forked from D-Net/dnet-hadoop
improved parallelization on transformation job
This commit is contained in:
parent
3ae67b7a1d
commit
cdfe01bbae
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@ -11,6 +11,9 @@ import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.function.Function;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoder;
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import org.apache.spark.sql.Encoders;
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@ -26,6 +29,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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import eu.dnetlib.dhp.message.MessageSender;
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import eu.dnetlib.dhp.schema.mdstore.MetadataRecord;
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import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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@ -33,6 +37,8 @@ public class TransformSparkJobNode {
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private static final Logger log = LoggerFactory.getLogger(TransformSparkJobNode.class);
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private static int RECORDS_PER_TASK = 200;
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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@ -67,6 +73,11 @@ public class TransformSparkJobNode {
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final String dateOfTransformation = parser.get("dateOfTransformation");
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log.info(String.format("dateOfTransformation: %s", dateOfTransformation));
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final Integer rpt = Optional
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.ofNullable(parser.get("recordsPerTask"))
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.map(Integer::valueOf)
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.orElse(RECORDS_PER_TASK);
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final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
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final VocabularyGroup vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService);
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@ -79,12 +90,12 @@ public class TransformSparkJobNode {
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isSparkSessionManaged,
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spark -> {
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transformRecords(
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parser.getObjectMap(), isLookupService, spark, inputPath, outputBasePath);
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parser.getObjectMap(), isLookupService, spark, inputPath, outputBasePath, rpt);
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});
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}
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public static void transformRecords(final Map<String, String> args, final ISLookUpService isLookUpService,
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final SparkSession spark, final String inputPath, final String outputBasePath)
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final SparkSession spark, final String inputPath, final String outputBasePath, final Integer rpt)
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throws DnetTransformationException, IOException {
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final LongAccumulator totalItems = spark.sparkContext().longAccumulator(CONTENT_TOTALITEMS);
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@ -99,18 +110,25 @@ public class TransformSparkJobNode {
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final String workflowId = args.get("workflowId");
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log.info("workflowId is {}", workflowId);
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MapFunction<MetadataRecord, MetadataRecord> x = TransformationFactory
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.getTransformationPlugin(args, ct, isLookUpService);
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final Dataset<MetadataRecord> inputMDStore = spark
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.read()
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.format("parquet")
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.load(inputPath)
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.as(encoder);
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final long totalInput = inputMDStore.count();
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final MessageSender messageSender = new MessageSender(dnetMessageManagerURL, workflowId);
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try (AggregatorReport report = new AggregatorReport(messageSender)) {
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try {
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final Dataset<MetadataRecord> mdstore = spark
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.read()
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.format("parquet")
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.load(inputPath)
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.as(encoder)
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.map(
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TransformationFactory.getTransformationPlugin(args, ct, isLookUpService),
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encoder);
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saveDataset(mdstore, outputBasePath + MDSTORE_DATA_PATH);
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JavaRDD<MetadataRecord> mdstore = inputMDStore
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.javaRDD()
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.repartition(getRepartitionNumber(totalInput, rpt))
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.map((Function<MetadataRecord, MetadataRecord>) x::call);
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saveDataset(spark.createDataset(mdstore.rdd(), encoder), outputBasePath + MDSTORE_DATA_PATH);
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log.info("Transformed item " + ct.getProcessedItems().count());
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log.info("Total item " + ct.getTotalItems().count());
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@ -2,6 +2,7 @@
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package eu.dnetlib.dhp.transformation.xslt;
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import java.io.ByteArrayInputStream;
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import java.io.Serializable;
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import java.io.StringWriter;
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import java.nio.charset.StandardCharsets;
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@ -15,7 +16,7 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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import eu.dnetlib.dhp.schema.mdstore.MetadataRecord;
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import net.sf.saxon.s9api.*;
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public class XSLTTransformationFunction implements MapFunction<MetadataRecord, MetadataRecord> {
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public class XSLTTransformationFunction implements MapFunction<MetadataRecord, MetadataRecord>, Serializable {
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public final static String QNAME_BASE_URI = "http://eu/dnetlib/transform";
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@ -27,6 +28,8 @@ public class XSLTTransformationFunction implements MapFunction<MetadataRecord, M
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private final long dateOfTransformation;
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private final VocabularyGroup vocabularies;
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public XSLTTransformationFunction(
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final AggregationCounter aggregationCounter,
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final String transformationRule,
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@ -35,6 +38,7 @@ public class XSLTTransformationFunction implements MapFunction<MetadataRecord, M
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throws Exception {
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this.aggregationCounter = aggregationCounter;
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this.transformationRule = transformationRule;
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this.vocabularies = vocabularies;
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this.dateOfTransformation = dateOfTransformation;
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cleanFunction = new Cleaner(vocabularies);
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}
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@ -73,4 +77,24 @@ public class XSLTTransformationFunction implements MapFunction<MetadataRecord, M
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throw new RuntimeException(e);
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}
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}
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public AggregationCounter getAggregationCounter() {
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return aggregationCounter;
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}
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public String getTransformationRule() {
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return transformationRule;
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}
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public Cleaner getCleanFunction() {
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return cleanFunction;
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}
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public long getDateOfTransformation() {
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return dateOfTransformation;
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}
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public VocabularyGroup getVocabularies() {
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return vocabularies;
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}
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}
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@ -37,6 +37,12 @@
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<name>dnetMessageManagerURL</name>
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<description>The URI of the Dnet Message Manager</description>
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</property>
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<property>
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<name>recordsPerTask</name>
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<value>200</value>
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<description>The URI of the Dnet Message Manager</description>
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</property>
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</parameters>
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<start to="BeginRead"/>
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@ -103,6 +109,7 @@
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<arg>--transformationPlugin</arg><arg>${transformationPlugin}</arg>
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<arg>--transformationRuleId</arg><arg>${transformationRuleId}</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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<arg>--recordsPerTask</arg><arg>${recordsPerTask}</arg>
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<arg>--workflowId</arg><arg>${workflowId}</arg>
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<arg>--dnetMessageManagerURL</arg><arg>${dnetMessageManagerURL}</arg>
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</spark>
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@ -48,6 +48,12 @@
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"paramDescription": "the identifier of the dnet Workflow",
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"paramRequired": true
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},
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{
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"paramName": "rpt",
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"paramLongName": "recordsPerTask",
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"paramDescription": "the number of records transformed by a single Task",
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"paramRequired": false
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},
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{
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"paramName": "tp",
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"paramLongName": "transformationPlugin",
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@ -180,7 +180,7 @@ public class GenerateNativeStoreSparkJobTest extends AbstractVocabularyTest {
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TransformSparkJobNode
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.transformRecords(
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parameters, isLookUpService, spark, mdStoreV2.getHdfsPath() + MDSTORE_DATA_PATH,
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mdStoreCleanedVersion.getHdfsPath());
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mdStoreCleanedVersion.getHdfsPath(), 200);
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final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
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final Dataset<MetadataRecord> mOutput = spark
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@ -167,7 +167,8 @@ public class TransformationJobTest extends AbstractVocabularyTest {
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}).collect(Collectors.toMap(data -> data[0], data -> data[1]));
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TransformSparkJobNode.transformRecords(parameters, isLookUpService, spark, mdstore_input, mdstore_output);
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TransformSparkJobNode
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.transformRecords(parameters, isLookUpService, spark, mdstore_input, mdstore_output, 200);
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// TODO introduce useful assertions
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@ -221,7 +222,8 @@ public class TransformationJobTest extends AbstractVocabularyTest {
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}).collect(Collectors.toMap(data -> data[0], data -> data[1]));
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TransformSparkJobNode.transformRecords(parameters, isLookUpService, spark, mdstore_input, mdstore_output);
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TransformSparkJobNode
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.transformRecords(parameters, isLookUpService, spark, mdstore_input, mdstore_output, 200);
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// TODO introduce useful assertions
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@ -1,16 +1,13 @@
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<xsl:stylesheet
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version="2.0"
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xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
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xmlns:oai="http://www.openarchives.org/OAI/2.0/"
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xmlns:oaf="http://namespace.openaire.eu/oaf"
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xmlns:vocabulary="http://eu/dnetlib/transform/clean"
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xmlns:dateCleaner="http://eu/dnetlib/transform/dateISO"
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xmlns:dr="http://www.driver-repository.eu/namespace/dr"
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exclude-result-prefixes="xsl vocabulary dateCleaner">
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<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
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xmlns:vocabulary="http://eu/dnetlib/transform/clean"
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xmlns:dateCleaner="http://eu/dnetlib/transform/dateISO"
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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:dr="http://www.driver-repository.eu/namespace/dr"
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exclude-result-prefixes="xsl vocabulary dateCleaner" version="2.0">
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<xsl:param name="varOfficialName"/>
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<xsl:param name="varDsType"/>
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<xsl:param name="varDataSourceId"/>
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<xsl:param name="varFP7" select="'corda_______::'"/>
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<xsl:param name="varH2020" select="'corda__h2020::'"/>
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<xsl:param name="varAKA" select="'aka_________::'"/>
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@ -29,34 +26,27 @@
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<xsl:param name="varRCUK" select="'rcuk________::'"/>
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<xsl:param name="varSFI" select="'sfi_________::'"/>
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<xsl:param name="varSGOV"
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select="'sgov________::'"/> <!-- SGOV awaiting DOI from Pilar, found project ids not in CSV list? -->
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select="'sgov________::'"/><!-- SGOV awaiting DOI from Pilar, found project ids not in CSV list? -->
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<xsl:param name="varSNSF" select="'snsf________::'"/>
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<xsl:param name="varTARA" select="'taraexp_____::'"/> <!-- TARA awaiting DOI from André -->
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<xsl:param name="varTARA" select="'taraexp_____::'"/><!-- TARA awaiting DOI from André -->
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<xsl:param name="varTUBITAK" select="'tubitakf____::'"/>
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<xsl:param name="varWT" select="'wt__________::'"/>
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<xsl:param name="index" select="0"/>
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<xsl:param name="transDate" select="current-dateTime()"/>
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<xsl:template match="/">
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<xsl:variable name="datasourcePrefix" select="normalize-space(//oaf:datasourceprefix)"/>
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<xsl:call-template name="validRecord"/>
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</xsl:template>
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<xsl:template name="validRecord">
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<record>
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<xsl:apply-templates select="//*[local-name() = 'header']"/>
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<metadata>
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<xsl:apply-templates select="//*[local-name() = 'metadata']//*[local-name() = 'resource']"/>
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<xsl:if test="//*[local-name()='date']/@dateType='Available'">
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<xsl:variable name='varEmbargoEndDate'
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<xsl:variable name="varEmbargoEndDate"
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select="dateCleaner:dateISO(normalize-space(//*[local-name()='date'][@dateType='Available']))"/>
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<xsl:choose>
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<xsl:when test="string-length($varEmbargoEndDate) > 0">
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<xsl:when test="string-length($varEmbargoEndDate) > 0">
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<oaf:embargoenddate>
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<xsl:value-of select="$varEmbargoEndDate"/>
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</oaf:embargoenddate>
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@ -68,55 +58,44 @@
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</xsl:otherwise>
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</xsl:choose>
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</xsl:if>
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<dr:CobjCategory>
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<xsl:variable name="varCobjCategory"
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select="vocabulary:clean( //*[local-name()='resourceType']/@resourceTypeGeneral, 'dnet:publication_resource')"/>
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<xsl:variable name="varSuperType"
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select="vocabulary:clean( $varCobjCategory, 'dnet:result_typologies')"/>
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<xsl:attribute name="type">
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<xsl:value-of select="$varSuperType"/>
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</xsl:attribute>
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<xsl:value-of select="$varCobjCategory"/>
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</dr:CobjCategory>
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<!-- review status -->
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<!-- Zenodo -->
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<xsl:variable name="varRefereedConvt" select="for $i in (//*[local-name()='resourceType']/(., @resourceTypeGeneral), //*[local-name()='version'])
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return vocabulary:clean(normalize-space($i), 'dnet:review_levels')"/>
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</dr:CobjCategory><!-- review status --><!-- Zenodo -->
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<xsl:variable name="varRefereedConvt"
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select="for $i in (//*[local-name()='resourceType']/(., @resourceTypeGeneral), //*[local-name()='version']) return vocabulary:clean(normalize-space($i), 'dnet:review_levels')"/>
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<xsl:variable name="varRefereedIdntf"
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select="//*[local-name()=('identifier', 'alternateIdentifier')][matches(lower-case(.), '.*([\s\-\.\\_/:]|%[2-7][0-9A-F])pre([\s\-\.\\_/:]|%[2-7][0-9A-F])?prints?([\s\-\.\\_/:%].*|$)')]/'0002' "/>
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<xsl:variable name="varRefereedReltn"
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select="//*[local-name()='relatedIdentifier'][./@relationType/lower-case(.)='isreviewedby']/'0001' "/>
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<xsl:variable name="varRefereedVersn" select="(//*[local-name()='version'][matches(lower-case(.), '.*peer[\s\-\.\\_/:%]?reviewed.*')]/'0001',
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//*[local-name()='version'][matches(normalize-space(lower-case(.)), '^(v|vs|version|rel|release)?[\s\.\-_]*0$')]/'0002',
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//*[local-name()='version'][matches(lower-case(.), '(^|[\s\-\.\\_/:%].*)(beta|draft|trial|test)([\s\-\.\\_/:%].*|$)')]/'0002',
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//*[local-name()='version'][matches(lower-case(.), '.*submi(tted|ssion|ttal).*')]/'0002') "/>
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<xsl:variable name="varRefereedOther" select="(//*[local-name()='publisher'][matches(lower-case(.), '.*[\s\-\.\\_/:%]pre[\s\-\.\\_/:%]?prints?([\s\-\.\\_/:%].*|$)')]/'0002',
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//*[local-name()='description'][matches(lower-case(.), '^peer[\s\-\.\\_/:%]?reviewed$')]/'0001',
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//*[local-name()='description'][matches(lower-case(.), '^pre[\s\-\.\\_/:%]?prints?$')]/'0002') "/>
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<xsl:variable name="varRefereedVersn"
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select="(//*[local-name()='version'][matches(lower-case(.), '.*peer[\s\-\.\\_/:%]?reviewed.*')]/'0001', //*[local-name()='version'][matches(normalize-space(lower-case(.)), '^(v|vs|version|rel|release)?[\s\.\-_]*0$')]/'0002', //*[local-name()='version'][matches(lower-case(.), '(^|[\s\-\.\\_/:%].*)(beta|draft|trial|test)([\s\-\.\\_/:%].*|$)')]/'0002', //*[local-name()='version'][matches(lower-case(.), '.*submi(tted|ssion|ttal).*')]/'0002') "/>
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<xsl:variable name="varRefereedOther"
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select="(//*[local-name()='publisher'][matches(lower-case(.), '.*[\s\-\.\\_/:%]pre[\s\-\.\\_/:%]?prints?([\s\-\.\\_/:%].*|$)')]/'0002', //*[local-name()='description'][matches(lower-case(.), '^peer[\s\-\.\\_/:%]?reviewed$')]/'0001', //*[local-name()='description'][matches(lower-case(.), '^pre[\s\-\.\\_/:%]?prints?$')]/'0002') "/>
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<xsl:variable name="varRefereed"
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select="($varRefereedConvt, $varRefereedIdntf, $varRefereedReltn, $varRefereedVersn, $varRefereedOther)"/>
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<xsl:choose>
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<xsl:when test="count($varRefereed[. = '0001']) > 0">
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<xsl:when test="count($varRefereed[. = '0001']) > 0">
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<oaf:refereed>
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<xsl:value-of select="'0001'"/>
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</oaf:refereed>
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</xsl:when>
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<xsl:when test="count($varRefereed[. = '0002']) > 0">
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<xsl:when test="count($varRefereed[. = '0002']) > 0">
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<oaf:refereed>
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<xsl:value-of select="'0002'"/>
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</oaf:refereed>
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</xsl:when>
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</xsl:choose>
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<oaf:dateAccepted>
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<xsl:value-of
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select="dateCleaner:dateISO(normalize-space(//*[local-name()='publicationYear']))"/>
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<xsl:value-of select="dateCleaner:dateISO(normalize-space(//*[local-name()='publicationYear']))"/>
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</oaf:dateAccepted>
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<xsl:choose>
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<xsl:when
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test="//*[local-name() = 'rights'][starts-with(normalize-space(.), 'info:eu-repo/semantics')]">
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<oaf:accessrights>
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@ -147,17 +126,12 @@
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</xsl:choose>
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</xsl:otherwise>
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</xsl:choose>
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<oaf:language>
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<xsl:value-of
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select="vocabulary:clean(//*[local-name()='language'], 'dnet:languages')"/>
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<xsl:value-of select="vocabulary:clean(//*[local-name()='language'], 'dnet:languages')"/>
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</oaf:language>
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<xsl:for-each
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select="//*[local-name()='nameIdentifier'][contains(., 'info:eu-repo/grantAgreement/')], //*[local-name()='fundingReference']/*[local-name()='awardNumber']">
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<xsl:choose>
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<xsl:when
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test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', 'i') or ../*[local-name() = 'funderIdentifier' and . = '10.13039/100011102']">
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<oaf:projectid>
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@ -308,13 +282,10 @@
|
|||
select="concat($varWT, replace(normalize-space(.), '(info:eu-repo/grantagreement/wt/.*?/)([^/]*)(/.*)?', '$2', 'i'))"/>
|
||||
</oaf:projectid>
|
||||
</xsl:when>
|
||||
|
||||
</xsl:choose>
|
||||
</xsl:for-each>
|
||||
|
||||
<xsl:for-each select="//*[local-name()='relatedIdentifier']">
|
||||
<xsl:if
|
||||
test="starts-with(./text(), 'https://zenodo.org/communities/')">
|
||||
<xsl:if test="starts-with(./text(), 'https://zenodo.org/communities/')">
|
||||
<oaf:concept>
|
||||
<xsl:attribute name="id">
|
||||
<xsl:value-of select="./text()"/>
|
||||
|
|
@ -322,7 +293,6 @@
|
|||
</oaf:concept>
|
||||
</xsl:if>
|
||||
</xsl:for-each>
|
||||
|
||||
<oaf:hostedBy>
|
||||
<xsl:attribute name="name">
|
||||
<xsl:value-of select="$varOfficialName"/>
|
||||
|
|
@ -343,24 +313,19 @@
|
|||
<xsl:copy-of select="//*[local-name() = 'about']"/>
|
||||
</record>
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template match="node()|@*">
|
||||
<xsl:copy>
|
||||
<xsl:apply-templates select="node()|@*"/>
|
||||
</xsl:copy>
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template match="//*[local-name() = 'metadata']//*[local-name() = 'resource']">
|
||||
<xsl:copy>
|
||||
<xsl:apply-templates select="node()|@*"/>
|
||||
</xsl:copy>
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template match="//*[local-name() = 'resource']/*[local-name()='alternateIdentifiers']">
|
||||
<xsl:element name="alternateIdentifiers" namespace="http://www.openarchives.org/OAI/2.0/">
|
||||
|
||||
<xsl:copy-of select="./*"/>
|
||||
|
||||
<xsl:if test="//*[local-name() = 'resource']/*[local-name()='identifier'][@identifierType='Handle']">
|
||||
<xsl:element name="alternateIdentifier" namespace="http://www.openarchives.org/OAI/2.0/">
|
||||
<xsl:attribute name="alternateIdentifierType">
|
||||
|
|
@ -370,7 +335,6 @@
|
|||
select="concat('http://hdl.handle.net/', //*[local-name() = 'resource']/*[local-name()='identifier'])"/>
|
||||
</xsl:element>
|
||||
</xsl:if>
|
||||
|
||||
<xsl:if test="//*[local-name() = 'resource']/*[local-name()='identifier'][@identifierType='URN']">
|
||||
<xsl:element name="alternateIdentifier" namespace="http://www.openarchives.org/OAI/2.0/">
|
||||
<xsl:attribute name="alternateIdentifierType">
|
||||
|
|
@ -380,7 +344,6 @@
|
|||
select="concat('http://nbn-resolving.org/', //*[local-name() = 'resource']/*[local-name()='identifier'])"/>
|
||||
</xsl:element>
|
||||
</xsl:if>
|
||||
|
||||
<xsl:if test="//*[local-name() = 'resource']/*[local-name()='identifier'][@identifierType='DOI']">
|
||||
<xsl:element name="alternateIdentifier" namespace="http://www.openarchives.org/OAI/2.0/">
|
||||
<xsl:attribute name="alternateIdentifierType">
|
||||
|
|
@ -390,11 +353,8 @@
|
|||
select="concat('http://dx.doi.org/', //*[local-name() = 'resource']/*[local-name()='identifier'])"/>
|
||||
</xsl:element>
|
||||
</xsl:if>
|
||||
|
||||
</xsl:element>
|
||||
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template match="//*[local-name() = 'resource']/*[local-name()='identifier']">
|
||||
<xsl:copy-of select="."/>
|
||||
<xsl:if test="not(//*[local-name() = 'resource']/*[local-name()='alternateIdentifiers'])">
|
||||
|
|
@ -404,8 +364,7 @@
|
|||
<xsl:attribute name="alternateIdentifierType">
|
||||
<xsl:value-of select="'URL'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:value-of
|
||||
select="concat('http://hdl.handle.net/', .)"/>
|
||||
<xsl:value-of select="concat('http://hdl.handle.net/', .)"/>
|
||||
</xsl:element>
|
||||
</xsl:if>
|
||||
<xsl:if test=".[@identifierType='URN']">
|
||||
|
|
@ -413,8 +372,7 @@
|
|||
<xsl:attribute name="alternateIdentifierType">
|
||||
<xsl:value-of select="'URL'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:value-of
|
||||
select="concat('http://nbn-resolving.org/', .)"/>
|
||||
<xsl:value-of select="concat('http://nbn-resolving.org/', .)"/>
|
||||
</xsl:element>
|
||||
</xsl:if>
|
||||
<xsl:if test=".[@identifierType='DOI']">
|
||||
|
|
@ -422,17 +380,12 @@
|
|||
<xsl:attribute name="alternateIdentifierType">
|
||||
<xsl:value-of select="'URL'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:value-of
|
||||
select="concat('http://dx.doi.org/', .)"/>
|
||||
<xsl:value-of select="concat('http://dx.doi.org/', .)"/>
|
||||
</xsl:element>
|
||||
</xsl:if>
|
||||
|
||||
</xsl:element>
|
||||
</xsl:if>
|
||||
|
||||
</xsl:template>
|
||||
|
||||
|
||||
<xsl:template match="//*[local-name() = 'header']">
|
||||
<xsl:copy>
|
||||
<xsl:apply-templates select="node()|@*"/>
|
||||
|
|
@ -441,5 +394,4 @@
|
|||
</xsl:element>
|
||||
</xsl:copy>
|
||||
</xsl:template>
|
||||
|
||||
</xsl:stylesheet>
|
||||
Loading…
Reference in New Issue