forked from D-Net/dnet-hadoop
conflict resolved on merge
This commit is contained in:
parent
6b34ba737e
commit
034304b33a
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@ -1,36 +1,35 @@
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package eu.dnetlib.dhp.utils;
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import java.io.*;
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import java.nio.charset.StandardCharsets;
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import java.security.MessageDigest;
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import java.util.List;
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import java.util.Map;
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import java.util.Properties;
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import java.util.zip.GZIPInputStream;
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import java.util.zip.GZIPOutputStream;
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import org.apache.commons.codec.binary.Base64;
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import org.apache.commons.codec.binary.Base64OutputStream;
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import org.apache.commons.codec.binary.Hex;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.SaveMode;
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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.ObjectMapper;
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import com.google.common.collect.Maps;
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import com.jayway.jsonpath.JsonPath;
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import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo;
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import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
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import net.minidev.json.JSONArray;
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import org.apache.commons.codec.binary.Hex;
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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.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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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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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.SaveMode;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import scala.collection.JavaConverters;
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import scala.collection.Seq;
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import java.io.*;
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import java.nio.charset.StandardCharsets;
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import java.security.MessageDigest;
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import java.util.*;
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import java.util.stream.Collectors;
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public class DHPUtils {
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private static final Logger log = LoggerFactory.getLogger(DHPUtils.class);
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@ -53,6 +52,45 @@ public class DHPUtils {
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}
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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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* @param includeEmpty include Empty mdstores
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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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public 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,
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boolean includeEmpty) 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 -> includeEmpty || 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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public static String generateIdentifier(final String originalId, final String nsPrefix) {
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return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId));
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}
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@ -52,7 +52,7 @@
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Incremental Download EBI Links</name>
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<class>eu.dnetllib.dhp.sx.bio.ebi.SparkDownloadEBILinks</class>
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<class>eu.dnetlib.dhp.sx.bio.ebi.SparkDownloadEBILinks</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -85,7 +85,7 @@
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Create OAF DataSet</name>
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<class>eu.dnetllib.dhp.sx.bio.ebi.SparkEBILinksToOaf</class>
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<class>eu.dnetlib.dhp.sx.bio.ebi.SparkEBILinksToOaf</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -30,7 +30,7 @@
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Convert Baseline to OAF Dataset</name>
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<class>eu.dnetllib.dhp.sx.bio.ebi.SparkCreateBaselineDataFrame</class>
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<class>eu.dnetlib.dhp.sx.bio.ebi.SparkCreateBaselineDataFrame</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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@ -1,118 +0,0 @@
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package eu.dnetlib.dhp.oa.graph.raw;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.*;
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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 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 scala.Tuple2;
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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 Set<String> paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation);
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final 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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final List<String> oafTypes = Lists.newArrayList(ModelSupport.oafTypes.keySet());
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runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, oafTypes, hdfsPath, paths));
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}
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public static void processPaths(final SparkSession spark,
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final List<String> oafTypes,
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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 (String type : oafTypes) {
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oaf
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.filter((FilterFunction<Oaf>) o -> o.getClass().getSimpleName().toLowerCase().equals(type))
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.map((MapFunction<Oaf, String>) OBJECT_MAPPER::writeValueAsString, Encoders.STRING())
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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 + "/" + type);
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}
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}
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}
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}
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@ -0,0 +1,74 @@
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package eu.dnetlib.dhp.oa.graph.raw
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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.schema.common.ModelSupport
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import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo
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import eu.dnetlib.dhp.schema.oaf.Oaf
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import eu.dnetlib.dhp.utils.DHPUtils
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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.http.client.methods.HttpGet
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import org.apache.http.impl.client.HttpClients
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import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
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import org.apache.spark.{SparkConf, SparkContext}
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import org.slf4j.LoggerFactory
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import scala.collection.JavaConverters._
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import scala.io.Source
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object CopyHdfsOafSparkApplication {
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def main(args: Array[String]): Unit = {
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val log = LoggerFactory.getLogger(getClass)
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val conf = new SparkConf()
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json")).mkString)
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parser.parseArgument(args)
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val spark =
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SparkSession
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.builder()
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.config(conf)
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.appName(getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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val sc: SparkContext = spark.sparkContext
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val mdstoreManagerUrl = parser.get("mdstoreManagerUrl")
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log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl)
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val mdFormat = parser.get("mdFormat")
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log.info("mdFormat: {}", mdFormat)
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val mdLayout = parser.get("mdLayout")
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log.info("mdLayout: {}", mdLayout)
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val mdInterpretation = parser.get("mdInterpretation")
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log.info("mdInterpretation: {}", mdInterpretation)
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val hdfsPath = parser.get("hdfsPath")
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log.info("hdfsPath: {}", hdfsPath)
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implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
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val paths = DHPUtils.mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation, true).asScala
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val validPaths: List[String] = paths.filter(p => HdfsSupport.exists(p, sc.hadoopConfiguration)).toList
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if (validPaths.nonEmpty) {
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val oaf = spark.read.load(validPaths: _*).as[Oaf]
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val mapper = new ObjectMapper()
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val l =ModelSupport.oafTypes.entrySet.asScala.map(e => e.getKey).toList
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l.foreach(
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e =>
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oaf.filter(o => o.getClass.getSimpleName.equalsIgnoreCase(e))
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.map(s => mapper.writeValueAsString(s))(Encoders.STRING)
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.write
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.option("compression", "gzip")
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.mode(SaveMode.Append)
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.text(s"$hdfsPath/${e}")
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)
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}
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}
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}
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@ -26,6 +26,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.utils.DHPUtils;
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public class AbstractMigrationApplication implements Closeable {
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@ -71,27 +72,7 @@ public class AbstractMigrationApplication implements Closeable {
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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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return DHPUtils.mdstorePaths(mdstoreManagerUrl, format, layout, interpretation, false);
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}
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private Configuration getConf() {
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@ -23,6 +23,12 @@
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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": "m",
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"paramLongName": "master",
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"paramDescription": "should be yarn or local",
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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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@ -553,7 +553,7 @@
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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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<class>eu.dnetlib.dhp.oa.graph.raw.CopyHdfsOafSparkApplication</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory ${sparkExecutorMemory}
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@ -568,6 +568,7 @@
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<arg>--mdstoreManagerUrl</arg><arg>${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>--master</arg><arg>yarn</arg>
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<arg>--mdInterpretation</arg><arg>graph</arg>
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</spark>
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<ok to="wait_graphs"/>
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