forked from antonis.lempesis/dnet-hadoop
data from last updated orcid
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@ -18,6 +18,7 @@ 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.util.LongAccumulator;
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import org.mortbay.log.Log;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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@ -30,6 +31,8 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.orcid.AuthorData;
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import eu.dnetlib.dhp.schema.orcid.AuthorSummary;
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import eu.dnetlib.dhp.schema.orcid.Work;
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import eu.dnetlib.dhp.schema.orcid.WorkDetail;
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import eu.dnetlib.doiboost.orcid.json.JsonHelper;
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import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf;
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@ -61,8 +64,6 @@ public class SparkGenEnrichedOrcidWorks {
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.orElse(Boolean.TRUE);
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final String workingPath = parser.get("workingPath");
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final String outputEnrichedWorksPath = parser.get("outputEnrichedWorksPath");
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final String outputWorksPath = parser.get("outputWorksPath");
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final String hdfsServerUri = parser.get("hdfsServerUri");
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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@ -71,26 +72,39 @@ public class SparkGenEnrichedOrcidWorks {
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spark -> {
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaPairRDD<Text, Text> summariesRDD = sc
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.sequenceFile(workingPath + "authors/authors.seq", Text.class, Text.class);
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Dataset<AuthorData> summariesDataset = spark
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Dataset<AuthorData> authorDataset = spark
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.createDataset(
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summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(),
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sc
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.textFile(workingPath.concat("last_orcid_dataset/authors/*"))
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.map(item -> OBJECT_MAPPER.readValue(item, AuthorSummary.class))
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.filter(authorSummary -> authorSummary.getAuthorData() != null)
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.map(authorSummary -> authorSummary.getAuthorData())
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.rdd(),
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Encoders.bean(AuthorData.class));
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logger.info("Authors data loaded: " + summariesDataset.count());
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logger.info("Authors data loaded: " + authorDataset.count());
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JavaPairRDD<Text, Text> activitiesRDD = sc
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.sequenceFile(workingPath + outputWorksPath + "*.seq", Text.class, Text.class);
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Dataset<WorkDetail> activitiesDataset = spark
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Dataset<WorkDetail> workDataset = spark
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.createDataset(
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activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(),
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sc
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.textFile(workingPath.concat("last_orcid_dataset/works/*"))
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.map(item -> OBJECT_MAPPER.readValue(item, Work.class))
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.filter(work -> work.getWorkDetail() != null)
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.map(work -> work.getWorkDetail())
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.filter(work -> work.getErrorCode() == null)
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.filter(
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work -> work
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.getExtIds()
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.stream()
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.filter(e -> e.getType() != null)
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.noneMatch(e -> e.getType().equalsIgnoreCase("doi")))
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.rdd(),
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Encoders.bean(WorkDetail.class));
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logger.info("Works data loaded: " + activitiesDataset.count());
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logger.info("Works data loaded: " + workDataset.count());
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JavaRDD<Tuple2<String, String>> enrichedWorksRDD = activitiesDataset
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JavaRDD<Tuple2<String, String>> enrichedWorksRDD = workDataset
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.joinWith(
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summariesDataset,
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activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner")
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authorDataset,
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workDataset.col("oid").equalTo(authorDataset.col("oid")), "inner")
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.map(
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(MapFunction<Tuple2<WorkDetail, AuthorData>, Tuple2<String, String>>) value -> {
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WorkDetail w = value._1;
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@ -150,31 +164,4 @@ public class SparkGenEnrichedOrcidWorks {
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logger.info("errorsInvalidType: " + errorsInvalidType.value().toString());
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});
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}
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private static AuthorData loadAuthorFromJson(Text orcidId, Text json) {
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AuthorData authorData = new AuthorData();
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authorData.setOid(orcidId.toString());
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JsonElement jElement = new JsonParser().parse(json.toString());
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authorData.setName(getJsonValue(jElement, "name"));
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authorData.setSurname(getJsonValue(jElement, "surname"));
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authorData.setCreditName(getJsonValue(jElement, "creditname"));
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return authorData;
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}
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private static WorkDetail loadWorkFromJson(Text orcidId, Text json) {
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WorkDetail workData = new Gson().fromJson(json.toString(), WorkDetail.class);
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return workData;
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}
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private static String getJsonValue(JsonElement jElement, String property) {
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if (jElement.getAsJsonObject().has(property)) {
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JsonElement name = null;
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name = jElement.getAsJsonObject().get(property);
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if (name != null && !name.isJsonNull()) {
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return name.getAsString();
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}
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}
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return new String("");
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}
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}
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@ -1,17 +1,18 @@
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<workflow-app name="gen_orcid_no_doi_dataset" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>spark2GenNoDoiDatasetMaxExecutors</name>
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<value>40</value>
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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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<name>spark2GenNoDoiDatasetExecutorMemory</name>
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<value>2G</value>
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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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@ -73,8 +74,9 @@
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<class>eu.dnetlib.doiboost.orcidnodoi.SparkGenEnrichedOrcidWorks</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--conf spark.dynamicAllocation.enabled=true
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--conf spark.dynamicAllocation.maxExecutors=${spark2GenNoDoiDatasetMaxExecutors}
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--executor-memory=${spark2GenNoDoiDatasetExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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