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Merge branch 'deduptesting' of https://code-repo.d4science.org/D-Net/dnet-hadoop into deduptesting

This commit is contained in:
Claudio Atzori 2020-04-16 12:18:32 +02:00
parent 376efd67de 6a089ec287
commit 76d23895e6
4 changed files with 23 additions and 16 deletions
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2
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java
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@ -24,7 +24,7 @@ abstract class AbstractSparkAction implements Serializable {
public ArgumentApplicationParser parser; //parameters for the spark action
public SparkSession spark; //the spark session
public AbstractSparkAction(ArgumentApplicationParser parser, SparkSession spark) throws Exception {
public AbstractSparkAction(ArgumentApplicationParser parser, SparkSession spark) {
this.parser = parser;
this.spark = spark;

9
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateConnectedComponent.java → dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java
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@ -16,7 +16,6 @@ import org.apache.commons.logging.LogFactory;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.graphx.Edge;
import org.apache.spark.rdd.RDD;
@ -31,11 +30,11 @@ import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
public class SparkCreateConnectedComponent extends AbstractSparkAction {
public class SparkCreateMergeRels extends AbstractSparkAction {
private static final Log log = LogFactory.getLog(SparkCreateConnectedComponent.class);
private static final Log log = LogFactory.getLog(SparkCreateMergeRels.class);
public SparkCreateConnectedComponent(ArgumentApplicationParser parser, SparkSession spark) throws Exception {
public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) throws Exception {
super(parser, spark);
}
@ -45,7 +44,7 @@ public class SparkCreateConnectedComponent extends AbstractSparkAction {
SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
parser.parseArgument(args);
new SparkCreateConnectedComponent(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
new SparkCreateMergeRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
}
@Override

2
dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml
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@ -108,7 +108,7 @@
<master>yarn</master>
<mode>cluster</mode>
<name>Create Merge Relations</name>
<class>eu.dnetlib.dhp.oa.dedup.SparkCreateConnectedComponent</class>
<class>eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels</class>
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}

26
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
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@ -22,6 +22,7 @@ import java.io.Serializable;
import java.net.URISyntaxException;
import java.nio.file.Paths;
import static java.nio.file.Files.createTempDirectory;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.Mockito.lenient;
@ -36,16 +37,20 @@ public class SparkDedupTest implements Serializable {
private static JavaSparkContext jsc;
private static String testGraphBasePath;
private final static String testOutputBasePath = "/tmp/test_dedup_workflow";
private static String testOutputBasePath;
private static String testDedupGraphBasePath;
private final static String testActionSetId = "test-orchestrator";
private final static String testDedupGraphBasePath = "/tmp/test_dedup_workflow/dedup_graph";
@BeforeAll
private static void cleanUp() throws IOException, URISyntaxException {
testGraphBasePath = Paths.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath();
testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString();
testDedupGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString();
FileUtils.deleteDirectory(new File(testOutputBasePath));
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
spark = SparkSession
.builder()
@ -54,7 +59,7 @@ public class SparkDedupTest implements Serializable {
.config(new SparkConf())
.getOrCreate();
jsc = new JavaSparkContext(spark.sparkContext());
jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
}
@ -69,7 +74,6 @@ public class SparkDedupTest implements Serializable {
lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
}
@Test
@ -97,11 +101,11 @@ public class SparkDedupTest implements Serializable {
@Test
@Order(2)
public void createCCTest() throws Exception {
public void createMergeRelsTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString(
SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
SparkCreateMergeRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
parser.parseArgument(new String[]{
"-mt", "local[*]",
"-i", testGraphBasePath,
@ -109,7 +113,7 @@ public class SparkDedupTest implements Serializable {
"-la", "lookupurl",
"-w", testOutputBasePath});
new SparkCreateConnectedComponent(parser, spark).run(isLookUpService);
new SparkCreateMergeRels(parser, spark).run(isLookUpService);
long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count();
long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count();
@ -185,8 +189,6 @@ public class SparkDedupTest implements Serializable {
assertEquals(mergedOrgs, deletedOrgs);
assertEquals(mergedPubs, deletedPubs);
//TODO check the size of other entities not deduplicated
}
@Test
@ -211,6 +213,12 @@ public class SparkDedupTest implements Serializable {
}
@AfterAll
public static void finalCleanUp() throws IOException {
FileUtils.deleteDirectory(new File(testOutputBasePath));
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
}
public boolean isDeletedByInference(String s) {
return s.contains("\"deletedbyinference\":true");
}