALIDATOR = new UrlValidator(UrlValidator.ALLOW_2_SLASHES);
private final boolean invisible; private final boolean invisible;

14
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
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@ -797,6 +797,20 @@ class MappersTest {
assertFalse(p_cleaned.getTitle().isEmpty()); assertFalse(p_cleaned.getTitle().isEmpty());
} }
@Test
void test_instance_url_validation() throws IOException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("idus_sevilla.xml")));
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
final Publication p = (Publication) list.get(0);
assertNotNull(p.getInstance());
assertFalse(p.getInstance().isEmpty());
assertNotNull(p.getInstance().get(0).getUrl());
assertFalse(p.getInstance().get(0).getUrl().isEmpty());
assertEquals("https://idus.us.es/handle//11441/118940", p.getInstance().get(0).getUrl().get(0));
}
@Test @Test
void testZenodo() throws IOException, DocumentException { void testZenodo() throws IOException, DocumentException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo.xml"))); final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo.xml")));

65
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/idus_sevilla.xml Normal file
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@ -0,0 +1,65 @@
<?xml version="1.0" encoding="UTF-8"?>
<record xmlns:dc="http://purl.org/dc/elements/1.1/"
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/"
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance"
xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<header xmlns="http://namespace.openaire.eu/">
<dri:objIdentifier>od______3272::6a4d00217a024a46ce9697ce98b13c2a</dri:objIdentifier>
<dri:recordIdentifier>oai:idus.us.es:11441/118940</dri:recordIdentifier>
<dri:dateOfCollection/>
<dri:mdFormat/>
<dri:mdFormatInterpretation/>
<dri:repositoryId/>
<dr:objectIdentifier/>
<dr:dateOfCollection>2021-08-20T12:32:32.826Z</dr:dateOfCollection>
<dr:dateOfTransformation>2023-07-04T15:47:55.397Z</dr:dateOfTransformation>
<oaf:datasourceprefix>od______3272</oaf:datasourceprefix>
</header>
<metadata xmlns="http://namespace.openaire.eu/">
<dc:title>El museo pictorico y escala optica : tomo I : theorica de la pintura en que se describe su origen ... y se aprueban con demonstraciomes mathematicas y filosoficas, sus mas radicales fundamentos</dc:title>
<dc:creator>Palomino de Castro y Velasco, Antonio, 1653-1726</dc:creator>
<dc:contributor>Rovira y Brocandel, Hipólito, 1693-1765</dc:contributor>
<dc:contributor>Palomino de Castro y Velasco, Antonio, 1653-1726</dc:contributor>
<dc:date>2021-08-12T08:59:53Z</dc:date>
<dc:date>1715</dc:date>
<dc:description>A 042(a)/063</dc:description>
<dc:format>application/pdf</dc:format>
<dc:identifier>https://idus.us.es/handle//11441/118940</dc:identifier>
<dc:language>spa</dc:language>
<dc:publisher>En Madrid : por Lucas Antonio de Bedmar ... : vendese en casa de Don Joseph de Villar y Villanueva, 1715</dc:publisher>
<dc:type>info:eu-repo/semantics/book</dc:type>
<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
<dr:CobjCategory type="publication">0002</dr:CobjCategory>
<oaf:dateAccepted>1715-01-01</oaf:dateAccepted>
<oaf:embargoenddate/>
<oaf:collectedDatasourceid>opendoar____::3272</oaf:collectedDatasourceid>
<oaf:accessrights>OPEN</oaf:accessrights>
<oaf:hostedBy id="opendoar____::3272" name="idUS. Depósito de Investigación de la Universidad de Sevilla."/>
<oaf:collectedFrom id="opendoar____::3272" name="idUS. Depósito de Investigación de la Universidad de Sevilla."/>
<oaf:identifier identifierType="landingPage">https://idus.us.es/handle//11441/118940</oaf:identifier>
<oaf:journal eissn="" ep="" iss="" issn="" sp="" vol=""/>
<oaf:license>http://creativecommons.org/licenses/by-nc-nd/4.0/</oaf:license>
</metadata>
<about>
<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="2021-08-20T12:32:32.826Z">
<baseURL>http%3A%2F%2Fidus.us.es%2Foai%2Fdriver</baseURL>
<identifier>oai:idus.us.es:11441/118940</identifier>
<datestamp>2021-08-12T08:59:54Z</datestamp>
<metadataNamespace>http://www.openarchives.org/OAI/2.0/oai_dc/</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:repository"
classname="sysimport:crosswalk:repository"
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
</oaf:datainfo>
</about>
</record>