Merge branch 'merge_entities_job' into beta
This commit is contained in:
commit
dc86018a5f
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@ -1,97 +0,0 @@
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package eu.dnetlib.dhp.oa.merge;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.Objects;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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public class DispatchEntitiesSparkJob {
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private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesSparkJob.class);
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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Objects
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.requireNonNull(
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DispatchEntitiesSparkJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/merge/dispatch_entities_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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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("inputPath");
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log.info("inputPath: {}", inputPath);
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String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible"));
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log.info("filterInvisible: {}", filterInvisible);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> dispatchEntities(spark, inputPath, outputPath, filterInvisible));
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}
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private static void dispatchEntities(
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SparkSession spark,
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String inputPath,
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String outputPath,
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boolean filterInvisible) {
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Dataset<String> df = spark.read().textFile(inputPath);
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ModelSupport.oafTypes.entrySet().parallelStream().forEach(entry -> {
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String entityType = entry.getKey();
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Class<?> clazz = entry.getValue();
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final String entityPath = outputPath + "/" + entityType;
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if (!entityType.equalsIgnoreCase("relation")) {
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HdfsSupport.remove(entityPath, spark.sparkContext().hadoopConfiguration());
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Dataset<Row> entityDF = spark
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.read()
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.schema(Encoders.bean(clazz).schema())
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.json(
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df
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.filter((FilterFunction<String>) s -> s.startsWith(clazz.getName()))
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.map(
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(MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"),
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Encoders.STRING()));
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if (filterInvisible) {
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entityDF = entityDF.filter("dataInfo.invisible != true");
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}
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entityDF
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(entityPath);
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}
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});
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}
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}
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@ -2,36 +2,28 @@
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package eu.dnetlib.dhp.oa.merge;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;
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import static org.apache.spark.sql.functions.col;
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import static org.apache.spark.sql.functions.when;
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import java.io.IOException;
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import java.util.List;
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import java.util.Objects;
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import java.util.Map;
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import java.util.Optional;
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import java.util.concurrent.ExecutionException;
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import java.util.concurrent.ForkJoinPool;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.ReduceFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.expressions.Aggregator;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.jayway.jsonpath.Configuration;
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import com.jayway.jsonpath.DocumentContext;
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import com.jayway.jsonpath.JsonPath;
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import com.jayway.jsonpath.Option;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import scala.Tuple2;
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@ -39,13 +31,9 @@ import scala.Tuple2;
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* Groups the graph content by entity identifier to ensure ID uniqueness
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*/
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public class GroupEntitiesSparkJob {
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private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class);
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private static final String ID_JPATH = "$.id";
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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private static final Encoder<OafEntity> OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class);
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public static void main(String[] args) throws Exception {
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@ -66,9 +54,15 @@ public class GroupEntitiesSparkJob {
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String graphInputPath = parser.get("graphInputPath");
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log.info("graphInputPath: {}", graphInputPath);
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String checkpointPath = parser.get("checkpointPath");
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log.info("checkpointPath: {}", checkpointPath);
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String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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boolean filterInvisible = Boolean.valueOf(parser.get("filterInvisible"));
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log.info("filterInvisible: {}", filterInvisible);
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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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conf.registerKryoClasses(ModelSupport.getOafModelClasses());
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@ -78,126 +72,95 @@ public class GroupEntitiesSparkJob {
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isSparkSessionManaged,
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spark -> {
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HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
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groupEntities(spark, graphInputPath, outputPath);
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groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible);
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});
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}
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private static void groupEntities(
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SparkSession spark,
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String inputPath,
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String outputPath) {
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String checkpointPath,
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String outputPath,
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boolean filterInvisible) {
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final TypedColumn<OafEntity, OafEntity> aggregator = new GroupingAggregator().toColumn();
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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spark
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.read()
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.textFile(toSeq(listEntityPaths(inputPath, sc)))
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.map((MapFunction<String, OafEntity>) GroupEntitiesSparkJob::parseOaf, Encoders.kryo(OafEntity.class))
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.filter((FilterFunction<OafEntity>) e -> StringUtils.isNotBlank(ModelSupport.idFn().apply(e)))
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.groupByKey((MapFunction<OafEntity, String>) oaf -> ModelSupport.idFn().apply(oaf), Encoders.STRING())
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.agg(aggregator)
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Dataset<OafEntity> allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC);
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for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
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String entity = e.getKey().name();
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Class<? extends OafEntity> entityClass = e.getValue();
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String entityInputPath = inputPath + "/" + entity;
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if (!HdfsSupport.exists(entityInputPath, spark.sparkContext().hadoopConfiguration())) {
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continue;
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}
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allEntities = allEntities
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.union(
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((Dataset<OafEntity>) spark
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.read()
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.schema(Encoders.bean(entityClass).schema())
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.json(entityInputPath)
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.filter("length(id) > 0")
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.as(Encoders.bean(entityClass)))
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.map((MapFunction<OafEntity, OafEntity>) r -> r, OAFENTITY_KRYO_ENC));
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}
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Dataset<?> groupedEntities = allEntities
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.groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING())
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.reduceGroups((ReduceFunction<OafEntity>) (b, a) -> OafMapperUtils.mergeEntities(b, a))
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.map(
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(MapFunction<Tuple2<String, OafEntity>, String>) t -> t._2().getClass().getName() +
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"|" + OBJECT_MAPPER.writeValueAsString(t._2()),
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Encoders.STRING())
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(MapFunction<Tuple2<String, OafEntity>, Tuple2<String, OafEntity>>) t -> new Tuple2(
|
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t._2().getClass().getName(), t._2()),
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Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC));
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// pivot on "_1" (classname of the entity)
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// created columns containing only entities of the same class
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for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
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String entity = e.getKey().name();
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Class<? extends OafEntity> entityClass = e.getValue();
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groupedEntities = groupedEntities
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.withColumn(
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entity,
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when(col("_1").equalTo(entityClass.getName()), col("_2")));
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}
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groupedEntities
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.drop("_1", "_2")
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.text(outputPath);
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}
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.option("compression", "gzip")
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.save(checkpointPath);
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public static class GroupingAggregator extends Aggregator<OafEntity, OafEntity, OafEntity> {
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ForkJoinPool parPool = new ForkJoinPool(ModelSupport.entityTypes.size());
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@Override
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public OafEntity zero() {
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return null;
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}
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|
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@Override
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public OafEntity reduce(OafEntity b, OafEntity a) {
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return mergeAndGet(b, a);
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}
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private OafEntity mergeAndGet(OafEntity b, OafEntity a) {
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if (Objects.nonNull(a) && Objects.nonNull(b)) {
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return OafMapperUtils.mergeEntities(b, a);
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}
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return Objects.isNull(a) ? b : a;
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}
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@Override
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public OafEntity merge(OafEntity b, OafEntity a) {
|
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return mergeAndGet(b, a);
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}
|
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|
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@Override
|
||||
public OafEntity finish(OafEntity j) {
|
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return j;
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}
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|
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@Override
|
||||
public Encoder<OafEntity> bufferEncoder() {
|
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return Encoders.kryo(OafEntity.class);
|
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}
|
||||
|
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@Override
|
||||
public Encoder<OafEntity> outputEncoder() {
|
||||
return Encoders.kryo(OafEntity.class);
|
||||
}
|
||||
|
||||
}
|
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|
||||
private static OafEntity parseOaf(String s) {
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||||
|
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DocumentContext dc = JsonPath
|
||||
.parse(s, Configuration.defaultConfiguration().addOptions(Option.SUPPRESS_EXCEPTIONS));
|
||||
final String id = dc.read(ID_JPATH);
|
||||
if (StringUtils.isNotBlank(id)) {
|
||||
|
||||
String prefix = StringUtils.substringBefore(id, "|");
|
||||
switch (prefix) {
|
||||
case "10":
|
||||
return parse(s, Datasource.class);
|
||||
case "20":
|
||||
return parse(s, Organization.class);
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||||
case "40":
|
||||
return parse(s, Project.class);
|
||||
case "50":
|
||||
String resultType = dc.read("$.resulttype.classid");
|
||||
switch (resultType) {
|
||||
case "publication":
|
||||
return parse(s, Publication.class);
|
||||
case "dataset":
|
||||
return parse(s, eu.dnetlib.dhp.schema.oaf.Dataset.class);
|
||||
case "software":
|
||||
return parse(s, Software.class);
|
||||
case "other":
|
||||
return parse(s, OtherResearchProduct.class);
|
||||
default:
|
||||
throw new IllegalArgumentException(String.format("invalid resultType: '%s'", resultType));
|
||||
}
|
||||
default:
|
||||
throw new IllegalArgumentException(String.format("invalid id prefix: '%s'", prefix));
|
||||
}
|
||||
} else {
|
||||
throw new IllegalArgumentException(String.format("invalid oaf: '%s'", s));
|
||||
}
|
||||
}
|
||||
|
||||
private static <T extends OafEntity> OafEntity parse(String s, Class<T> clazz) {
|
||||
try {
|
||||
return OBJECT_MAPPER.readValue(s, clazz);
|
||||
} catch (IOException e) {
|
||||
throw new IllegalArgumentException(e);
|
||||
}
|
||||
}
|
||||
|
||||
private static List<String> listEntityPaths(String inputPath, JavaSparkContext sc) {
|
||||
return HdfsSupport
|
||||
.listFiles(inputPath, sc.hadoopConfiguration())
|
||||
ModelSupport.entityTypes
|
||||
.entrySet()
|
||||
.stream()
|
||||
.filter(f -> !f.toLowerCase().contains("relation"))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
.map(e -> parPool.submit(() -> {
|
||||
String entity = e.getKey().name();
|
||||
Class<? extends OafEntity> entityClass = e.getValue();
|
||||
|
||||
spark
|
||||
.read()
|
||||
.load(checkpointPath)
|
||||
.select(col(entity).as("value"))
|
||||
.filter("value IS NOT NULL")
|
||||
.as(OAFENTITY_KRYO_ENC)
|
||||
.map((MapFunction<OafEntity, OafEntity>) r -> r, (Encoder<OafEntity>) Encoders.bean(entityClass))
|
||||
.filter(filterInvisible ? "dataInfo.invisible != TRUE" : "TRUE")
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath + "/" + entity);
|
||||
}))
|
||||
.collect(Collectors.toList())
|
||||
.forEach(t -> {
|
||||
try {
|
||||
t.get();
|
||||
} catch (InterruptedException | ExecutionException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
});
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,26 +0,0 @@
|
|||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "i",
|
||||
"paramLongName": "inputPath",
|
||||
"paramDescription": "the source path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "o",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "path of the output graph",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "fi",
|
||||
"paramLongName": "filterInvisible",
|
||||
"paramDescription": "if true filters out invisible entities",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -8,13 +8,25 @@
|
|||
{
|
||||
"paramName": "gin",
|
||||
"paramLongName": "graphInputPath",
|
||||
"paramDescription": "the graph root path",
|
||||
"paramDescription": "the input graph root path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "cp",
|
||||
"paramLongName": "checkpointPath",
|
||||
"paramDescription": "checkpoint directory",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "out",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the output merged graph root path",
|
||||
"paramDescription": "the output graph root path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "fi",
|
||||
"paramLongName": "filterInvisible",
|
||||
"paramDescription": "if true filters out invisible entities",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -152,31 +152,7 @@
|
|||
--conf spark.sql.shuffle.partitions=15000
|
||||
</spark-opts>
|
||||
<arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
</spark>
|
||||
<ok to="dispatch_entities"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_entities">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch grouped entitities</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryOverhead}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--checkpointPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}</arg>
|
||||
<arg>--filterInvisible</arg><arg>${filterInvisible}</arg>
|
||||
</spark>
|
||||
|
|
|
|||
|
|
@ -96,30 +96,7 @@
|
|||
--conf spark.sql.shuffle.partitions=15000
|
||||
</spark-opts>
|
||||
<arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
</spark>
|
||||
<ok to="dispatch_entities"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_entities">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch grouped entities</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--checkpointPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}</arg>
|
||||
<arg>--filterInvisible</arg><arg>${filterInvisible}</arg>
|
||||
</spark>
|
||||
|
|
|
|||
|
|
@ -1,16 +1,15 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.group;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.nio.file.Paths;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
|
|
@ -19,118 +18,108 @@ import org.apache.spark.sql.Encoders;
|
|||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.*;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import java.io.IOException;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.nio.file.Paths;
|
||||
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
||||
public class GroupEntitiesSparkJobTest {
|
||||
|
||||
private static SparkSession spark;
|
||||
private static SparkSession spark;
|
||||
|
||||
private static ObjectMapper mapper = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
private static ObjectMapper mapper = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
|
||||
private static Path workingDir;
|
||||
private Path dataInputPath;
|
||||
private static Path workingDir;
|
||||
private Path dataInputPath;
|
||||
|
||||
private Path groupEntityPath;
|
||||
private Path dispatchEntityPath;
|
||||
private Path checkpointPath;
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName());
|
||||
private Path outputPath;
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName());
|
||||
conf.setMaster("local");
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
||||
spark = SparkSession.builder().config(conf).getOrCreate();
|
||||
}
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName());
|
||||
|
||||
@BeforeEach
|
||||
public void beforeEach() throws IOException, URISyntaxException {
|
||||
dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI());
|
||||
groupEntityPath = workingDir.resolve("grouped_entity");
|
||||
dispatchEntityPath = workingDir.resolve("dispatched_entity");
|
||||
}
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName());
|
||||
conf.setMaster("local");
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
||||
spark = SparkSession.builder().config(conf).getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
spark.stop();
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
}
|
||||
@BeforeEach
|
||||
public void beforeEach() throws IOException, URISyntaxException {
|
||||
dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI());
|
||||
checkpointPath = workingDir.resolve("grouped_entity");
|
||||
outputPath = workingDir.resolve("dispatched_entity");
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(1)
|
||||
void testGroupEntities() throws Exception {
|
||||
GroupEntitiesSparkJob.main(new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-graphInputPath",
|
||||
dataInputPath.toString(),
|
||||
"-outputPath",
|
||||
groupEntityPath.toString()
|
||||
});
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
spark.stop();
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
}
|
||||
|
||||
Dataset<Result> output = spark
|
||||
.read()
|
||||
.textFile(groupEntityPath.toString())
|
||||
.map((MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"), Encoders.STRING())
|
||||
.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
|
||||
@Test
|
||||
@Order(1)
|
||||
void testGroupEntities() throws Exception {
|
||||
GroupEntitiesSparkJob.main(new String[]{
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-graphInputPath",
|
||||
dataInputPath.toString(),
|
||||
"-checkpointPath",
|
||||
checkpointPath.toString(),
|
||||
"-outputPath",
|
||||
outputPath.toString(),
|
||||
"-filterInvisible",
|
||||
Boolean.FALSE.toString()
|
||||
});
|
||||
|
||||
assertEquals(
|
||||
1,
|
||||
output
|
||||
.filter(
|
||||
(FilterFunction<Result>) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9"
|
||||
.equals(r.getId()) &&
|
||||
r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
|
||||
.count());
|
||||
}
|
||||
Dataset<OafEntity> checkpointTable = spark
|
||||
.read()
|
||||
.load(checkpointPath.toString())
|
||||
.selectExpr("COALESCE(*)")
|
||||
.as(Encoders.kryo(OafEntity.class));
|
||||
|
||||
@Test
|
||||
@Order(2)
|
||||
void testDispatchEntities() throws Exception {
|
||||
DispatchEntitiesSparkJob.main(new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-inputPath",
|
||||
groupEntityPath.toString(),
|
||||
"-outputPath",
|
||||
dispatchEntityPath.resolve(".").toString(),
|
||||
"-filterInvisible",
|
||||
Boolean.TRUE.toString()
|
||||
});
|
||||
|
||||
Dataset<Result> output = spark
|
||||
.read()
|
||||
.textFile(
|
||||
DHPUtils
|
||||
.toSeq(
|
||||
HdfsSupport
|
||||
.listFiles(dispatchEntityPath.toString(), spark.sparkContext().hadoopConfiguration())))
|
||||
.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
|
||||
assertEquals(
|
||||
1,
|
||||
checkpointTable
|
||||
.filter(
|
||||
(FilterFunction<OafEntity>) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9"
|
||||
.equals(r.getId()) &&
|
||||
r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
|
||||
.count());
|
||||
|
||||
assertEquals(3, output.count());
|
||||
assertEquals(
|
||||
2,
|
||||
output
|
||||
.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
|
||||
.filter((FilterFunction<String>) s -> s.equals("publication"))
|
||||
.count());
|
||||
assertEquals(
|
||||
1,
|
||||
output
|
||||
.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
|
||||
.filter((FilterFunction<String>) s -> s.equals("dataset"))
|
||||
.count());
|
||||
}
|
||||
}
|
||||
|
||||
Dataset<Result> output = spark
|
||||
.read()
|
||||
.textFile(
|
||||
DHPUtils
|
||||
.toSeq(
|
||||
HdfsSupport
|
||||
.listFiles(outputPath.toString(), spark.sparkContext().hadoopConfiguration())))
|
||||
.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
|
||||
|
||||
assertEquals(3, output.count());
|
||||
assertEquals(
|
||||
2,
|
||||
output
|
||||
.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
|
||||
.filter((FilterFunction<String>) s -> s.equals("publication"))
|
||||
.count());
|
||||
assertEquals(
|
||||
1,
|
||||
output
|
||||
.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
|
||||
.filter((FilterFunction<String>) s -> s.equals("dataset"))
|
||||
.count());
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue