[AffiliationFromPublisher]refactoring after compilation
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@ -89,64 +89,66 @@ public class PrepareAffiliationRelations implements Serializable {
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isSparkSessionManaged,
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spark -> {
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Constants.removeOutputDir(spark, outputPath);
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createActionSet(spark, crossrefInputPath, pubmedInputPath, openapcInputPath, dataciteInputPath, webcrawlInputPath, publisherInputPath, outputPath);
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createActionSet(
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spark, crossrefInputPath, pubmedInputPath, openapcInputPath, dataciteInputPath, webcrawlInputPath,
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publisherInputPath, outputPath);
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});
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}
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private static void createActionSet(SparkSession spark, String crossrefInputPath, String pubmedInputPath, String openapcInputPath, String dataciteInputPath, String webcrawlInputPath, String publisherlInputPath, String outputPath) {
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private static void createActionSet(SparkSession spark, String crossrefInputPath, String pubmedInputPath,
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String openapcInputPath, String dataciteInputPath, String webcrawlInputPath, String publisherlInputPath,
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String outputPath) {
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List<KeyValue> collectedFromCrossref = OafMapperUtils
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.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
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JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
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spark, crossrefInputPath, collectedFromCrossref);
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spark, crossrefInputPath, collectedFromCrossref);
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List<KeyValue> collectedFromPubmed = OafMapperUtils
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.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
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JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
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spark, pubmedInputPath, collectedFromPubmed);
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spark, pubmedInputPath, collectedFromPubmed);
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List<KeyValue> collectedFromOpenAPC = OafMapperUtils
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.listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC");
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JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations(
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spark, openapcInputPath, collectedFromOpenAPC);
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spark, openapcInputPath, collectedFromOpenAPC);
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List<KeyValue> collectedFromDatacite = OafMapperUtils
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.listKeyValues(ModelConstants.DATACITE_ID, "Datacite");
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JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
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spark, dataciteInputPath, collectedFromDatacite);
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spark, dataciteInputPath, collectedFromDatacite);
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List<KeyValue> collectedFromWebCrawl = OafMapperUtils
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.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
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JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
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spark, webcrawlInputPath, collectedFromWebCrawl);
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spark, webcrawlInputPath, collectedFromWebCrawl);
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List<KeyValue> collectedfromPublisher = OafMapperUtils
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.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
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.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
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JavaPairRDD<Text, Text> publisherRelations = prepareAffiliationRelationFromPublisher(
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spark, publisherlInputPath, collectedfromPublisher);
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spark, publisherlInputPath, collectedfromPublisher);
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crossrefRelations
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.union(pubmedRelations)
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.union(openAPCRelations)
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.union(dataciteRelations)
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.union(webCrawlRelations)
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.union(publisherRelations)
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.union(publisherRelations)
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.saveAsHadoopFile(
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
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}
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private static JavaPairRDD<Text,Text> prepareAffiliationRelationFromPublisher(SparkSession spark, String inputPath,
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List<KeyValue> collectedfrom){
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private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisher(SparkSession spark, String inputPath,
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List<KeyValue> collectedfrom) {
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Dataset<Row> df = spark
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.read()
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.schema("`DOI` STRING, `Organizations` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
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.json(inputPath)
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.where("DOI is not null");
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.read()
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.schema("`DOI` STRING, `Organizations` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
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.json(inputPath)
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.where("DOI is not null");
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return getTextTextJavaPairRDD(collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"));
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}
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private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
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@ -174,41 +176,41 @@ public class PrepareAffiliationRelations implements Serializable {
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// prepare action sets for affiliation relations
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return df
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.toJavaRDD()
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.flatMap((FlatMapFunction<Row, Relation>) row -> {
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.toJavaRDD()
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.flatMap((FlatMapFunction<Row, Relation>) row -> {
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// DOI to OpenAIRE id
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final String paperId = ID_PREFIX
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", row.getAs("doi")));
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// DOI to OpenAIRE id
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final String paperId = ID_PREFIX
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", row.getAs("doi")));
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// ROR id to OpenAIRE id
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final String affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("rorid"));
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// ROR id to OpenAIRE id
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final String affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("rorid"));
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Qualifier qualifier = OafMapperUtils
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.qualifier(
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BIP_AFFILIATIONS_CLASSID,
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BIP_AFFILIATIONS_CLASSNAME,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS);
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Qualifier qualifier = OafMapperUtils
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.qualifier(
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BIP_AFFILIATIONS_CLASSID,
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BIP_AFFILIATIONS_CLASSNAME,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS);
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// format data info; setting `confidence` into relation's `trust`
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DataInfo dataInfo = OafMapperUtils
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.dataInfo(
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false,
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BIP_INFERENCE_PROVENANCE,
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true,
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false,
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qualifier,
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Double.toString(row.getAs("confidence")));
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// format data info; setting `confidence` into relation's `trust`
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DataInfo dataInfo = OafMapperUtils
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.dataInfo(
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false,
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BIP_INFERENCE_PROVENANCE,
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true,
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false,
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qualifier,
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Double.toString(row.getAs("confidence")));
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// return bi-directional relations
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return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
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// return bi-directional relations
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return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
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})
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.map(p -> new AtomicAction(Relation.class, p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))));
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})
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.map(p -> new AtomicAction(Relation.class, p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))));
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}
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private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,
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@ -79,8 +79,8 @@ public class PrepareAffiliationRelationsTest {
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.getPath();
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String publisherAffiliationRelationPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers")
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.getPath();
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers")
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.getPath();
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String outputPath = workingDir.toString() + "/actionSet";
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@ -93,7 +93,7 @@ public class PrepareAffiliationRelationsTest {
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"-openapcInputPath", crossrefAffiliationRelationPath,
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"-dataciteInputPath", crossrefAffiliationRelationPath,
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"-webCrawlInputPath", crossrefAffiliationRelationPath,
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"-publisherInputPath", publisherAffiliationRelationPath,
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"-publisherInputPath", publisherAffiliationRelationPath,
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"-outputPath", outputPath
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});
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@ -1,3 +1,4 @@
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package eu.dnetlib.dhp.broker.oa.matchers.simple;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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@ -16,7 +17,8 @@ class EnrichMissingAuthorOrcidTest {
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final EnrichMissingAuthorOrcid matcher = new EnrichMissingAuthorOrcid();
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@BeforeEach
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void setUp() throws Exception {}
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void setUp() throws Exception {
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}
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@Test
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void testFindDifferences_1() {
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@ -23,7 +23,8 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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public class ConversionUtilsTest {
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@BeforeEach
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public void setUp() throws Exception {}
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public void setUp() throws Exception {
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}
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@Test
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public void testAllResultPids() {
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@ -20,7 +20,6 @@ import javax.xml.transform.*;
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import javax.xml.transform.dom.DOMSource;
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import javax.xml.transform.stream.StreamResult;
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import eu.dnetlib.dhp.oa.provision.model.*;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.tuple.ImmutablePair;
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import org.apache.commons.lang3.tuple.Pair;
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@ -42,6 +41,7 @@ import com.google.common.collect.Sets;
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import com.mycila.xmltool.XMLDoc;
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import com.mycila.xmltool.XMLTag;
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import eu.dnetlib.dhp.oa.provision.model.*;
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import eu.dnetlib.dhp.schema.common.*;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.Result;
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