D-Net
/
dnet-hadoop
14
5
Fork 11
Code Issues 14 Pull Requests 12 Projects 2 Releases 2 Wiki Activity

fixed test

This commit is contained in:
Sandro La Bruzzo 2021-02-04 10:30:49 +01:00
parent 3ea8c328ac
commit 69c253710b
3 changed files with 148 additions and 97 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

52
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/aggregation/AbstractVocabularyTest.java Normal file
View File

@ -0,0 +1,52 @@
package eu.dnetlib.dhp.aggregation;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.transformation.TransformationFactory;
import eu.dnetlib.dhp.transformation.TransformationJobTest;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.io.IOUtils;
import org.mockito.Mock;
import java.io.IOException;
import java.util.Collections;
import java.util.List;
import static org.mockito.Mockito.lenient;
public abstract class AbstractVocabularyTest {
@Mock
protected ISLookUpService isLookUpService;
protected VocabularyGroup vocabularies;
public void setUpVocabulary() throws ISLookUpException, IOException {
lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs());
lenient()
.when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY))
.thenReturn(synonyms());
vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService);
}
private static List<String> vocs() throws IOException {
return IOUtils
.readLines(TransformationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/terms.txt"));
}
private static List<String> synonyms() throws IOException {
return IOUtils
.readLines(TransformationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/synonyms.txt"));
}
protected void mockupTrasformationRule(final String trule, final String path) throws Exception {
final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path));
lenient()
.when(isLookUpService.quickSearchProfile(String.format(TransformationFactory.TRULE_XQUERY, trule)))
.thenReturn(Collections.singletonList(trValue));
}
}

105
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/aggregation/AggregationJobTest.java
View File

@ -1,44 +1,47 @@
package eu.dnetlib.dhp.aggregation; package eu.dnetlib.dhp.aggregation;
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.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.transformation.TransformSparkJobNode;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.junit.jupiter.MockitoExtension;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File; import java.io.File;
import java.io.FileOutputStream; import java.io.FileOutputStream;
import java.io.FileReader; import java.io.FileReader;
import java.io.IOException; import java.io.IOException;
import java.nio.file.Files; import java.nio.file.Files;
import java.nio.file.Path; import java.nio.file.Path;
import java.util.HashMap;
import java.util.Map; import java.util.Map;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import java.util.stream.Stream; import java.util.stream.Stream;
import org.apache.commons.io.FileUtils; import static eu.dnetlib.dhp.aggregation.common.AggregationConstants.MDSTORE_DATA_PATH;
import org.apache.commons.io.IOUtils; import static org.junit.jupiter.api.Assertions.assertEquals;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
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.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) @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
public class AggregationJobTest { @ExtendWith(MockitoExtension.class)
public class AggregationJobTest extends AbstractVocabularyTest{
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
@ -55,6 +58,8 @@ public class AggregationJobTest {
private static final Logger log = LoggerFactory.getLogger(AggregationJobTest.class); private static final Logger log = LoggerFactory.getLogger(AggregationJobTest.class);
@BeforeAll @BeforeAll
public static void beforeAll() throws IOException { public static void beforeAll() throws IOException {
provenance = IOUtils provenance = IOUtils
@ -81,6 +86,8 @@ public class AggregationJobTest {
.getOrCreate(); .getOrCreate();
} }
@AfterAll @AfterAll
public static void afterAll() throws IOException { public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile()); FileUtils.deleteDirectory(workingDir.toFile());
@ -149,19 +156,45 @@ public class AggregationJobTest {
@Order(3) @Order(3)
public void testTransformSparkJob() throws Exception { public void testTransformSparkJob() throws Exception {
setUpVocabulary();
MDStoreVersion mdStoreV2 = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreVersion_2.json"); MDStoreVersion mdStoreV2 = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreVersion_2.json");
MDStoreVersion mdStoreCleanedVersion = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreCleanedVersion.json"); MDStoreVersion mdStoreCleanedVersion = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreCleanedVersion.json");
TransformSparkJobNode.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(), mockupTrasformationRule("simpleTRule", "/eu/dnetlib/dhp/transform/ext_simple.xsl");
"-dateOfTransformation", dateOfCollection,
"-mdstoreInputVersion", OBJECT_MAPPER.writeValueAsString(mdStoreV2), final Map<String, String> parameters = Stream.of(new String[][] {
"-mdstoreOutputVersion", OBJECT_MAPPER.writeValueAsString(mdStoreCleanedVersion), {
"-transformationPlugin", "XSLT_TRANSFORM", "dateOfTransformation", "1234"
"-isLookupUrl", "https://dev-openaire.d4science.org/is/services/isLookUp", },
"-transformationRuleId", {
"183dde52-a69b-4db9-a07e-1ef2be105294_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU=" "transformationPlugin", "XSLT_TRANSFORM"
}); },
{
"transformationRuleId", "simpleTRule"
},
}).collect(Collectors.toMap(data -> data[0], data -> data[1]));
TransformSparkJobNode.transformRecords(parameters, isLookUpService, spark, mdStoreV2.getHdfsPath()+MDSTORE_DATA_PATH, mdStoreCleanedVersion.getHdfsPath());
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mOutput = spark.read().format("parquet").load(mdStoreCleanedVersion.getHdfsPath()+MDSTORE_DATA_PATH).as(encoder);
final Long total = mOutput.count();
final long recordTs = mOutput
.filter((FilterFunction<MetadataRecord>) p -> p.getDateOfTransformation() == 1234)
.count();
final long recordNotEmpty = mOutput
.filter((FilterFunction<MetadataRecord>) p -> !StringUtils.isBlank(p.getBody()))
.count();
assertEquals(total, recordTs);
assertEquals(total, recordNotEmpty);
} }

88
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java
View File

@ -1,20 +1,12 @@
package eu.dnetlib.dhp.transformation; package eu.dnetlib.dhp.transformation;
import static org.junit.jupiter.api.Assertions.assertEquals; import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest;
import static org.junit.jupiter.api.Assertions.assertNotNull; import eu.dnetlib.dhp.aggregation.common.AggregationCounter;
import static org.mockito.Mockito.lenient; import eu.dnetlib.dhp.collection.CollectionJobTest;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import java.io.IOException; import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction;
import java.io.StringWriter; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import javax.xml.transform.stream.StreamSource;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
@ -24,52 +16,42 @@ import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.apache.spark.util.LongAccumulator; import org.apache.spark.util.LongAccumulator;
import org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.junit.jupiter.api.*; import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.api.io.TempDir; import org.junit.jupiter.api.io.TempDir;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
import eu.dnetlib.dhp.aggregation.common.AggregationCounter; import java.io.IOException;
import eu.dnetlib.dhp.collection.CollectionJobTest; import java.nio.file.Files;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import java.nio.file.Path;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord; import java.util.Collections;
import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction; import java.util.Map;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import java.util.stream.Collectors;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import java.util.stream.Stream;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import static eu.dnetlib.dhp.aggregation.common.AggregationConstants.MDSTORE_DATA_PATH;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.Mockito.lenient;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
public class TransformationJobTest { public class TransformationJobTest extends AbstractVocabularyTest {
private static SparkSession spark; private static SparkSession spark;
@Mock
private ISLookUpService isLookUpService;
private VocabularyGroup vocabularies;
@BeforeEach
public void setUp() throws ISLookUpException, IOException {
lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs());
lenient()
.when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY))
.thenReturn(synonyms());
vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService);
}
@BeforeAll @BeforeAll
public static void beforeAll() { public static void beforeAll() throws IOException, ISLookUpException {
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.setAppName(CollectionJobTest.class.getSimpleName()); conf.setAppName(CollectionJobTest.class.getSimpleName());
conf.setMaster("local"); conf.setMaster("local");
spark = SparkSession.builder().config(conf).getOrCreate(); spark = SparkSession.builder().config(conf).getOrCreate();
} }
@BeforeEach
public void setUp() throws IOException, ISLookUpException {
setUpVocabulary();
}
@AfterAll @AfterAll
public static void afterAll() { public static void afterAll() {
spark.stop(); spark.stop();
@ -101,8 +83,6 @@ public class TransformationJobTest {
mockupTrasformationRule("simpleTRule", "/eu/dnetlib/dhp/transform/ext_simple.xsl"); mockupTrasformationRule("simpleTRule", "/eu/dnetlib/dhp/transform/ext_simple.xsl");
// final String arguments = "-issm true -i %s -o %s -d 1 -w 1 -tp XSLT_TRANSFORM -tr simpleTRule";
final Map<String, String> parameters = Stream.of(new String[][] { final Map<String, String> parameters = Stream.of(new String[][] {
{ {
"dateOfTransformation", "1234" "dateOfTransformation", "1234"
@ -111,7 +91,7 @@ public class TransformationJobTest {
"transformationPlugin", "XSLT_TRANSFORM" "transformationPlugin", "XSLT_TRANSFORM"
}, },
{ {
"transformationRuleTitle", "simpleTRule" "transformationRuleId", "simpleTRule"
}, },
}).collect(Collectors.toMap(data -> data[0], data -> data[1])); }).collect(Collectors.toMap(data -> data[0], data -> data[1]));
@ -121,7 +101,7 @@ public class TransformationJobTest {
// TODO introduce useful assertions // TODO introduce useful assertions
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class); final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mOutput = spark.read().format("parquet").load(mdstore_output).as(encoder); final Dataset<MetadataRecord> mOutput = spark.read().format("parquet").load(mdstore_output+MDSTORE_DATA_PATH).as(encoder);
final Long total = mOutput.count(); final Long total = mOutput.count();
@ -151,13 +131,7 @@ public class TransformationJobTest {
Files.deleteIfExists(tempDirWithPrefix); Files.deleteIfExists(tempDirWithPrefix);
} }
private void mockupTrasformationRule(final String trule, final String path) throws Exception {
final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path));
lenient()
.when(isLookUpService.quickSearchProfile(String.format(TransformationFactory.TRULE_XQUERY, trule)))
.thenReturn(Collections.singletonList(trValue));
}
private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception { private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception {
final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path)); final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path));
@ -165,13 +139,5 @@ public class TransformationJobTest {
return new XSLTTransformationFunction(new AggregationCounter(la, la, la), trValue, 0, vocabularies); return new XSLTTransformationFunction(new AggregationCounter(la, la, la), trValue, 0, vocabularies);
} }
private List<String> vocs() throws IOException {
return IOUtils
.readLines(TransformationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/terms.txt"));
}
private List<String> synonyms() throws IOException {
return IOUtils
.readLines(TransformationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/synonyms.txt"));
}
} }