lsmyrnaios
/
dnet-hadoop
forked from D-Net/dnet-hadoop
1
0
Fork 0
Code Pull Requests Activity

code formatting

This commit is contained in:
Claudio Atzori 2021-02-02 12:34:14 +01:00
parent 75807ea5ae
commit bb89b99b24
6 changed files with 164 additions and 167 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/common/AggregationConstants.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.aggregation.common;
public class AggregationConstants {
@ -10,6 +11,4 @@ public class AggregationConstants {
public static final String CONTENT_INVALIDRECORDS = "InvalidRecords";
public static final String CONTENT_TRANSFORMEDRECORDS = "transformedItems";
}

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/common/AggregationUtility.java
View File

@ -5,7 +5,6 @@ import java.io.BufferedOutputStream;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
@ -15,6 +14,8 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;

32
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java
View File

@ -1,11 +1,16 @@
package eu.dnetlib.dhp.collection;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.model.mdstore.Provenance;
import static eu.dnetlib.dhp.aggregation.common.AggregationConstants.*;
import static eu.dnetlib.dhp.aggregation.common.AggregationUtility.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.IntWritable;
@ -22,18 +27,15 @@ import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.model.mdstore.Provenance;
import scala.Tuple2;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.Objects;
import java.util.Optional;
import static eu.dnetlib.dhp.aggregation.common.AggregationConstants.*;
import static eu.dnetlib.dhp.aggregation.common.AggregationUtility.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
public class GenerateNativeStoreSparkJob {
private static final Logger log = LoggerFactory.getLogger(GenerateNativeStoreSparkJob.class);

14
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformSparkJobNode.java
View File

@ -1,19 +1,17 @@
package eu.dnetlib.dhp.transformation;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static eu.dnetlib.dhp.aggregation.common.AggregationUtility.*;
import static eu.dnetlib.dhp.aggregation.common.AggregationConstants.*;
import static eu.dnetlib.dhp.aggregation.common.AggregationUtility.saveDataset;
import static eu.dnetlib.dhp.aggregation.common.AggregationUtility.writeTotalSizeOnHDFS;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.util.Map;
import java.util.Optional;
import eu.dnetlib.dhp.aggregation.common.AggregationConstants;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
@ -25,7 +23,6 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
import eu.dnetlib.dhp.aggregation.common.AggregationCounter;
import eu.dnetlib.dhp.aggregation.common.AggregationUtility;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
@ -67,7 +64,6 @@ public class TransformSparkJobNode {
final String dateOfTransformation = parser.get("dateOfTransformation");
log.info(String.format("dateOfTransformation: %s", dateOfTransformation));
final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
final VocabularyGroup vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService);
@ -94,7 +90,8 @@ public class TransformSparkJobNode {
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
saveDataset(
spark.read()
spark
.read()
.format("parquet")
.load(inputPath)
.as(encoder)
@ -103,7 +100,6 @@ public class TransformSparkJobNode {
encoder),
outputPath + MDSTORE_DATA_PATH);
log.info("Transformed item " + ct.getProcessedItems().count());
log.info("Total item " + ct.getTotalItems().count());
log.info("Transformation Error item " + ct.getErrorItems().count());

24
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/aggregation/AggregationJobTest.java
View File

@ -12,11 +12,6 @@ import java.util.Map;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.transformation.TransformSparkJobNode;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.IntWritable;
@ -35,7 +30,12 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
import eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.transformation.TransformSparkJobNode;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
public class AggregationJobTest {
@ -57,7 +57,8 @@ public class AggregationJobTest {
@BeforeAll
public static void beforeAll() throws IOException {
provenance = IOUtils.toString(AggregationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/collection/provenance.json"));
provenance = IOUtils
.toString(AggregationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/collection/provenance.json"));
workingDir = Files.createTempDirectory(AggregationJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
@ -100,7 +101,7 @@ public class AggregationJobTest {
GenerateNativeStoreSparkJob
.main(
new String[]{
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-encoding", encoding,
"-dateOfCollection", dateOfCollection,
@ -130,7 +131,7 @@ public class AggregationJobTest {
GenerateNativeStoreSparkJob
.main(
new String[]{
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-encoding", encoding,
"-dateOfCollection", dateOfCollection,
@ -144,7 +145,6 @@ public class AggregationJobTest {
verify(mdStoreV2);
}
@Test
@Order(3)
public void testTransformSparkJob() throws Exception {
@ -152,14 +152,16 @@ public class AggregationJobTest {
MDStoreVersion mdStoreV2 = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreVersion_2.json");
MDStoreVersion mdStoreCleanedVersion = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreCleanedVersion.json");
TransformSparkJobNode.main(new String[]{
TransformSparkJobNode.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-dateOfTransformation", dateOfCollection,
"-mdstoreInputVersion", OBJECT_MAPPER.writeValueAsString(mdStoreV2),
"-mdstoreOutputVersion", OBJECT_MAPPER.writeValueAsString(mdStoreCleanedVersion),
"-transformationPlugin", "XSLT_TRANSFORM",
"-isLookupUrl", "https://dev-openaire.d4science.org/is/services/isLookUp",
"-transformationRuleId", "183dde52-a69b-4db9-a07e-1ef2be105294_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU="});
"-transformationRuleId",
"183dde52-a69b-4db9-a07e-1ef2be105294_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU="
});
}

3
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java
View File

@ -75,9 +75,6 @@ public class TransformationJobTest {
spark.stop();
}
@Test
@DisplayName("Test Transform Single XML using XSLTTransformator")
public void testTransformSaxonHE() throws Exception {