forked from D-Net/dnet-hadoop
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
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476a4708d6
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1cc09adfaa
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@ -65,7 +65,10 @@ public class CreateActionSetSparkJob implements Serializable {
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}", outputPath);
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final boolean shouldDuplicateRels = Boolean.valueOf(parser.get("shouldDuplicateRels"));
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final boolean shouldDuplicateRels =
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Optional.ofNullable(parser.get("shouldDuplicateRels"))
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.map(Boolean::valueOf)
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.orElse(Boolean.FALSE);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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@ -1,176 +0,0 @@
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package eu.dnetlib.dhp.actionmanager.opencitations;
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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.io.Serializable;
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import java.util.*;
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import org.apache.commons.cli.ParseException;
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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.hadoop.mapred.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.FlatMapFunction;
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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.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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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.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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import scala.Tuple2;
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public class CreateRelationsJson implements Serializable {
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public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
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public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
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private static final String ID_PREFIX = "50|doi_________::";
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private static final String TRUST = "0.91";
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private static final Logger log = LoggerFactory.getLogger(CreateRelationsJson.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(final String[] args) throws IOException, ParseException {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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Objects
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.requireNonNull(
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CreateRelationsJson.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/opencitations/as_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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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("inputPath");
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log.info("inputPath {}", inputPath.toString());
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}", outputPath);
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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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extractContent(spark, inputPath, outputPath);
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});
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}
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private static void extractContent(SparkSession spark, String inputPath, String outputPath) {
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spark
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.sqlContext()
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.createDataset(spark.sparkContext().textFile(inputPath + "/*", 6000), Encoders.STRING())
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.flatMap(
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(FlatMapFunction<String, Relation>) value -> createRelation(value).iterator(),
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Encoders.bean(Relation.class))
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.filter((FilterFunction<Relation>) value -> value != null)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath);
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}
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private static List<Relation> createRelation(String value) {
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String[] line = value.split(",");
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if (!line[1].startsWith("10.")) {
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return new ArrayList<>();
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}
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List<Relation> relationList = new ArrayList<>();
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String citing = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[1]));
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final String cited = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[2]));
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relationList
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.addAll(
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getRelations(
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citing,
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cited));
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if (line[1].endsWith(".refs")) {
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citing = ID_PREFIX + IdentifierFactory
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.md5(CleaningFunctions.normalizePidValue("doi", line[1].substring(0, line[1].indexOf(".refs"))));
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relationList.addAll(getRelations(citing, cited));
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}
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return relationList;
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}
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private static Collection<Relation> getRelations(String citing, String cited) {
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return Arrays
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.asList(
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getRelation(citing, cited, ModelConstants.CITES),
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getRelation(cited, citing, ModelConstants.IS_CITED_BY));
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}
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public static Relation getRelation(
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String source,
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String target,
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String relclass) {
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Relation r = new Relation();
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r.setCollectedfrom(getCollectedFrom());
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r.setSource(source);
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r.setTarget(target);
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r.setRelClass(relclass);
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r.setRelType(ModelConstants.RESULT_RESULT);
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r.setSubRelType(ModelConstants.CITATION);
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r
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.setDataInfo(
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getDataInfo());
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return r;
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}
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public static List<KeyValue> getCollectedFrom() {
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KeyValue kv = new KeyValue();
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kv.setKey(ModelConstants.OPENOCITATIONS_ID);
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kv.setValue(ModelConstants.OPENOCITATIONS_NAME);
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return Arrays.asList(kv);
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}
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public static DataInfo getDataInfo() {
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DataInfo di = new DataInfo();
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di.setInferred(false);
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di.setDeletedbyinference(false);
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di.setTrust(TRUST);
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di
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.setProvenanceaction(
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getQualifier(OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS));
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return di;
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}
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public static Qualifier getQualifier(String class_id, String class_name,
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String qualifierSchema) {
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Qualifier pa = new Qualifier();
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pa.setClassid(class_id);
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pa.setClassname(class_name);
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pa.setSchemeid(qualifierSchema);
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pa.setSchemename(qualifierSchema);
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return pa;
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}
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}
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@ -1,5 +0,0 @@
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package eu.dnetlib.dhp.actionmanager.opencitations;
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public class OpenCitationModel {
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}
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@ -84,6 +84,8 @@ public class CreateOpenCitationsASTest {
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-shouldDuplicateRels",
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Boolean.TRUE.toString(),
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"-inputPath",
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inputPath,
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"-outputPath",
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@ -99,7 +101,39 @@ public class CreateOpenCitationsASTest {
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assertEquals(60, tmp.count());
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tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
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// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
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}
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@Test
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void testNumberofRelations2() throws Exception {
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String inputPath = getClass()
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.getResource(
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"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
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.getPath();
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CreateActionSetSparkJob
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.main(
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-inputPath",
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inputPath,
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"-outputPath",
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workingDir.toString() + "/actionSet"
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Relation> tmp = sc
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.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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assertEquals(44, tmp.count());
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// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
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}
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@ -206,8 +240,8 @@ public class CreateOpenCitationsASTest {
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assertEquals("citation", r.getSubRelType());
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assertEquals("resultResult", r.getRelType());
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});
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assertEquals(30, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
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assertEquals(30, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
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assertEquals(22, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
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assertEquals(22, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
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}
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