Merge branch 'stable_ids' of code-repo.d4science.org:D-Net/dnet-hadoop into stable_id_scholexplorer
This commit is contained in:
commit
a167543637
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@ -18,7 +18,7 @@ import eu.dnetlib.dhp.schema.oaf.Field;
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public class DatePicker {
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public static final String DATE_PATTERN = "^\\d{4}-\\d{2}-\\d{2}$";
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public static final String DATE_PATTERN = "^(\\d{4})-(\\d{2})-(\\d{2})";
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private static final String DATE_DEFAULT_SUFFIX = "01-01";
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private static final int YEAR_LB = 1300;
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private static final int YEAR_UB = Year.now().getValue() + 5;
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@ -28,6 +28,7 @@ public class DatePicker {
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final Map<String, Integer> frequencies = dateofacceptance
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.parallelStream()
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.filter(StringUtils::isNotBlank)
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.map(d -> substringBefore(d, "T"))
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.collect(Collectors.toConcurrentMap(w -> w, w -> 1, Integer::sum));
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if (frequencies.isEmpty()) {
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@ -0,0 +1,44 @@
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package eu.dnetlib.dhp.oa.dedup;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import java.util.Collection;
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import org.junit.jupiter.api.Test;
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import com.clearspring.analytics.util.Lists;
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public class DatePickerTest {
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Collection<String> dates = Lists.newArrayList();
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@Test
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public void testPickISO() {
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dates.add("2016-01-01T12:00:00Z");
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dates.add("2016-06-16T12:00:00Z");
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dates.add("2020-01-01T12:00:00Z");
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dates.add("2020-10-01T12:00:00Z");
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assertEquals("2020-10-01", DatePicker.pick(dates).getValue());
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}
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@Test
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public void testPickSimple() {
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dates.add("2016-01-01");
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dates.add("2016-06-16");
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dates.add("2020-01-01");
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dates.add("2020-10-01");
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assertEquals("2020-10-01", DatePicker.pick(dates).getValue());
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}
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@Test
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public void testPickFrequent() {
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dates.add("2016-02-01");
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dates.add("2016-02-01");
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dates.add("2016-02-01");
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dates.add("2020-10-01");
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assertEquals("2016-02-01", DatePicker.pick(dates).getValue());
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}
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}
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@ -1,6 +1,11 @@
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package eu.dnetlib.doiboost.crossref
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.doiboost.crossref.CrossrefDataset.to_item
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import eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries.getClass
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import org.apache.hadoop.io.{IntWritable, Text}
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import org.apache.hadoop.io.compress.GzipCodec
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import org.apache.spark.rdd.RDD
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import org.apache.spark.{SparkConf, SparkContext}
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import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
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import org.json4s
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@ -17,13 +22,6 @@ object GenerateCrossrefDataset {
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implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
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def extractDump(input:String):List[String] = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: json4s.JValue = parse(input)
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val a = (json \ "items").extract[JArray]
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a.arr.map(s => compact(render(s)))
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}
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def crossrefElement(meta: String): CrossrefDT = {
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@ -44,7 +42,7 @@ object GenerateCrossrefDataset {
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val targetPath = parser.get("targetPath")
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val spark: SparkSession = SparkSession.builder().config(conf)
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.appName(GenerateCrossrefDataset.getClass.getSimpleName)
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.appName(UnpackCrtossrefEntries.getClass.getSimpleName)
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.master(master)
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.getOrCreate()
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val sc: SparkContext = spark.sparkContext
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@ -52,19 +50,14 @@ object GenerateCrossrefDataset {
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import spark.implicits._
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def extractDump(input:String):List[String] = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: json4s.JValue = parse(input)
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val tmp : RDD[String] = sc.textFile(sourcePath,6000)
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val a = (json \ "items").extract[JArray]
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a.arr.map(s => compact(render(s)))
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}
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sc.wholeTextFiles(sourcePath,6000).flatMap(d =>extractDump(d._2))
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.map(meta => crossrefElement(meta))
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.toDS()//.as[CrossrefDT]
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spark.createDataset(tmp)
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.map(entry => crossrefElement(entry))
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.write.mode(SaveMode.Overwrite).save(targetPath)
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// .map(meta => crossrefElement(meta))
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// .toDS.as[CrossrefDT]
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// .write.mode(SaveMode.Overwrite).save(targetPath)
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}
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@ -4,9 +4,9 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset}
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import org.apache.commons.io.IOUtils
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import org.apache.hadoop.io.{IntWritable, Text}
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import org.apache.spark.SparkConf
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import org.apache.spark.rdd.RDD
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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@ -17,6 +17,7 @@ object SparkMapDumpIntoOAF {
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def main(args: Array[String]): Unit = {
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implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
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val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
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val conf: SparkConf = new SparkConf()
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@ -35,7 +36,6 @@ object SparkMapDumpIntoOAF {
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implicit val mapEncoderDatasets: Encoder[oaf.Dataset] = Encoders.kryo[OafDataset]
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val targetPath = parser.get("targetPath")
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import spark.implicits._
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spark.read.load(parser.get("sourcePath")).as[CrossrefDT]
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.flatMap(k => Crossref2Oaf.convert(k.json))
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@ -0,0 +1,54 @@
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package eu.dnetlib.doiboost.crossref
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import org.apache.hadoop.io.compress.GzipCodec
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import org.apache.spark.{SparkConf, SparkContext}
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import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
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import org.json4s
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import org.json4s.DefaultFormats
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import org.json4s.JsonAST.JArray
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import org.json4s.jackson.JsonMethods.{compact, parse, render}
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import org.slf4j.{Logger, LoggerFactory}
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import scala.io.Source
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object UnpackCrtossrefEntries {
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val log: Logger = LoggerFactory.getLogger(UnpackCrtossrefEntries.getClass)
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def extractDump(input:String):List[String] = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: json4s.JValue = parse(input)
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val a = (json \ "items").extract[JArray]
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a.arr.map(s => compact(render(s)))
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}
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def main(args: Array[String]): Unit = {
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val conf = new SparkConf
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json")).mkString)
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parser.parseArgument(args)
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val master = parser.get("master")
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val sourcePath = parser.get("sourcePath")
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val targetPath = parser.get("targetPath")
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val spark: SparkSession = SparkSession.builder().config(conf)
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.appName(UnpackCrtossrefEntries.getClass.getSimpleName)
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.master(master)
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.getOrCreate()
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val sc: SparkContext = spark.sparkContext
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sc.wholeTextFiles(sourcePath,6000).flatMap(d =>extractDump(d._2))
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.saveAsTextFile(targetPath, classOf[GzipCodec])
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}
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}
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@ -24,7 +24,7 @@
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</parameters>
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<start to="ImportCrossRef"/>
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<start to="GenerateCrossrefDataset"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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@ -40,11 +40,37 @@
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<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
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<arg>--outputPath</arg><arg>${workingDir}/files/</arg>
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</java>
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<ok to="generateCrossrefDataset"/>
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<ok to="UnpackCrossrefEntries"/>
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<error to="Kill"/>
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</action>
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<action name="generateCrossrefDataset">
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<action name="UnpackCrossrefEntries">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>SparkGenerateCrossrefDataset</name>
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<class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--master</arg><arg>yarn-cluster</arg>
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<arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
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<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
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</spark>
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<ok to="GenerateCrossrefDataset"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateCrossrefDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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@ -62,31 +88,31 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--master</arg><arg>yarn-cluster</arg>
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<arg>--sourcePath</arg><arg>${workingDir}/files</arg>
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<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds_updated</arg>
|
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<arg>--sourcePath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
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<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds_updates</arg>
|
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|
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</spark>
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<ok to="removeFiles"/>
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<error to="Kill"/>
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</action>
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<action name="removeFiles">
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<fs>
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<delete path="${workingDir}/files"/>
|
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</fs>
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<ok to="renameDataset"/>
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<error to="Kill"/>
|
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</action>
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|
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<action name="renameDataset">
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<fs>
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<delete path="${inputPathCrossref}/crossref_ds"/>
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<move source="${inputPathCrossref}/crossref_ds_updated"
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target="${inputPathCrossref}/crossref_ds"/>
|
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</fs>
|
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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|
||||
<!-- <action name="removeFiles">-->
|
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<!-- <fs>-->
|
||||
<!-- <delete path="${workingDir}/files"/>-->
|
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<!-- </fs>-->
|
||||
<!-- <ok to="renameDataset"/>-->
|
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<!-- <error to="Kill"/>-->
|
||||
<!-- </action>-->
|
||||
|
||||
<!-- <action name="renameDataset">-->
|
||||
<!-- <fs>-->
|
||||
<!-- <delete path="${inputPathCrossref}/crossref_ds"/>-->
|
||||
<!-- <move source="${inputPathCrossref}/crossref_ds_updated"-->
|
||||
<!-- target="${inputPathCrossref}/crossref_ds"/>-->
|
||||
<!-- </fs>-->
|
||||
<!-- <ok to="End"/>-->
|
||||
<!-- <error to="Kill"/>-->
|
||||
<!-- </action>-->
|
||||
|
||||
<end name="End"/>
|
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</workflow-app>
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||||
|
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@ -142,6 +142,32 @@
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|||
<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${crossrefDumpPath}/files/</arg>
|
||||
</java>
|
||||
<ok to="UnpackCrossrefEntries"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="UnpackCrossrefEntries">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>SparkUnpackCrossrefEntries</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
|
||||
<arg>--targetPath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="GenerateCrossrefDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
|
@ -154,9 +180,9 @@
|
|||
<class>eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-memory=7G
|
||||
--executor-cores=2
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--driver-memory=7G
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
|
|
@ -164,7 +190,7 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/files/</arg>
|
||||
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
|
||||
<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
|
||||
|
||||
</spark>
|
||||
|
|
@ -174,7 +200,8 @@
|
|||
|
||||
<action name="removeFiles">
|
||||
<fs>
|
||||
<delete path="${crossrefDumpPath}/files"/>
|
||||
<!-- <delete path="${crossrefDumpPath}/files"/>-->
|
||||
<delete path="${crossrefDumpPath}/crossref_unpack/"/>
|
||||
</fs>
|
||||
<ok to="ResetMagWorkingPath"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
|||
|
|
@ -395,4 +395,71 @@ class CrossrefMappingTest {
|
|||
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Test
|
||||
def testSetDateOfAcceptanceCrossRef2Oaf(): Unit = {
|
||||
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("dump_file.json")).mkString
|
||||
assertNotNull(json)
|
||||
|
||||
assertFalse(json.isEmpty);
|
||||
|
||||
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
|
||||
|
||||
assertTrue(resultList.nonEmpty)
|
||||
|
||||
val items = resultList.filter(p => p.isInstanceOf[Publication])
|
||||
|
||||
assert(items.nonEmpty)
|
||||
assert(items.size == 1)
|
||||
val result: Result = items.head.asInstanceOf[Publication]
|
||||
assertNotNull(result)
|
||||
|
||||
logger.info(mapper.writeValueAsString(result));
|
||||
|
||||
// assertNotNull(result.getDataInfo, "Datainfo test not null Failed");
|
||||
// assertNotNull(
|
||||
// result.getDataInfo.getProvenanceaction,
|
||||
// "DataInfo/Provenance test not null Failed");
|
||||
// assertFalse(
|
||||
// result.getDataInfo.getProvenanceaction.getClassid.isEmpty,
|
||||
// "DataInfo/Provenance/classId test not null Failed");
|
||||
// assertFalse(
|
||||
// result.getDataInfo.getProvenanceaction.getClassname.isEmpty,
|
||||
// "DataInfo/Provenance/className test not null Failed");
|
||||
// assertFalse(
|
||||
// result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty,
|
||||
// "DataInfo/Provenance/SchemeId test not null Failed");
|
||||
// assertFalse(
|
||||
// result.getDataInfo.getProvenanceaction.getSchemename.isEmpty,
|
||||
// "DataInfo/Provenance/SchemeName test not null Failed");
|
||||
//
|
||||
// assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed");
|
||||
// assertFalse(result.getCollectedfrom.isEmpty);
|
||||
//
|
||||
// val collectedFromList = result.getCollectedfrom.asScala
|
||||
// assert(collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")), "Wrong collected from assertion")
|
||||
//
|
||||
// assert(collectedFromList.exists(c => c.getValue.equalsIgnoreCase("crossref")), "Wrong collected from assertion")
|
||||
//
|
||||
//
|
||||
// val relevantDates = result.getRelevantdate.asScala
|
||||
//
|
||||
// assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("created")), "Missing relevant date of type created")
|
||||
//
|
||||
// val rels = resultList.filter(p => p.isInstanceOf[Relation]).asInstanceOf[List[Relation]]
|
||||
// assertFalse(rels.isEmpty)
|
||||
// rels.foreach(relation => {
|
||||
// assertNotNull(relation)
|
||||
// assertFalse(relation.getSource.isEmpty)
|
||||
// assertFalse(relation.getTarget.isEmpty)
|
||||
// assertFalse(relation.getRelClass.isEmpty)
|
||||
// assertFalse(relation.getRelType.isEmpty)
|
||||
// assertFalse(relation.getSubRelType.isEmpty)
|
||||
//
|
||||
// })
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1 @@
|
|||
{"indexed":{"date-parts":[[2020,4,10]],"date-time":"2020-04-10T00:38:19Z","timestamp":1586479099385},"reference-count":0,"publisher":"American Medical Association (AMA)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Archives of Internal Medicine"],"published-print":{"date-parts":[[2006,2,27]]},"DOI":"10.1001/.389","type":"journal-article","created":{"date-parts":[[2006,2,27]],"date-time":"2006-02-27T21:28:23Z","timestamp":1141075703000},"page":"389-390","source":"Crossref","is-referenced-by-count":0,"title":["Decision Making at the Fringe of Evidence: Take What You Can Get"],"prefix":"10.1001","volume":"166","author":[{"given":"N. F.","family":"Col","affiliation":[]}],"member":"10","container-title":["Archives of Internal Medicine"],"original-title":[],"deposited":{"date-parts":[[2007,2,13]],"date-time":"2007-02-13T20:56:13Z","timestamp":1171400173000},"score":null,"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,2,27]]},"references-count":0,"URL":"http://dx.doi.org/10.1001/.389","relation":{},"ISSN":["0003-9926"],"issn-type":[{"value":"0003-9926","type":"print"}],"subject":["Internal Medicine"]}
|
||||
2
pom.xml
2
pom.xml
|
|
@ -736,7 +736,7 @@
|
|||
<mockito-core.version>3.3.3</mockito-core.version>
|
||||
<mongodb.driver.version>3.4.2</mongodb.driver.version>
|
||||
<vtd.version>[2.12,3.0)</vtd.version>
|
||||
<dhp-schemas.version>[2.5.12]</dhp-schemas.version>
|
||||
<dhp-schemas.version>[2.6.13]</dhp-schemas.version>
|
||||
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
|
||||
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
|
||||
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
|
||||
|
|
|
|||
Loading…
Reference in New Issue