[dhp-actionmanager] partitioning spark job added
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przemek
parent
f9f7350bb9
commit
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package eu.dnetlib.dhp.actionmanager.partition;
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import eu.dnetlib.dhp.actionmanager.common.HdfsSupport;
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import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.types.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.List;
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import java.util.Optional;
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import static eu.dnetlib.dhp.actionmanager.common.SparkSessionSupport.runWithSparkSession;
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import static org.apache.spark.sql.functions.*;
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/**
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* Partitions given set of action sets by payload type.
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*/
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public class PartitionActionSetsByPayloadTypeJob {
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private static final Logger logger = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class);
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private static final StructType KV_SCHEMA = StructType$.MODULE$.apply(
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Arrays.asList(
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StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()),
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StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty())
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));
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private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$.apply(
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Arrays.asList(
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StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()),
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StructField$.MODULE$.apply("payload", DataTypes.StringType, false, Metadata.empty())
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));
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private static final String INPUT_ACTION_SET_PATHS_SEPARATOR = ",";
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils.toString(
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PromoteActionPayloadForGraphTableJob.class
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.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputActionSetPaths = parser.get("inputActionSetPaths");
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logger.info("inputActionSetPaths: {}", inputActionSetPaths);
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String outputPath = parser.get("outputPath");
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logger.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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runWithSparkSession(conf, isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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readAndWriteActionSetsFromPaths(spark,
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Arrays.asList(inputActionSetPaths.split(INPUT_ACTION_SET_PATHS_SEPARATOR)),
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outputPath);
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});
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}
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private static void removeOutputDir(SparkSession spark, String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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private static void readAndWriteActionSetsFromPaths(SparkSession spark,
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List<String> inputActionSetPaths,
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String outputPath) {
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inputActionSetPaths
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.forEach(inputActionSetPath -> {
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Dataset<Row> actionDS = readActionSetFromPath(spark, inputActionSetPath);
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saveActions(actionDS, outputPath);
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});
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}
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private static Dataset<Row> readActionSetFromPath(SparkSession spark,
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String path) {
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logger.info("Reading actions from path: {}", path);
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List<String> files = HdfsSupport.listFiles(path, spark.sparkContext().hadoopConfiguration());
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logger.info("Found files: {}", String.join(",", files));
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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return files
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.stream()
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.map(file -> {
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JavaRDD<Row> rdd = sc
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.sequenceFile(file, Text.class, Text.class)
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.map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
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return spark.createDataFrame(rdd, KV_SCHEMA)
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.withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
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.select(expr("atomic_action.*"));
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})
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.reduce(spark.createDataFrame(Collections.emptyList(), ATOMIC_ACTION_SCHEMA), Dataset::union);
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}
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private static void saveActions(Dataset<Row> actionDS,
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String path) {
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logger.info("Saving actions to path: {}", path);
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actionDS
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.write()
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.partitionBy("clazz")
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.mode(SaveMode.Append)
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.parquet(path);
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}
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}
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[
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{
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "TODO",
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"paramRequired": false
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},
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{
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"paramName": "iasp",
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"paramLongName": "inputActionSetPaths",
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"paramDescription": "TODO",
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"paramRequired": true
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},
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{
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"paramName": "opasp",
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"paramLongName": "outputPath",
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"paramDescription": "TODO",
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"paramRequired": true
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}
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]
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@ -0,0 +1,190 @@
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package eu.dnetlib.dhp.actionmanager.partition;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.mapreduce.Job;
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import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.Row;
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import org.apache.spark.sql.SparkSession;
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import org.apache.spark.sql.types.*;
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import org.junit.jupiter.api.*;
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import org.junit.jupiter.api.io.TempDir;
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import scala.Tuple2;
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import scala.collection.mutable.Seq;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.util.*;
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import java.util.stream.Collectors;
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import static eu.dnetlib.dhp.actionmanager.common.ThrowingSupport.rethrowAsRuntimeException;
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import static org.apache.spark.sql.functions.*;
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import static org.junit.jupiter.api.Assertions.assertIterableEquals;
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import static scala.collection.JavaConversions.mutableSeqAsJavaList;
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public class PartitionActionSetsByPayloadTypeJobTest {
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private static final ClassLoader cl = PartitionActionSetsByPayloadTypeJobTest.class.getClassLoader();
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private static Configuration configuration;
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private static SparkSession spark;
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$.apply(
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Arrays.asList(
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StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()),
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StructField$.MODULE$.apply("payload", DataTypes.StringType, false, Metadata.empty())
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));
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@BeforeAll
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public static void beforeAll() throws IOException {
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configuration = Job.getInstance().getConfiguration();
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SparkConf conf = new SparkConf();
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conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName());
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conf.setMaster("local");
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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spark = SparkSession.builder().config(conf).getOrCreate();
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}
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@AfterAll
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public static void afterAll() {
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spark.stop();
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}
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@DisplayName("Job")
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@Nested
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class Main {
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@Test
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public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception {
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// given
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Path inputActionSetsDir = workingDir.resolve("input").resolve("action_sets");
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Path outputDir = workingDir.resolve("output");
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Map<String, List<String>> oafsByClassName = createActionSets(inputActionSetsDir);
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// when
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PartitionActionSetsByPayloadTypeJob.main(new String[]{
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputActionSetPaths", inputActionSetsDir.toString(),
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"-outputPath", outputDir.toString()
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});
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// then
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Files.exists(outputDir);
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assertForOafType(outputDir, oafsByClassName, eu.dnetlib.dhp.schema.oaf.Dataset.class);
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assertForOafType(outputDir, oafsByClassName, Datasource.class);
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assertForOafType(outputDir, oafsByClassName, Organization.class);
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assertForOafType(outputDir, oafsByClassName, OtherResearchProduct.class);
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assertForOafType(outputDir, oafsByClassName, Project.class);
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assertForOafType(outputDir, oafsByClassName, Publication.class);
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assertForOafType(outputDir, oafsByClassName, Result.class);
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assertForOafType(outputDir, oafsByClassName, Relation.class);
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assertForOafType(outputDir, oafsByClassName, Software.class);
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}
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}
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private static Map<String, List<String>> createActionSets(Path inputActionSetsDir) throws IOException {
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Path inputActionSetJsonDumpsDir = Paths
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.get(Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/partition/input/"))
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.getFile());
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Map<String, List<String>> oafsByType = new HashMap<>();
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Files
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.list(inputActionSetJsonDumpsDir)
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.forEach(inputActionSetJsonDumpFile -> {
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String inputActionSetId = inputActionSetJsonDumpFile.getFileName().toString();
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Path inputActionSetDir = inputActionSetsDir.resolve(inputActionSetId);
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Dataset<String> actionDS = readActionsFromJsonDump(inputActionSetJsonDumpFile.toString())
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.cache();
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writeActionsAsJobInput(actionDS, inputActionSetId, inputActionSetDir.toString());
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Map<String, List<String>> actionSetOafsByType = actionDS
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.withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
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.select(expr("atomic_action.*"))
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.groupBy(col("clazz"))
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.agg(collect_list(col("payload")).as("payload_list"))
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.collectAsList()
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.stream()
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.map(row -> new AbstractMap.SimpleEntry<>(row.<String>getAs("clazz"),
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mutableSeqAsJavaList(row.<Seq<String>>getAs("payload_list"))))
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.collect(Collectors.toMap(AbstractMap.SimpleEntry::getKey, AbstractMap.SimpleEntry::getValue));
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actionSetOafsByType.keySet()
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.forEach(x -> {
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if (oafsByType.containsKey(x)) {
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List<String> collected = new ArrayList<>();
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collected.addAll(oafsByType.get(x));
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collected.addAll(actionSetOafsByType.get(x));
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oafsByType.put(x, collected);
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} else {
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oafsByType.put(x, actionSetOafsByType.get(x));
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}
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});
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});
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return oafsByType;
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}
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private static Dataset<String> readActionsFromJsonDump(String path) {
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return spark
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.read()
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.textFile(path);
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}
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private static void writeActionsAsJobInput(Dataset<String> actionDS,
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String inputActionSetId,
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String path) {
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actionDS
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.javaRDD()
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.mapToPair(json -> new Tuple2<>(new Text(inputActionSetId), new Text(json)))
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.saveAsNewAPIHadoopFile(path,
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Text.class,
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Text.class,
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SequenceFileOutputFormat.class,
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configuration);
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}
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private static <T extends Oaf> void assertForOafType(Path outputDir, Map<String, List<String>> oafsByClassName, Class<T> clazz) {
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Path outputDatasetDir = outputDir.resolve(String.format("clazz=%s", clazz.getCanonicalName()));
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Files.exists(outputDatasetDir);
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List<T> actuals = readActionPayloadFromJobOutput(outputDatasetDir.toString(), clazz).collectAsList();
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actuals.sort(Comparator.comparingInt(Object::hashCode));
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List<T> expecteds = oafsByClassName.get(clazz.getCanonicalName()).stream()
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.map(json -> mapToOaf(json, clazz))
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.sorted(Comparator.comparingInt(Object::hashCode))
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.collect(Collectors.toList());
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assertIterableEquals(expecteds, actuals);
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}
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private static <T extends Oaf> Dataset<T> readActionPayloadFromJobOutput(String path,
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Class<T> clazz) {
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return spark
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.read()
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.parquet(path)
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.map((MapFunction<Row, T>) value -> OBJECT_MAPPER.readValue(value.<String>getAs("payload"), clazz),
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Encoders.bean(clazz));
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}
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private static <T extends Oaf> T mapToOaf(String json, Class<T> clazz) {
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return rethrowAsRuntimeException(
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() -> OBJECT_MAPPER.readValue(json, clazz),
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String.format("failed to map json to class: json=%s, class=%s", json, clazz.getCanonicalName())
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);
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}
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}
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