forked from D-Net/dnet-hadoop
[Dump] resolved conflicts with beta and merging
This commit is contained in:
commit
56409d1281
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@ -3,8 +3,6 @@
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*.iws
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*.ipr
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*.iml
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*.ipr
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*.iws
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*~
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.vscode
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.metals
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|
|
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|||
|
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@ -57,9 +57,17 @@ public class VocabularyGroup implements Serializable {
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final String syn = arr[2].trim();
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vocs.addSynonyms(vocId, termId, syn);
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}
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}
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// add the term names as synonyms
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vocs.vocs.values().forEach(voc -> {
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voc.getTerms().values().forEach(term -> {
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voc.addSynonym(term.getName().toLowerCase(), term.getId());
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});
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});
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return vocs;
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}
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|
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@ -16,6 +16,8 @@ import com.github.sisyphsu.dateparser.DateParserUtils;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Sets;
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import eu.dnetlib.dhp.common.vocabulary.Vocabulary;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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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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@ -86,6 +88,22 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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}
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public static <T extends Oaf> boolean filter(T value) {
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if (Boolean.TRUE
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.equals(
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Optional
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.ofNullable(value)
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.map(
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o -> Optional
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.ofNullable(o.getDataInfo())
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.map(
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d -> Optional
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.ofNullable(d.getInvisible())
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.orElse(true))
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.orElse(true))
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.orElse(true))) {
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return false;
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}
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if (value instanceof Datasource) {
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// nothing to evaluate here
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} else if (value instanceof Project) {
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@ -115,7 +133,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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return true;
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}
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public static <T extends Oaf> T cleanup(T value) {
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public static <T extends Oaf> T cleanup(T value, VocabularyGroup vocs) {
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if (value instanceof Datasource) {
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// nothing to clean here
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} else if (value instanceof Project) {
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@ -212,6 +230,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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.map(GraphCleaningFunctions::cleanValue)
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.collect(Collectors.toList()));
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}
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if (Objects.nonNull(r.getFormat())) {
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r
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.setFormat(
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r
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.getFormat()
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.stream()
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.map(GraphCleaningFunctions::cleanValue)
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.collect(Collectors.toList()));
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}
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if (Objects.nonNull(r.getDescription())) {
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r
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.setDescription(
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@ -234,6 +261,38 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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if (Objects.nonNull(r.getInstance())) {
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for (Instance i : r.getInstance()) {
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if (!vocs.termExists(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getClassid())) {
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if (r instanceof Publication) {
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i
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.setInstancetype(
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OafMapperUtils
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.qualifier(
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"0038", "Other literature type", ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE));
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} else if (r instanceof Dataset) {
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i
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.setInstancetype(
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OafMapperUtils
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.qualifier(
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"0039", "Other dataset type", ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE));
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} else if (r instanceof Software) {
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i
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.setInstancetype(
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OafMapperUtils
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.qualifier(
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"0040", "Other software type", ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE));
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} else if (r instanceof OtherResearchProduct) {
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i
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.setInstancetype(
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OafMapperUtils
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.qualifier(
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"0020", "Other ORP type", ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE));
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}
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}
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if (Objects.nonNull(i.getPid())) {
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i.setPid(processPidCleaning(i.getPid()));
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}
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|
|
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|
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@ -107,7 +107,7 @@ class OafMapperUtilsTest {
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assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("2006-01-02T15:04:05+0000").get());
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assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09-07:00").get());
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assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09").get());
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assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get());
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assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get());
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assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.3186369").get());
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assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000").get());
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assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.123").get());
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|
|
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|
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@ -1,69 +0,0 @@
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package eu.dnetlib.dhp.actionmanager.scholix
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
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import org.apache.spark.SparkConf
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import org.apache.spark.sql._
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import org.slf4j.{Logger, LoggerFactory}
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import scala.io.Source
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object SparkCreateActionset {
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def main(args: Array[String]): Unit = {
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val log: Logger = LoggerFactory.getLogger(getClass)
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/generate_actionset.json")).mkString)
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parser.parseArgument(args)
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val spark: SparkSession =
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SparkSession
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.builder()
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.config(conf)
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.appName(getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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val sourcePath = parser.get("sourcePath")
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log.info(s"sourcePath -> $sourcePath")
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val targetPath = parser.get("targetPath")
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log.info(s"targetPath -> $targetPath")
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val workingDirFolder = parser.get("workingDirFolder")
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log.info(s"workingDirFolder -> $workingDirFolder")
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implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
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implicit val resultEncoders: Encoder[Result] = Encoders.kryo[Result]
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implicit val relationEncoders: Encoder[Relation] = Encoders.kryo[Relation]
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import spark.implicits._
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val relation = spark.read.load(s"$sourcePath/relation").as[Relation]
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relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
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.flatMap(r => List(r.getSource, r.getTarget)).distinct().write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/id_relation")
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val idRelation = spark.read.load(s"$workingDirFolder/id_relation").as[String]
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log.info("extract source and target Identifier involved in relations")
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log.info("save relation filtered")
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relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
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.write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/actionSetOaf")
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log.info("saving entities")
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val entities: Dataset[(String, Result)] = spark.read.load(s"$sourcePath/entities/*").as[Result].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING, resultEncoders))
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entities
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.joinWith(idRelation, entities("_1").equalTo(idRelation("value")))
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.map(p => p._1._2)
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.write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
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}
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}
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@ -1,86 +0,0 @@
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package eu.dnetlib.dhp.actionmanager.scholix
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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.oaf.{Oaf, Dataset => OafDataset,Publication, Software, OtherResearchProduct, Relation}
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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.sql.{Encoder, Encoders, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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import scala.io.Source
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object SparkSaveActionSet {
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def toActionSet(item: Oaf): (String, String) = {
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val mapper = new ObjectMapper()
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item match {
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case dataset: OafDataset =>
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val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset]
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a.setClazz(classOf[OafDataset])
|
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a.setPayload(dataset)
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(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case publication: Publication =>
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val a: AtomicAction[Publication] = new AtomicAction[Publication]
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a.setClazz(classOf[Publication])
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a.setPayload(publication)
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(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case software: Software =>
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val a: AtomicAction[Software] = new AtomicAction[Software]
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a.setClazz(classOf[Software])
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a.setPayload(software)
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(software.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case orp: OtherResearchProduct =>
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val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct]
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a.setClazz(classOf[OtherResearchProduct])
|
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a.setPayload(orp)
|
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(orp.getClass.getCanonicalName, mapper.writeValueAsString(a))
|
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|
||||
case relation: Relation =>
|
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val a: AtomicAction[Relation] = new AtomicAction[Relation]
|
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a.setClazz(classOf[Relation])
|
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a.setPayload(relation)
|
||||
(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
|
||||
case _ =>
|
||||
null
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||
val conf: SparkConf = new SparkConf()
|
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/save_actionset.json")).mkString)
|
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parser.parseArgument(args)
|
||||
|
||||
|
||||
val spark: SparkSession =
|
||||
SparkSession
|
||||
.builder()
|
||||
.config(conf)
|
||||
.appName(getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
|
||||
|
||||
val sourcePath = parser.get("sourcePath")
|
||||
log.info(s"sourcePath -> $sourcePath")
|
||||
|
||||
val targetPath = parser.get("targetPath")
|
||||
log.info(s"targetPath -> $targetPath")
|
||||
|
||||
implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||
implicit val tEncoder: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
|
||||
|
||||
spark.read.load(sourcePath).as[Oaf]
|
||||
.map(o => toActionSet(o))
|
||||
.filter(o => o != null)
|
||||
.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text, Text]], classOf[GzipCodec])
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,8 +1,8 @@
|
|||
package eu.dnetlib.dhp.datacite
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
|
||||
import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
|
||||
|
||||
import java.io.InputStream
|
||||
import java.time.format.DateTimeFormatter
|
||||
|
|
@ -6,7 +6,7 @@ import eu.dnetlib.dhp.datacite.DataciteModelConstants._
|
|||
import eu.dnetlib.dhp.schema.action.AtomicAction
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
|
||||
import eu.dnetlib.dhp.schema.oaf.{AccessRight, Author, DataInfo, Instance, KeyValue, Oaf, OtherResearchProduct, Publication, Qualifier, Relation, Result, Software, StructuredProperty, Dataset => OafDataset}
|
||||
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _}
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import org.apache.commons.lang3.StringUtils
|
||||
import org.json4s.DefaultFormats
|
||||
|
|
@ -29,6 +29,7 @@ object DataciteToOAFTransformation {
|
|||
/**
|
||||
* This method should skip record if json contains invalid text
|
||||
* defined in gile datacite_filter
|
||||
*
|
||||
* @param json
|
||||
* @return True if the record should be skipped
|
||||
*/
|
||||
|
|
@ -7,6 +7,7 @@ import org.json4s.DefaultFormats
|
|||
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||
import org.json4s.jackson.JsonMethods.{compact, parse, render}
|
||||
import collection.JavaConverters._
|
||||
|
||||
object BioDBToOAF {
|
||||
|
||||
case class EBILinkItem(id: Long, links: String) {}
|
||||
|
|
@ -1,9 +1,9 @@
|
|||
package eu.dnetlib.dhp.sx.bio
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||
import BioDBToOAF.ScholixResolved
|
||||
import eu.dnetlib.dhp.collection.CollectionUtils
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
|
|
@ -3,7 +3,7 @@ package eu.dnetlib.dhp.sx.bio.ebi
|
|||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||
import eu.dnetlib.dhp.schema.oaf.Result
|
||||
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
|
||||
import eu.dnetlib.dhp.sx.bio.pubmed._
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.conf.Configuration
|
||||
|
|
@ -1,9 +1,8 @@
|
|||
package eu.dnetlib.dhp.sx.bio.ebi
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
|
||||
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
|
||||
import eu.dnetlib.dhp.sx.bio.pubmed.PMJournal
|
||||
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.http.client.config.RequestConfig
|
||||
import org.apache.http.client.methods.HttpGet
|
||||
|
|
@ -1,11 +1,10 @@
|
|||
package eu.dnetlib.dhp.sx.bio.ebi
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.collection.CollectionUtils
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||
import eu.dnetlib.dhp.sx.bio.BioDBToOAF
|
||||
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
|
||||
import BioDBToOAF.EBILinkItem
|
||||
import eu.dnetlib.dhp.collection.CollectionUtils
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql._
|
||||
|
|
@ -4,7 +4,7 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
|||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType}
|
||||
import eu.dnetlib.dhp.schema.oaf._
|
||||
import scala.collection.JavaConverters._
|
||||
import collection.JavaConverters._
|
||||
|
||||
import java.util.regex.Pattern
|
||||
|
||||
|
|
@ -22,10 +22,10 @@ object PubMedToOaf {
|
|||
val collectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Cleaning the DOI Applying regex in order to
|
||||
* remove doi starting with URL
|
||||
*
|
||||
* @param doi input DOI
|
||||
* @return cleaned DOI
|
||||
*/
|
||||
|
|
@ -93,7 +93,6 @@ object PubMedToOaf {
|
|||
* @param vocabularyName the input vocabulary name
|
||||
* @param vocabularies all the vocabularies
|
||||
* @param term the term to find
|
||||
*
|
||||
* @return the cleaned term value
|
||||
*/
|
||||
def getVocabularyTerm(vocabularyName: String, vocabularies: VocabularyGroup, term: String): Qualifier = {
|
||||
|
|
@ -106,7 +105,6 @@ object PubMedToOaf {
|
|||
/**
|
||||
* Map the Pubmed Article into the OAF instance
|
||||
*
|
||||
*
|
||||
* @param article the pubmed articles
|
||||
* @param vocabularies the vocabularies
|
||||
* @return The OAF instance if the mapping did not fail
|
||||
|
|
@ -185,7 +183,6 @@ object PubMedToOaf {
|
|||
//--------------------------------------------------------------------------------------
|
||||
|
||||
|
||||
|
||||
// RESULT MAPPING
|
||||
//--------------------------------------------------------------------------------------
|
||||
result.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo))
|
||||
|
|
@ -89,13 +89,13 @@ public class CreateOpenCitationsASTest {
|
|||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
workingDir.toString() + "/actionSet1"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
|
|
@ -121,13 +121,13 @@ public class CreateOpenCitationsASTest {
|
|||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
workingDir.toString() + "/actionSet2"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.sequenceFile(workingDir.toString() + "/actionSet2", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
|
|
@ -153,13 +153,13 @@ public class CreateOpenCitationsASTest {
|
|||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
workingDir.toString() + "/actionSet3"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.sequenceFile(workingDir.toString() + "/actionSet3", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
|
|
@ -186,13 +186,13 @@ public class CreateOpenCitationsASTest {
|
|||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
workingDir.toString() + "/actionSet4"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.sequenceFile(workingDir.toString() + "/actionSet4", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
|
|
@ -226,13 +226,13 @@ public class CreateOpenCitationsASTest {
|
|||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
workingDir.toString() + "/actionSet5"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.sequenceFile(workingDir.toString() + "/actionSet5", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
|
|
@ -261,13 +261,13 @@ public class CreateOpenCitationsASTest {
|
|||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
workingDir.toString() + "/actionSet6"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.sequenceFile(workingDir.toString() + "/actionSet6", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
|
|
@ -306,13 +306,13 @@ public class CreateOpenCitationsASTest {
|
|||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
workingDir.toString() + "/actionSet7"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.sequenceFile(workingDir.toString() + "/actionSet7", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@ import org.apache.commons.io.FileUtils
|
|||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.functions.{col, count}
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
||||
import org.junit.jupiter.api.Assertions._
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.junit.jupiter.api.{AfterEach, BeforeEach, Test}
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
|
|
@ -17,7 +18,7 @@ import java.nio.file.{Files, Path}
|
|||
import java.text.SimpleDateFormat
|
||||
import java.util.Locale
|
||||
import scala.io.Source
|
||||
import org.junit.jupiter.api.Assertions._
|
||||
|
||||
@ExtendWith(Array(classOf[MockitoExtension]))
|
||||
class DataciteToOAFTest extends AbstractVocabularyTest{
|
||||
|
||||
|
|
@ -90,7 +90,7 @@ public class ReadBlacklistFromDB implements Closeable {
|
|||
inverse.setSource(target_direct);
|
||||
|
||||
String encoding = rs.getString("relationship");
|
||||
RelationInverse ri = ModelSupport.relationInverseMap.get(encoding);
|
||||
RelationInverse ri = ModelSupport.findInverse(encoding);
|
||||
direct.setRelClass(ri.getRelClass());
|
||||
inverse.setRelClass(ri.getInverseRelClass());
|
||||
direct.setRelType(ri.getRelType());
|
||||
|
|
|
|||
|
|
@ -1,21 +1,19 @@
|
|||
package eu.dnetlib.doiboost
|
||||
|
||||
import java.time.LocalDate
|
||||
import java.time.format.DateTimeFormatter
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.schema.action.AtomicAction
|
||||
import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Dataset, Field, Instance, KeyValue, Oaf, OpenAccessRoute, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf._
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import org.apache.commons.lang3.StringUtils
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{getClosedAccessQualifier, getEmbargoedAccessQualifier, getUnknownQualifier}
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import java.time.LocalDate
|
||||
import java.time.format.DateTimeFormatter
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
|
||||
|
|
@ -8,11 +8,12 @@ import org.apache.hadoop.io.Text
|
|||
import org.apache.hadoop.io.compress.GzipCodec
|
||||
import org.apache.hadoop.mapred.SequenceFileOutputFormat
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkGenerateDOIBoostActionSet {
|
||||
val logger: Logger = LoggerFactory.getLogger(getClass)
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
||||
val conf: SparkConf = new SparkConf()
|
||||
|
|
@ -55,7 +56,6 @@ object SparkGenerateDOIBoostActionSet {
|
|||
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
||||
|
||||
|
||||
|
||||
val asCRelation = spark.read.load(crossRefRelation).as[Relation]
|
||||
.filter(r => r != null && r.getSource != null && r.getTarget != null)
|
||||
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
||||
|
|
@ -65,23 +65,12 @@ object SparkGenerateDOIBoostActionSet {
|
|||
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
val d: Dataset[(String, String)] = asDataset.union(asPublication).union(asOrganization).union(asCRelation).union(asRelAffiliation)
|
||||
|
||||
|
||||
|
||||
d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text, Text]], classOf[GzipCodec])
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -9,14 +9,12 @@ import org.apache.commons.io.IOUtils
|
|||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.expressions.Aggregator
|
||||
import org.apache.spark.sql.functions.col
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
import org.apache.spark.sql._
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST.{JField, JObject, JString,JArray}
|
||||
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
import scala.collection.JavaConverters._
|
||||
object SparkGenerateDoiBoost {
|
||||
|
||||
|
||||
|
|
@ -38,7 +36,6 @@ object SparkGenerateDoiBoost {
|
|||
}
|
||||
|
||||
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
||||
val logger: Logger = LoggerFactory.getLogger(getClass)
|
||||
|
|
@ -118,8 +115,7 @@ object SparkGenerateDoiBoost {
|
|||
val crossrefPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/crossrefPublication").as[Publication].map(p => (p.getId, p))
|
||||
val uwPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/uwPublication").as[Publication].map(p => (p.getId, p))
|
||||
|
||||
def applyMerge(item:((String, Publication), (String, Publication))) : Publication =
|
||||
{
|
||||
def applyMerge(item: ((String, Publication), (String, Publication))): Publication = {
|
||||
val crossrefPub = item._1._2
|
||||
if (item._2 != null) {
|
||||
val otherPub = item._2._2
|
||||
|
|
@ -130,6 +126,7 @@ object SparkGenerateDoiBoost {
|
|||
}
|
||||
crossrefPub
|
||||
}
|
||||
|
||||
crossrefPublication.joinWith(uwPublication, crossrefPublication("_1").equalTo(uwPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/firstJoin")
|
||||
logger.info("Phase 3) Join Result with ORCID")
|
||||
val fj: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/firstJoin").as[Publication].map(p => (p.getId, p))
|
||||
|
|
@ -169,7 +166,6 @@ object SparkGenerateDoiBoost {
|
|||
.select(col("_1.PaperId"), col("_2.AffiliationId"), col("_2.GridId"), col("_2.OfficialPage"), col("_2.DisplayName")).as[DoiBoostAffiliation]
|
||||
|
||||
|
||||
|
||||
val magPubs: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/doiBoostPublicationFiltered").as[Publication]
|
||||
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p))(tupleForJoinEncoder).filter(s => s._1 != null)
|
||||
|
||||
|
|
@ -198,8 +194,6 @@ object SparkGenerateDoiBoost {
|
|||
})(mapEncoderRel).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved")
|
||||
|
||||
|
||||
|
||||
|
||||
val unresolvedRels: Dataset[(String, Relation)] = spark.read.load(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved").as[Relation].map(r => {
|
||||
|
||||
if (r.getSource.startsWith("unresolved"))
|
||||
|
|
@ -4,20 +4,19 @@ import eu.dnetlib.dhp.schema.common.ModelConstants
|
|||
import eu.dnetlib.dhp.schema.oaf._
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{decideAccessRight, _}
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
||||
import org.apache.commons.lang.StringUtils
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST.{JValue, _}
|
||||
import org.json4s.JsonAST._
|
||||
import org.json4s.jackson.JsonMethods._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import java.util
|
||||
import scala.collection.JavaConverters._
|
||||
import scala.collection.mutable
|
||||
import scala.util.matching.Regex
|
||||
import java.util
|
||||
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||
|
||||
case class CrossrefDT(doi: String, json:String, timestamp: Long) {}
|
||||
|
||||
|
|
@ -6,7 +6,7 @@ import org.apache.commons.io.IOUtils
|
|||
import org.apache.hadoop.io.{IntWritable, Text}
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.expressions.Aggregator
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql.{Dataset, Encoder, SaveMode, SparkSession}
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
|
|
@ -30,7 +30,6 @@ object CrossrefDataset {
|
|||
def main(args: Array[String]): Unit = {
|
||||
|
||||
|
||||
|
||||
val conf: SparkConf = new SparkConf()
|
||||
val parser = new ArgumentApplicationParser(IOUtils.toString(CrossrefDataset.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json")))
|
||||
parser.parseArgument(args)
|
||||
|
|
@ -2,17 +2,12 @@ package eu.dnetlib.doiboost.crossref
|
|||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||
import eu.dnetlib.doiboost.crossref.CrossrefDataset.to_item
|
||||
import eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries.getClass
|
||||
import org.apache.hadoop.io.{IntWritable, Text}
|
||||
import org.apache.hadoop.io.compress.GzipCodec
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.{SparkConf, SparkContext}
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.{SparkConf, SparkContext}
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST.JArray
|
||||
import org.json4s.jackson.JsonMethods.{compact, parse, render}
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.io.Source
|
||||
|
|
@ -24,7 +19,6 @@ object GenerateCrossrefDataset {
|
|||
implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
|
||||
|
||||
|
||||
|
||||
def crossrefElement(meta: String): CrossrefDT = {
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
lazy val json: json4s.JValue = parse(meta)
|
||||
|
|
@ -4,10 +4,8 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
|||
import eu.dnetlib.dhp.schema.oaf
|
||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset}
|
||||
import org.apache.commons.io.IOUtils
|
||||
|
||||
import org.apache.spark.SparkConf
|
||||
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
|
||||
|
|
@ -2,8 +2,8 @@ package eu.dnetlib.doiboost.crossref
|
|||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import org.apache.hadoop.io.compress.GzipCodec
|
||||
import org.apache.spark.sql.SparkSession
|
||||
import org.apache.spark.{SparkConf, SparkContext}
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST.JArray
|
||||
|
|
@ -17,8 +17,6 @@ object UnpackCrtossrefEntries {
|
|||
val log: Logger = LoggerFactory.getLogger(UnpackCrtossrefEntries.getClass)
|
||||
|
||||
|
||||
|
||||
|
||||
def extractDump(input: String): List[String] = {
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
lazy val json: json4s.JValue = parse(input)
|
||||
|
|
@ -30,7 +28,6 @@ object UnpackCrtossrefEntries {
|
|||
}
|
||||
|
||||
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
val conf = new SparkConf
|
||||
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json")).mkString)
|
||||
|
|
@ -5,10 +5,10 @@ import eu.dnetlib.dhp.schema.common.ModelConstants
|
|||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
|
||||
import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty}
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
import scala.collection.mutable
|
||||
|
|
@ -3,8 +3,8 @@ package eu.dnetlib.doiboost.mag
|
|||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{SaveMode, SparkSession}
|
||||
import org.apache.spark.sql.types._
|
||||
import org.apache.spark.sql.{SaveMode, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkImportMagIntoDataset {
|
||||
|
|
@ -75,7 +75,6 @@ object SparkImportMagIntoDataset {
|
|||
.master(parser.get("master")).getOrCreate()
|
||||
|
||||
|
||||
|
||||
stream.foreach { case (k, v) =>
|
||||
val s: StructType = getSchema(k)
|
||||
val df = spark.read
|
||||
|
|
@ -5,13 +5,10 @@ import eu.dnetlib.dhp.schema.oaf.Publication
|
|||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql.functions._
|
||||
import org.apache.spark.sql.functions.{col, collect_list, struct}
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
object SparkProcessMAG {
|
||||
|
||||
def getDistinctResults(d: Dataset[MagPapers]): Dataset[MagPapers] = {
|
||||
|
|
@ -20,7 +17,7 @@ object SparkProcessMAG {
|
|||
.reduceGroups((p1: MagPapers, p2: MagPapers) => ConversionUtil.choiceLatestMagArtitcle(p1, p2))
|
||||
.map(_._2)(Encoders.product[MagPapers])
|
||||
.map(mp => {
|
||||
new MagPapers(mp.PaperId, mp.Rank, DoiBoostMappingUtil.normalizeDoi(mp.Doi),
|
||||
MagPapers(mp.PaperId, mp.Rank, DoiBoostMappingUtil.normalizeDoi(mp.Doi),
|
||||
mp.DocType, mp.PaperTitle, mp.OriginalTitle,
|
||||
mp.BookTitle, mp.Year, mp.Date, mp.Publisher: String,
|
||||
mp.JournalId, mp.ConferenceSeriesId, mp.ConferenceInstanceId,
|
||||
|
|
@ -153,6 +150,5 @@ object SparkProcessMAG {
|
|||
.write.mode(SaveMode.Overwrite).save(s"$targetPath/magPublication")
|
||||
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -4,17 +4,16 @@ import com.fasterxml.jackson.databind.ObjectMapper
|
|||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
|
||||
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication}
|
||||
import eu.dnetlib.dhp.schema.orcid.{AuthorData, OrcidDOI}
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{createSP, generateDataInfo}
|
||||
import org.apache.commons.lang.StringUtils
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST._
|
||||
import org.json4s.jackson.JsonMethods._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
|
||||
case class ORCIDItem(doi:String, authors:List[OrcidAuthor]){}
|
||||
|
|
@ -1,15 +1,12 @@
|
|||
package eu.dnetlib.doiboost.orcid
|
||||
|
||||
import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper}
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.oa.merge.AuthorMerger
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication
|
||||
import eu.dnetlib.dhp.schema.orcid.OrcidDOI
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql.functions._
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql.functions.{col, collect_list}
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkPreprocessORCID {
|
||||
|
|
@ -1,16 +1,14 @@
|
|||
package eu.dnetlib.doiboost.uw
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication
|
||||
import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
|
||||
object SparkMapUnpayWallToOAF {
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
|
@ -4,14 +4,13 @@ import eu.dnetlib.dhp.schema.common.ModelConstants
|
|||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
|
||||
import eu.dnetlib.dhp.schema.oaf.{AccessRight, Instance, OpenAccessRoute, Publication}
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
||||
import eu.dnetlib.doiboost.uw.UnpayWallToOAF.get_unpaywall_color
|
||||
|
||||
|
||||
|
||||
|
|
@ -1,70 +0,0 @@
|
|||
package eu.dnetlib.dhp.doiboost
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.{Publication, Dataset => OafDataset}
|
||||
import eu.dnetlib.doiboost.{DoiBoostMappingUtil, HostedByItemType}
|
||||
import eu.dnetlib.doiboost.SparkGenerateDoiBoost.getClass
|
||||
import eu.dnetlib.doiboost.mag.ConversionUtil
|
||||
import eu.dnetlib.doiboost.orcid.ORCIDElement
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
|
||||
import org.junit.jupiter.api.Test
|
||||
|
||||
import scala.io.Source
|
||||
|
||||
class DoiBoostHostedByMapTest {
|
||||
|
||||
|
||||
|
||||
// @Test
|
||||
// def testMerge():Unit = {
|
||||
// val conf: SparkConf = new SparkConf()
|
||||
// val spark: SparkSession =
|
||||
// SparkSession
|
||||
// .builder()
|
||||
// .config(conf)
|
||||
// .appName(getClass.getSimpleName)
|
||||
// .master("local[*]").getOrCreate()
|
||||
//
|
||||
//
|
||||
//
|
||||
// implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
|
||||
// implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
|
||||
// implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub)
|
||||
//
|
||||
//
|
||||
// import spark.implicits._
|
||||
// val dataset:RDD[String]= spark.sparkContext.textFile("/home/sandro/Downloads/hbMap.gz")
|
||||
//
|
||||
//
|
||||
// val hbMap:Dataset[(String, HostedByItemType)] =spark.createDataset(dataset.map(DoiBoostMappingUtil.toHostedByItem))
|
||||
//
|
||||
//
|
||||
// hbMap.show()
|
||||
//
|
||||
//
|
||||
//
|
||||
//
|
||||
//
|
||||
//
|
||||
//
|
||||
//
|
||||
//
|
||||
//
|
||||
// }
|
||||
|
||||
|
||||
@Test
|
||||
def idDSGeneration():Unit = {
|
||||
val s ="doajarticles::0066-782X"
|
||||
|
||||
|
||||
|
||||
println(DoiBoostMappingUtil.generateDSId(s))
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,20 @@
|
|||
package eu.dnetlib.dhp.doiboost
|
||||
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||
import org.junit.jupiter.api.Test
|
||||
|
||||
class DoiBoostHostedByMapTest {
|
||||
|
||||
@Test
|
||||
def idDSGeneration():Unit = {
|
||||
val s ="doajarticles::0066-782X"
|
||||
|
||||
|
||||
|
||||
println(DoiBoostMappingUtil.generateDSId(s))
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -1,7 +1,8 @@
|
|||
package eu.dnetlib.doiboost.crossref
|
||||
package eu.dnetlib.dhp.doiboost.crossref
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf._
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
|
||||
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
|
||||
import org.junit.jupiter.api.Assertions._
|
||||
import org.junit.jupiter.api.Test
|
||||
|
|
@ -21,9 +22,9 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testFunderRelationshipsMapping(): Unit = {
|
||||
val template = Source.fromInputStream(getClass.getResourceAsStream("article_funder_template.json")).mkString
|
||||
val funder_doi = Source.fromInputStream(getClass.getResourceAsStream("funder_doi")).mkString
|
||||
val funder_name = Source.fromInputStream(getClass.getResourceAsStream("funder_doi")).mkString
|
||||
val template = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article_funder_template.json")).mkString
|
||||
val funder_doi = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/funder_doi")).mkString
|
||||
val funder_name = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/funder_doi")).mkString
|
||||
|
||||
|
||||
for (line <- funder_doi.lines) {
|
||||
|
|
@ -72,7 +73,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testOrcidID() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("orcid_data.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/orcid_data.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
|
|
@ -93,7 +94,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testEmptyTitle() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("empty_title.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/empty_title.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
|
|
@ -115,7 +116,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testPeerReviewed(): Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("prwTest.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/prwTest.json")).mkString
|
||||
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
|
||||
|
||||
assertNotNull(json)
|
||||
|
|
@ -156,7 +157,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testJournalRelation(): Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("awardTest.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/awardTest.json")).mkString
|
||||
assertNotNull(json)
|
||||
|
||||
assertFalse(json.isEmpty)
|
||||
|
|
@ -177,7 +178,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testConvertBookFromCrossRef2Oaf(): Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("book.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/book.json")).mkString
|
||||
assertNotNull(json)
|
||||
|
||||
assertFalse(json.isEmpty);
|
||||
|
|
@ -233,7 +234,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testConvertPreprintFromCrossRef2Oaf(): Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("preprint.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/preprint.json")).mkString
|
||||
assertNotNull(json)
|
||||
|
||||
assertFalse(json.isEmpty);
|
||||
|
|
@ -291,7 +292,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testConvertDatasetFromCrossRef2Oaf(): Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("dataset.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/dataset.json")).mkString
|
||||
assertNotNull(json)
|
||||
|
||||
assertFalse(json.isEmpty);
|
||||
|
|
@ -332,7 +333,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testConvertArticleFromCrossRef2Oaf(): Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("article.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article.json")).mkString
|
||||
assertNotNull(json)
|
||||
|
||||
assertFalse(json.isEmpty);
|
||||
|
|
@ -400,7 +401,7 @@ class CrossrefMappingTest {
|
|||
@Test
|
||||
def testSetDateOfAcceptanceCrossRef2Oaf(): Unit = {
|
||||
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("dump_file.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/dump_file.json")).mkString
|
||||
assertNotNull(json)
|
||||
|
||||
assertFalse(json.isEmpty);
|
||||
|
|
@ -415,55 +416,12 @@ class CrossrefMappingTest {
|
|||
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)
|
||||
//
|
||||
// })
|
||||
}
|
||||
|
||||
@Test
|
||||
def testNormalizeDOI(): Unit = {
|
||||
val template = Source.fromInputStream(getClass.getResourceAsStream("article_funder_template.json")).mkString
|
||||
val template = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article_funder_template.json")).mkString
|
||||
val line :String = "\"funder\": [{\"name\": \"Wellcome Trust Masters Fellowship\",\"award\": [\"090633\"]}],"
|
||||
val json = template.replace("%s", line)
|
||||
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
|
||||
|
|
@ -479,7 +437,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testNormalizeDOI2(): Unit = {
|
||||
val template = Source.fromInputStream(getClass.getResourceAsStream("article.json")).mkString
|
||||
val template = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article.json")).mkString
|
||||
|
||||
val resultList: List[Oaf] = Crossref2Oaf.convert(template)
|
||||
assertTrue(resultList.nonEmpty)
|
||||
|
|
@ -494,7 +452,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testLicenseVorClosed() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_vor.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_vor.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
|
|
@ -521,7 +479,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testLicenseOpen() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_open.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_open.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
|
|
@ -544,7 +502,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testLicenseEmbargoOpen() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo_open.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo_open.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
|
|
@ -567,7 +525,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testLicenseEmbargo() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
|
|
@ -591,7 +549,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testLicenseEmbargoDateTime() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo_datetime.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo_datetime.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
|
|
@ -614,7 +572,7 @@ class CrossrefMappingTest {
|
|||
|
||||
@Test
|
||||
def testMultipleURLs() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("multiple_urls.json")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/multiple_urls.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
|
|
@ -1,11 +1,12 @@
|
|||
package eu.dnetlib.doiboost.mag
|
||||
package eu.dnetlib.dhp.doiboost.mag
|
||||
|
||||
import eu.dnetlib.doiboost.mag.{ConversionUtil, MagPapers, SparkProcessMAG}
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Dataset, SparkSession}
|
||||
import org.codehaus.jackson.map.ObjectMapper
|
||||
import org.json4s.DefaultFormats
|
||||
import org.junit.jupiter.api.Assertions._
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.json4s.DefaultFormats
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import java.sql.Timestamp
|
||||
|
|
@ -47,7 +48,7 @@ class MAGMappingTest {
|
|||
|
||||
@Test
|
||||
def buildInvertedIndexTest(): Unit = {
|
||||
val json_input = Source.fromInputStream(getClass.getResourceAsStream("invertedIndex.json")).mkString
|
||||
val json_input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/mag/invertedIndex.json")).mkString
|
||||
val description = ConversionUtil.convertInvertedIndexString(json_input)
|
||||
assertNotNull(description)
|
||||
assertTrue(description.nonEmpty)
|
||||
|
|
@ -71,7 +72,7 @@ class MAGMappingTest {
|
|||
.appName(getClass.getSimpleName)
|
||||
.config(conf)
|
||||
.getOrCreate()
|
||||
val path = getClass.getResource("magPapers.json").getPath
|
||||
val path = getClass.getResource("/eu/dnetlib/doiboost/mag/magPapers.json").getPath
|
||||
|
||||
import org.apache.spark.sql.Encoders
|
||||
val schema = Encoders.product[MagPapers].schema
|
||||
|
|
@ -101,7 +102,7 @@ class MAGMappingTest {
|
|||
.appName(getClass.getSimpleName)
|
||||
.config(conf)
|
||||
.getOrCreate()
|
||||
val path = getClass.getResource("duplicatedMagPapers.json").getPath
|
||||
val path = getClass.getResource("/eu/dnetlib/doiboost/mag/duplicatedMagPapers.json").getPath
|
||||
|
||||
import org.apache.spark.sql.Encoders
|
||||
val schema = Encoders.product[MagPapers].schema
|
||||
|
|
@ -1,7 +1,8 @@
|
|||
package eu.dnetlib.doiboost.orcid
|
||||
package eu.dnetlib.dhp.doiboost.orcid
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication
|
||||
import eu.dnetlib.doiboost.orcid._
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
||||
import org.junit.jupiter.api.Assertions._
|
||||
|
|
@ -10,9 +11,8 @@ import org.junit.jupiter.api.io.TempDir
|
|||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import java.nio.file.Path
|
||||
import scala.io.Source
|
||||
|
||||
import scala.collection.JavaConversions._
|
||||
import scala.io.Source
|
||||
|
||||
class MappingORCIDToOAFTest {
|
||||
val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass)
|
||||
|
|
@ -20,7 +20,7 @@ class MappingORCIDToOAFTest {
|
|||
|
||||
@Test
|
||||
def testExtractData():Unit ={
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("dataOutput")).mkString
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/orcid/dataOutput")).mkString
|
||||
assertNotNull(json)
|
||||
assertFalse(json.isEmpty)
|
||||
json.lines.foreach(s => {
|
||||
|
|
@ -1,13 +1,13 @@
|
|||
package eu.dnetlib.doiboost.uw
|
||||
|
||||
package eu.dnetlib.dhp.doiboost.uw
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.schema.oaf.OpenAccessRoute
|
||||
import eu.dnetlib.doiboost.uw.UnpayWallToOAF
|
||||
import org.junit.jupiter.api.Assertions._
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.io.Source
|
||||
import org.junit.jupiter.api.Assertions._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
class UnpayWallMappingTest {
|
||||
|
||||
|
|
@ -18,7 +18,7 @@ class UnpayWallMappingTest {
|
|||
@Test
|
||||
def testMappingToOAF():Unit ={
|
||||
|
||||
val Ilist = Source.fromInputStream(getClass.getResourceAsStream("input.json")).mkString
|
||||
val Ilist = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/uw/input.json")).mkString
|
||||
|
||||
var i:Int = 0
|
||||
for (line <-Ilist.lines) {
|
||||
|
|
@ -88,7 +88,7 @@ public class CleanGraphSparkJob {
|
|||
readTableFromPath(spark, inputPath, clazz)
|
||||
.map((MapFunction<T, T>) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz))
|
||||
.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
|
||||
.map((MapFunction<T, T>) GraphCleaningFunctions::cleanup, Encoders.bean(clazz))
|
||||
.map((MapFunction<T, T>) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz))
|
||||
.filter((FilterFunction<T>) GraphCleaningFunctions::filter)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
|
|
|
|||
|
|
@ -1,8 +1,8 @@
|
|||
package eu.dnetlib.dhp.oa.graph.hostedbymap
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, TypedColumn}
|
||||
import org.apache.spark.sql.expressions.Aggregator
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, TypedColumn}
|
||||
|
||||
|
||||
case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {}
|
||||
|
|
@ -2,13 +2,12 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap
|
|||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.SparkApplyHostedByMapToResult.{applyHBtoPubs, getClass}
|
||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.{Datasource, Publication}
|
||||
import eu.dnetlib.dhp.schema.oaf.Datasource
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql._
|
||||
import org.json4s.DefaultFormats
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
|
|
@ -5,16 +5,14 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
|||
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
|
||||
import eu.dnetlib.dhp.schema.oaf.{Datasource, Instance, OpenAccessRoute, Publication}
|
||||
import eu.dnetlib.dhp.schema.oaf.{Instance, OpenAccessRoute, Publication}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql._
|
||||
import org.json4s.DefaultFormats
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
|
||||
object SparkApplyHostedByMapToResult {
|
||||
|
||||
def applyHBtoPubs(join: Dataset[EntityInfo], pubs: Dataset[Publication]) = {
|
||||
|
|
@ -25,7 +23,7 @@ object SparkApplyHostedByMapToResult {
|
|||
val ei: EntityInfo = t2._2
|
||||
val i = p.getInstance().asScala
|
||||
if (i.size == 1) {
|
||||
val inst: Instance = i(0)
|
||||
val inst: Instance = i.head
|
||||
inst.getHostedby.setKey(ei.getHostedById)
|
||||
inst.getHostedby.setValue(ei.getName)
|
||||
if (ei.getOpenAccess) {
|
||||
|
|
@ -39,6 +37,7 @@ object SparkApplyHostedByMapToResult {
|
|||
p
|
||||
})(Encoders.bean(classOf[Publication]))
|
||||
}
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
||||
|
||||
|
|
@ -3,18 +3,15 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap
|
|||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.{Journal, Publication}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql._
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
|
||||
|
||||
object SparkPrepareHostedByInfoToApply {
|
||||
|
||||
implicit val mapEncoderPInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo])
|
||||
|
|
@ -1,22 +1,20 @@
|
|||
package eu.dnetlib.dhp.oa.graph.hostedbymap
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.{DOAJModel, UnibiGoldModel}
|
||||
import eu.dnetlib.dhp.schema.oaf.Datasource
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.conf.Configuration
|
||||
import org.apache.hadoop.fs.{FileSystem, Path}
|
||||
import org.apache.hadoop.io.compress.GzipCodec
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
||||
import org.json4s.DefaultFormats
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import org.apache.hadoop.conf.Configuration
|
||||
import org.apache.hadoop.fs.FileSystem
|
||||
import org.apache.hadoop.fs.Path
|
||||
|
||||
import java.io.PrintWriter
|
||||
|
||||
import org.apache.hadoop.io.compress.GzipCodec
|
||||
|
||||
|
||||
object SparkProduceHostedByMap {
|
||||
|
||||
|
||||
|
|
@ -52,7 +50,6 @@ object SparkProduceHostedByMap {
|
|||
}
|
||||
|
||||
|
||||
|
||||
def getHostedByItemType(id: String, officialname: String, issn: String, eissn: String, issnl: String, oa: Boolean): HostedByItemType = {
|
||||
if (issn != null) {
|
||||
if (eissn != null) {
|
||||
|
|
@ -163,7 +160,6 @@ object SparkProduceHostedByMap {
|
|||
}
|
||||
|
||||
|
||||
|
||||
def writeToHDFS(input: Array[String], outputPath: String, hdfsNameNode: String): Unit = {
|
||||
val conf = new Configuration()
|
||||
|
||||
|
|
@ -182,7 +178,6 @@ object SparkProduceHostedByMap {
|
|||
}
|
||||
|
||||
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
||||
val logger: Logger = LoggerFactory.getLogger(getClass)
|
||||
|
|
@ -4,17 +4,11 @@ import com.fasterxml.jackson.databind.ObjectMapper
|
|||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.common.HdfsSupport
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport
|
||||
import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.commons.lang3.StringUtils
|
||||
import org.apache.http.client.methods.HttpGet
|
||||
import org.apache.http.impl.client.HttpClients
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.{SparkConf, SparkContext}
|
||||
import org.slf4j.LoggerFactory
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
import scala.io.Source
|
||||
|
||||
|
|
@ -2,9 +2,8 @@ package eu.dnetlib.dhp.oa.graph.resolution
|
|||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.common.HdfsSupport
|
||||
import eu.dnetlib.dhp.schema.common.EntityType
|
||||
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Result, Software, Dataset => OafDataset}
|
||||
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset,_}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.fs.{FileSystem, Path}
|
||||
import org.apache.spark.SparkConf
|
||||
|
|
@ -3,7 +3,7 @@ package eu.dnetlib.dhp.oa.graph.resolution
|
|||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.common.HdfsSupport
|
||||
import eu.dnetlib.dhp.schema.oaf.{Relation, Result}
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.fs.{FileSystem, Path}
|
||||
|
|
@ -18,7 +18,6 @@ object SparkDataciteToOAF {
|
|||
.config(conf)
|
||||
.appName(getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
import spark.implicits._
|
||||
|
||||
|
||||
val sc = spark.sparkContext
|
||||
|
|
@ -2,7 +2,7 @@ package eu.dnetlib.dhp.sx.graph
|
|||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, OtherResearchProduct, Publication, Result, Software, Dataset => OafDataset}
|
||||
import eu.dnetlib.dhp.schema.oaf.Result
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.io.compress.GzipCodec
|
||||
import org.apache.spark.SparkConf
|
||||
|
|
@ -5,10 +5,10 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
|||
import eu.dnetlib.dhp.schema.sx.scholix.Scholix
|
||||
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.io.compress.GzipCodec
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
import org.apache.hadoop.io.compress._
|
||||
|
||||
object SparkConvertObjectToJson {
|
||||
|
||||
|
|
@ -2,11 +2,12 @@ package eu.dnetlib.dhp.sx.graph
|
|||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset}
|
||||
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Software,Dataset => OafDataset}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkConvertRDDtoDataset {
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
|
@ -1,14 +1,12 @@
|
|||
package eu.dnetlib.dhp.sx.graph
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset}
|
||||
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset,_}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
|
||||
|
||||
object SparkCreateInputGraph {
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
|
@ -41,9 +39,6 @@ object SparkCreateInputGraph {
|
|||
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
val sourcePath = parser.get("sourcePath")
|
||||
log.info(s"sourcePath -> $sourcePath")
|
||||
val targetPath = parser.get("targetPath")
|
||||
|
|
@ -9,7 +9,7 @@ import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils.RelatedEntities
|
|||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.functions.count
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkCreateScholix {
|
||||
|
|
@ -6,7 +6,7 @@ import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
|
|||
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkCreateSummaryObject {
|
||||
|
|
@ -5,6 +5,7 @@ import org.apache.spark.sql.{Encoder, Encoders}
|
|||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
|
||||
import java.util.regex.Pattern
|
||||
import scala.language.postfixOps
|
||||
import scala.xml.{Elem, Node, XML}
|
||||
|
|
@ -2,11 +2,11 @@ package eu.dnetlib.dhp.sx.graph.pangaea
|
|||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.{SparkConf, SparkContext}
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.{SparkConf, SparkContext}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
import scala.io.Source
|
||||
|
||||
object SparkGeneratePanagaeaDataset {
|
||||
|
|
@ -46,7 +46,4 @@ object SparkGeneratePanagaeaDataset {
|
|||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -1,6 +1,5 @@
|
|||
package eu.dnetlib.dhp.sx.graph.scholix
|
||||
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Result, StructuredProperty}
|
||||
import eu.dnetlib.dhp.schema.sx.scholix._
|
||||
import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, Typology}
|
||||
|
|
@ -10,10 +9,8 @@ import org.apache.spark.sql.{Encoder, Encoders}
|
|||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
import scala.io.Source
|
||||
import scala.language.postfixOps
|
||||
|
||||
object ScholixUtils {
|
||||
|
||||
|
|
@ -21,6 +18,7 @@ object ScholixUtils {
|
|||
val DNET_IDENTIFIER_SCHEMA: String = "DNET Identifier"
|
||||
|
||||
val DATE_RELATION_KEY: String = "RelationDate"
|
||||
|
||||
case class RelationVocabulary(original: String, inverse: String) {}
|
||||
|
||||
case class RelatedEntities(id: String, relatedDataset: Long, relatedPublication: Long) {}
|
||||
|
|
@ -66,7 +64,6 @@ object ScholixUtils {
|
|||
}
|
||||
|
||||
|
||||
|
||||
val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] = new Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] with Serializable {
|
||||
override def zero: RelatedEntities = null
|
||||
|
||||
|
|
@ -85,8 +82,7 @@ object ScholixUtils {
|
|||
if (b1 != null && b2 != null)
|
||||
RelatedEntities(b1.id, b1.relatedDataset + b2.relatedDataset, b1.relatedPublication + b2.relatedPublication)
|
||||
|
||||
else
|
||||
if (b1!= null)
|
||||
else if (b1 != null)
|
||||
b1
|
||||
else
|
||||
b2
|
||||
|
|
@ -144,7 +140,6 @@ object ScholixUtils {
|
|||
s
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -203,8 +198,7 @@ object ScholixUtils {
|
|||
|
||||
if (summaryObject.getDate != null && !summaryObject.getDate.isEmpty)
|
||||
r.setPublicationDate(summaryObject.getDate.get(0))
|
||||
if (summaryObject.getPublisher!= null && !summaryObject.getPublisher.isEmpty)
|
||||
{
|
||||
if (summaryObject.getPublisher != null && !summaryObject.getPublisher.isEmpty) {
|
||||
val plist: List[ScholixEntityId] = summaryObject.getPublisher.asScala.map(p => new ScholixEntityId(p, null)).toList
|
||||
|
||||
if (plist.nonEmpty)
|
||||
|
|
@ -228,9 +222,6 @@ object ScholixUtils {
|
|||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
def scholixFromSource(relation: Relation, source: ScholixSummary): Scholix = {
|
||||
|
||||
if (relation == null || source == null)
|
||||
|
|
@ -74,6 +74,53 @@ public class GraphCleaningFunctionsTest {
|
|||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
void testFilter_false() throws Exception {
|
||||
|
||||
assertNotNull(vocabularies);
|
||||
assertNotNull(mapping);
|
||||
|
||||
String json = IOUtils
|
||||
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json"));
|
||||
Publication p_in = MAPPER.readValue(json, Publication.class);
|
||||
|
||||
assertTrue(p_in instanceof Result);
|
||||
assertTrue(p_in instanceof Publication);
|
||||
|
||||
assertEquals(false, GraphCleaningFunctions.filter(p_in));
|
||||
}
|
||||
|
||||
@Test
|
||||
void testFilter_true() throws Exception {
|
||||
|
||||
assertNotNull(vocabularies);
|
||||
assertNotNull(mapping);
|
||||
|
||||
String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json"));
|
||||
Publication p_in = MAPPER.readValue(json, Publication.class);
|
||||
|
||||
assertTrue(p_in instanceof Result);
|
||||
assertTrue(p_in instanceof Publication);
|
||||
|
||||
assertEquals(true, GraphCleaningFunctions.filter(p_in));
|
||||
}
|
||||
|
||||
@Test
|
||||
void testFilter_missing_invisible() throws Exception {
|
||||
|
||||
assertNotNull(vocabularies);
|
||||
assertNotNull(mapping);
|
||||
|
||||
String json = IOUtils
|
||||
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json"));
|
||||
Publication p_in = MAPPER.readValue(json, Publication.class);
|
||||
|
||||
assertTrue(p_in instanceof Result);
|
||||
assertTrue(p_in instanceof Publication);
|
||||
|
||||
assertEquals(true, GraphCleaningFunctions.filter(p_in));
|
||||
}
|
||||
|
||||
@Test
|
||||
void testCleaning() throws Exception {
|
||||
|
||||
|
|
@ -104,6 +151,12 @@ public class GraphCleaningFunctionsTest {
|
|||
assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid());
|
||||
assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname());
|
||||
|
||||
assertEquals("0027", p_out.getInstance().get(1).getInstancetype().getClassid());
|
||||
assertEquals("Model", p_out.getInstance().get(1).getInstancetype().getClassname());
|
||||
|
||||
assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassid());
|
||||
assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassname());
|
||||
|
||||
assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid());
|
||||
assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname());
|
||||
|
||||
|
|
@ -117,7 +170,7 @@ public class GraphCleaningFunctionsTest {
|
|||
|
||||
List<Instance> poi = p_out.getInstance();
|
||||
assertNotNull(poi);
|
||||
assertEquals(1, poi.size());
|
||||
assertEquals(3, poi.size());
|
||||
|
||||
final Instance poii = poi.get(0);
|
||||
assertNotNull(poii);
|
||||
|
|
@ -145,7 +198,7 @@ public class GraphCleaningFunctionsTest {
|
|||
|
||||
assertEquals(5, p_out.getTitle().size());
|
||||
|
||||
Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out);
|
||||
Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
|
||||
|
||||
assertEquals(3, p_cleaned.getTitle().size());
|
||||
|
||||
|
|
@ -164,9 +217,12 @@ public class GraphCleaningFunctionsTest {
|
|||
|
||||
assertEquals("1970-10-07", p_cleaned.getDateofacceptance().getValue());
|
||||
|
||||
assertEquals("0038", p_cleaned.getInstance().get(2).getInstancetype().getClassid());
|
||||
assertEquals("Other literature type", p_cleaned.getInstance().get(2).getInstancetype().getClassname());
|
||||
|
||||
final List<Instance> pci = p_cleaned.getInstance();
|
||||
assertNotNull(pci);
|
||||
assertEquals(1, pci.size());
|
||||
assertEquals(3, pci.size());
|
||||
|
||||
final Instance pcii = pci.get(0);
|
||||
assertNotNull(pcii);
|
||||
|
|
@ -234,7 +290,7 @@ public class GraphCleaningFunctionsTest {
|
|||
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub.json"));
|
||||
Publication p_in = MAPPER.readValue(json, Publication.class);
|
||||
Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
|
||||
Publication cleaned = GraphCleaningFunctions.cleanup(p_out);
|
||||
Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
|
||||
|
||||
Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));
|
||||
}
|
||||
|
|
@ -245,7 +301,7 @@ public class GraphCleaningFunctionsTest {
|
|||
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub2.json"));
|
||||
Publication p_in = MAPPER.readValue(json, Publication.class);
|
||||
Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
|
||||
Publication cleaned = GraphCleaningFunctions.cleanup(p_out);
|
||||
Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
|
||||
|
||||
Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));
|
||||
|
||||
|
|
|
|||
|
|
@ -171,30 +171,6 @@ public class DumpJobTest {
|
|||
|
||||
GraphResult gr = verificationDataset.first();
|
||||
|
||||
Assertions.assertEquals(1, gr.getInstance().size());
|
||||
|
||||
Assertions.assertEquals(2, gr.getInstance().get(0).getMeasures().size());
|
||||
Assertions
|
||||
.assertTrue(
|
||||
gr
|
||||
.getInstance()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.anyMatch(
|
||||
m -> m.getKey().equals("influence")
|
||||
&& m.getValue().equals("1.62759106106e-08")));
|
||||
Assertions
|
||||
.assertTrue(
|
||||
gr
|
||||
.getInstance()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.anyMatch(
|
||||
m -> m.getKey().equals("popularity")
|
||||
&& m.getValue().equals("0.22519296")));
|
||||
|
||||
Assertions.assertEquals(6, gr.getAuthor().size());
|
||||
Assertions
|
||||
.assertTrue(
|
||||
|
|
@ -363,8 +339,6 @@ public class DumpJobTest {
|
|||
|
||||
Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId());
|
||||
|
||||
System.out.println(gr.getOriginalId().size());
|
||||
|
||||
Assertions.assertEquals(1, gr.getOriginalId().size());
|
||||
Assertions
|
||||
.assertTrue(
|
||||
|
|
|
|||
|
|
@ -708,7 +708,7 @@ class MappersTest {
|
|||
assertEquals(1, p.getTitle().size());
|
||||
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
||||
|
||||
final Publication p_cleaned = cleanup(fixVocabularyNames(p));
|
||||
final Publication p_cleaned = cleanup(fixVocabularyNames(p), vocs);
|
||||
|
||||
assertNotNull(p_cleaned.getTitle());
|
||||
assertFalse(p_cleaned.getTitle().isEmpty());
|
||||
|
|
|
|||
|
|
@ -403,6 +403,178 @@
|
|||
"http://juuli.fi/Record/0275158616",
|
||||
"http://dx.doi.org/10.1007/s109090161569x"
|
||||
]
|
||||
},
|
||||
{
|
||||
"pid": [
|
||||
{
|
||||
"dataInfo": null,
|
||||
"qualifier": {
|
||||
"classid": "doi",
|
||||
"classname": "doi",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
},
|
||||
"value": "10.1002/s21010127267xy"
|
||||
},
|
||||
{
|
||||
"dataInfo": null,
|
||||
"qualifier": {
|
||||
"classid": "doi",
|
||||
"classname": "doi",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
},
|
||||
"value": "10.1008/abcd"
|
||||
}
|
||||
],
|
||||
"alternateIdentifier": [
|
||||
{
|
||||
"dataInfo": null,
|
||||
"qualifier": {
|
||||
"classid": "doi",
|
||||
"classname": "doi",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
},
|
||||
"value": "10.1007/s109090161569x"
|
||||
},
|
||||
{
|
||||
"dataInfo": null,
|
||||
"qualifier": {
|
||||
"classid": "doi",
|
||||
"classname": "doi",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
},
|
||||
"value": "10.1009/qwerty"
|
||||
}
|
||||
],
|
||||
"accessright": {
|
||||
"classid": "CLOSED",
|
||||
"classname": "CLOSED",
|
||||
"schemeid": "dnet:access_modes",
|
||||
"schemename": "dnet:access_modes"
|
||||
},
|
||||
"collectedfrom": {
|
||||
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
|
||||
"value": "VIRTA"
|
||||
},
|
||||
"dateofacceptance": {
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"value": "2016-01-01"
|
||||
},
|
||||
"distributionlocation": "",
|
||||
"hostedby": {
|
||||
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
|
||||
"value": "VIRTA"
|
||||
},
|
||||
"instancetype": {
|
||||
"classid": "Model",
|
||||
"classname": "Model",
|
||||
"schemeid": "dnet:publication_resource",
|
||||
"schemename": "dnet:publication_resource"
|
||||
},
|
||||
"url": [
|
||||
"http://dx.doi.org/10.1002/s21010127267xy"
|
||||
]
|
||||
},
|
||||
{
|
||||
"pid": [
|
||||
{
|
||||
"dataInfo": null,
|
||||
"qualifier": {
|
||||
"classid": "doi",
|
||||
"classname": "doi",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
},
|
||||
"value": "10.1002/s21010127267xy"
|
||||
},
|
||||
{
|
||||
"dataInfo": null,
|
||||
"qualifier": {
|
||||
"classid": "doi",
|
||||
"classname": "doi",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
},
|
||||
"value": "10.1008/abcd"
|
||||
}
|
||||
],
|
||||
"alternateIdentifier": [
|
||||
{
|
||||
"dataInfo": null,
|
||||
"qualifier": {
|
||||
"classid": "doi",
|
||||
"classname": "doi",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
},
|
||||
"value": "10.1007/s109090161569x"
|
||||
},
|
||||
{
|
||||
"dataInfo": null,
|
||||
"qualifier": {
|
||||
"classid": "doi",
|
||||
"classname": "doi",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
},
|
||||
"value": "10.1009/qwerty"
|
||||
}
|
||||
],
|
||||
"accessright": {
|
||||
"classid": "CLOSED",
|
||||
"classname": "CLOSED",
|
||||
"schemeid": "dnet:access_modes",
|
||||
"schemename": "dnet:access_modes"
|
||||
},
|
||||
"collectedfrom": {
|
||||
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
|
||||
"value": "VIRTA"
|
||||
},
|
||||
"dateofacceptance": {
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"value": "2016-01-01"
|
||||
},
|
||||
"distributionlocation": "",
|
||||
"hostedby": {
|
||||
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
|
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"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "",
|
||||
"classname": "",
|
||||
"schemeid": "",
|
||||
"schemename": ""
|
||||
},
|
||||
"value": "lens antennas"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "",
|
||||
"classname": "",
|
||||
"schemeid": "",
|
||||
"schemename": ""
|
||||
},
|
||||
"value": "silicon"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "",
|
||||
"classname": "",
|
||||
"schemeid": "",
|
||||
"schemename": ""
|
||||
},
|
||||
"value": "slot antennas"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "",
|
||||
"classname": "",
|
||||
"schemeid": "",
|
||||
"schemename": ""
|
||||
},
|
||||
"value": "strained silicon"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "",
|
||||
"classname": "",
|
||||
"schemeid": "",
|
||||
"schemename": ""
|
||||
},
|
||||
"value": "cold electron bolometers"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "",
|
||||
"classname": "",
|
||||
"schemeid": "",
|
||||
"schemename": ""
|
||||
},
|
||||
"value": "doped silicon"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "",
|
||||
"classname": "",
|
||||
"schemeid": "",
|
||||
"schemename": ""
|
||||
},
|
||||
"value": "measure noise"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "",
|
||||
"classname": "",
|
||||
"schemeid": "",
|
||||
"schemename": ""
|
||||
},
|
||||
"value": "noise equivalent power"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "",
|
||||
"classname": "",
|
||||
"schemeid": "",
|
||||
"schemename": ""
|
||||
},
|
||||
"value": "optical characterisation"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "",
|
||||
"classname": "",
|
||||
"schemeid": "",
|
||||
"schemename": ""
|
||||
},
|
||||
"value": "optical response"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "",
|
||||
"classname": "",
|
||||
"schemeid": "",
|
||||
"schemename": ""
|
||||
},
|
||||
"value": "photon noise"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "",
|
||||
"classname": "",
|
||||
"schemeid": "",
|
||||
"schemename": ""
|
||||
},
|
||||
"value": "silicon absorbers"
|
||||
}
|
||||
],
|
||||
"title": [
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "main title",
|
||||
"classname": "main title",
|
||||
"schemeid": "dnet:dataCite_title",
|
||||
"schemename": "dnet:dataCite_title"
|
||||
},
|
||||
"value": "Optical response of strained- and unstrained-silicon cold-electron bolometers test"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "main title",
|
||||
"classname": "main title",
|
||||
"schemeid": "dnet:dataCite_title",
|
||||
"schemename": "dnet:dataCite_title"
|
||||
},
|
||||
"value": "test test 123 test"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "main title",
|
||||
"classname": "main title",
|
||||
"schemeid": "dnet:dataCite_title",
|
||||
"schemename": "dnet:dataCite_title"
|
||||
},
|
||||
"value": "omic"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "main title",
|
||||
"classname": "main title",
|
||||
"schemeid": "dnet:dataCite_title",
|
||||
"schemename": "dnet:dataCite_title"
|
||||
},
|
||||
"value": "｢マキャベリ的知性と心の理論の進化論｣ リチャード・バーン， アンドリュー・ホワイトゥン 編／藤田和生， 山下博志， 友永雅巳 監訳"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "main title",
|
||||
"classname": "main title",
|
||||
"schemeid": "dnet:dataCite_title",
|
||||
"schemename": "dnet:dataCite_title"
|
||||
},
|
||||
"value": "-"
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -3,13 +3,9 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap
|
|||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.SparkPrepareHostedByInfoToApply.{joinResHBM, prepareResultInfo, toEntityInfo}
|
||||
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
|
||||
import eu.dnetlib.dhp.schema.oaf.{Datasource, OpenAccessRoute, Publication}
|
||||
import javax.management.openmbean.OpenMBeanAttributeInfo
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import org.junit.jupiter.api.Assertions.{assertEquals, assertTrue}
|
||||
import org.junit.jupiter.api.Test
|
||||
|
||||
|
|
@ -4,10 +4,9 @@ import eu.dnetlib.dhp.schema.oaf.Datasource
|
|||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
|
||||
import org.json4s.DefaultFormats
|
||||
import org.junit.jupiter.api.Assertions.{assertNotNull, assertTrue}
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.Assertions._
|
||||
import org.json4s.jackson.Serialization.write
|
||||
import org.junit.jupiter.api.Assertions._
|
||||
import org.junit.jupiter.api.Test
|
||||
|
||||
class TestPreprocess extends java.io.Serializable{
|
||||
|
||||
|
|
@ -37,7 +37,8 @@ class ScholixGraphTest extends AbstractVocabularyTest{
|
|||
val input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/scholix/result.json")).mkString
|
||||
val res =SparkResolveRelation.extractPidsFromRecord(input)
|
||||
assertNotNull(res)
|
||||
assertTrue(res._2.size == 2)
|
||||
|
||||
assertEquals(1,res._2.size)
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,158 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.provision.model;
|
||||
|
||||
import java.util.Set;
|
||||
|
||||
import com.google.common.collect.Sets;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import scala.Serializable;
|
||||
|
||||
public class XmlInstance implements Serializable {
|
||||
|
||||
public static final AccessRight UNKNOWN_ACCESS_RIGHT;
|
||||
|
||||
static {
|
||||
UNKNOWN_ACCESS_RIGHT = new AccessRight();
|
||||
UNKNOWN_ACCESS_RIGHT.setClassid(ModelConstants.UNKNOWN);
|
||||
UNKNOWN_ACCESS_RIGHT.setClassname(ModelConstants.UNKNOWN);
|
||||
UNKNOWN_ACCESS_RIGHT.setSchemeid(ModelConstants.DNET_ACCESS_MODES);
|
||||
UNKNOWN_ACCESS_RIGHT.setSchemename(ModelConstants.DNET_ACCESS_MODES);
|
||||
}
|
||||
|
||||
private String url;
|
||||
|
||||
private AccessRight accessright;
|
||||
|
||||
private Set<KeyValue> collectedfrom = Sets.newHashSet();
|
||||
|
||||
private Set<KeyValue> hostedby = Sets.newHashSet();
|
||||
|
||||
private Set<Qualifier> instancetype = Sets.newHashSet();
|
||||
|
||||
private Set<String> license = Sets.newHashSet();
|
||||
|
||||
// other research products specifc
|
||||
private Set<String> distributionlocation = Sets.newHashSet();
|
||||
|
||||
private Set<StructuredProperty> pid = Sets.newHashSet();
|
||||
|
||||
private Set<StructuredProperty> alternateIdentifier = Sets.newHashSet();
|
||||
|
||||
private Set<String> dateofacceptance = Sets.newHashSet();
|
||||
|
||||
// ( article | book ) processing charges. Defined here to cope with possible wrongly typed
|
||||
// results
|
||||
private String processingchargeamount;
|
||||
|
||||
// currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly
|
||||
// typed results
|
||||
private String processingchargecurrency;
|
||||
|
||||
private Set<Qualifier> refereed = Sets.newHashSet();; // peer-review status
|
||||
|
||||
public String getUrl() {
|
||||
return url;
|
||||
}
|
||||
|
||||
public void setUrl(String url) {
|
||||
this.url = url;
|
||||
}
|
||||
|
||||
public AccessRight getAccessright() {
|
||||
return accessright;
|
||||
}
|
||||
|
||||
public void setAccessright(AccessRight accessright) {
|
||||
this.accessright = accessright;
|
||||
}
|
||||
|
||||
public Set<KeyValue> getCollectedfrom() {
|
||||
return collectedfrom;
|
||||
}
|
||||
|
||||
public void setCollectedfrom(Set<KeyValue> collectedfrom) {
|
||||
this.collectedfrom = collectedfrom;
|
||||
}
|
||||
|
||||
public Set<KeyValue> getHostedby() {
|
||||
return hostedby;
|
||||
}
|
||||
|
||||
public void setHostedby(Set<KeyValue> hostedby) {
|
||||
this.hostedby = hostedby;
|
||||
}
|
||||
|
||||
public Set<Qualifier> getInstancetype() {
|
||||
return instancetype;
|
||||
}
|
||||
|
||||
public void setInstancetype(Set<Qualifier> instancetype) {
|
||||
this.instancetype = instancetype;
|
||||
}
|
||||
|
||||
public Set<String> getLicense() {
|
||||
return license;
|
||||
}
|
||||
|
||||
public void setLicense(Set<String> license) {
|
||||
this.license = license;
|
||||
}
|
||||
|
||||
public Set<String> getDistributionlocation() {
|
||||
return distributionlocation;
|
||||
}
|
||||
|
||||
public void setDistributionlocation(Set<String> distributionlocation) {
|
||||
this.distributionlocation = distributionlocation;
|
||||
}
|
||||
|
||||
public Set<StructuredProperty> getPid() {
|
||||
return pid;
|
||||
}
|
||||
|
||||
public void setPid(Set<StructuredProperty> pid) {
|
||||
this.pid = pid;
|
||||
}
|
||||
|
||||
public Set<StructuredProperty> getAlternateIdentifier() {
|
||||
return alternateIdentifier;
|
||||
}
|
||||
|
||||
public void setAlternateIdentifier(Set<StructuredProperty> alternateIdentifier) {
|
||||
this.alternateIdentifier = alternateIdentifier;
|
||||
}
|
||||
|
||||
public Set<String> getDateofacceptance() {
|
||||
return dateofacceptance;
|
||||
}
|
||||
|
||||
public void setDateofacceptance(Set<String> dateofacceptance) {
|
||||
this.dateofacceptance = dateofacceptance;
|
||||
}
|
||||
|
||||
public String getProcessingchargeamount() {
|
||||
return processingchargeamount;
|
||||
}
|
||||
|
||||
public void setProcessingchargeamount(String processingchargeamount) {
|
||||
this.processingchargeamount = processingchargeamount;
|
||||
}
|
||||
|
||||
public String getProcessingchargecurrency() {
|
||||
return processingchargecurrency;
|
||||
}
|
||||
|
||||
public void setProcessingchargecurrency(String processingchargecurrency) {
|
||||
this.processingchargecurrency = processingchargecurrency;
|
||||
}
|
||||
|
||||
public Set<Qualifier> getRefereed() {
|
||||
return refereed;
|
||||
}
|
||||
|
||||
public void setRefereed(Set<Qualifier> refereed) {
|
||||
this.refereed = refereed;
|
||||
}
|
||||
}
|
||||
|
|
@ -8,11 +8,16 @@ import java.io.IOException;
|
|||
import java.util.ArrayList;
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import javax.swing.text.html.Option;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.stringtemplate.v4.ST;
|
||||
|
||||
import com.google.common.collect.Lists;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
|
||||
|
|
@ -94,13 +99,15 @@ public class TemplateFactory {
|
|||
}
|
||||
|
||||
public String getInstance(
|
||||
final String resultId, final List<String> instancemetadata, final List<String> webresources) {
|
||||
final List<String> instancemetadata, final String url) {
|
||||
return getTemplate(resources.getInstance())
|
||||
.add("instanceId", escapeXml(removePrefix(resultId)))
|
||||
.add("metadata", instancemetadata)
|
||||
.add(
|
||||
"webresources",
|
||||
(webresources != null ? webresources : new ArrayList<String>())
|
||||
Optional
|
||||
.ofNullable(url)
|
||||
.map(u -> Lists.newArrayList(url))
|
||||
.orElse(Lists.newArrayList())
|
||||
.stream()
|
||||
.filter(StringUtils::isNotBlank)
|
||||
.map(this::getWebResource)
|
||||
|
|
|
|||
|
|
@ -10,24 +10,18 @@ import java.io.IOException;
|
|||
import java.io.Serializable;
|
||||
import java.io.StringReader;
|
||||
import java.io.StringWriter;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Objects;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
import java.net.URL;
|
||||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
import java.util.stream.Stream;
|
||||
|
||||
import javax.xml.transform.OutputKeys;
|
||||
import javax.xml.transform.Transformer;
|
||||
import javax.xml.transform.TransformerConfigurationException;
|
||||
import javax.xml.transform.TransformerException;
|
||||
import javax.xml.transform.TransformerFactory;
|
||||
import javax.xml.transform.*;
|
||||
import javax.xml.transform.dom.DOMSource;
|
||||
import javax.xml.transform.stream.StreamResult;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.commons.lang3.tuple.ImmutablePair;
|
||||
import org.apache.commons.lang3.tuple.Pair;
|
||||
import org.apache.spark.util.LongAccumulator;
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.DocumentException;
|
||||
|
|
@ -49,25 +43,10 @@ import com.mycila.xmltool.XMLTag;
|
|||
import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
|
||||
import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
|
||||
import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
|
||||
import eu.dnetlib.dhp.schema.common.EntityType;
|
||||
import eu.dnetlib.dhp.schema.common.MainEntityType;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
import eu.dnetlib.dhp.schema.oaf.Datasource;
|
||||
import eu.dnetlib.dhp.schema.oaf.ExternalReference;
|
||||
import eu.dnetlib.dhp.schema.oaf.ExtraInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Instance;
|
||||
import eu.dnetlib.dhp.schema.oaf.Journal;
|
||||
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
import eu.dnetlib.dhp.schema.oaf.Organization;
|
||||
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.oa.provision.model.XmlInstance;
|
||||
import eu.dnetlib.dhp.schema.common.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.oaf.Software;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
|
||||
public class XmlRecordFactory implements Serializable {
|
||||
|
|
@ -1112,37 +1091,64 @@ public class XmlRecordFactory implements Serializable {
|
|||
if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) {
|
||||
final List<Instance> instances = ((Result) entity).getInstance();
|
||||
if (instances != null) {
|
||||
for (final Instance instance : ((Result) entity).getInstance()) {
|
||||
|
||||
groupInstancesByUrl(((Result) entity).getInstance()).forEach(instance -> {
|
||||
final List<String> fields = Lists.newArrayList();
|
||||
|
||||
if (instance.getAccessright() != null && !instance.getAccessright().isBlank()) {
|
||||
fields
|
||||
.add(XmlSerializationUtils.mapQualifier("accessright", instance.getAccessright()));
|
||||
}
|
||||
if (instance.getCollectedfrom() != null && kvNotBlank(instance.getCollectedfrom())) {
|
||||
if (instance.getCollectedfrom() != null) {
|
||||
fields
|
||||
.add(XmlSerializationUtils.mapKeyValue("collectedfrom", instance.getCollectedfrom()));
|
||||
.addAll(
|
||||
instance
|
||||
.getCollectedfrom()
|
||||
.stream()
|
||||
.filter(cf -> kvNotBlank(cf))
|
||||
.map(cf -> XmlSerializationUtils.mapKeyValue("collectedfrom", cf))
|
||||
.collect(Collectors.toList()));
|
||||
}
|
||||
if (instance.getHostedby() != null && kvNotBlank(instance.getHostedby())) {
|
||||
fields.add(XmlSerializationUtils.mapKeyValue("hostedby", instance.getHostedby()));
|
||||
}
|
||||
if (instance.getDateofacceptance() != null
|
||||
&& isNotBlank(instance.getDateofacceptance().getValue())) {
|
||||
|
||||
if (instance.getHostedby() != null) {
|
||||
fields
|
||||
.add(
|
||||
XmlSerializationUtils
|
||||
.asXmlElement("dateofacceptance", instance.getDateofacceptance().getValue()));
|
||||
.addAll(
|
||||
instance
|
||||
.getHostedby()
|
||||
.stream()
|
||||
.filter(hb -> kvNotBlank(hb))
|
||||
.map(hb -> XmlSerializationUtils.mapKeyValue("hostedby", hb))
|
||||
.collect(Collectors.toList()));
|
||||
}
|
||||
if (instance.getInstancetype() != null && !instance.getInstancetype().isBlank()) {
|
||||
if (instance.getDateofacceptance() != null) {
|
||||
fields
|
||||
.add(XmlSerializationUtils.mapQualifier("instancetype", instance.getInstancetype()));
|
||||
.addAll(
|
||||
instance
|
||||
.getDateofacceptance()
|
||||
.stream()
|
||||
.filter(d -> isNotBlank(d))
|
||||
.map(d -> XmlSerializationUtils.asXmlElement("dateofacceptance", d))
|
||||
.collect(Collectors.toList()));
|
||||
}
|
||||
if (isNotBlank(instance.getDistributionlocation())) {
|
||||
if (instance.getInstancetype() != null) {
|
||||
fields
|
||||
.add(
|
||||
XmlSerializationUtils
|
||||
.asXmlElement("distributionlocation", instance.getDistributionlocation()));
|
||||
.addAll(
|
||||
instance
|
||||
.getInstancetype()
|
||||
.stream()
|
||||
.filter(t -> !t.isBlank())
|
||||
.map(t -> XmlSerializationUtils.mapQualifier("instancetype", t))
|
||||
.collect(Collectors.toList()));
|
||||
}
|
||||
if (instance.getDistributionlocation() != null) {
|
||||
fields
|
||||
.addAll(
|
||||
instance
|
||||
.getDistributionlocation()
|
||||
.stream()
|
||||
.filter(d -> isNotBlank(d))
|
||||
.map(d -> XmlSerializationUtils.asXmlElement("distributionlocation", d))
|
||||
.collect(Collectors.toList()));
|
||||
}
|
||||
if (instance.getPid() != null) {
|
||||
fields
|
||||
|
|
@ -1165,32 +1171,50 @@ public class XmlRecordFactory implements Serializable {
|
|||
.collect(Collectors.toList()));
|
||||
}
|
||||
|
||||
if (instance.getRefereed() != null && !instance.getRefereed().isBlank()) {
|
||||
if (instance.getRefereed() != null) {
|
||||
fields
|
||||
.add(XmlSerializationUtils.mapQualifier("refereed", instance.getRefereed()));
|
||||
.addAll(
|
||||
instance
|
||||
.getRefereed()
|
||||
.stream()
|
||||
.filter(Objects::nonNull)
|
||||
.filter(r -> !r.isBlank())
|
||||
.map(r -> XmlSerializationUtils.mapQualifier("refereed", r))
|
||||
.collect(Collectors.toList()));
|
||||
}
|
||||
if (instance.getProcessingchargeamount() != null
|
||||
&& isNotBlank(instance.getProcessingchargeamount().getValue())) {
|
||||
&& isNotBlank(instance.getProcessingchargeamount())) {
|
||||
fields
|
||||
.add(
|
||||
XmlSerializationUtils
|
||||
.asXmlElement(
|
||||
"processingchargeamount", instance.getProcessingchargeamount().getValue()));
|
||||
"processingchargeamount", instance.getProcessingchargeamount()));
|
||||
}
|
||||
if (instance.getProcessingchargecurrency() != null
|
||||
&& isNotBlank(instance.getProcessingchargecurrency().getValue())) {
|
||||
&& isNotBlank(instance.getProcessingchargecurrency())) {
|
||||
fields
|
||||
.add(
|
||||
XmlSerializationUtils
|
||||
.asXmlElement(
|
||||
"processingchargecurrency", instance.getProcessingchargecurrency().getValue()));
|
||||
"processingchargecurrency", instance.getProcessingchargecurrency()));
|
||||
}
|
||||
|
||||
if (instance.getLicense() != null) {
|
||||
fields
|
||||
.addAll(
|
||||
instance
|
||||
.getLicense()
|
||||
.stream()
|
||||
.filter(d -> isNotBlank(d))
|
||||
.map(d -> XmlSerializationUtils.asXmlElement("license", d))
|
||||
.collect(Collectors.toList()));
|
||||
}
|
||||
|
||||
children
|
||||
.add(
|
||||
templateFactory
|
||||
.getInstance(instance.getHostedby().getKey(), fields, instance.getUrl()));
|
||||
}
|
||||
.getInstance(fields, instance.getUrl()));
|
||||
});
|
||||
}
|
||||
final List<ExternalReference> ext = ((Result) entity).getExternalReference();
|
||||
if (ext != null) {
|
||||
|
|
@ -1234,6 +1258,97 @@ public class XmlRecordFactory implements Serializable {
|
|||
return children;
|
||||
}
|
||||
|
||||
private Stream<XmlInstance> groupInstancesByUrl(List<Instance> instance) {
|
||||
return instance
|
||||
.stream()
|
||||
.filter(i -> Objects.nonNull(i.getUrl()))
|
||||
.map(i -> {
|
||||
i
|
||||
.setUrl(
|
||||
i
|
||||
.getUrl()
|
||||
.stream()
|
||||
.filter(this::isValidUrl)
|
||||
.collect(Collectors.toList()));
|
||||
return i;
|
||||
})
|
||||
.filter(
|
||||
i -> Optional
|
||||
.ofNullable(i.getUrl())
|
||||
.map(u -> !u.isEmpty())
|
||||
.orElse(false))
|
||||
.map(this::pickByUrl)
|
||||
.collect(Collectors.groupingBy(ImmutablePair::getLeft))
|
||||
.values()
|
||||
.stream()
|
||||
.filter(Objects::nonNull)
|
||||
.map(this::mergeInstances);
|
||||
}
|
||||
|
||||
private boolean isValidUrl(String url) {
|
||||
try {
|
||||
new URL(url).toURI();
|
||||
return true;
|
||||
} catch (Exception e) {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
||||
private ImmutablePair<String, Instance> pickByUrl(Instance i) {
|
||||
return new ImmutablePair<>(i.getUrl().get(0), i);
|
||||
}
|
||||
|
||||
private XmlInstance mergeInstances(List<ImmutablePair<String, Instance>> instances) {
|
||||
|
||||
final XmlInstance instance = new XmlInstance();
|
||||
|
||||
instance.setUrl(instances.get(0).getLeft());
|
||||
instance
|
||||
.setAccessright(
|
||||
instances
|
||||
.stream()
|
||||
.map(Pair::getValue)
|
||||
.map(Instance::getAccessright)
|
||||
.min(new AccessRightComparator<AccessRight>())
|
||||
.orElse(XmlInstance.UNKNOWN_ACCESS_RIGHT));
|
||||
|
||||
instances.forEach(p -> {
|
||||
final Instance i = p.getRight();
|
||||
instance.getCollectedfrom().add(i.getCollectedfrom());
|
||||
instance.getHostedby().add(i.getHostedby());
|
||||
instance.getInstancetype().add(i.getInstancetype());
|
||||
instance.getRefereed().add(i.getRefereed());
|
||||
instance
|
||||
.setProcessingchargeamount(
|
||||
Optional.ofNullable(i.getProcessingchargeamount()).map(apc -> apc.getValue()).orElse(null));
|
||||
instance
|
||||
.setProcessingchargecurrency(
|
||||
Optional.ofNullable(i.getProcessingchargecurrency()).map(c -> c.getValue()).orElse(null));
|
||||
Optional
|
||||
.ofNullable(i.getPid())
|
||||
.ifPresent(pid -> instance.getPid().addAll(pid));
|
||||
Optional
|
||||
.ofNullable(i.getAlternateIdentifier())
|
||||
.ifPresent(altId -> instance.getAlternateIdentifier().addAll(altId));
|
||||
Optional
|
||||
.ofNullable(i.getDateofacceptance())
|
||||
.ifPresent(d -> instance.getDateofacceptance().add(d.getValue()));
|
||||
Optional
|
||||
.ofNullable(i.getLicense())
|
||||
.ifPresent(license -> instance.getLicense().add(license.getValue()));
|
||||
Optional
|
||||
.ofNullable(i.getDistributionlocation())
|
||||
.ifPresent(dl -> instance.getDistributionlocation().add(dl));
|
||||
});
|
||||
|
||||
if (instance.getHostedby().size() > 1
|
||||
&& instance.getHostedby().stream().anyMatch(hb -> ModelConstants.UNKNOWN_REPOSITORY.equals(hb))) {
|
||||
instance.getHostedby().remove(ModelConstants.UNKNOWN_REPOSITORY);
|
||||
}
|
||||
|
||||
return instance;
|
||||
}
|
||||
|
||||
private boolean isDuplicate(final RelatedEntityWrapper link) {
|
||||
return ModelConstants.DEDUP.equalsIgnoreCase(link.getRelation().getSubRelType());
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
<instance id="$instanceId$">
|
||||
<instance>
|
||||
$metadata:{ it | $it$ }$
|
||||
$webresources:{ it | $it$ }$
|
||||
</instance>
|
||||
|
|
@ -12,7 +12,6 @@ import org.apache.commons.io.IOUtils;
|
|||
import org.dom4j.Document;
|
||||
import org.dom4j.DocumentException;
|
||||
import org.dom4j.io.SAXReader;
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
|
|
@ -54,18 +53,19 @@ public class XmlRecordFactoryTest {
|
|||
|
||||
System.out.println(doc.asXML());
|
||||
|
||||
Assertions.assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid"));
|
||||
Assertions.assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending"));
|
||||
assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid"));
|
||||
assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending"));
|
||||
|
||||
Assertions.assertEquals("0000-0001-9613-9956", doc.valueOf("//creator[@rank = '2']/@orcid"));
|
||||
Assertions.assertEquals("", doc.valueOf("//creator[@rank = '2']/@orcid_pending"));
|
||||
assertEquals("0000-0001-9613-9956", doc.valueOf("//creator[@rank = '2']/@orcid"));
|
||||
assertEquals("", doc.valueOf("//creator[@rank = '2']/@orcid_pending"));
|
||||
|
||||
Assertions.assertEquals("doi", doc.valueOf("//instance/pid/@classid"));
|
||||
Assertions.assertEquals("10.1109/TED.2018.2853550", doc.valueOf("//instance/pid/text()"));
|
||||
assertEquals("doi", doc.valueOf("//instance/pid/@classid"));
|
||||
assertEquals("10.1109/TED.2018.2853550", doc.valueOf("//instance/pid/text()"));
|
||||
|
||||
Assertions.assertEquals("doi", doc.valueOf("//instance/alternateidentifier/@classid"));
|
||||
Assertions.assertEquals("10.5689/LIB.2018.2853550", doc.valueOf("//instance/alternateidentifier/text()"));
|
||||
// TODO add assertions based of values extracted from the XML record
|
||||
assertEquals("doi", doc.valueOf("//instance/alternateidentifier/@classid"));
|
||||
assertEquals("10.5689/LIB.2018.2853550", doc.valueOf("//instance/alternateidentifier/text()"));
|
||||
|
||||
assertEquals(3, doc.selectNodes("//instance").size());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -96,7 +96,7 @@ public class XmlRecordFactoryTest {
|
|||
final Document doc = new SAXReader().read(new StringReader(xml));
|
||||
assertNotNull(doc);
|
||||
System.out.println(doc.asXML());
|
||||
Assertions.assertEquals("2021-01-01", doc.valueOf("//validated/@date"));
|
||||
assertEquals("2021-01-01", doc.valueOf("//validated/@date"));
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
|||
|
|
@ -412,9 +412,800 @@
|
|||
"value": ""
|
||||
},
|
||||
"url": [
|
||||
"http://juuli.fi/Record/0331473718",
|
||||
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|||
Loading…
Reference in New Issue