forked from D-Net/dnet-hadoop
code formatting
This commit is contained in:
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75807ea5ae
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@ -1,3 +1,4 @@
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package eu.dnetlib.dhp.aggregation.common;
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public class AggregationConstants {
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@ -10,6 +11,4 @@ public class AggregationConstants {
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public static final String CONTENT_INVALIDRECORDS = "InvalidRecords";
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public static final String CONTENT_TRANSFORMEDRECORDS = "transformedItems";
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}
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@ -5,7 +5,6 @@ import java.io.BufferedOutputStream;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import org.apache.hadoop.fs.FSDataOutputStream;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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@ -15,6 +14,8 @@ import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob;
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import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
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@ -1,11 +1,16 @@
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package eu.dnetlib.dhp.collection;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
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import eu.dnetlib.dhp.model.mdstore.Provenance;
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import static eu.dnetlib.dhp.aggregation.common.AggregationConstants.*;
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import static eu.dnetlib.dhp.aggregation.common.AggregationUtility.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.ByteArrayInputStream;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import java.util.Objects;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.hadoop.io.IntWritable;
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@ -22,18 +27,15 @@ import org.dom4j.Node;
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import org.dom4j.io.SAXReader;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
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import eu.dnetlib.dhp.model.mdstore.Provenance;
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import scala.Tuple2;
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import java.io.ByteArrayInputStream;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import java.util.Objects;
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import java.util.Optional;
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import static eu.dnetlib.dhp.aggregation.common.AggregationConstants.*;
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import static eu.dnetlib.dhp.aggregation.common.AggregationUtility.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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public class GenerateNativeStoreSparkJob {
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private static final Logger log = LoggerFactory.getLogger(GenerateNativeStoreSparkJob.class);
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@ -1,19 +1,17 @@
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package eu.dnetlib.dhp.transformation;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static eu.dnetlib.dhp.aggregation.common.AggregationUtility.*;
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import static eu.dnetlib.dhp.aggregation.common.AggregationConstants.*;
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import static eu.dnetlib.dhp.aggregation.common.AggregationUtility.saveDataset;
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import static eu.dnetlib.dhp.aggregation.common.AggregationUtility.writeTotalSizeOnHDFS;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.util.Map;
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import java.util.Optional;
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import eu.dnetlib.dhp.aggregation.common.AggregationConstants;
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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.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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import org.apache.spark.sql.SparkSession;
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@ -25,7 +23,6 @@ import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
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import eu.dnetlib.dhp.aggregation.common.AggregationCounter;
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import eu.dnetlib.dhp.aggregation.common.AggregationUtility;
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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.model.mdstore.MetadataRecord;
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@ -67,7 +64,6 @@ 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 ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
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final VocabularyGroup vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService);
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@ -94,7 +90,8 @@ public class TransformSparkJobNode {
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final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
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saveDataset(
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spark.read()
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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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@ -103,7 +100,6 @@ public class TransformSparkJobNode {
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encoder),
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outputPath + 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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log.info("Transformation Error item " + ct.getErrorItems().count());
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@ -12,11 +12,6 @@ import java.util.Map;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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import eu.dnetlib.dhp.transformation.TransformSparkJobNode;
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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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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.IntWritable;
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@ -35,7 +30,12 @@ import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
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import eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
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import eu.dnetlib.dhp.transformation.TransformSparkJobNode;
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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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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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public class AggregationJobTest {
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@ -57,7 +57,8 @@ public class AggregationJobTest {
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@BeforeAll
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public static void beforeAll() throws IOException {
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provenance = IOUtils.toString(AggregationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/collection/provenance.json"));
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provenance = IOUtils
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.toString(AggregationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/collection/provenance.json"));
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workingDir = Files.createTempDirectory(AggregationJobTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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@ -100,7 +101,7 @@ public class AggregationJobTest {
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GenerateNativeStoreSparkJob
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.main(
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new String[]{
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-encoding", encoding,
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"-dateOfCollection", dateOfCollection,
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@ -130,7 +131,7 @@ public class AggregationJobTest {
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GenerateNativeStoreSparkJob
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.main(
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new String[]{
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-encoding", encoding,
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"-dateOfCollection", dateOfCollection,
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@ -144,7 +145,6 @@ public class AggregationJobTest {
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verify(mdStoreV2);
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}
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@Test
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@Order(3)
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public void testTransformSparkJob() throws Exception {
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@ -152,14 +152,16 @@ public class AggregationJobTest {
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MDStoreVersion mdStoreV2 = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreVersion_2.json");
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MDStoreVersion mdStoreCleanedVersion = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreCleanedVersion.json");
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TransformSparkJobNode.main(new String[]{
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TransformSparkJobNode.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-dateOfTransformation", dateOfCollection,
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"-mdstoreInputVersion", OBJECT_MAPPER.writeValueAsString(mdStoreV2),
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"-mdstoreOutputVersion", OBJECT_MAPPER.writeValueAsString(mdStoreCleanedVersion),
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"-transformationPlugin", "XSLT_TRANSFORM",
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"-isLookupUrl", "https://dev-openaire.d4science.org/is/services/isLookUp",
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"-transformationRuleId", "183dde52-a69b-4db9-a07e-1ef2be105294_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU="});
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"-transformationRuleId",
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"183dde52-a69b-4db9-a07e-1ef2be105294_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU="
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});
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}
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@ -75,9 +75,6 @@ public class TransformationJobTest {
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spark.stop();
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}
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@Test
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@DisplayName("Test Transform Single XML using XSLTTransformator")
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public void testTransformSaxonHE() throws Exception {
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