code formatting
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eed9fe0902
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@ -33,7 +33,7 @@ import scala.Tuple2;
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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 Encoder<OafEntity> OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class);
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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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@ -114,7 +114,7 @@ public class GroupEntitiesSparkJob {
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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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// 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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@ -67,60 +67,60 @@ public class SparkPropagateRelation extends AbstractSparkAction {
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log.info("graphOutputPath: '{}'", graphOutputPath);
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Dataset<Relation> mergeRels = spark
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.read()
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.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
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.as(REL_BEAN_ENC);
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.read()
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.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
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.as(REL_BEAN_ENC);
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// <mergedObjectID, dedupID>
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Dataset<Row> idsToMerge = mergeRels
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.where(col("relClass").equalTo(ModelConstants.MERGES))
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.select(col("source").as("dedupID"), col("target").as("mergedObjectID"))
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.distinct();
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.where(col("relClass").equalTo(ModelConstants.MERGES))
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.select(col("source").as("dedupID"), col("target").as("mergedObjectID"))
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.distinct();
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Dataset<Row> allRels = spark
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.read()
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.schema(REL_BEAN_ENC.schema())
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.json(graphBasePath + "/relation");
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.read()
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.schema(REL_BEAN_ENC.schema())
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.json(graphBasePath + "/relation");
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Dataset<Relation> dedupedRels = allRels
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.joinWith(idsToMerge, allRels.col("source").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
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.joinWith(idsToMerge, col("_1.target").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
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.select("_1._1", "_1._2.dedupID", "_2.dedupID")
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.as(Encoders.tuple(REL_BEAN_ENC, Encoders.STRING(), Encoders.STRING()))
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.map((MapFunction<Tuple3<Relation, String, String>, Relation>) t -> {
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Relation rel = t._1();
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String newSource = t._2();
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String newTarget = t._3();
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.joinWith(idsToMerge, allRels.col("source").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
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.joinWith(idsToMerge, col("_1.target").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
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.select("_1._1", "_1._2.dedupID", "_2.dedupID")
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.as(Encoders.tuple(REL_BEAN_ENC, Encoders.STRING(), Encoders.STRING()))
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.map((MapFunction<Tuple3<Relation, String, String>, Relation>) t -> {
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Relation rel = t._1();
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String newSource = t._2();
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String newTarget = t._3();
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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if (newSource != null || newTarget != null) {
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rel.getDataInfo().setDeletedbyinference(false);
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if (newSource != null || newTarget != null) {
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rel.getDataInfo().setDeletedbyinference(false);
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if (newSource != null)
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rel.setSource(newSource);
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if (newSource != null)
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rel.setSource(newSource);
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if (newTarget != null)
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rel.setTarget(newTarget);
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}
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if (newTarget != null)
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rel.setTarget(newTarget);
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}
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return rel;
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}, REL_BEAN_ENC);
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return rel;
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}, REL_BEAN_ENC);
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// ids of records that are both not deletedbyinference and not invisible
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Dataset<Row> ids = validIds(spark, graphBasePath);
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// filter relations that point to valid records, can force them to be visible
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Dataset<Relation> cleanedRels = dedupedRels
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.join(ids, col("source").equalTo(ids.col("id")), "leftsemi")
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.join(ids, col("target").equalTo(ids.col("id")), "leftsemi")
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.as(REL_BEAN_ENC)
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.map((MapFunction<Relation, Relation>) r -> {
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r.getDataInfo().setInvisible(false);
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return r;
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}, REL_KRYO_ENC);
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.join(ids, col("source").equalTo(ids.col("id")), "leftsemi")
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.join(ids, col("target").equalTo(ids.col("id")), "leftsemi")
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.as(REL_BEAN_ENC)
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.map((MapFunction<Relation, Relation>) r -> {
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r.getDataInfo().setInvisible(false);
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return r;
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}, REL_KRYO_ENC);
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Dataset<Relation> distinctRels = cleanedRels
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.groupByKey(
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@ -1,14 +1,14 @@
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package eu.dnetlib.dhp.oa.graph.group;
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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 eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import java.io.IOException;
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import java.net.URISyntaxException;
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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 org.apache.commons.io.FileUtils;
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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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@ -18,108 +18,108 @@ import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.*;
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import java.io.IOException;
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import java.net.URISyntaxException;
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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 com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.utils.DHPUtils;
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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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public class GroupEntitiesSparkJobTest {
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private static SparkSession spark;
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private static SparkSession spark;
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private static ObjectMapper mapper = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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private static ObjectMapper mapper = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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private static Path workingDir;
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private Path dataInputPath;
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private static Path workingDir;
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private Path dataInputPath;
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private Path checkpointPath;
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private Path checkpointPath;
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private Path outputPath;
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private Path outputPath;
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName());
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName());
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SparkConf conf = new SparkConf();
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conf.setAppName(GroupEntitiesSparkJob.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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conf.registerKryoClasses(ModelSupport.getOafModelClasses());
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spark = SparkSession.builder().config(conf).getOrCreate();
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}
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SparkConf conf = new SparkConf();
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conf.setAppName(GroupEntitiesSparkJob.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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conf.registerKryoClasses(ModelSupport.getOafModelClasses());
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spark = SparkSession.builder().config(conf).getOrCreate();
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}
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@BeforeEach
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public void beforeEach() throws IOException, URISyntaxException {
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dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI());
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checkpointPath = workingDir.resolve("grouped_entity");
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outputPath = workingDir.resolve("dispatched_entity");
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}
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@BeforeEach
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public void beforeEach() throws IOException, URISyntaxException {
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dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI());
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checkpointPath = workingDir.resolve("grouped_entity");
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outputPath = workingDir.resolve("dispatched_entity");
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}
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@AfterAll
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public static void afterAll() throws IOException {
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spark.stop();
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FileUtils.deleteDirectory(workingDir.toFile());
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}
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@AfterAll
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public static void afterAll() throws IOException {
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spark.stop();
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FileUtils.deleteDirectory(workingDir.toFile());
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}
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@Test
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@Order(1)
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void testGroupEntities() throws Exception {
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GroupEntitiesSparkJob.main(new String[]{
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-graphInputPath",
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dataInputPath.toString(),
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"-checkpointPath",
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checkpointPath.toString(),
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"-outputPath",
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outputPath.toString(),
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"-filterInvisible",
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Boolean.FALSE.toString()
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});
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@Test
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@Order(1)
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void testGroupEntities() throws Exception {
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GroupEntitiesSparkJob.main(new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-graphInputPath",
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dataInputPath.toString(),
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"-checkpointPath",
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checkpointPath.toString(),
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"-outputPath",
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outputPath.toString(),
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"-filterInvisible",
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Boolean.FALSE.toString()
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});
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Dataset<OafEntity> checkpointTable = spark
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.read()
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.load(checkpointPath.toString())
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.selectExpr("COALESCE(*)")
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.as(Encoders.kryo(OafEntity.class));
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Dataset<OafEntity> checkpointTable = spark
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.read()
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.load(checkpointPath.toString())
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.selectExpr("COALESCE(*)")
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.as(Encoders.kryo(OafEntity.class));
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assertEquals(
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1,
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checkpointTable
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.filter(
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(FilterFunction<OafEntity>) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9"
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.equals(r.getId()) &&
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r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
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.count());
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assertEquals(
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1,
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checkpointTable
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.filter(
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(FilterFunction<OafEntity>) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9"
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.equals(r.getId()) &&
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r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
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.count());
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Dataset<Result> output = spark
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.read()
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.textFile(
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DHPUtils
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.toSeq(
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HdfsSupport
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.listFiles(outputPath.toString(), spark.sparkContext().hadoopConfiguration())))
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.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
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Dataset<Result> output = spark
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.read()
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.textFile(
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DHPUtils
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.toSeq(
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HdfsSupport
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.listFiles(outputPath.toString(), spark.sparkContext().hadoopConfiguration())))
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.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
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assertEquals(3, output.count());
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assertEquals(
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2,
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output
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.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
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.filter((FilterFunction<String>) s -> s.equals("publication"))
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.count());
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assertEquals(
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1,
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output
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.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
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.filter((FilterFunction<String>) s -> s.equals("dataset"))
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.count());
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}
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}
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assertEquals(3, output.count());
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assertEquals(
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2,
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output
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.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
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.filter((FilterFunction<String>) s -> s.equals("publication"))
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.count());
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assertEquals(
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1,
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output
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.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
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.filter((FilterFunction<String>) s -> s.equals("dataset"))
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.count());
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}
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}
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