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joined summaries and activities dataset

This commit is contained in:
Enrico Ottonello 2020-05-19 12:57:21 +02:00
parent ca722d4d18
commit 934ad570e0
2 changed files with 26 additions and 12 deletions
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34
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java
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@ -2,6 +2,8 @@
package eu.dnetlib.doiboost.orcid; package eu.dnetlib.doiboost.orcid;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static org.apache.spark.sql.functions.col;
import static org.apache.spark.sql.functions.collect_list;
import java.io.IOException; import java.io.IOException;
import java.text.SimpleDateFormat; import java.text.SimpleDateFormat;
@ -22,7 +24,9 @@ import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.Function; import org.apache.spark.api.java.function.Function;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.RelationalGroupedDataset;
import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.TypedColumn;
import org.apache.spark.util.LongAccumulator; import org.apache.spark.util.LongAccumulator;
import org.mortbay.log.Log; import org.mortbay.log.Log;
import org.slf4j.Logger; import org.slf4j.Logger;
@ -60,7 +64,6 @@ public class SparkGenerateDoiAuthorList {
logger.info("workingPath: ", workingPath); logger.info("workingPath: ", workingPath);
final String outputDoiAuthorListPath = parser.get("outputDoiAuthorListPath"); final String outputDoiAuthorListPath = parser.get("outputDoiAuthorListPath");
logger.info("outputDoiAuthorListPath: ", outputDoiAuthorListPath); logger.info("outputDoiAuthorListPath: ", outputDoiAuthorListPath);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
runWithSparkSession( runWithSparkSession(
@ -69,20 +72,31 @@ public class SparkGenerateDoiAuthorList {
spark -> { spark -> {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaPairRDD<Text, Text> summariesRDD = sc.sequenceFile(workingPath + "../orcid_summaries/output/authors.seq", Text.class, Text.class); JavaPairRDD<Text, Text> summariesRDD = sc
.sequenceFile(workingPath + "../orcid_summaries/output/authors.seq", Text.class, Text.class);
Dataset<AuthorData> summariesDataset = spark Dataset<AuthorData> summariesDataset = spark
.createDataset(summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(), .createDataset(
summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(),
Encoders.bean(AuthorData.class)); Encoders.bean(AuthorData.class));
JavaPairRDD<Text, Text> activitiesRDD = sc.sequenceFile(workingPath + "/output/*.seq", Text.class, Text.class); JavaPairRDD<Text, Text> activitiesRDD = sc
.sequenceFile(workingPath + "/output/*.seq", Text.class, Text.class);
Dataset<WorkData> activitiesDataset = spark Dataset<WorkData> activitiesDataset = spark
.createDataset(activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(), .createDataset(
Encoders.bean(WorkData.class)); activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(),
Encoders.bean(WorkData.class));
RelationalGroupedDataset group = activitiesDataset
.where("oid='0000-0002-9710-779X'")
.joinWith(
summariesDataset,
activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner")
.groupBy(col("doi"));
}); });
} }
private static AuthorData loadAuthorFromJson(Text orcidId, Text json) { private static AuthorData loadAuthorFromJson(Text orcidId, Text json) {
AuthorData authorData = new AuthorData(); AuthorData authorData = new AuthorData();
authorData.setOid(orcidId.toString()); authorData.setOid(orcidId.toString());
@ -92,7 +106,7 @@ public class SparkGenerateDoiAuthorList {
authorData.setCreditName(getJsonValue(jElement, "creditname")); authorData.setCreditName(getJsonValue(jElement, "creditname"));
return authorData; return authorData;
} }
private static WorkData loadWorkFromJson(Text orcidId, Text json) { private static WorkData loadWorkFromJson(Text orcidId, Text json) {
WorkData workData = new WorkData(); WorkData workData = new WorkData();
workData.setOid(orcidId.toString()); workData.setOid(orcidId.toString());
@ -100,7 +114,7 @@ public class SparkGenerateDoiAuthorList {
workData.setDoi(getJsonValue(jElement, "doi")); workData.setDoi(getJsonValue(jElement, "doi"));
return workData; return workData;
} }
private static String getJsonValue(JsonElement jElement, String property) { private static String getJsonValue(JsonElement jElement, String property) {
if (jElement.getAsJsonObject().has(property)) { if (jElement.getAsJsonObject().has(property)) {
JsonElement name = null; JsonElement name = null;

4
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/workflow.xml
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@ -1,4 +1,4 @@
<workflow-app name="Gen Orcid Authors" xmlns="uri:oozie:workflow:0.5"> <workflow-app name="Gen_Doi_Author_List_WF" xmlns="uri:oozie:workflow:0.5">
<parameters> <parameters>
<property> <property>
<name>workingPath</name> <name>workingPath</name>
@ -42,7 +42,7 @@
<name>Gen_Doi_Author_List</name> <name>Gen_Doi_Author_List</name>
<class>eu.dnetlib.doiboost.orcid.SparkGenerateDoiAuthorList</class> <class>eu.dnetlib.doiboost.orcid.SparkGenerateDoiAuthorList</class>
<jar>dhp-doiboost-1.2.1-SNAPSHOT.jar</jar> <jar>dhp-doiboost-1.2.1-SNAPSHOT.jar</jar>
<spark-opts>--num-executors 1 --conf spark.yarn.jars=&quot;hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2&quot; --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} <spark-opts>--num-executors 5 --conf spark.yarn.jars=&quot;hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2&quot; --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory}
</spark-opts> </spark-opts>
<arg>-w</arg><arg>${workingPath}/</arg> <arg>-w</arg><arg>${workingPath}/</arg>
<arg>-o</arg><arg>doi_author_list/</arg> <arg>-o</arg><arg>doi_author_list/</arg>