[BypassAS] addition of OC relations
parent
6f7ca539c6
commit
9e214ce0eb
@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.bypassactionset;
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package eu.dnetlib.dhp.bypassactionset.bipfinder;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.bypassactionset.model.BipScore;
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package eu.dnetlib.dhp.bypassactionset.opencitations;
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import java.io.*;
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import java.io.Serializable;
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import java.util.Objects;
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import java.util.zip.GZIPOutputStream;
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import java.util.zip.ZipEntry;
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import java.util.zip.ZipInputStream;
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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.conf.Configuration;
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import org.apache.hadoop.fs.FSDataInputStream;
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import org.apache.hadoop.fs.FSDataOutputStream;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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public class GetOpenCitationsRefs implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(GetOpenCitationsRefs.class);
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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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GetOpenCitationsRefs.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/bypassactionset/opencitations/input_parameters.json"))));
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parser.parseArgument(args);
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final String[] inputFile = parser.get("inputFile").split(";");
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log.info("inputFile {}", inputFile.toString());
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final String workingPath = parser.get("workingPath");
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log.info("workingPath {}", workingPath);
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final String hdfsNameNode = parser.get("hdfsNameNode");
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log.info("hdfsNameNode {}", hdfsNameNode);
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(conf);
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GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
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for (String file : inputFile) {
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ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem);
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}
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}
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private void doExtract(String inputFile, String workingPath, FileSystem fileSystem)
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throws IOException {
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final Path path = new Path(inputFile);
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FSDataInputStream oc_zip = fileSystem.open(path);
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int count = 1;
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try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
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ZipEntry entry = null;
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while ((entry = zis.getNextEntry()) != null) {
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if (!entry.isDirectory()) {
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String fileName = entry.getName();
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fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
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count++;
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try (
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FSDataOutputStream out = fileSystem
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.create(new Path(workingPath + "/COCI/" + fileName + ".gz"));
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GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
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IOUtils.copy(zis, gzipOs);
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}
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}
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}
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}
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}
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}
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@ -0,0 +1,158 @@
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package eu.dnetlib.dhp.bypassactionset.opencitations;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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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.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.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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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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public class SparkUpdateOCRels implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkUpdateOCRels.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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SparkUpdateOCRels.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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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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conf,
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isSparkSessionManaged,
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spark ->
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addOCRelations(spark, inputPath, outputPath, shouldDuplicateRels)
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);
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}
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private static void addOCRelations(SparkSession spark, String inputPath, String outputPath,
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boolean shouldDuplicateRels) {
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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, shouldDuplicateRels).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.Append)
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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, boolean duplicate) {
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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 (duplicate && line[1].endsWith(REF_DOI)) {
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citing = ID_PREFIX + IdentifierFactory
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.md5(CleaningFunctions.normalizePidValue(DOI, line[1].substring(0, line[1].indexOf(REF_DOI))));
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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(UPDATE_DATA_INFO_TYPE, OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME,
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ModelConstants.DNET_PROVENANCE_ACTIONS, OC_TRUST, false));
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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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}
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