Addressing comments in #340\#issuecomment-10592
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@ -12,6 +12,7 @@ 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.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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@ -26,9 +27,12 @@ import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
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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.common.ModelSupport;
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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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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import scala.Tuple2;
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public class CreateActionSetSparkJob implements Serializable {
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@ -68,9 +72,6 @@ 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 String prefix = parser.get("prefix");
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log.info("prefix {}", prefix);
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final boolean shouldDuplicateRels = Optional
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.ofNullable(parser.get("shouldDuplicateRels"))
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.map(Boolean::valueOf)
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@ -81,47 +82,62 @@ public class CreateActionSetSparkJob implements Serializable {
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conf,
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isSparkSessionManaged,
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spark -> {
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extractContent(spark, inputPath, outputPath, shouldDuplicateRels, prefix);
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extractContent(spark, inputPath, outputPath, shouldDuplicateRels);
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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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boolean shouldDuplicateRels) {
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getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, "COCI")
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.union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, "POCI"))
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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}
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private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath,
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boolean shouldDuplicateRels, String prefix) {
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spark
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return spark
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.read()
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.textFile(inputPath + "/*")
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.textFile(inputPath + "/" + prefix + "/" + prefix + "_JSON/*")
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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(value, shouldDuplicateRels, prefix)
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.iterator(),
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(FlatMapFunction<COCI, Relation>) value -> createRelation(
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value, shouldDuplicateRels, prefix)
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.iterator(),
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Encoders.bean(Relation.class))
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.filter((FilterFunction<Relation>) value -> value != null)
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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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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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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, boolean duplicate, String p) {
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List<Relation> relationList = new ArrayList<>();
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String prefix;
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String citing;
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String cited;
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if (p.equals("COCI")) {
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prefix = DOI_PREFIX;
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citing = prefix
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCiting()));
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cited = prefix
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCited()));
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} else {
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prefix = PMID_PREFIX;
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}
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citing = prefix
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("pmid", value.getCiting()));
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cited = prefix
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("pmid", value.getCited()));
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String citing = prefix
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCiting()));
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final String cited = prefix
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCited()));
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}
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if (!citing.equals(cited)) {
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relationList
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@ -143,59 +159,30 @@ public class CreateActionSetSparkJob implements Serializable {
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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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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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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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@ -110,7 +110,7 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingPath}/${prefix}_JSON</arg>
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<arg>--inputPath</arg><arg>${workingPath}</arg>
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<arg>--outputPath</arg><arg>${outputPath}</arg>
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<arg>--prefix</arg><arg>${prefix}</arg>
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</spark>
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