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unit test for GraphHiveImporterJob

This commit is contained in:
Claudio Atzori 2020-04-08 13:24:43 +02:00
parent ba9f07a6fe
commit 47f3d9b757
11 changed files with 204 additions and 151 deletions
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14
dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java
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@ -29,6 +29,20 @@ public class SparkSessionSupport {
runWithSparkSession(c -> SparkSession.builder().config(c).getOrCreate(), conf, isSparkSessionManaged, fn);
}
/**
* Runs a given function using SparkSession created with hive support and using default builder and supplied SparkConf.
* Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession created externally.
*
* @param conf SparkConf instance
* @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession
*/
public static void runWithSparkHiveSession(SparkConf conf,
Boolean isSparkSessionManaged,
ThrowingConsumer<SparkSession, Exception> fn) {
runWithSparkSession(c -> SparkSession.builder().config(c).enableHiveSupport().getOrCreate(), conf, isSparkSessionManaged, fn);
}
/**
* Runs a given function using SparkSession created using supplied builder and supplied SparkConf. Stops SparkSession
* when SparkSession is managed. Allows to reuse SparkSession created externally.

30
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java
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@ -1,6 +1,7 @@
package eu.dnetlib.dhp.actionmanager.promote;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
@ -45,34 +46,7 @@ public class PromoteActionPayloadForGraphTableJobTest {
conf.setAppName(PromoteActionPayloadForGraphTableJobTest.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
});
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
spark = SparkSession.builder().config(conf).getOrCreate();
}

69
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJob.java Normal file
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@ -0,0 +1,69 @@
package eu.dnetlib.dhp.oa.graph;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Optional;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
public class GraphHiveImporterJob {
private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJob.class);
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString(GraphHiveImporterJob.class.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/input_graph_hive_parameters.json")));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath);
String hiveMetastoreUris = parser.get("hiveMetastoreUris");
log.info("hiveMetastoreUris: {}", hiveMetastoreUris);
String hiveDbName = parser.get("hiveDbName");
log.info("hiveDbName: {}", hiveDbName);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", hiveMetastoreUris);
runWithSparkHiveSession(conf, isSparkSessionManaged,
spark -> loadGraphAsHiveDB(spark, inputPath, hiveDbName));
}
// protected for testing
private static void loadGraphAsHiveDB(SparkSession spark, String inputPath, String hiveDbName) {
spark.sql(String.format("DROP DATABASE IF EXISTS %s CASCADE", hiveDbName));
spark.sql(String.format("CREATE DATABASE IF NOT EXISTS %s", hiveDbName));
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
// Read the input file and convert it into RDD of serializable object
ModelSupport.oafTypes.forEach((name, clazz) -> spark.createDataset(sc.textFile(inputPath + "/" + name)
.map(s -> new ObjectMapper().readValue(s, clazz))
.rdd(), Encoders.bean(clazz))
.write()
.mode(SaveMode.Overwrite)
.saveAsTable(hiveDbName + "." + name));
}
}

62
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/SparkGraphImporterJob.java
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@ -1,62 +0,0 @@
package eu.dnetlib.dhp.oa.graph;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
public class SparkGraphImporterJob {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString(SparkGraphImporterJob.class.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/input_graph_parameters.json")));
parser.parseArgument(args);
new SparkGraphImporterJob().run(parser);
}
private void run(ArgumentApplicationParser parser) {
try(SparkSession spark = getSparkSession(parser)) {
final String inputPath = parser.get("sourcePath");
final String hiveDbName = parser.get("hive_db_name");
runWith(spark, inputPath, hiveDbName);
}
}
// protected for testing
protected void runWith(SparkSession spark, String inputPath, String hiveDbName) {
spark.sql(String.format("DROP DATABASE IF EXISTS %s CASCADE", hiveDbName));
spark.sql(String.format("CREATE DATABASE IF NOT EXISTS %s", hiveDbName));
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
// Read the input file and convert it into RDD of serializable object
ModelSupport.oafTypes.forEach((name, clazz) -> spark.createDataset(sc.textFile(inputPath + "/" + name)
.map(s -> new ObjectMapper().readValue(s, clazz))
.rdd(), Encoders.bean(clazz))
.write()
.mode(SaveMode.Overwrite)
.saveAsTable(hiveDbName + "." + name));
}
private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
return SparkSession
.builder()
.appName(SparkGraphImporterJob.class.getSimpleName())
.master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate();
}
}

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/oozie_app/config-default.xml → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/config-default.xml
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0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/oozie_app/lib/scripts/postprocessing.sql → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/postprocessing.sql
View File

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/oozie_app/workflow.xml → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml
View File

@ -49,7 +49,7 @@
<master>yarn</master>
<mode>cluster</mode>
<name>MapGraphAsHiveDB</name>
<class>eu.dnetlib.dhp.oa.graph.SparkGraphImporterJob</class>
<class>eu.dnetlib.dhp.oa.graph.GraphHiveImporterJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}

26
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_graph_hive_parameters.json Normal file
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@ -0,0 +1,26 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "in",
"paramLongName": "inputPath",
"paramDescription": "the path to the graph data dump to read",
"paramRequired": true
},
{
"paramName": "hmu",
"paramLongName": "hiveMetastoreUris",
"paramDescription": "the hive metastore uris",
"paramRequired": true
},
{
"paramName": "db",
"paramLongName": "hiveDbName",
"paramDescription": "the target hive database name",
"paramRequired": true
}
]

6
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_graph_parameters.json
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@ -1,6 +0,0 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
{"paramName":"h", "paramLongName":"hive_metastore_uris","paramDescription": "the hive metastore uris", "paramRequired": true},
{"paramName":"db", "paramLongName":"hive_db_name", "paramDescription": "the target hive database name", "paramRequired": true}
]

92
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java Normal file
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@ -0,0 +1,92 @@
package eu.dnetlib.dhp.oa.graph;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang3.RandomStringUtils;
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.jupiter.api.*;
import org.junit.jupiter.api.io.TempDir;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Objects;
public class GraphHiveImporterJobTest {
private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJobTest.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ClassLoader cl = GraphHiveImporterJobTest.class.getClassLoader();
public static final String JDBC_DERBY_TEMPLATE = "jdbc:derby:;databaseName=%s/junit_metastore_db;create=true";
private static SparkSession spark;
private static Path workingDir;
private static String dbName;
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(GraphHiveImporterJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
dbName = RandomStringUtils.randomAlphabetic(5);
log.info("using DB name {}", "test_" + dbName);
SparkConf conf = new SparkConf();
conf.setAppName(GraphHiveImporterJobTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
conf.set("javax.jdo.option.ConnectionURL", String.format(JDBC_DERBY_TEMPLATE, workingDir.resolve("warehouse").toString()));
spark = SparkSession
.builder()
.appName(GraphHiveImporterJobTest.class.getSimpleName())
.config(conf)
.enableHiveSupport()
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public void testImportGraphAsHiveDB() throws Exception {
GraphHiveImporterJob.main(new String[]{
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-inputPath", getClass().getResource("/eu/dnetlib/dhp/oa/graph/sample").getPath(),
"-hiveMetastoreUris", "",
"-hiveDbName", dbName
});
ModelSupport.oafTypes.forEach((name, clazz) -> {
long count = spark.read().table(dbName + "." + name).count();
int expected = name.equals("relation") ? 100 : 10;
Assertions.assertEquals(expected, count, String.format("%s should be %s", name, expected));
});
}
}

54
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/SparkGraphImporterJobTest.java
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@ -1,54 +0,0 @@
package eu.dnetlib.dhp.oa.graph;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
import java.nio.file.Path;
public class SparkGraphImporterJobTest {
private final static String TEST_DB_NAME = "test";
@Test
public void testImport(@TempDir Path outPath) {
try(SparkSession spark = testSparkSession(outPath.toString())) {
new SparkGraphImporterJob().runWith(
spark,
getClass().getResource("/eu/dnetlib/dhp/oa/graph/sample").getPath(),
TEST_DB_NAME);
GraphMappingUtils.types.forEach((name, clazz) -> {
final long count = spark.read().table(TEST_DB_NAME + "." + name).count();
if (name.equals("relation")) {
Assertions.assertEquals(100, count, String.format("%s should be 100", name));
} else {
Assertions.assertEquals(10, count, String.format("%s should be 10", name));
}
});
}
}
private SparkSession testSparkSession(final String inputPath) {
SparkConf conf = new SparkConf();
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("hive.metastore.warehouse.dir", inputPath + "/warehouse");
conf.set("spark.sql.warehouse.dir", inputPath);
conf.set("javax.jdo.option.ConnectionURL", String.format("jdbc:derby:;databaseName=%s/junit_metastore_db;create=true", inputPath));
conf.set("spark.ui.enabled", "false");
return SparkSession
.builder()
.appName(SparkGraphImporterJobTest.class.getSimpleName())
.master("local[*]")
.config(conf)
.enableHiveSupport()
.getOrCreate();
}
}