graph cleaning, suggestions from ticket 8898 - round 2 #356
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@ -12,6 +12,7 @@ import org.apache.hadoop.io.Text;
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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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import org.apache.spark.api.java.function.FlatMapFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.Dataset;
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@ -57,11 +58,14 @@ public class PrepareAffiliationRelations implements Serializable {
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Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("inputPath");
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log.info("inputPath {}: ", inputPath);
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final String crossrefInputPath = parser.get("crossrefInputPath");
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log.info("crossrefInputPath: {}", crossrefInputPath);
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final String pubmedInputPath = parser.get("pubmedInputPath");
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log.info("pubmedInputPath: {}", pubmedInputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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log.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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@ -70,12 +74,28 @@ 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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prepareAffiliationRelations(spark, inputPath, 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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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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crossrefRelations
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.union(pubmedRelations)
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.saveAsHadoopFile(
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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});
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}
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private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath,
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String outputPath) {
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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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@ -92,7 +112,7 @@ public class PrepareAffiliationRelations implements Serializable {
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new Column("matching.Confidence").as("confidence"));
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// prepare action sets for affiliation relations
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df
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return df
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.toJavaRDD()
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.flatMap((FlatMapFunction<Row, Relation>) row -> {
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@ -120,8 +140,6 @@ public class PrepareAffiliationRelations implements Serializable {
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qualifier,
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Double.toString(row.getAs("confidence")));
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List<KeyValue> collectedfrom = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
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// return bi-directional relations
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return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
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@ -129,9 +147,7 @@ public class PrepareAffiliationRelations implements Serializable {
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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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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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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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@ -6,9 +6,15 @@
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"paramRequired": false
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},
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{
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"paramName": "ip",
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"paramLongName": "inputPath",
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"paramDescription": "the URL from where to get the programme file",
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"paramName": "cip",
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"paramLongName": "crossrefInputPath",
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"paramDescription": "the path to get the input data from Crossref",
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"paramRequired": true
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},
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{
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"paramName": "pip",
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"paramLongName": "pubmedInputPath",
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"paramDescription": "the path to get the input data from Pubmed",
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"paramRequired": true
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},
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{
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|
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@ -31,5 +31,6 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
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# The following is needed as a property of a workflow
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oozie.wf.application.path=${oozieTopWfApplicationPath}
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inputPath=/data/bip-affiliations/data.json
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crossrefInputPath=/data/bip-affiliations/data.json
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pubmedInputPath=/data/bip-affiliations/pubmed-data.json
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outputPath=/tmp/crossref-affiliations-output-v5
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@ -2,8 +2,12 @@
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<parameters>
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<property>
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<name>inputPath</name>
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<description>the path where to find the inferred affiliation relations</description>
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<name>crossrefInputPath</name>
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<description>the path where to find the inferred affiliation relations from Crossref</description>
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</property>
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<property>
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<name>pubmedInputPath</name>
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<description>the path where to find the inferred affiliation relations from Pubmed</description>
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</property>
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<property>
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<name>outputPath</name>
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@ -83,7 +87,7 @@
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Produces the atomic action with the inferred by BIP! affiliation relations from Crossref</name>
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<name>Produces the atomic action with the inferred by BIP! affiliation relations (from Crossref and Pubmed)</name>
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<class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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@ -96,7 +100,8 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--inputPath</arg><arg>${inputPath}</arg>
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<arg>--crossrefInputPath</arg><arg>${crossrefInputPath}</arg>
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<arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
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<arg>--outputPath</arg><arg>${outputPath}</arg>
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</spark>
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<ok to="End"/>
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@ -74,17 +74,22 @@ public class PrepareAffiliationRelationsTest {
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@Test
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void testMatch() throws Exception {
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String affiliationRelationsPath = getClass()
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String crossrefAffiliationRelationPath = 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 pubmedAffiliationRelationsPath = 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 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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"-inputPath", affiliationRelationsPath,
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"-crossrefInputPath", crossrefAffiliationRelationPath,
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"-pubmedInputPath", pubmedAffiliationRelationsPath,
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"-outputPath", outputPath
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});
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@ -101,7 +106,7 @@ public class PrepareAffiliationRelationsTest {
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// );
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// }
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// count the number of relations
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assertEquals(20, tmp.count());
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assertEquals(40, tmp.count());
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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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@ -112,7 +117,7 @@ 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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10, execVerification
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20, execVerification
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.filter(
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"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
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.collectAsList()
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@ -120,7 +125,7 @@ public class PrepareAffiliationRelationsTest {
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Assertions
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.assertEquals(
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10, execVerification
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20, 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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|
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@ -29,7 +29,7 @@ public abstract class AbstractMdRecordToOafMapper {
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protected final VocabularyGroup vocs;
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protected static final UrlValidator URL_VALIDATOR = UrlValidator.getInstance();
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protected static final UrlValidator URL_VALIDATOR = new UrlValidator(UrlValidator.ALLOW_2_SLASHES);
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private final boolean invisible;
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|
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@ -797,6 +797,20 @@ class MappersTest {
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assertFalse(p_cleaned.getTitle().isEmpty());
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}
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@Test
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void test_instance_url_validation() throws IOException {
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final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("idus_sevilla.xml")));
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final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
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final Publication p = (Publication) list.get(0);
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assertNotNull(p.getInstance());
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assertFalse(p.getInstance().isEmpty());
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assertNotNull(p.getInstance().get(0).getUrl());
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assertFalse(p.getInstance().get(0).getUrl().isEmpty());
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assertEquals("https://idus.us.es/handle//11441/118940", p.getInstance().get(0).getUrl().get(0));
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}
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@Test
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void testZenodo() throws IOException, DocumentException {
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final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo.xml")));
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@ -0,0 +1,65 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<record xmlns:dc="http://purl.org/dc/elements/1.1/"
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xmlns:dr="http://www.driver-repository.eu/namespace/dr"
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xmlns:dri="http://www.driver-repository.eu/namespace/dri"
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xmlns:oaf="http://namespace.openaire.eu/oaf"
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xmlns:oai="http://www.openarchives.org/OAI/2.0/"
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xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance"
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xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<header xmlns="http://namespace.openaire.eu/">
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<dri:objIdentifier>od______3272::6a4d00217a024a46ce9697ce98b13c2a</dri:objIdentifier>
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<dri:recordIdentifier>oai:idus.us.es:11441/118940</dri:recordIdentifier>
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||||
<dri:dateOfCollection/>
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||||
<dri:mdFormat/>
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||||
<dri:mdFormatInterpretation/>
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||||
<dri:repositoryId/>
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||||
<dr:objectIdentifier/>
|
||||
<dr:dateOfCollection>2021-08-20T12:32:32.826Z</dr:dateOfCollection>
|
||||
<dr:dateOfTransformation>2023-07-04T15:47:55.397Z</dr:dateOfTransformation>
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||||
<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>
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<dc:creator>Palomino de Castro y Velasco, Antonio, 1653-1726</dc:creator>
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||||
<dc:contributor>Rovira y Brocandel, Hipólito, 1693-1765</dc:contributor>
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||||
<dc:contributor>Palomino de Castro y Velasco, Antonio, 1653-1726</dc:contributor>
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||||
<dc:date>2021-08-12T08:59:53Z</dc:date>
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||||
<dc:date>1715</dc:date>
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||||
<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>
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||||
<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>
|
||||
Loading…
Reference in New Issue