[OpenAireAffiliations] changed the code to handle mixed model in input. To be able to update some links for as many datasources as possible. So far crossref and openapc
This commit is contained in:
parent
0765641979
commit
371154d74f
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@ -10,7 +10,6 @@ import java.util.List;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.BZip2Codec;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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@ -46,6 +45,8 @@ public class PrepareAffiliationRelations implements Serializable {
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public static final String BIP_INFERENCE_PROVENANCE = "openaire:affiliation";
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public static final String OPENAIRE_DATASOURCE_ID = "10|infrastruct_::f66f1bd369679b5b077dcdf006089556";
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public static final String OPENAIRE_DATASOURCE_NAME = "OpenAIRE";
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public static final String DOI_URL_PREFIX = "https://doi.org/";
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public static final int DOI_URL_PREFIX_LENGTH = 16;
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public static <I extends Result> void main(String[] args) throws Exception {
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@ -101,13 +102,13 @@ public class PrepareAffiliationRelations implements Serializable {
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List<KeyValue> collectedfromOpenAIRE = OafMapperUtils
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.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
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JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
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JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelationsNewModel(
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spark, crossrefInputPath, collectedfromOpenAIRE);
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JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
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spark, pubmedInputPath, collectedfromOpenAIRE);
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JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations(
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JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelationsNewModel(
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spark, openapcInputPath, collectedfromOpenAIRE);
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JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
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@ -129,7 +130,7 @@ public class PrepareAffiliationRelations implements Serializable {
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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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private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisherNewModel(SparkSession spark, String inputPath,
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List<KeyValue> collectedfrom) {
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Dataset<Row> df = spark
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@ -143,7 +144,35 @@ public class PrepareAffiliationRelations implements Serializable {
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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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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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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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String inputPath,
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List<KeyValue> collectedfrom) {
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// load and parse affiliation relations from HDFS
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Dataset<Row> df = spark
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.read()
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.schema("`DOI` STRING, `Matchings` 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);
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}
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private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelationsNewModel(SparkSession spark,
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String inputPath,
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List<KeyValue> collectedfrom) {
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// load and parse affiliation relations from HDFS
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@ -154,10 +183,58 @@ public class PrepareAffiliationRelations implements Serializable {
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.json(inputPath)
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.where("DOI is not null");
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return getTextTextJavaPairRDD(collectedfrom, df);
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return getTextTextJavaPairRDDNew(collectedfrom, df);
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}
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private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(List<KeyValue> collectedfrom, Dataset<Row> df) {
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// unroll nested arrays
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df = df
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.withColumn("matching", functions.explode(new Column("Matchings")))
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.select(
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new Column("DOI").as("doi"),
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new Column("matching.RORid").as("rorid"),
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new Column("matching.Confidence").as("confidence"));
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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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// DOI to OpenAIRE id
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final String paperId = ID_PREFIX
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", removePrefix(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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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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// 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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private static JavaPairRDD<Text, Text> getTextTextJavaPairRDDNew(List<KeyValue> collectedfrom, Dataset<Row> df) {
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// unroll nested arrays
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df = df
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.withColumn("matching", functions.explode(new Column("Matchings")))
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@ -176,7 +253,7 @@ public class PrepareAffiliationRelations implements Serializable {
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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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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", removePrefix(row.getAs("doi"))));
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// Organization to OpenAIRE identifier
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String affId = null;
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@ -214,6 +291,12 @@ public class PrepareAffiliationRelations implements Serializable {
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new Text(OBJECT_MAPPER.writeValueAsString(aa))));
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}
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private static String removePrefix(String doi) {
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if(doi.startsWith(DOI_URL_PREFIX))
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return doi.substring(DOI_URL_PREFIX_LENGTH);
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return doi;
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}
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private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,
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DataInfo dataInfo) {
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return Arrays
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@ -74,26 +74,34 @@ public class PrepareAffiliationRelationsTest {
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@Test
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void testMatch() throws Exception {
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String crossrefAffiliationRelationPath = getClass()
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String crossrefAffiliationRelationPathNew = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
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.getPath();
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String crossrefAffiliationRelationPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json")
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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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String publisherAffiliationRelationOldPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old")
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.getPath();
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String outputPath = workingDir.toString() + "/actionSet";
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PrepareAffiliationRelations
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-crossrefInputPath", crossrefAffiliationRelationPath,
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"-crossrefInputPath", crossrefAffiliationRelationPathNew,
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"-pubmedInputPath", crossrefAffiliationRelationPath,
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"-openapcInputPath", crossrefAffiliationRelationPath,
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"-openapcInputPath", crossrefAffiliationRelationPathNew,
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"-dataciteInputPath", crossrefAffiliationRelationPath,
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"-webCrawlInputPath", crossrefAffiliationRelationPath,
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"-publisherInputPath", publisherAffiliationRelationPath,
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"-publisherInputPath", publisherAffiliationRelationOldPath,
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"-outputPath", outputPath
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});
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@ -104,13 +112,9 @@ public class PrepareAffiliationRelationsTest {
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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// for (Relation r : tmp.collect()) {
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// System.out.println(
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// r.getSource() + "\t" + r.getTarget() + "\t" + r.getRelType() + "\t" + r.getRelClass() + "\t" + r.getSubRelType() + "\t" + r.getValidationDate() + "\t" + r.getDataInfo().getTrust() + "\t" + r.getDataInfo().getInferred()
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// );
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// }
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// count the number of relations
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assertEquals(168, tmp.count());// 150 +
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assertEquals(150, tmp.count());// 18 + 24 *3 + 30 * 2 =
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Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
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dataset.createOrReplaceTempView("result");
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@ -121,7 +125,7 @@ public class PrepareAffiliationRelationsTest {
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// verify that we have equal number of bi-directional relations
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Assertions
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.assertEquals(
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84, execVerification
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75, execVerification
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.filter(
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"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
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.collectAsList()
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@ -129,7 +133,7 @@ public class PrepareAffiliationRelationsTest {
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Assertions
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.assertEquals(
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84, execVerification
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75, execVerification
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.filter(
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"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
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.collectAsList()
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@ -156,7 +160,7 @@ public class PrepareAffiliationRelationsTest {
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Assertions
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.assertEquals(
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5, execVerification.filter("source = '" + publisherid + "' and target = '" + rorId + "'").count());
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2, execVerification.filter("source = '" + publisherid + "' and target = '" + rorId + "'").count());
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Assertions
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.assertEquals(
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@ -168,5 +172,19 @@ public class PrepareAffiliationRelationsTest {
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+ "' and target = '" + "20|ror_________::"
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+ IdentifierFactory.md5("https://ror.org/03265fv13") + "'")
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.count());
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Assertions
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.assertEquals(
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3, execVerification
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.filter(
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"source = '" + ID_PREFIX
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+ IdentifierFactory
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.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/3-540-47984-8_14"))
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+ "' and target = '" + "20|ror_________::"
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+ IdentifierFactory.md5("https://ror.org/00a0n9e72") + "'")
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.count());
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}
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}
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@ -0,0 +1,9 @@
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{"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}]}
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{"DOI":"10.1105\/tpc.8.3.343","Matchings":[{"RORid":"https:\/\/ror.org\/02k40bc56","Confidence":0.7071067812}]}
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{"DOI":"10.1161\/01.cir.0000013305.01850.37","Matchings":[{"RORid":"https:\/\/ror.org\/00qjgza05","Confidence":1}]}
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{"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":"https:\/\/ror.org\/035xkbk20","Confidence":1},{"RORid":"https:\/\/ror.org\/05apxxy63","Confidence":1}]}
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{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":"https:\/\/ror.org\/04j198w64","Confidence":0.82}]}
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{"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}]}
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{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":"https:\/\/ror.org\/057xtrt18","Confidence":0.7071067812}]}
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{"DOI": "10.1080/13669877.2015.1042504", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/03265fv13"}]}
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{"DOI": "https://doi.org/10.1007/3-540-47984-8_14", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/00a0n9e72"}]}
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@ -0,0 +1,6 @@
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{"DOI": "10.1007/s00217-010-1268-9", "Authors": [{"Name": {"Full": "Martin Zarnkow", "First": null, "Last": null}, "Raw_affiliations": ["TU M\u00fcnchen, Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Andrea Faltermaier", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Werner Back", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Technologie der Brauerei I"], "Organization_PIDs": []}, {"Name": {"Full": "Martina Gastl", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Elkek K. Arendt", "First": null, "Last": null}, "Raw_affiliations": ["University College Cork"], "Organization_PIDs": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}
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{"DOI": "10.1007/BF01154707", "Authors": [{"Name": {"Full": "Buggy, M.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Materials Science and Technology, University of Limerick, Limerick, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/00a0n9e72", "Confidence": 1}]}, {"Name": {"Full": "Carew, A.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Materials Science and Technology, University of Limerick, Limerick, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/00a0n9e72", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/00a0n9e72", "Confidence": 1}]}
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{"DOI": "10.1007/s10237-017-0974-7", "Authors": [{"Name": {"Full": "Donnacha J. McGrath", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}]}, {"Name": {"Full": "Anja Lena Thiebes", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Christian G. Cornelissen", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Barry O\u2019Brien", "First": null, "Last": null}, "Raw_affiliations": ["Department for Internal Medicine \u2013 Section for Pneumology, Medical Faculty, RWTH Aachen University, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/04xfq0f34", "Confidence": 1}]}, {"Name": {"Full": "Stefan Jockenhoevel", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}]}, {"Name": {"Full": "Mark Bruzzi", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Peter E. McHugh", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}, {"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 1}]}
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{"DOI": "10.1007/BF03168973", "Authors": [{"Name": {"Full": "Sheehan, G.", "First": null, "Last": null}, "Raw_affiliations": ["Dept of Infectious Diseases, Mater Misercordiae Hospital, Dublin 7"], "Organization_PIDs": []}, {"Name": {"Full": "Chew, N.", "First": null, "Last": null}, "Raw_affiliations": ["Dept of Infectious Diseases, Mater Misercordiae Hospital, Dublin 7"], "Organization_PIDs": []}], "Organizations": []}
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{"DOI": "10.1007/s00338-009-0480-1", "Authors": [{"Name": {"Full": "Gleason, D. F.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biology, Georgia Southern University, Statesboro, USA"], "Organization_PIDs": [{"RORid": "https://ror.org/04agmb972", "Confidence": 1}]}, {"Name": {"Full": "Danilowicz, B. S.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biology, Georgia Southern University, Statesboro, USA"], "Organization_PIDs": [{"RORid": "https://ror.org/04agmb972", "Confidence": 1}]}, {"Name": {"Full": "Nolan, C. J.", "First": null, "Last": null}, "Raw_affiliations": ["School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/05m7pjf47", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/04agmb972", "Confidence": 1}, {"RORid": "https://ror.org/05m7pjf47", "Confidence": 1}]}
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{"DOI": "10.1007/s10993-010-9187-y", "Authors": [{"Name": {"Full": "Martin Howard", "First": null, "Last": null}, "Raw_affiliations": ["University College Cork"], "Organization_PIDs": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}
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