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Opencitations: chenaged the test class to mirror the creation or not of duplicate dois for .refs oc original plus added optional parameter to duplicate the relation

This commit is contained in:
Miriam Baglioni 2021-10-18 14:11:27 +02:00
parent 476a4708d6
commit 1cc09adfaa
4 changed files with 41 additions and 185 deletions

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@ -65,7 +65,10 @@ public class CreateActionSetSparkJob implements Serializable {
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final boolean shouldDuplicateRels = Boolean.valueOf(parser.get("shouldDuplicateRels"));
final boolean shouldDuplicateRels =
Optional.ofNullable(parser.get("shouldDuplicateRels"))
.map(Boolean::valueOf)
.orElse(Boolean.FALSE);
SparkConf conf = new SparkConf();
runWithSparkSession(

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@ -1,176 +0,0 @@
package eu.dnetlib.dhp.actionmanager.opencitations;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.io.Serializable;
import java.util.*;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import scala.Tuple2;
public class CreateRelationsJson implements Serializable {
public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
private static final String ID_PREFIX = "50|doi_________::";
private static final String TRUST = "0.91";
private static final Logger log = LoggerFactory.getLogger(CreateRelationsJson.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws IOException, ParseException {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
CreateRelationsJson.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json"))));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}", inputPath.toString());
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
extractContent(spark, inputPath, outputPath);
});
}
private static void extractContent(SparkSession spark, String inputPath, String outputPath) {
spark
.sqlContext()
.createDataset(spark.sparkContext().textFile(inputPath + "/*", 6000), Encoders.STRING())
.flatMap(
(FlatMapFunction<String, Relation>) value -> createRelation(value).iterator(),
Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) value -> value != null)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
private static List<Relation> createRelation(String value) {
String[] line = value.split(",");
if (!line[1].startsWith("10.")) {
return new ArrayList<>();
}
List<Relation> relationList = new ArrayList<>();
String citing = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[1]));
final String cited = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[2]));
relationList
.addAll(
getRelations(
citing,
cited));
if (line[1].endsWith(".refs")) {
citing = ID_PREFIX + IdentifierFactory
.md5(CleaningFunctions.normalizePidValue("doi", line[1].substring(0, line[1].indexOf(".refs"))));
relationList.addAll(getRelations(citing, cited));
}
return relationList;
}
private static Collection<Relation> getRelations(String citing, String cited) {
return Arrays
.asList(
getRelation(citing, cited, ModelConstants.CITES),
getRelation(cited, citing, ModelConstants.IS_CITED_BY));
}
public static Relation getRelation(
String source,
String target,
String relclass) {
Relation r = new Relation();
r.setCollectedfrom(getCollectedFrom());
r.setSource(source);
r.setTarget(target);
r.setRelClass(relclass);
r.setRelType(ModelConstants.RESULT_RESULT);
r.setSubRelType(ModelConstants.CITATION);
r
.setDataInfo(
getDataInfo());
return r;
}
public static List<KeyValue> getCollectedFrom() {
KeyValue kv = new KeyValue();
kv.setKey(ModelConstants.OPENOCITATIONS_ID);
kv.setValue(ModelConstants.OPENOCITATIONS_NAME);
return Arrays.asList(kv);
}
public static DataInfo getDataInfo() {
DataInfo di = new DataInfo();
di.setInferred(false);
di.setDeletedbyinference(false);
di.setTrust(TRUST);
di
.setProvenanceaction(
getQualifier(OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS));
return di;
}
public static Qualifier getQualifier(String class_id, String class_name,
String qualifierSchema) {
Qualifier pa = new Qualifier();
pa.setClassid(class_id);
pa.setClassname(class_name);
pa.setSchemeid(qualifierSchema);
pa.setSchemename(qualifierSchema);
return pa;
}
}

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@ -1,5 +0,0 @@
package eu.dnetlib.dhp.actionmanager.opencitations;
public class OpenCitationModel {
}

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@ -84,6 +84,8 @@ public class CreateOpenCitationsASTest {
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-shouldDuplicateRels",
Boolean.TRUE.toString(),
"-inputPath",
inputPath,
"-outputPath",
@ -99,7 +101,39 @@ public class CreateOpenCitationsASTest {
assertEquals(60, tmp.count());
tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
}
@Test
void testNumberofRelations2() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
.getPath();
CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
assertEquals(44, tmp.count());
// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
}
@ -206,8 +240,8 @@ public class CreateOpenCitationsASTest {
assertEquals("citation", r.getSubRelType());
assertEquals("resultResult", r.getRelType());
});
assertEquals(30, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
assertEquals(30, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
assertEquals(22, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
assertEquals(22, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
}