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WIP: promote job tests and test resources implementation snapshot

This commit is contained in:
Przemysław Jacewicz 2020-03-11 17:06:29 +01:00
parent 2e996d610f
commit 3f24593e51
37 changed files with 651 additions and 130 deletions
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179
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctionsTest.java
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@ -2,9 +2,8 @@ package eu.dnetlib.dhp.actionmanager;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Column;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
@ -13,13 +12,11 @@ import org.junit.BeforeClass;
import org.junit.Test;
import java.io.IOException;
import java.io.Serializable;
import java.util.Arrays;
import java.util.List;
import java.util.function.BiFunction;
import java.util.stream.Collectors;
import java.util.function.Function;
import static org.apache.spark.sql.functions.get_json_object;
import static org.junit.Assert.assertEquals;
public class PromoteActionSetFromHDFSFunctionsTest {
@ -32,6 +29,7 @@ public class PromoteActionSetFromHDFSFunctionsTest {
conf.setMaster("local");
conf.setAppName(PromoteActionSetFromHDFSFunctionsTest.class.getSimpleName());
conf.set("spark.driver.host", "localhost");
spark = SparkSession.builder().config(conf).getOrCreate();
}
@ -40,24 +38,93 @@ public class PromoteActionSetFromHDFSFunctionsTest {
spark.stop();
}
@Test
public void shouldJoinWithActionPayloadUsingIdAndMerge() {
// given
String id1 = "id1";
String id2 = "id2";
String id3 = "id3";
String id4 = "id4";
List<OafImpl> oafData = Arrays.asList(
createOafImpl(id1), createOafImpl(id2), createOafImpl(id3), createOafImpl(id4)
);
Dataset<OafImpl> oafDS = spark.createDataset(oafData, Encoders.bean(OafImpl.class));
List<String> actionPayloadData = Arrays.asList(
createActionPayload(id1),
createActionPayload(id2), createActionPayload(id2),
createActionPayload(id3), createActionPayload(id3), createActionPayload(id3)
);
Dataset<String> actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.STRING());
SerializableSupplier<Function<OafImpl, String>> oafIdFn = () -> OafImpl::getId;
SerializableSupplier<BiFunction<String, Class<OafImpl>, OafImpl>> actionPayloadToOafFn = () -> (s, clazz) -> {
try {
JsonNode jsonNode = new ObjectMapper().readTree(s);
String id = jsonNode.at("/id").asText();
return createOafImpl(id);
} catch (IOException e) {
throw new RuntimeException(e);
}
};
SerializableSupplier<BiFunction<OafImpl, OafImpl, OafImpl>> mergeAndGetFn = () -> (x, y) -> {
x.mergeFrom(y);
return x;
};
// when
List<OafImpl> results = PromoteActionSetFromHDFSFunctions
.joinOafEntityWithActionPayloadAndMerge(oafDS,
actionPayloadDS,
oafIdFn,
actionPayloadToOafFn,
mergeAndGetFn,
OafImpl.class)
.collectAsList();
// System.out.println(results.stream().map(x -> String.format("%s:%d", x.getId(), x.merged)).collect(Collectors.joining(",")));
// then
assertEquals(7, results.size());
results.forEach(result -> {
switch (result.getId()) {
case "id1":
case "id2":
case "id3":
assertEquals(2, result.merged);
break;
case "id4":
assertEquals(1, result.merged);
break;
}
});
}
@Test
public void shouldGroupOafEntitiesByIdAndMergeWithinGroup() {
// given
String id1 = "id1";
String id2 = "id2";
String id3 = "id3";
List<OafEntityImpl> entityData = Arrays.asList(
createOafEntityImpl(id1),
createOafEntityImpl(id2), createOafEntityImpl(id2),
createOafEntityImpl(id3), createOafEntityImpl(id3), createOafEntityImpl(id3)
List<OafImpl> oafData = Arrays.asList(
createOafImpl(id1),
createOafImpl(id2), createOafImpl(id2),
createOafImpl(id3), createOafImpl(id3), createOafImpl(id3)
);
Dataset<OafEntityImpl> entityDS = spark.createDataset(entityData, Encoders.bean(OafEntityImpl.class));
Dataset<OafImpl> oafDS = spark.createDataset(oafData, Encoders.bean(OafImpl.class));
SerializableSupplier<Function<OafImpl, String>> idFn = () -> OafImpl::getId;
SerializableSupplier<BiFunction<OafImpl, OafImpl, OafImpl>> mergeAndGetFn = () -> (x, y) -> {
x.mergeFrom(y);
return x;
};
// when
List<OafEntityImpl> results = PromoteActionSetFromHDFSFunctions
.groupEntitiesByIdAndMerge(entityDS, OafEntityImpl.class)
List<OafImpl> results = PromoteActionSetFromHDFSFunctions
.groupOafByIdAndMerge(oafDS,
idFn,
mergeAndGetFn,
OafImpl.class)
.collectAsList();
System.out.println(results.stream().map(x -> String.format("%s:%d", x.getId(), x.merged)).collect(Collectors.joining(",")));
// System.out.println(results.stream().map(x -> String.format("%s:%d", x.getId(), x.merged)).collect(Collectors.joining(",")));
// then
assertEquals(3, results.size());
@ -76,76 +143,20 @@ public class PromoteActionSetFromHDFSFunctionsTest {
});
}
@Test
public void shouldJoinWithActionPayloadUsingIdAndMerge() {
// given
String id1 = "id1";
String id2 = "id2";
String id3 = "id3";
String id4 = "id4";
List<OafEntityImpl> entityData = Arrays.asList(
createOafEntityImpl(id1), createOafEntityImpl(id2), createOafEntityImpl(id3), createOafEntityImpl(id4)
);
Dataset<OafEntityImpl> entityDS = spark.createDataset(entityData, Encoders.bean(OafEntityImpl.class));
List<String> actionPayloadData = Arrays.asList(
actionPayload(id1),
actionPayload(id2), actionPayload(id2),
actionPayload(id3), actionPayload(id3), actionPayload(id3)
);
Dataset<String> actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.STRING());
BiFunction<Dataset<OafEntityImpl>, Dataset<String>, Column> entityToActionPayloadJoinExpr = (left, right) ->
left.col("id").equalTo(get_json_object(right.col("value"), "$.id"));
BiFunction<String, Class<OafEntityImpl>, OafEntityImpl> actionPayloadToEntityFn =
(BiFunction<String, Class<OafEntityImpl>, OafEntityImpl> & Serializable) (s, clazz) -> {
try {
JsonNode jsonNode = new ObjectMapper().readTree(s);
String id = jsonNode.at("/id").asText();
OafEntityImpl x = new OafEntityImpl();
x.setId(id);
return x;
} catch (IOException e) {
throw new RuntimeException(e);
}
};
// when
List<OafEntityImpl> results = PromoteActionSetFromHDFSFunctions
.joinEntitiesWithActionPayloadAndMerge(entityDS,
actionPayloadDS,
entityToActionPayloadJoinExpr,
actionPayloadToEntityFn,
OafEntityImpl.class)
.collectAsList();
System.out.println(results.stream().map(x -> String.format("%s:%d", x.getId(), x.merged)).collect(Collectors.joining(",")));
// then
assertEquals(7, results.size());
results.forEach(result -> {
switch (result.getId()) {
case "id1":
assertEquals(2, result.merged);
break;
case "id2":
assertEquals(2, result.merged);
break;
case "id3":
assertEquals(2, result.merged);
break;
case "id4":
assertEquals(1, result.merged);
break;
}
});
}
public static class OafEntityImpl extends OafEntity {
public static class OafImpl extends Oaf {
private String id;
private int merged = 1;
@Override
public void mergeFrom(OafEntity e) {
merged += ((OafEntityImpl) e).merged;
public void mergeFrom(Oaf e) {
merged += ((OafImpl) e).merged;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public int getMerged() {
@ -157,13 +168,13 @@ public class PromoteActionSetFromHDFSFunctionsTest {
}
}
private static OafEntityImpl createOafEntityImpl(String id) {
OafEntityImpl x = new OafEntityImpl();
private static OafImpl createOafImpl(String id) {
OafImpl x = new OafImpl();
x.setId(id);
return x;
}
private static String actionPayload(String id) {
private static String createActionPayload(String id) {
return String.format("{\"id\":\"%s\"}", id);
}
}

278
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJobTest.java
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@ -1,79 +1,269 @@
package eu.dnetlib.dhp.actionmanager;
import org.junit.Before;
import org.junit.Test;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.*;
import scala.Tuple2;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Comparator;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import static org.apache.spark.sql.functions.base64;
import static org.apache.spark.sql.functions.col;
import static org.junit.Assert.*;
public class PromoteActionSetFromHDFSJobTest {
private ClassLoader cl = getClass().getClassLoader();
private static SparkSession spark;
private static Configuration configuration;
private Path workingDir;
private Path inputDir;
private Path inputGraphDir;
private Path inputActionSetsDir;
private Path outputDir;
private ClassLoader cl = getClass().getClassLoader();
@BeforeClass
public static void beforeClass() throws IOException {
SparkConf conf = new SparkConf();
conf.setAppName(PromoteActionSetFromHDFSJobTest.class.getSimpleName());
conf.setMaster("local");
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(new Class[]{
Author.class,
Context.class,
Country.class,
DataInfo.class,
eu.dnetlib.dhp.schema.oaf.Dataset.class,
Datasource.class,
ExternalReference.class,
ExtraInfo.class,
Field.class,
GeoLocation.class,
Instance.class,
Journal.class,
KeyValue.class,
Oaf.class,
OafEntity.class,
OAIProvenance.class,
Organization.class,
OriginDescription.class,
OtherResearchProduct.class,
Project.class,
Publication.class,
Qualifier.class,
Relation.class,
Result.class,
Software.class,
StructuredProperty.class
});
spark = SparkSession.builder().config(conf).getOrCreate();
configuration = Job.getInstance().getConfiguration();
}
@Before
public void before() throws IOException {
workingDir = Files.createTempDirectory("promote_action_set");
inputDir = workingDir.resolve("input");
inputGraphDir = inputDir.resolve("graph");
inputActionSetsDir = inputDir.resolve("action_sets");
outputDir = workingDir.resolve("output");
}
// @After
// public void after() throws IOException {
// FileUtils.deleteDirectory(workingDir.toFile());
// }
@After
public void after() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
}
@AfterClass
public static void afterAll() {
spark.stop();
}
@Test
public void shouldReadAtomicActionsFromHDFSAndWritePartitionedAsParquetFiles() throws Exception {
public void shouldThrowWhenGraphTableIsInvalid() {
fail("not yet implemented");
}
@Test
public void shouldReadActionsFromHDFSAndPromoteThemForDatasetsUsingMergeFromStrategy() throws Exception {
readActionsFromHDFSAndPromoteThemFor("dataset",
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
eu.dnetlib.dhp.schema.oaf.Dataset.class);
}
@Test
public void shouldReadActionsFromHDFSAndPromoteThemForDatasourcesUsingMergeFromStrategy() throws Exception {
readActionsFromHDFSAndPromoteThemFor("datasource",
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
Datasource.class);
}
@Test
public void shouldReadActionsFromHDFSAndPromoteThemForOrganizationUsingMergeFromStrategy() throws Exception {
readActionsFromHDFSAndPromoteThemFor("organization",
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
Organization.class);
}
@Test
public void shouldReadActionsFromHDFSAndPromoteThemForOtherResearchProductUsingMergeFromStrategy() throws Exception {
readActionsFromHDFSAndPromoteThemFor("otherresearchproduct",
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
OtherResearchProduct.class);
}
@Test
public void shouldReadActionsFromHDFSAndPromoteThemForProjectUsingMergeFromStrategy() throws Exception {
readActionsFromHDFSAndPromoteThemFor("project",
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
Project.class);
}
@Test
public void shouldReadActionsFromHDFSAndPromoteThemForPublicationUsingMergeFromStrategy() throws Exception {
readActionsFromHDFSAndPromoteThemFor("publication",
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
Publication.class);
}
@Test
public void shouldReadActionsFromHDFSAndPromoteThemForRelationUsingMergeFromStrategy() throws Exception {
readActionsFromHDFSAndPromoteThemFor("relation",
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
Relation.class);
}
@Test
public void shouldReadActionsFromHDFSAndPromoteThemForSoftwareUsingMergeFromStrategy() throws Exception {
readActionsFromHDFSAndPromoteThemFor("software",
OafMergeAndGet.Strategy.MERGE_FROM_AND_GET,
Software.class);
}
private <T extends Oaf> void readActionsFromHDFSAndPromoteThemFor(String graphTableName,
OafMergeAndGet.Strategy strategy,
Class<T> clazz) throws Exception {
// given
// NOTE: test resource should contain atomic actions in a human readable form, probably as json files; here the
// files should be converted to a serialized format and written out to workingDir/input
// for current testing: actions from iis export, given as sequence file are copied to workingDir/input/
//graph
Path inputGraphDir = inputDir.resolve("graph");
Files.createDirectories(inputGraphDir);
copyFiles(Paths.get(Objects.requireNonNull(cl.getResource("graph")).getFile()), inputGraphDir);
//actions
Path inputActionsDir = inputDir.resolve("actions");
Files.createDirectories(inputActionsDir);
Path inputEntitiesPatentDir = inputActionsDir.resolve("entities_patent");
Files.createDirectories(inputEntitiesPatentDir);
copyFiles(Paths.get(Objects.requireNonNull(cl.getResource("actions/entities_patent")).getFile()), inputEntitiesPatentDir);
Path inputEntitiesSoftwareDir = inputActionsDir.resolve("entities_software");
Files.createDirectories(inputEntitiesSoftwareDir);
copyFiles(Paths.get(Objects.requireNonNull(cl.getResource("actions/entities_software")).getFile()), inputEntitiesSoftwareDir);
String inputActionSetPaths = String.join(",", inputEntitiesSoftwareDir.toString()); //inputEntitiesPatentDir.toString(),
String inputGraphTableJsonDumpPath =
String.format("%s/%s.json", "eu/dnetlib/dhp/actionmanager/input/graph", graphTableName);
createGraphTableFor(inputGraphTableJsonDumpPath, graphTableName, clazz);
String inputActionSetPaths = createActionSets();
Path outputGraphDir = outputDir.resolve("graph");
// when
PromoteActionSetFromHDFSJob.main(new String[]{
"-master", "local[*]",
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-inputGraphPath", inputGraphDir.toString(),
"-inputActionSetPaths", inputActionSetPaths,
"-outputGraphPath", outputDir.toString()
"-graphTableName", graphTableName,
"-outputGraphPath", outputGraphDir.toString(),
"mergeAndGetStrategy", strategy.name()
});
// then
Path outputGraphTableDir = outputGraphDir.resolve(graphTableName);
assertTrue(Files.exists(outputGraphDir));
List<T> outputGraphTableRows = readGraphTableFromParquet(outputGraphTableDir.toString(), clazz).collectAsList();
outputGraphTableRows.sort(Comparator.comparingInt(Object::hashCode));
assertEquals(10, outputGraphTableRows.size());
String expectedOutputGraphTableJsonDumpPath =
String.format("%s/%s/%s.json", "eu/dnetlib/dhp/actionmanager/output/graph", strategy.name().toLowerCase(), graphTableName);
Path expectedOutputGraphTableJsonDumpFile = Paths
.get(Objects.requireNonNull(cl.getResource(expectedOutputGraphTableJsonDumpPath)).getFile());
List<T> expectedOutputGraphTableRows = readGraphTableFromJSON(
expectedOutputGraphTableJsonDumpFile, clazz)
.collectAsList();
expectedOutputGraphTableRows.sort(Comparator.comparingInt(Object::hashCode));
assertArrayEquals(expectedOutputGraphTableRows.toArray(), outputGraphTableRows.toArray());
}
private static void copyFiles(Path source, Path target) throws IOException {
Files.list(source).forEach(f -> {
try {
if (Files.isDirectory(f)) {
Path subTarget = Files.createDirectories(target.resolve(f.getFileName()));
copyFiles(f, subTarget);
} else {
Files.copy(f, target.resolve(f.getFileName()));
}
} catch (IOException e) {
e.printStackTrace();
throw new RuntimeException(e);
private <T extends Oaf> void createGraphTableFor(String inputGraphTableJsonDumpPath,
String inputGraphTableDirRelativePath,
Class<T> clazz) {
Path inputGraphTableJsonDumpFile = Paths
.get(Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)).getFile());
Dataset<T> inputGraphTableDS = readGraphTableFromJSON(inputGraphTableJsonDumpFile, clazz);
Path inputGraphTableDir = inputGraphDir.resolve(inputGraphTableDirRelativePath);
inputGraphTableDS
.toJSON()
.javaRDD()
.mapToPair(json -> new Tuple2<>(new Text(clazz.getCanonicalName()), new Text(json)))
.saveAsNewAPIHadoopFile(inputGraphTableDir.toString(),
Text.class,
Text.class,
SequenceFileOutputFormat.class,
configuration);
}
private String createActionSets() throws IOException {
Path inputActionPayloadJsonDumpsDir = Paths
.get(Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/input/action_sets/"))
.getFile());
Files
.list(inputActionPayloadJsonDumpsDir)
.forEach(inputActionPayloadJsonDump -> {
String inputActionSetId = inputActionPayloadJsonDump.getFileName().toString();
Path inputActionSetDir = inputActionSetsDir.resolve(inputActionPayloadJsonDump.getFileName());
spark.read()
.textFile(inputActionPayloadJsonDump.toString())
.withColumn("TargetValue", base64(col("value")))
.select("TargetValue")
.toJSON()
.javaRDD()
.mapToPair(json -> new Tuple2<>(new Text(inputActionSetId), new Text(json)))
.saveAsNewAPIHadoopFile(inputActionSetDir.toString(),
Text.class,
Text.class,
SequenceFileOutputFormat.class,
configuration);
});
return Files.list(inputActionSetsDir).map(Path::toString).collect(Collectors.joining(","));
}
private static <T extends Oaf> Dataset<T> readGraphTableFromJSON(Path path, Class<T> clazz) {
return spark.read()
.format("json")
.load(path.toString())
.toJSON()
.map((MapFunction<String, T>) json -> newObjectMapper().readValue(json, clazz), Encoders.bean(clazz));
}
//TODO: enable strict deserialization later
private static ObjectMapper newObjectMapper() {
return new ObjectMapper().disable(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES);
}
private static <T extends Oaf> Dataset<T> readGraphTableFromParquet(String outputGraphTablePath, Class<T> clazz) {
return spark.read()
.format("parquet")
.load(outputGraphTablePath)
.as(Encoders.bean(clazz));
}
}

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@ -0,0 +1,20 @@
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::007a4870b31056f89b768cf508e1538e"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::007a4870b31056f89b768cf508e1538e"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::9ea9c0996c87e1dc7fc69f94b5ed0010"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::9ea9c0996c87e1dc7fc69f94b5ed0010"}
{"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::d0bbea1f5bed5864d1904eb602e608a6"}
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