forked from D-Net/dnet-hadoop
workflow to generate seq(doi,AuthorList)
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package eu.dnetlib.doiboost.orcid;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.text.SimpleDateFormat;
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import java.util.Date;
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import java.util.List;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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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.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.Function;
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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.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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import com.google.gson.JsonElement;
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import com.google.gson.JsonParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.scholexplorer.DLIRelation;
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import eu.dnetlib.doiboost.orcid.model.AuthorData;
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import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData;
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import eu.dnetlib.doiboost.orcid.model.WorkData;
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import scala.Tuple2;
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public class SparkGenerateDoiAuthorList {
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public static void main(String[] args) throws IOException, Exception {
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Logger logger = LoggerFactory.getLogger(SparkGenerateDoiAuthorList.class);
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logger.info("[ SparkGenerateDoiAuthorList STARTED]");
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkGenerateDoiAuthorList.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/gen_doi_author_list_orcid_parameters.json")));
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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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logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String workingPath = parser.get("workingPath");
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logger.info("workingPath: ", workingPath);
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final String outputDoiAuthorListPath = parser.get("outputDoiAuthorListPath");
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logger.info("outputDoiAuthorListPath: ", outputDoiAuthorListPath);
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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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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaPairRDD<Text, Text> summariesRDD = sc.sequenceFile(workingPath + "../orcid_summaries/output/authors.seq", Text.class, Text.class);
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Dataset<AuthorData> summariesDataset = spark
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.createDataset(summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(),
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Encoders.bean(AuthorData.class));
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JavaPairRDD<Text, Text> activitiesRDD = sc.sequenceFile(workingPath + "/output/*.seq", Text.class, Text.class);
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Dataset<WorkData> activitiesDataset = spark
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.createDataset(activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(),
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Encoders.bean(WorkData.class));
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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 WorkData loadWorkFromJson(Text orcidId, Text json) {
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WorkData workData = new WorkData();
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workData.setOid(orcidId.toString());
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JsonElement jElement = new JsonParser().parse(json.toString());
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workData.setDoi(getJsonValue(jElement, "doi"));
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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.isJsonObject()) {
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return name.getAsString();
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}
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}
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return null;
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}
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}
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@ -0,0 +1,3 @@
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[{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path", "paramRequired": true},
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{"paramName":"o", "paramLongName":"outputDoiAuthorListPath", "paramDescription": "the relative folder of the sequencial file to write the data", "paramRequired": true}
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]
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@ -0,0 +1,18 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>hadoop-rm3.garr-pa1.d4science.org:8032</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://hadoop-rm1.garr-pa1.d4science.org:8020</value>
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</property>
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<property>
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<name>queueName</name>
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<value>default</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>spark2</value>
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</property>
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</configuration>
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@ -0,0 +1,55 @@
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<workflow-app name="Gen Orcid Authors" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>workingPath</name>
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<description>the working dir base path</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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</parameters>
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<start to="ResetWorkingPath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ResetWorkingPath">
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<fs>
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<delete path='${workingPath_activities}/doi_author_list'/>
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</fs>
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<ok to="Gen_Doi_Author_List"/>
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<error to="Kill"/>
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</action>
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<action name="Gen_Doi_Author_List">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Gen_Doi_Author_List</name>
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<class>eu.dnetlib.doiboost.orcid.SparkGenerateDoiAuthorList</class>
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<jar>dhp-doiboost-1.2.1-SNAPSHOT.jar</jar>
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<spark-opts>--num-executors 1 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory}
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</spark-opts>
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<arg>-w</arg><arg>${workingPath}/</arg>
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<arg>-o</arg><arg>doi_author_list/</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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<end name="End"/>
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</workflow-app>
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