From e21bb89dbdbbf3d605272f74520dc0732bcad41f Mon Sep 17 00:00:00 2001 From: pjacewicz Date: Wed, 1 Apr 2020 18:41:29 +0200 Subject: [PATCH] [dhp-actionmanager] partitioning spark job added --- .../PartitionActionSetsByPayloadTypeJob.java | 120 +++++++++++ ...sets_by_payload_type_input_parameters.json | 20 ++ ...rtitionActionSetsByPayloadTypeJobTest.java | 190 ++++++++++++++++++ .../partition/input/action_set_1_payload.json | 90 +++++++++ .../partition/input/action_set_2_payload.json | 90 +++++++++ 5 files changed, 510 insertions(+) create mode 100644 dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java create mode 100644 dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json create mode 100644 dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/partition/input/action_set_1_payload.json create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/partition/input/action_set_2_payload.json diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java new file mode 100644 index 000000000..5b977c4ff --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java @@ -0,0 +1,120 @@ +package eu.dnetlib.dhp.actionmanager.partition; + +import eu.dnetlib.dhp.actionmanager.common.HdfsSupport; +import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.*; +import org.apache.spark.sql.types.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.Arrays; +import java.util.Collections; +import java.util.List; +import java.util.Optional; + +import static eu.dnetlib.dhp.actionmanager.common.SparkSessionSupport.runWithSparkSession; +import static org.apache.spark.sql.functions.*; + +/** + * Partitions given set of action sets by payload type. + */ +public class PartitionActionSetsByPayloadTypeJob { + + private static final Logger logger = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class); + + private static final StructType KV_SCHEMA = StructType$.MODULE$.apply( + Arrays.asList( + StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()), + StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty()) + )); + + private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$.apply( + Arrays.asList( + StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()), + StructField$.MODULE$.apply("payload", DataTypes.StringType, false, Metadata.empty()) + )); + + private static final String INPUT_ACTION_SET_PATHS_SEPARATOR = ","; + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils.toString( + PromoteActionPayloadForGraphTableJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputActionSetPaths = parser.get("inputActionSetPaths"); + logger.info("inputActionSetPaths: {}", inputActionSetPaths); + + String outputPath = parser.get("outputPath"); + logger.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + + runWithSparkSession(conf, isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + readAndWriteActionSetsFromPaths(spark, + Arrays.asList(inputActionSetPaths.split(INPUT_ACTION_SET_PATHS_SEPARATOR)), + outputPath); + }); + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + private static void readAndWriteActionSetsFromPaths(SparkSession spark, + List inputActionSetPaths, + String outputPath) { + inputActionSetPaths + .forEach(inputActionSetPath -> { + Dataset actionDS = readActionSetFromPath(spark, inputActionSetPath); + saveActions(actionDS, outputPath); + }); + } + + private static Dataset readActionSetFromPath(SparkSession spark, + String path) { + logger.info("Reading actions from path: {}", path); + + List files = HdfsSupport.listFiles(path, spark.sparkContext().hadoopConfiguration()); + logger.info("Found files: {}", String.join(",", files)); + + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + return files + .stream() + .map(file -> { + JavaRDD rdd = sc + .sequenceFile(file, Text.class, Text.class) + .map(x -> RowFactory.create(x._1().toString(), x._2().toString())); + return spark.createDataFrame(rdd, KV_SCHEMA) + .withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA)) + .select(expr("atomic_action.*")); + }) + .reduce(spark.createDataFrame(Collections.emptyList(), ATOMIC_ACTION_SCHEMA), Dataset::union); + } + + private static void saveActions(Dataset actionDS, + String path) { + logger.info("Saving actions to path: {}", path); + actionDS + .write() + .partitionBy("clazz") + .mode(SaveMode.Append) + .parquet(path); + } +} diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json new file mode 100644 index 000000000..38630bc92 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "TODO", + "paramRequired": false + }, + { + "paramName": "iasp", + "paramLongName": "inputActionSetPaths", + "paramDescription": "TODO", + "paramRequired": true + }, + { + "paramName": "opasp", + "paramLongName": "outputPath", + "paramDescription": "TODO", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java new file mode 100644 index 000000000..644bf19e5 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java @@ -0,0 +1,190 @@ +package eu.dnetlib.dhp.actionmanager.partition; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest; +import eu.dnetlib.dhp.schema.oaf.*; +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.Row; +import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.types.*; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.io.TempDir; +import scala.Tuple2; +import scala.collection.mutable.Seq; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.*; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.actionmanager.common.ThrowingSupport.rethrowAsRuntimeException; +import static org.apache.spark.sql.functions.*; +import static org.junit.jupiter.api.Assertions.assertIterableEquals; +import static scala.collection.JavaConversions.mutableSeqAsJavaList; + +public class PartitionActionSetsByPayloadTypeJobTest { + private static final ClassLoader cl = PartitionActionSetsByPayloadTypeJobTest.class.getClassLoader(); + + private static Configuration configuration; + private static SparkSession spark; + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$.apply( + Arrays.asList( + StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()), + StructField$.MODULE$.apply("payload", DataTypes.StringType, false, Metadata.empty()) + )); + + @BeforeAll + public static void beforeAll() throws IOException { + configuration = Job.getInstance().getConfiguration(); + SparkConf conf = new SparkConf(); + conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName()); + conf.setMaster("local"); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + spark = SparkSession.builder().config(conf).getOrCreate(); + } + + @AfterAll + public static void afterAll() { + spark.stop(); + } + + @DisplayName("Job") + @Nested + class Main { + + @Test + public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception { + // given + Path inputActionSetsDir = workingDir.resolve("input").resolve("action_sets"); + Path outputDir = workingDir.resolve("output"); + + Map> oafsByClassName = createActionSets(inputActionSetsDir); + + // when + PartitionActionSetsByPayloadTypeJob.main(new String[]{ + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-inputActionSetPaths", inputActionSetsDir.toString(), + "-outputPath", outputDir.toString() + }); + + // then + Files.exists(outputDir); + + assertForOafType(outputDir, oafsByClassName, eu.dnetlib.dhp.schema.oaf.Dataset.class); + assertForOafType(outputDir, oafsByClassName, Datasource.class); + assertForOafType(outputDir, oafsByClassName, Organization.class); + assertForOafType(outputDir, oafsByClassName, OtherResearchProduct.class); + assertForOafType(outputDir, oafsByClassName, Project.class); + assertForOafType(outputDir, oafsByClassName, Publication.class); + assertForOafType(outputDir, oafsByClassName, Result.class); + assertForOafType(outputDir, oafsByClassName, Relation.class); + assertForOafType(outputDir, oafsByClassName, Software.class); + } + } + + private static Map> createActionSets(Path inputActionSetsDir) throws IOException { + Path inputActionSetJsonDumpsDir = Paths + .get(Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/partition/input/")) + .getFile()); + + Map> oafsByType = new HashMap<>(); + Files + .list(inputActionSetJsonDumpsDir) + .forEach(inputActionSetJsonDumpFile -> { + String inputActionSetId = inputActionSetJsonDumpFile.getFileName().toString(); + Path inputActionSetDir = inputActionSetsDir.resolve(inputActionSetId); + + Dataset actionDS = readActionsFromJsonDump(inputActionSetJsonDumpFile.toString()) + .cache(); + + writeActionsAsJobInput(actionDS, inputActionSetId, inputActionSetDir.toString()); + + Map> actionSetOafsByType = actionDS + .withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA)) + .select(expr("atomic_action.*")) + .groupBy(col("clazz")) + .agg(collect_list(col("payload")).as("payload_list")) + .collectAsList() + .stream() + .map(row -> new AbstractMap.SimpleEntry<>(row.getAs("clazz"), + mutableSeqAsJavaList(row.>getAs("payload_list")))) + .collect(Collectors.toMap(AbstractMap.SimpleEntry::getKey, AbstractMap.SimpleEntry::getValue)); + + actionSetOafsByType.keySet() + .forEach(x -> { + if (oafsByType.containsKey(x)) { + List collected = new ArrayList<>(); + collected.addAll(oafsByType.get(x)); + collected.addAll(actionSetOafsByType.get(x)); + oafsByType.put(x, collected); + } else { + oafsByType.put(x, actionSetOafsByType.get(x)); + } + }); + }); + + return oafsByType; + } + + private static Dataset readActionsFromJsonDump(String path) { + return spark + .read() + .textFile(path); + } + + private static void writeActionsAsJobInput(Dataset actionDS, + String inputActionSetId, + String path) { + actionDS + .javaRDD() + .mapToPair(json -> new Tuple2<>(new Text(inputActionSetId), new Text(json))) + .saveAsNewAPIHadoopFile(path, + Text.class, + Text.class, + SequenceFileOutputFormat.class, + configuration); + } + + private static void assertForOafType(Path outputDir, Map> oafsByClassName, Class clazz) { + Path outputDatasetDir = outputDir.resolve(String.format("clazz=%s", clazz.getCanonicalName())); + Files.exists(outputDatasetDir); + + List actuals = readActionPayloadFromJobOutput(outputDatasetDir.toString(), clazz).collectAsList(); + actuals.sort(Comparator.comparingInt(Object::hashCode)); + + List expecteds = oafsByClassName.get(clazz.getCanonicalName()).stream() + .map(json -> mapToOaf(json, clazz)) + .sorted(Comparator.comparingInt(Object::hashCode)) + .collect(Collectors.toList()); + + assertIterableEquals(expecteds, actuals); + } + + private static Dataset readActionPayloadFromJobOutput(String path, + Class clazz) { + return spark + .read() + .parquet(path) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value.getAs("payload"), clazz), + Encoders.bean(clazz)); + } + + private static T mapToOaf(String json, Class clazz) { + return rethrowAsRuntimeException( + () -> OBJECT_MAPPER.readValue(json, clazz), + String.format("failed to map json to class: json=%s, class=%s", json, clazz.getCanonicalName()) + ); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/partition/input/action_set_1_payload.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/partition/input/action_set_1_payload.json new file mode 100644 index 000000000..7a8778172 --- /dev/null +++ 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