WIP: worflow nodes for including Scholexplorer records in the RAW graph
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parent
51a03c0a50
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package eu.dnetlib.dhp.oa.graph.raw;
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import com.clearspring.analytics.util.Lists;
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import com.fasterxml.jackson.databind.ObjectMapper;
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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.common.vocabulary.VocabularyGroup;
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import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
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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.Oaf;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import org.apache.commons.io.IOUtils;
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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.FlatMapFunction;
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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.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.util.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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public class CopyHdfsOafApplication extends AbstractMigrationApplication {
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private static final Logger log = LoggerFactory.getLogger(CopyHdfsOafApplication.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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CopyHdfsOafApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json")));
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parser.parseArgument(args);
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final 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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final String mdstoreManagerUrl = parser.get("mdstoreManagerUrl");
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log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl);
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final String mdFormat = parser.get("mdFormat");
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log.info("mdFormat: {}", mdFormat);
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final String mdLayout = parser.get("mdLayout");
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log.info("mdLayout: {}", mdLayout);
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final String mdInterpretation = parser.get("mdInterpretation");
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log.info("mdInterpretation: {}", mdInterpretation);
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final String hdfsPath = parser.get("hdfsPath");
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log.info("hdfsPath: {}", hdfsPath);
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final String isLookupUrl = parser.get("isLookupUrl");
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log.info("isLookupUrl: {}", isLookupUrl);
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final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
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final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService);
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final Set<String> paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation);
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final SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, vocs, hdfsPath, paths));
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}
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public static void processPaths(final SparkSession spark,
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final VocabularyGroup vocs,
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final String outputPath,
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final Set<String> paths) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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log.info("Found {} mdstores", paths.size());
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paths.forEach(log::info);
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final String[] validPaths = paths
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.stream()
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.filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration()))
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.toArray(String[]::new);
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log.info("Non empty mdstores {}", validPaths.length);
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if (validPaths.length > 0) {
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// load the dataset
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Dataset<Oaf> oaf = spark
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.read()
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.load(validPaths)
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.as(Encoders.kryo(Oaf.class));
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// dispatch each entity type individually in the respective graph subdirectory in append mode
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for(Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
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oaf
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.filter((FilterFunction<Oaf>) o -> o.getClass().getSimpleName().toLowerCase().equals(e.getKey().toString()))
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.map((MapFunction<Oaf, String>) OBJECT_MAPPER::writeValueAsString, Encoders.bean(e.getValue()))
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Append)
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.text(outputPath + "/" + e.getKey());
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}
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oaf
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.flatMap((FlatMapFunction<Oaf, Relation>) o -> {
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Relation rel = (Relation) o;
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List<Relation> rels = Lists.newArrayList();
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rels.add(getInverse(rel, vocs));
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return rels.iterator();
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}, Encoders.bean(Relation.class));
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}
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}
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private static Relation getInverse(Relation rel, VocabularyGroup vocs) {
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final Relation inverse = new Relation();
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inverse.setProperties(rel.getProperties());
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inverse.setValidated(rel.getValidated());
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inverse.setValidationDate(rel.getValidationDate());
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inverse.setCollectedfrom(rel.getCollectedfrom());
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inverse.setDataInfo(rel.getDataInfo());
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inverse.setLastupdatetimestamp(rel.getLastupdatetimestamp());
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inverse.setSource(rel.getTarget());
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inverse.setTarget(rel.getSource());
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inverse.setRelType(rel.getRelType());
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inverse.setSubRelType(rel.getSubRelType());
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return inverse;
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}
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}
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@ -135,30 +135,4 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication
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}
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}
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private static Set<String> mdstorePaths(final String mdstoreManagerUrl,
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final String format,
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final String layout,
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final String interpretation) throws IOException {
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final String url = mdstoreManagerUrl + "/mdstores/";
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final ObjectMapper objectMapper = new ObjectMapper();
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final HttpGet req = new HttpGet(url);
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try (final CloseableHttpClient client = HttpClients.createDefault()) {
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try (final CloseableHttpResponse response = client.execute(req)) {
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final String json = IOUtils.toString(response.getEntity().getContent());
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final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class);
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return Arrays
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.stream(mdstores)
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.filter(md -> md.getFormat().equalsIgnoreCase(format))
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.filter(md -> md.getLayout().equalsIgnoreCase(layout))
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.filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation))
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.filter(md -> StringUtils.isNotBlank(md.getHdfsPath()))
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.filter(md -> StringUtils.isNotBlank(md.getCurrentVersion()))
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.filter(md -> md.getSize() > 0)
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.map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store")
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.collect(Collectors.toSet());
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}
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}
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}
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}
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@ -3,8 +3,14 @@ package eu.dnetlib.dhp.oa.graph.raw.common;
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import java.io.Closeable;
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import java.io.IOException;
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import java.util.Arrays;
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import java.util.Set;
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import java.util.concurrent.atomic.AtomicInteger;
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import java.util.stream.Collectors;
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import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo;
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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.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.hadoop.conf.Configuration;
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@ -16,6 +22,10 @@ import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpGet;
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import org.apache.http.impl.client.CloseableHttpClient;
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import org.apache.http.impl.client.HttpClients;
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public class AbstractMigrationApplication implements Closeable {
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@ -47,6 +57,43 @@ public class AbstractMigrationApplication implements Closeable {
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SequenceFile.Writer.valueClass(Text.class));
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}
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/**
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* Retrieves from the metadata store manager application the list of paths associated with mdstores characterized
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* by he given format, layout, interpretation
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* @param mdstoreManagerUrl the URL of the mdstore manager service
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* @param format the mdstore format
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* @param layout the mdstore layout
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* @param interpretation the mdstore interpretation
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* @return the set of hdfs paths
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* @throws IOException in case of HTTP communication issues
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*/
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protected static Set<String> mdstorePaths(final String mdstoreManagerUrl,
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final String format,
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final String layout,
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final String interpretation) throws IOException {
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final String url = mdstoreManagerUrl + "/mdstores/";
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final ObjectMapper objectMapper = new ObjectMapper();
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final HttpGet req = new HttpGet(url);
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try (final CloseableHttpClient client = HttpClients.createDefault()) {
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try (final CloseableHttpResponse response = client.execute(req)) {
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final String json = IOUtils.toString(response.getEntity().getContent());
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final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class);
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return Arrays
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.stream(mdstores)
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.filter(md -> md.getFormat().equalsIgnoreCase(format))
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.filter(md -> md.getLayout().equalsIgnoreCase(layout))
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.filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation))
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.filter(md -> StringUtils.isNotBlank(md.getHdfsPath()))
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.filter(md -> StringUtils.isNotBlank(md.getCurrentVersion()))
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.filter(md -> md.getSize() > 0)
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.map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store")
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.collect(Collectors.toSet());
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}
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}
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}
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private Configuration getConf() {
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return new Configuration();
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/*
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[
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{
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"paramName": "p",
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"paramLongName": "hdfsPath",
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"paramDescription": "the path where storing the sequential file",
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"paramRequired": true
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},
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{
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"paramName": "u",
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"paramLongName": "mdstoreManagerUrl",
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"paramDescription": "the MdstoreManager url",
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"paramRequired": true
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},
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{
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"paramName": "f",
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"paramLongName": "mdFormat",
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"paramDescription": "metadata format",
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"paramRequired": true
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},
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{
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"paramName": "l",
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"paramLongName": "mdLayout",
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"paramDescription": "metadata layout",
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"paramRequired": true
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},
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{
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"paramName": "i",
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"paramLongName": "mdInterpretation",
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"paramDescription": "metadata interpretation",
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"paramRequired": true
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},
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{
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"paramName": "isu",
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"paramLongName": "isLookupUrl",
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"paramDescription": "the url of the ISLookupService",
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"paramRequired": true
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}
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]
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@ -544,6 +544,33 @@
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<arg>--sourcePath</arg><arg>${workingDir}/entities</arg>
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<arg>--graphRawPath</arg><arg>${workingDir}/graph_raw</arg>
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</spark>
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<ok to="Import_oaf_store_graph"/>
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<error to="Kill"/>
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</action>
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<action name="Import_oaf_store_graph">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ImportOAF_hdfs_graph</name>
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<class>eu.dnetlib.dhp.oa.graph.raw.CopyHdfsOafApplication</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory ${sparkExecutorMemory}
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--executor-cores ${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--hdfsPath</arg><arg>${workingDir}/graph_raw</arg>
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<arg>--mdstoreManagerUrl</arg><arg>${mdstoreManagerUrl}</arg>
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<arg>--mdFormat</arg><arg>OAF</arg>
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<arg>--mdLayout</arg><arg>store</arg>
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<arg>--mdInterpretation</arg><arg>graph</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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</spark>
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<ok to="wait_graphs"/>
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<error to="Kill"/>
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</action>
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