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wf doi_authors generates one json data foreach row

This commit is contained in:
Enrico Ottonello 2020-12-07 15:28:10 +01:00
parent fa1855a4b8
commit 5c65e602d3
3 changed files with 25 additions and 27 deletions
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29
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java
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@ -1,24 +1,25 @@
package eu.dnetlib.dhp.schema.orcid;
import java.util.List;
public class OrcidDOI {
private String doi;
private List<AuthorData> authors;
private String doi;
private List<AuthorData> authors;
public String getDoi() {
return doi;
}
public String getDoi() {
return doi;
}
public void setDoi(String doi) {
this.doi = doi;
}
public void setDoi(String doi) {
this.doi = doi;
}
public List<AuthorData> getAuthors() {
return authors;
}
public List<AuthorData> getAuthors() {
return authors;
}
public void setAuthors(List<AuthorData> authors) {
this.authors = authors;
}
public void setAuthors(List<AuthorData> authors) {
this.authors = authors;
}
}

21
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java
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@ -3,37 +3,32 @@ package eu.dnetlib.doiboost.orcid;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.Function;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.rdd.RDD;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.esotericsoftware.minlog.Log;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.JsonElement;
import com.google.gson.JsonParser;
import com.ximpleware.ParseException;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.parser.utility.VtdException;
import eu.dnetlib.dhp.schema.orcid.AuthorData;
import eu.dnetlib.dhp.schema.orcid.OrcidDOI;
import eu.dnetlib.doiboost.orcid.model.WorkData;
import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
@ -154,11 +149,13 @@ public class SparkGenerateDoiAuthorList {
authorList.removeIf(a -> !oidsAlreadySeen.add(a.getOid()));
return new Tuple2<>(s._1(), authorList);
})
.mapToPair(
s -> {
return new Tuple2<>(s._1(), JsonWriter.create(s._2()));
})
.saveAsTextFile(workingPath + outputDoiAuthorListPath);
.map(s -> {
OrcidDOI orcidDOI = new OrcidDOI();
orcidDOI.setDoi(s._1());
orcidDOI.setAuthors(s._2());
return JsonWriter.create(orcidDOI);
})
.saveAsTextFile(workingPath + outputDoiAuthorListPath, GzipCodec.class);
});
}

2
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/workflow.xml
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@ -14,7 +14,7 @@
</property>
<property>
<name>spark2MaxExecutors</name>
<value>40</value>
<value>20</value>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>