forked from D-Net/dnet-hadoop
code, workflow and parameters for the dump of the results associated to funders
This commit is contained in:
parent
57cac36898
commit
46ba3793f6
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package eu.dnetlib.dhp.oa.graph.dump.funderresults;
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import java.io.Serializable;
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import java.util.List;
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import eu.dnetlib.dhp.schema.dump.oaf.Result;
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public class FunderResults implements Serializable {
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private List<Result> results;
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public List<Result> getResults() {
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return results;
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}
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public void setResults(List<Result> results) {
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this.results = results;
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}
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}
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package eu.dnetlib.dhp.oa.graph.dump.funderresults;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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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.function.MapFunction;
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import org.apache.spark.api.java.function.MapGroupsFunction;
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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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.schema.dump.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import scala.Tuple2;
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/**
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* Preparation of the Project information to be added to the dumped results. For each result associated to at least one
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* Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the
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* list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to
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*/
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public class SparkPrepareResultProject implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultProject.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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SparkPrepareResultProject.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/project_prep_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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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final String communityMapPath = parser.get("communityMapPath");
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log.info("communityMapPath: {}", communityMapPath);
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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 -> {
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Utils.removeOutputDir(spark, outputPath);
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prepareResultProjectList2(spark, inputPath, outputPath, communityMapPath);
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});
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}
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private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath,
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String communityMapPath) {
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CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
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Dataset<Relation> relation = Utils
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.readPath(spark, inputPath + "/relation", Relation.class)
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.filter("dataInfo.deletedbyinference = false and relClass = 'produces'");
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Dataset<eu.dnetlib.dhp.schema.oaf.Result> result = Utils
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.readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class)
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.union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class))
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.union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class))
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.union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class));
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result
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.joinWith(relation, result.col("id").equalTo(relation.col("target")))
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.groupByKey(
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(MapFunction<Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation>, String>) value -> value
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._2()
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.getSource()
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.substring(3, 15),
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Encoders.STRING())
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.mapGroups(
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(MapGroupsFunction<String, Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation>, Tuple2<String, FunderResults>>) (
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s, it) -> {
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Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation> first = it.next();
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FunderResults fr = new FunderResults();
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List<Result> resultList = new ArrayList<>();
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resultList.add(ResultMapper.map(first._1(), communityMap, true));
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it.forEachRemaining(c -> {
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resultList.add(ResultMapper.map(c._1(), communityMap, true));
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});
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fr.setResults(resultList);
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return new Tuple2<>(s, fr);
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}, Encoders.tuple(Encoders.STRING(), Encoders.bean(FunderResults.class)))
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.foreach(t -> {
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String funder = t._1();
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spark
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.createDataFrame(t._2.getResults(), Result.class)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + "/" + funder);
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});
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}
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private static void prepareResultProjectList2(SparkSession spark, String inputPath, String outputPath,
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String communityMapPath) {
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CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
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Dataset<Relation> relation = Utils
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.readPath(spark, inputPath + "/relation", Relation.class)
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.filter("dataInfo.deletedbyinference = false and relClass = 'produces'");
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Dataset<eu.dnetlib.dhp.schema.oaf.Result> result = Utils
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.readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class)
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.union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class))
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.union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class))
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.union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class));
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result
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.joinWith(relation, result.col("id").equalTo(relation.col("target")))
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.groupByKey(
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(MapFunction<Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation>, String>) value -> value
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._2()
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.getSource()
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.substring(3, 15),
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Encoders.STRING())
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.mapGroups(
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(MapGroupsFunction<String, Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation>, String>) (s, it) -> {
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Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation> first = it.next();
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List<Result> resultList = new ArrayList<>();
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resultList.add(ResultMapper.map(first._1(), communityMap, true));
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it.forEachRemaining(c -> {
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resultList.add(ResultMapper.map(c._1(), communityMap, true));
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});
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spark
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.createDataFrame(resultList, Result.class)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + "/" + s);
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return new String();
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}, Encoders.STRING());
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}
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}
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[
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{
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"paramName":"s",
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"paramLongName":"sourcePath",
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"paramDescription": "the path of the sequencial file to read",
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"paramRequired": true
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},
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{
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"paramName": "out",
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"paramLongName": "outputPath",
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"paramDescription": "the path used to store temporary output files",
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"paramRequired": true
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},
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{
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"paramName": "ssm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "true if the spark session is managed, false otherwise",
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"paramRequired": false
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},
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{
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"paramName": "cmp",
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"paramLongName": "communityMapPath",
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"paramDescription": "the community map path",
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"paramRequired": true
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}
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]
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>hiveMetastoreUris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>hiveJdbcUrl</name>
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<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
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</property>
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<property>
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<name>hiveDbName</name>
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<value>openaire</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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</configuration>
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<workflow-app name="dump_funder_results" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the source path</description>
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</property>
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<property>
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<name>isLookUpUrl</name>
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<description>the isLookup service endpoint</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>the output path</description>
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</property>
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<property>
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<name>accessToken</name>
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<description>the access token used for the deposition in Zenodo</description>
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</property>
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<property>
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<name>connectionUrl</name>
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<description>the connection url for Zenodo</description>
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</property>
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<property>
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<name>metadata</name>
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<description> the metadata associated to the deposition</description>
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</property>
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<property>
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<name>depositionType</name>
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<description>the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided)</description>
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</property>
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<property>
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<name>conceptRecordId</name>
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<description>for new version, the id of the record for the old deposition</description>
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</property>
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<property>
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<name>depositionId</name>
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<description>the depositionId of a deposition open that has to be added content</description>
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</property>
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<property>
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<name>hiveDbName</name>
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<description>the target hive database name</description>
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</property>
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<property>
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<name>hiveJdbcUrl</name>
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<description>hive server jdbc url</description>
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</property>
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<property>
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<name>hiveMetastoreUris</name>
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<description>hive server metastore URIs</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>oozieActionShareLibForSpark2</name>
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<description>oozie action sharelib for spark 2.*</description>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
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<description>spark 2.* extra listeners classname</description>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
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<description>spark 2.* sql query execution listeners classname</description>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<description>spark 2.* yarn history server address</description>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<description>spark 2.* event log dir location</description>
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</property>
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</parameters>
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="reset_outputpath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="reset_outputpath">
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<fs>
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<delete path="${outputPath}"/>
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<mkdir path="${outputPath}"/>
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</fs>
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<ok to="save_community_map"/>
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<error to="Kill"/>
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</action>
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<action name="save_community_map">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap</main-class>
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<arg>--outputPath</arg><arg>${workingDir}/communityMap</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
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</java>
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<ok to="dump_funder_results"/>
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<error to="Kill"/>
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</action>
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<action name="dump_funder_results">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump funder results </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkPrepareResultProject</class>
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<jar>dhp-graph-mapper-${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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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--outputPath</arg><arg>${workingDir}/result</arg>
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<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<action name="send_zenodo">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS</main-class>
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<arg>--hdfsPath</arg><arg>${outputPath}</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--accessToken</arg><arg>${accessToken}</arg>
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<arg>--connectionUrl</arg><arg>${connectionUrl}</arg>
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<arg>--metadata</arg><arg>${metadata}</arg>
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<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
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<arg>--conceptRecordId</arg><arg>${conceptRecordId}</arg>
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<arg>--depositionType</arg><arg>${depositionType}</arg>
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<arg>--depositionId</arg><arg>${depositionId}</arg>
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</java>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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