[AffRo] removing package
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package eu.dnetlib.dhp.oa.graph.openorgsforaffro;
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import com.fasterxml.jackson.core.JsonProcessingException;
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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.Relation;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
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import eu.dnetlib.dhp.schema.oaf.utils.PidType;
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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.*;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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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.JavaPairRDD;
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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.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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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 scala.Tuple2;
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import java.io.BufferedOutputStream;
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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 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 static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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public class ExtractAffRoInfoFromOpenOrgs 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 DOI_PREFIX = "50|doi_________::";
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private static final String PMID_PREFIX = "50|pmid________::";
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private static final String ARXIV_PREFIX = "50|arXiv_______::";
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private static final String PMCID_PREFIX = "50|pmcid_______::";
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private static final String TRUST = "0.91";
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private static final Logger log = LoggerFactory.getLogger(ExtractAffRoInfoFromOpenOrgs.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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ExtractAffRoInfoFromOpenOrgs.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);
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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 -> extractContent(spark, inputPath, outputPath));
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}
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private static void extractContent(SparkSession spark, String inputPath, String outputPath) {
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getTextTextJavaPairRDD(spark, inputPath)
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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}
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private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath) {
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return spark
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.read()
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.textFile(inputPath)
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.map(
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(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
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Encoders.bean(COCI.class))
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.flatMap(
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(FlatMapFunction<COCI, Relation>) value -> createRelation(
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value)
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.iterator(),
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Encoders.bean(Relation.class))
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.filter((FilterFunction<Relation>) Objects::nonNull)
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.toJavaRDD()
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.map(p -> new AtomicAction(p.getClass(), p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))));
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}
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private static List<Relation> createRelation(COCI value) throws JsonProcessingException {
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List<Relation> relationList = new ArrayList<>();
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String citing;
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String cited;
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switch (value.getCiting_pid()) {
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case "doi":
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citing = DOI_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
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break;
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case "pmid":
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citing = PMID_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
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break;
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case "arxiv":
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citing = ARXIV_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCiting()));
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break;
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case "pmcid":
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citing = PMCID_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCiting()));
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break;
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case "isbn":
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case "issn":
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return relationList;
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default:
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throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
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}
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switch (value.getCited_pid()) {
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case "doi":
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cited = DOI_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCited()));
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break;
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case "pmid":
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cited = PMID_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCited()));
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break;
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case "arxiv":
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cited = ARXIV_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCited()));
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break;
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case "pmcid":
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cited = PMCID_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCited()));
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break;
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case "isbn":
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case "issn":
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return relationList;
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default:
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throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
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}
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if (!citing.equals(cited)) {
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relationList
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.add(
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getRelation(
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citing,
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cited, ModelConstants.CITES));
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}
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return relationList;
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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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return OafMapperUtils
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.getRelation(
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source,
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target,
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ModelConstants.RESULT_RESULT,
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ModelConstants.CITATION,
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relClass,
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Arrays
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.asList(
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OafMapperUtils.keyValue(ModelConstants.OPENOCITATIONS_ID, ModelConstants.OPENOCITATIONS_NAME)),
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OafMapperUtils
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.dataInfo(
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false, null, false, false,
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OafMapperUtils
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.qualifier(
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OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME,
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ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
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TRUST),
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null);
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}
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}
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