diff --git a/README.md b/README.md index 39d4d98e4..0a0bd82ab 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,2 @@ # dnet-hadoop -Dnet-hadoop is a tool for \ No newline at end of file +Dnet-hadoop is the project that defined all the OOZIE workflows for the OpenAIRE Graph construction, processing, provisioning. \ No newline at end of file diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 74f31cf35..4c7810c47 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -25,6 +25,11 @@ com.github.sisyphsu dateparser + + me.xuender + unidecode + + org.apache.spark spark-core_2.11 diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java index 0b602b774..7a8e55a6e 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java @@ -67,6 +67,7 @@ public class AuthorMerger { a -> a .getPid() .stream() + .filter(Objects::nonNull) .map(p -> new Tuple2<>(pidToComparableString(p), a))) .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); @@ -78,6 +79,7 @@ public class AuthorMerger { a -> a .getPid() .stream() + .filter(Objects::nonNull) .filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p))) .map(p -> new Tuple2<>(p, a))) .collect(Collectors.toList()); @@ -150,7 +152,7 @@ public class AuthorMerger { } private static boolean hasPid(Author a) { - if (a == null || a.getPid() == null || a.getPid().size() == 0) + if (a == null || a.getPid() == null || a.getPid().isEmpty()) return false; return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue())); } @@ -159,7 +161,10 @@ public class AuthorMerger { if (StringUtils.isNotBlank(author.getSurname())) { return new Person(author.getSurname() + ", " + author.getName(), false); } else { - return new Person(author.getFullname(), false); + if (StringUtils.isNotBlank(author.getFullname())) + return new Person(author.getFullname(), false); + else + return new Person("", false); } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index a75cc52e6..1d002ed7e 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -7,22 +7,19 @@ import java.time.format.DateTimeFormatter; import java.time.format.DateTimeParseException; import java.util.*; import java.util.function.Function; -import java.util.regex.Matcher; -import java.util.regex.Pattern; import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.lang3.StringUtils; -import org.jetbrains.annotations.NotNull; import com.github.sisyphsu.dateparser.DateParserUtils; import com.google.common.collect.Lists; -import com.google.common.collect.Maps; import com.google.common.collect.Sets; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; +import me.xuender.unidecode.Unidecode; public class GraphCleaningFunctions extends CleaningFunctions { @@ -98,7 +95,7 @@ public class GraphCleaningFunctions extends CleaningFunctions { Result r = (Result) value; - if (Objects.nonNull(r.getTitle()) && r.getTitle().isEmpty()) { + if (Objects.isNull(r.getTitle()) || r.getTitle().isEmpty()) { return false; } @@ -194,11 +191,15 @@ public class GraphCleaningFunctions extends CleaningFunctions { .filter(Objects::nonNull) .filter(sp -> StringUtils.isNotBlank(sp.getValue())) .filter( - sp -> sp - .getValue() - .toLowerCase() - .replaceAll(TITLE_FILTER_REGEX, "") - .length() > TITLE_FILTER_RESIDUAL_LENGTH) + sp -> { + final String title = sp + .getValue() + .toLowerCase(); + final String residual = Unidecode + .decode(title) + .replaceAll(TITLE_FILTER_REGEX, ""); + return residual.length() > TITLE_FILTER_RESIDUAL_LENGTH; + }) .map(GraphCleaningFunctions::cleanValue) .collect(Collectors.toList())); } diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java index eefa1e9a3..8d519a93f 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java @@ -4,12 +4,8 @@ package eu.dnetlib.dhp.schema.oaf.utils; import static org.junit.jupiter.api.Assertions.*; import java.io.IOException; -import java.time.LocalDate; -import java.time.format.DateTimeFormatter; import java.util.HashSet; import java.util.List; -import java.util.Locale; -import java.util.Optional; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; @@ -19,13 +15,32 @@ import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; +import me.xuender.unidecode.Unidecode; public class OafMapperUtilsTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + @Test + public void testUnidecode() { + + assertEquals("Liu Ben Mu hiruzuSen tawa", Unidecode.decode("六本木ヒルズ森タワ")); + assertEquals("Nan Wu A Mi Tuo Fo", Unidecode.decode("南无阿弥陀佛")); + assertEquals("Yi Tiao Hui Zou Lu De Yu", Unidecode.decode("一条会走路的鱼")); + assertEquals("amidaniyorai", Unidecode.decode("あみだにょらい")); + assertEquals("T`owrk`iayi", Unidecode.decode("Թուրքիայի")); + assertEquals("Obzor tematiki", Unidecode.decode("Обзор тематики")); + assertEquals("GERMANSKIE IaZYKI", Unidecode.decode("ГЕРМАНСКИЕ ЯЗЫКИ")); + assertEquals("Diereunese tes ikanopoieses", Unidecode.decode("Διερεύνηση της ικανοποίησης")); + assertEquals("lqDy l'wly@", Unidecode.decode("القضايا الأولية")); + assertEquals("abc def ghi", Unidecode.decode("abc def ghi")); + } + @Test public void testDateValidation() { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala index 8df203283..92a870e37 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala @@ -1,9 +1,10 @@ package eu.dnetlib.dhp.actionmanager.datacite import org.apache.commons.io.IOUtils +import org.apache.http.client.config.RequestConfig import org.apache.http.client.methods.{HttpGet, HttpPost, HttpRequestBase, HttpUriRequest} import org.apache.http.entity.StringEntity -import org.apache.http.impl.client.HttpClients +import org.apache.http.impl.client.{HttpClientBuilder, HttpClients} import java.io.IOException @@ -56,31 +57,31 @@ abstract class AbstractRestClient extends Iterator[String]{ private def doHTTPRequest[A <: HttpUriRequest](r: A) :String ={ - val client = HttpClients.createDefault + val timeout = 60; // seconds + val config = RequestConfig.custom() + .setConnectTimeout(timeout * 1000) + .setConnectionRequestTimeout(timeout * 1000) + .setSocketTimeout(timeout * 1000).build() + val client =HttpClientBuilder.create().setDefaultRequestConfig(config).build() var tries = 4 - try { - while (tries > 0) { - + while (tries > 0) { println(s"requesting ${r.getURI}") - val response = client.execute(r) - println(s"get response with status${response.getStatusLine.getStatusCode}") - if (response.getStatusLine.getStatusCode > 400) { - tries -= 1 + try { + val response = client.execute(r) + println(s"get response with status${response.getStatusLine.getStatusCode}") + if (response.getStatusLine.getStatusCode > 400) { + tries -= 1 + } + else + return IOUtils.toString(response.getEntity.getContent) + } catch { + case e: Throwable => + println(s"Error on requesting ${r.getURI}") + e.printStackTrace() + tries-=1 } - else - return IOUtils.toString(response.getEntity.getContent) } "" - } catch { - case e: Throwable => - throw new RuntimeException("Error on executing request ", e) - } finally try client.close() - catch { - case e: IOException => - throw new RuntimeException("Unable to close client ", e) - } - } - + } getBufferData() - } \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala index 0cdf0accb..cfdd98d30 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala @@ -367,7 +367,7 @@ object DataciteToOAFTransformation { result.setDateofcollection(ISO8601FORMAT.format(d)) - result.setDateoftransformation(ISO8601FORMAT.format(ts)) + result.setDateoftransformation(ISO8601FORMAT.format(d)) result.setDataInfo(dataInfo) val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List()) @@ -532,11 +532,11 @@ object DataciteToOAFTransformation { JField("awardUri", JString(awardUri)) <- fundingReferences } yield awardUri + result.setId(IdentifierFactory.createIdentifier(result)) var relations: List[Relation] = awardUris.flatMap(a => get_projectRelation(a, result.getId)).filter(r => r != null) - fix_figshare(result) - result.setId(IdentifierFactory.createIdentifier(result)) + if (result.getId == null) return List() diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala index 931ac06f6..2b73d2955 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala @@ -140,7 +140,7 @@ object ImportDatacite { private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs:Int): Long = { var from:Long = timestamp * 1000 - val delta:Long = 50000000L + val delta:Long = 100000000L var client: DataciteAPIImporter = null val now :Long =System.currentTimeMillis() var i = 0 diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkCreateActionset.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkCreateActionset.scala new file mode 100644 index 000000000..b78f411ee --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkCreateActionset.scala @@ -0,0 +1,73 @@ +package eu.dnetlib.dhp.actionmanager.scholix + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result} +import org.apache.spark.SparkConf +import org.apache.spark.sql._ +import org.slf4j.{Logger, LoggerFactory} + +import scala.io.Source + +object SparkCreateActionset { + + def main(args: Array[String]): Unit = { + val log: Logger = LoggerFactory.getLogger(getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/generate_actionset.json")).mkString) + 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") + + val workingDirFolder = parser.get("workingDirFolder") + log.info(s"workingDirFolder -> $workingDirFolder") + + implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf] + implicit val resultEncoders: Encoder[Result] = Encoders.kryo[Result] + implicit val relationEncoders: Encoder[Relation] = Encoders.kryo[Relation] + + import spark.implicits._ + + val relation = spark.read.load(s"$sourcePath/relation").as[Relation] + + relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge")) + .flatMap(r => List(r.getSource, r.getTarget)).distinct().write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/id_relation") + + + val idRelation = spark.read.load(s"$workingDirFolder/id_relation").as[String] + + log.info("extract source and target Identifier involved in relations") + + + log.info("save relation filtered") + + relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge")) + .write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/actionSetOaf") + + log.info("saving entities") + + val entities: Dataset[(String, Result)] = spark.read.load(s"$sourcePath/entities/*").as[Result].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING, resultEncoders)) + + + entities.filter(r => r.isInstanceOf[Result]).map(r => r.asInstanceOf[Result]) + entities + .joinWith(idRelation, entities("_1").equalTo(idRelation("value"))) + .map(p => p._1._2) + .write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf") + + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkSaveActionSet.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkSaveActionSet.scala new file mode 100644 index 000000000..1df7ea3fb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkSaveActionSet.scala @@ -0,0 +1,86 @@ +package eu.dnetlib.dhp.actionmanager.scholix + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.action.AtomicAction +import eu.dnetlib.dhp.schema.oaf.{Oaf, Dataset => OafDataset,Publication, Software, OtherResearchProduct, Relation} +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.{Encoder, Encoders, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +import scala.io.Source + +object SparkSaveActionSet { + + + def toActionSet(item: Oaf): (String, String) = { + val mapper = new ObjectMapper() + + item match { + case dataset: OafDataset => + val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset] + a.setClazz(classOf[OafDataset]) + a.setPayload(dataset) + (dataset.getClass.getCanonicalName, mapper.writeValueAsString(a)) + case publication: Publication => + val a: AtomicAction[Publication] = new AtomicAction[Publication] + a.setClazz(classOf[Publication]) + a.setPayload(publication) + (publication.getClass.getCanonicalName, mapper.writeValueAsString(a)) + case software: Software => + val a: AtomicAction[Software] = new AtomicAction[Software] + a.setClazz(classOf[Software]) + a.setPayload(software) + (software.getClass.getCanonicalName, mapper.writeValueAsString(a)) + case orp: OtherResearchProduct => + val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct] + a.setClazz(classOf[OtherResearchProduct]) + a.setPayload(orp) + (orp.getClass.getCanonicalName, mapper.writeValueAsString(a)) + + case relation: Relation => + val a: AtomicAction[Relation] = new AtomicAction[Relation] + a.setClazz(classOf[Relation]) + 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() + val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/save_actionset.json")).mkString) + 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]) + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml index 036178b37..021704f54 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml @@ -16,7 +16,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/actionset/generate_actionset.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/actionset/generate_actionset.json new file mode 100644 index 000000000..0563808ea --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/actionset/generate_actionset.json @@ -0,0 +1,6 @@ +[ + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"s", "paramLongName":"sourcePath","paramDescription": "source path", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingDirFolder","paramDescription": "the working Dir Folder", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath","paramDescription": "the target path ", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/actionset/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/actionset/oozie_app/config-default.xml new file mode 100644 index 000000000..dd3c32c62 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/actionset/oozie_app/config-default.xml @@ -0,0 +1,23 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/actionset/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/actionset/oozie_app/workflow.xml new file mode 100644 index 000000000..2d97b5163 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/actionset/oozie_app/workflow.xml @@ -0,0 +1,76 @@ + + + + sourcePath + the path of the consistent graph + + + workingDirFolder + the path of working dir ActionSet + + + outputPath + the path of Scholexplorer ActionSet + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn-cluster + cluster + Create Action Set + eu.dnetlib.dhp.actionmanager.scholix.SparkCreateActionset + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${sourcePath} + --targetPath${outputPath} + --workingDirFolder${workingDirFolder} + --masteryarn-cluster + + + + + + + + + yarn-cluster + cluster + Save Action Set + eu.dnetlib.dhp.actionmanager.scholix.SparkSaveActionSet + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${workingDirFolder}/actionSetOaf + --targetPath${outputPath} + --masteryarn-cluster + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/actionset/save_actionset.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/actionset/save_actionset.json new file mode 100644 index 000000000..0264c825f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/actionset/save_actionset.json @@ -0,0 +1,5 @@ +[ + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"s", "paramLongName":"sourcePath","paramDescription": "source path", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath","paramDescription": "the target path ", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala index 0d10c41dc..a795a910d 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala @@ -3,13 +3,14 @@ package eu.dnetlib.dhp.actionmanager.datacite import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.SerializationFeature - import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest import eu.dnetlib.dhp.schema.oaf.Oaf import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.{BeforeEach, Test} import org.mockito.junit.jupiter.MockitoExtension +import java.text.SimpleDateFormat +import java.util.Locale import scala.io.Source @ExtendWith(Array(classOf[MockitoExtension])) @@ -22,6 +23,18 @@ class DataciteToOAFTest extends AbstractVocabularyTest{ super.setUpVocabulary() } + + @Test + def testDateMapping:Unit = { + val inputDate = "2021-07-14T11:52:54+0000" + val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US) + val dt = ISO8601FORMAT.parse(inputDate) + println(dt.getTime) + + + } + + @Test def testMapping() :Unit = { val record =Source.fromInputStream(getClass.getResourceAsStream("record.json")).mkString diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record.json index 3ae10be73..f5aa65940 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record.json +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record.json @@ -1 +1 @@ -{"id":"10.7282/t3-sjyd-1r46","type":"dois","attributes":{"doi":"10.7282/t3-sjyd-1r46","identifiers":[],"creators":[{"name":"Huang, Xu","nameType":"Personal","givenName":"Xu","familyName":"Huang","affiliation":[],"nameIdentifiers":[]},{"name":"Guo, Zhixiong","nameType":"Personal","givenName":"Zhixiong","familyName":"Guo","nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0003-0481-2738","nameIdentifierScheme":"ORCID"}],"affiliation":[]}],"titles":[{"title":"High thermal conductance across c-BN/diamond interface"}],"publisher":"Rutgers University","container":{},"publicationYear":2099,"subjects":[{"subject":"Diamond"},{"subject":"Cubic boron nitride"},{"subject":"Thermal conductivity"},{"subject":"Interface"},{"subject":"Phonon"},{"subject":"Thermal conductance"}],"contributors":[],"dates":[{"date":"2099-12-31","dateType":"Accepted"},{"date":"2099","dateType":"Issued"}],"language":"en","types":{"ris":"RPRT","bibtex":"article","citeproc":"article-journal","schemaOrg":"ScholarlyArticle","resourceType":"Accepted manuscript","resourceTypeGeneral":"Text"},"relatedIdentifiers":[],"sizes":[],"formats":["application/pdf"],"version":null,"rightsList":[{"rights":"Embargo"}],"descriptions":[{"description":"High thermal conductivity electronic components with low interfacial thermal resistance are of technological importance and fundamental interest of research. Diamond, a superhard material with ultrahigh thermal conductivity at room temperature, is desirable for microelectronics thermal management. Cubic polymorph of boron nitride (c-BN) is a promising material due to wide bandgap and diamond like structure and properties. To understand the nature in thermal transport of diamond, c-BN and the most commonly used silicon (Si) semiconductor, ab initio phonon Boltzmann transport equations are employed to investigate lattice vibrational properties of these three materials. At 300 K, the predicted thermal conductivity of Si, diamond and c-BN reached 142, 2112, and 736 W/(m��K), respectively. What's more, heat transport phenomena across the interfaces of Si/diamond, c-BN/diamond and Si/c-BN are unfolded. In comparison, the interfacial thermal conductance of c-BN/diamond is ten-fold of Si/diamond; besides, the thermal conductance across Si/c-BN interface is 20.2% larger than that of Si/diamond at 300 K and 18.9% larger at 340 K. These findings provide us new vision and potential solution to heat dissipation of high-local-power density devices, shedding light on future thermal management of c-BN and diamond related electronics.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://scholarship.libraries.rutgers.edu/discovery/fulldisplay/alma991031549917804646/01RUT_INST:ResearchRepository","contentUrl":null,"metadataVersion":1,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2020-06-30T21:12:19Z","registered":"2020-07-02T16:45:07Z","published":null,"updated":"2021-01-14T18:24:19Z"},"relationships":{"client":{"data":{"id":"rutgers.lib","type":"clients"}}}} \ No newline at end of file +{"id":"10.5517/ccdc.csd.cc25rpzm","type":"dois","attributes":{"doi":"10.5517/ccdc.csd.cc25rpzm","prefix":"10.5517","suffix":"ccdc.csd.cc25rpzm","identifiers":[{"identifier":"2018781","identifierType":"CCDC"}],"alternateIdentifiers":[{"alternateIdentifierType":"CCDC","alternateIdentifier":"2018781"}],"creators":[{"name":"Ling, Irene","affiliation":[],"nameIdentifiers":[]},{"name":"Sobolev, Alexandre N.","affiliation":[],"nameIdentifiers":[]},{"name":"Raston, Colin L.","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"CCDC 2018781: Experimental Crystal Structure Determination"}],"publisher":"Cambridge Crystallographic Data Centre","container":{},"publicationYear":2021,"subjects":[{"subject":"Crystal Structure"},{"subject":"Experimental 3D Coordinates"},{"subject":"Crystal System"},{"subject":"Space Group"},{"subject":"Cell Parameters"},{"subject":"Crystallography"},{"subject":"bis[penta-aqua-copper(ii)] bis(mu-5,11,17,23-tetra-sulfonato-25,26,27,28-tetrahydroxycalix(4)arene)-dodeca-aqua-tri-copper(ii) bis(nitrate) heptahydrate"}],"contributors":[],"dates":[],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/00958972.2020.1849642","relatedIdentifierType":"DOI"}],"sizes":[],"formats":["CIF"],"version":null,"rightsList":[],"descriptions":[{"description":"Related Article: Irene Ling, Alexandre N. Sobolev, Colin L. 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\ No newline at end of file diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsReferencedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsReferencedBy.java index 21786687e..bcbcf755f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsReferencedBy.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsReferencedBy.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.schema.common.ModelConstants; public class EnrichMissingDatasetIsReferencedBy extends AbstractEnrichMissingDataset { @@ -11,7 +12,7 @@ public class EnrichMissingDatasetIsReferencedBy extends AbstractEnrichMissingDat @Override protected boolean filterByType(final String relType) { - return relType.equals("isReferencedBy"); + return relType.equals(ModelConstants.IS_REFERENCED_BY); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsRelatedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsRelatedTo.java index 0f3739434..4125974ce 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsRelatedTo.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsRelatedTo.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.schema.common.ModelConstants; public class EnrichMissingDatasetIsRelatedTo extends AbstractEnrichMissingDataset { @@ -11,7 +12,7 @@ public class EnrichMissingDatasetIsRelatedTo extends AbstractEnrichMissingDatase @Override protected boolean filterByType(final String relType) { - return relType.equals("isRelatedTo"); + return relType.equals(ModelConstants.IS_RELATED_TO); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedBy.java index cde227fee..480daf666 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedBy.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedBy.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.schema.common.ModelConstants; public class EnrichMissingDatasetIsSupplementedBy extends AbstractEnrichMissingDataset { @@ -11,7 +12,7 @@ public class EnrichMissingDatasetIsSupplementedBy extends AbstractEnrichMissingD @Override protected boolean filterByType(final String relType) { - return relType.equals("isSupplementedBy"); + return relType.equals(ModelConstants.IS_SUPPLEMENTED_BY); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedTo.java index 750165ff5..97b1eb8bd 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedTo.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedTo.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.schema.common.ModelConstants; public class EnrichMissingDatasetIsSupplementedTo extends AbstractEnrichMissingDataset { @@ -11,7 +12,7 @@ public class EnrichMissingDatasetIsSupplementedTo extends AbstractEnrichMissingD @Override protected boolean filterByType(final String relType) { - return relType.equals("isSupplementedTo"); + return relType.equals(ModelConstants.IS_SUPPLEMENT_TO); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetReferences.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetReferences.java index b1c0afe16..0978486a3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetReferences.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetReferences.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.schema.common.ModelConstants; public class EnrichMissingDatasetReferences extends AbstractEnrichMissingDataset { @@ -11,7 +12,7 @@ public class EnrichMissingDatasetReferences extends AbstractEnrichMissingDataset @Override protected boolean filterByType(final String relType) { - return relType.equals("references"); + return relType.equals(ModelConstants.REFERENCES); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsReferencedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsReferencedBy.java index eebb5c1a6..ff9155c9d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsReferencedBy.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsReferencedBy.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.schema.common.ModelConstants; public class EnrichMissingPublicationIsReferencedBy extends AbstractEnrichMissingPublication { @@ -11,6 +12,6 @@ public class EnrichMissingPublicationIsReferencedBy extends AbstractEnrichMissin @Override protected boolean filterByType(final String relType) { - return relType.equals("isReferencedBy"); + return relType.equals(ModelConstants.IS_REFERENCED_BY); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsRelatedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsRelatedTo.java index a8aa550d4..1051559c9 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsRelatedTo.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsRelatedTo.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.schema.common.ModelConstants; public class EnrichMissingPublicationIsRelatedTo extends AbstractEnrichMissingPublication { @@ -11,7 +12,7 @@ public class EnrichMissingPublicationIsRelatedTo extends AbstractEnrichMissingPu @Override protected boolean filterByType(final String relType) { - return relType.equals("isRelatedTo"); + return relType.equals(ModelConstants.IS_RELATED_TO); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedBy.java index 762ac942e..d97f46f09 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedBy.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedBy.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.schema.common.ModelConstants; public class EnrichMissingPublicationIsSupplementedBy extends AbstractEnrichMissingPublication { @@ -11,6 +12,6 @@ public class EnrichMissingPublicationIsSupplementedBy extends AbstractEnrichMiss @Override protected boolean filterByType(final String relType) { - return relType.equals("isSupplementedBy"); + return relType.equals(ModelConstants.IS_SUPPLEMENTED_BY); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedTo.java index fc7196a01..b33b340e3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedTo.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedTo.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.schema.common.ModelConstants; public class EnrichMissingPublicationIsSupplementedTo extends AbstractEnrichMissingPublication { @@ -11,7 +12,7 @@ public class EnrichMissingPublicationIsSupplementedTo extends AbstractEnrichMiss @Override protected boolean filterByType(final String relType) { - return relType.equals("isSupplementedTo"); + return relType.equals(ModelConstants.IS_SUPPLEMENT_TO); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationReferences.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationReferences.java index da1994454..fe0f96b6e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationReferences.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationReferences.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.schema.common.ModelConstants; public class EnrichMissingPublicationReferences extends AbstractEnrichMissingPublication { @@ -11,7 +12,7 @@ public class EnrichMissingPublicationReferences extends AbstractEnrichMissingPub @Override protected boolean filterByType(final String relType) { - return relType.equals("references"); + return relType.equals(ModelConstants.REFERENCES); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java index c7be633a9..7c4ca1d22 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java @@ -17,6 +17,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; public class ClusterUtils { @@ -52,15 +53,15 @@ public class ClusterUtils { } public static boolean isDedupRoot(final String id) { - return id.contains("dedup_wf_"); + return id.contains("dedup"); } public static final boolean isValidResultResultClass(final String s) { - return s.equals("isReferencedBy") - || s.equals("isRelatedTo") - || s.equals("references") - || s.equals("isSupplementedBy") - || s.equals("isSupplementedTo"); + return s.equals(ModelConstants.IS_REFERENCED_BY) + || s.equals(ModelConstants.IS_RELATED_TO) + || s.equals(ModelConstants.REFERENCES) + || s.equals(ModelConstants.IS_SUPPLEMENTED_BY) + || s.equals(ModelConstants.IS_SUPPLEMENT_TO); } public static T incrementAccumulator(final T o, final LongAccumulator acc) { diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java index 03709c8fe..fdef7f77d 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java @@ -23,6 +23,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; @@ -77,48 +78,54 @@ public class SparkUpdateEntity extends AbstractSparkAction { (type, clazz) -> { final String outputPath = dedupGraphPath + "/" + type; removeOutputDir(spark, outputPath); + final String ip = DedupUtility.createEntityPath(graphBasePath, type.toString()); + if (HdfsSupport.exists(ip, sc.hadoopConfiguration())) { + JavaRDD sourceEntity = sc + .textFile(DedupUtility.createEntityPath(graphBasePath, type.toString())); - JavaRDD sourceEntity = sc - .textFile(DedupUtility.createEntityPath(graphBasePath, type.toString())); + if (mergeRelExists(workingPath, type.toString())) { - if (mergeRelExists(workingPath, type.toString())) { + final String mergeRelPath = DedupUtility + .createMergeRelPath(workingPath, "*", type.toString()); + final String dedupRecordPath = DedupUtility + .createDedupRecordPath(workingPath, "*", type.toString()); - final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, "*", type.toString()); - final String dedupRecordPath = DedupUtility - .createDedupRecordPath(workingPath, "*", type.toString()); + final Dataset rel = spark + .read() + .load(mergeRelPath) + .as(Encoders.bean(Relation.class)); - final Dataset rel = spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class)); + final JavaPairRDD mergedIds = rel + .where("relClass == 'merges'") + .where("source != target") + .select(rel.col("target")) + .distinct() + .toJavaRDD() + .mapToPair( + (PairFunction) r -> new Tuple2<>(r.getString(0), "d")); - final JavaPairRDD mergedIds = rel - .where("relClass == 'merges'") - .where("source != target") - .select(rel.col("target")) - .distinct() - .toJavaRDD() - .mapToPair( - (PairFunction) r -> new Tuple2<>(r.getString(0), "d")); + JavaPairRDD entitiesWithId = sourceEntity + .mapToPair( + (PairFunction) s -> new Tuple2<>( + MapDocumentUtil.getJPathString(IDJSONPATH, s), s)); + if (type == EntityType.organization) // exclude root records from organizations + entitiesWithId = excludeRootOrgs(entitiesWithId, rel); - JavaPairRDD entitiesWithId = sourceEntity - .mapToPair( - (PairFunction) s -> new Tuple2<>( - MapDocumentUtil.getJPathString(IDJSONPATH, s), s)); - if (type == EntityType.organization) // exclude root records from organizations - entitiesWithId = excludeRootOrgs(entitiesWithId, rel); + JavaRDD map = entitiesWithId + .leftOuterJoin(mergedIds) + .map(k -> { + if (k._2()._2().isPresent()) { + return updateDeletedByInference(k._2()._1(), clazz); + } + return k._2()._1(); + }); - JavaRDD map = entitiesWithId - .leftOuterJoin(mergedIds) - .map(k -> { - if (k._2()._2().isPresent()) { - return updateDeletedByInference(k._2()._1(), clazz); - } - return k._2()._1(); - }); + sourceEntity = map.union(sc.textFile(dedupRecordPath)); - sourceEntity = map.union(sc.textFile(dedupRecordPath)); + } + sourceEntity.saveAsTextFile(outputPath, GzipCodec.class); } - - sourceEntity.saveAsTextFile(outputPath, GzipCodec.class); }); } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala index c0939fec1..e68880433 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala @@ -1,12 +1,16 @@ package eu.dnetlib.doiboost +import java.time.LocalDate +import java.time.format.DateTimeFormatter + import eu.dnetlib.dhp.schema.action.AtomicAction -import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty} +import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Dataset, Field, Instance, KeyValue, Oaf, OpenAccessRoute, Organization, Publication, Qualifier, Relation, Result, StructuredProperty} 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 @@ -118,14 +122,92 @@ object DoiBoostMappingUtil { } + def decideAccessRight(lic : Field[String], date:String) : AccessRight = { + if(lic == null){ + //Default value Unknown + return getUnknownQualifier() + } + val license : String = lic.getValue + //CC licenses + if(license.startsWith("cc") || + license.startsWith("http://creativecommons.org/licenses") || + license.startsWith("https://creativecommons.org/licenses") || + + //ACS Publications Author choice licenses (considered OPEN also by Unpaywall) + license.equals("http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html") || + license.equals("http://pubs.acs.org/page/policy/authorchoice_termsofuse.html") || + license.equals("http://pubs.acs.org/page/policy/authorchoice_ccbyncnd_termsofuse.html") || + + //APA (considered OPEN also by Unpaywall) + license.equals("http://www.apa.org/pubs/journals/resources/open-access.aspx")){ + + val oaq : AccessRight = getOpenAccessQualifier() + oaq.setOpenAccessRoute(OpenAccessRoute.hybrid) + return oaq + } + + //OUP (BUT ONLY AFTER 12 MONTHS FROM THE PUBLICATION DATE, OTHERWISE THEY ARE EMBARGOED) + if(license.equals("https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model")){ + val now = java.time.LocalDate.now + + try{ + val pub_date = LocalDate.parse(date, DateTimeFormatter.ofPattern("yyyy-MM-dd")) + if (((now.toEpochDay - pub_date.toEpochDay)/365.0) > 1){ + val oaq : AccessRight = getOpenAccessQualifier() + oaq.setOpenAccessRoute(OpenAccessRoute.hybrid) + return oaq + } + else{ + return getEmbargoedAccessQualifier() + } + }catch { + case e: Exception => { + try{ + val pub_date = LocalDate.parse(date, DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'")) + if (((now.toEpochDay - pub_date.toEpochDay)/365.0) > 1){ + val oaq : AccessRight = getOpenAccessQualifier() + oaq.setOpenAccessRoute(OpenAccessRoute.hybrid) + return oaq + } + else{ + return getEmbargoedAccessQualifier() + } + }catch{ + case ex: Exception => return getClosedAccessQualifier() + } + } + + } + + } + + return getClosedAccessQualifier() + + } + def getOpenAccessQualifier():AccessRight = { - OafMapperUtils.accessRight("OPEN","Open Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES) + + OafMapperUtils.accessRight(ModelConstants.ACCESS_RIGHT_OPEN,"Open Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES) } def getRestrictedQualifier():AccessRight = { - OafMapperUtils.accessRight("RESTRICTED","Restricted",ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES) + OafMapperUtils.accessRight( "RESTRICTED","Restricted",ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES) + } + + + def getUnknownQualifier():AccessRight = { + OafMapperUtils.accessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE,ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES) + } + + + def getEmbargoedAccessQualifier():AccessRight = { + OafMapperUtils.accessRight("EMBARGO","Embargo",ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES) + } + + def getClosedAccessQualifier():AccessRight = { + OafMapperUtils.accessRight("CLOSED","Closed Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES) } @@ -150,10 +232,11 @@ object DoiBoostMappingUtil { if (item != null) { hb.setValue(item.officialname) hb.setKey(generateDSId(item.id)) - if (item.openAccess) + if (item.openAccess) { i.setAccessright(getOpenAccessQualifier()) - val ar = getOpenAccessQualifier() - publication.setBestaccessright(OafMapperUtils.qualifier(ar.getClassid, ar.getClassname, ar.getSchemeid, ar.getSchemename)) + i.getAccessright.setOpenAccessRoute(OpenAccessRoute.gold) + } + } else { hb = ModelConstants.UNKNOWN_REPOSITORY @@ -161,17 +244,8 @@ object DoiBoostMappingUtil { i.setHostedby(hb) }) - val ar = publication.getInstance().asScala.filter(i => i.getInstancetype != null && i.getAccessright!= null && i.getAccessright.getClassid!= null).map(f=> f.getAccessright.getClassid) - if (ar.nonEmpty) { - if(ar.contains(ModelConstants.ACCESS_RIGHT_OPEN)){ - val ar = getOpenAccessQualifier() - publication.setBestaccessright(OafMapperUtils.qualifier(ar.getClassid, ar.getClassname, ar.getSchemeid, ar.getSchemename)) - } - else { - val ar = getRestrictedQualifier() - publication.setBestaccessright(OafMapperUtils.qualifier(ar.getClassid, ar.getClassname, ar.getSchemeid, ar.getSchemename)) - } - } + publication.setBestaccessright(OafMapperUtils.createBestAccessRights(publication.getInstance())) + publication } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index fb96717d9..25f0ff381 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -4,7 +4,7 @@ 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._ +import eu.dnetlib.doiboost.DoiBoostMappingUtil.{decideAccessRight, _} import org.apache.commons.lang.StringUtils import org.json4s import org.json4s.DefaultFormats @@ -168,12 +168,22 @@ case object Crossref2Oaf { // Mapping instance val instance = new Instance() val license = for { - JString(lic) <- json \ "license" \ "URL" - } yield asField(lic) - val l = license.filter(d => StringUtils.isNotBlank(d.getValue)) - if (l.nonEmpty) - instance.setLicense(l.head) - + JObject(license) <- json \ "license" + JField("URL", JString(lic)) <- license + JField("content-version", JString(content_version)) <- license + } yield (asField(lic), content_version) + val l = license.filter(d => StringUtils.isNotBlank(d._1.getValue)) + if (l.nonEmpty){ + if (l exists (d => d._2.equals("vor"))){ + for(d <- l){ + if (d._2.equals("vor")){ + instance.setLicense(d._1) + } + } + } + else{ + instance.setLicense(l.head._1)} + } // Ticket #6281 added pid to Instance instance.setPid(result.getPid) @@ -185,7 +195,7 @@ case object Crossref2Oaf { OafMapperUtils.qualifier("0001", "peerReviewed", ModelConstants.DNET_REVIEW_LEVELS, ModelConstants.DNET_REVIEW_LEVELS)) } - instance.setAccessright(getRestrictedQualifier()) + instance.setAccessright(decideAccessRight(instance.getLicense, result.getDateofacceptance.getValue)) instance.setInstancetype(OafMapperUtils.qualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)) result.setResourcetype(OafMapperUtils.qualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala index cc758bcae..c8324cde1 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala @@ -11,6 +11,7 @@ import org.slf4j.{Logger, LoggerFactory} import scala.collection.JavaConverters._ import eu.dnetlib.doiboost.DoiBoostMappingUtil._ +import eu.dnetlib.doiboost.uw.UnpayWallToOAF.get_unpaywall_color @@ -23,6 +24,21 @@ case class OALocation(evidence:Option[String], host_type:Option[String], is_best object UnpayWallToOAF { val logger: Logger = LoggerFactory.getLogger(getClass) + + def get_unpaywall_color(input:String):Option[OpenAccessRoute] = { + if(input == null || input.equalsIgnoreCase("close")) + return None + if(input.equalsIgnoreCase("green")) + return Some(OpenAccessRoute.green) + if(input.equalsIgnoreCase("bronze")) + return Some(OpenAccessRoute.bronze) + if(input.equalsIgnoreCase("hybrid")) + return Some(OpenAccessRoute.hybrid) + else + return Some(OpenAccessRoute.gold) + + } + def get_color(is_oa:Boolean, location: OALocation, journal_is_oa:Boolean):Option[OpenAccessRoute] = { if (is_oa) { if (location.host_type.isDefined) { @@ -65,7 +81,7 @@ object UnpayWallToOAF { val oaLocation:OALocation = (json \ "best_oa_location").extractOrElse[OALocation](null) - val colour = get_color(is_oa, oaLocation, journal_is_oa) + val colour = get_unpaywall_color((json \ "oa_status").extractOrElse[String](null)) pub.setCollectedfrom(List(createUnpayWallCollectedFrom()).asJava) pub.setDataInfo(generateDataInfo()) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml index a1b8804fa..ecaeda709 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml @@ -1,4 +1,4 @@ - + sparkDriverMemory diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml index e75e1d8e1..831ff5a57 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml @@ -1,4 +1,4 @@ - + sparkDriverMemory @@ -100,7 +100,7 @@ --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 + --conf spark.sql.shuffle.partitions=7680 --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} @@ -125,7 +125,7 @@ --executor-memory=${sparkExecutorIntersectionMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 + --conf spark.sql.shuffle.partitions=7680 --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala index 0fa34d88e..75fb3f787 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala @@ -492,6 +492,124 @@ class CrossrefMappingTest { } + @Test + def testLicenseVorClosed() :Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_vor.json")).mkString + assertNotNull(json) + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + + val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result] + + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + println(mapper.writeValueAsString(item)) + + assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://www.springer.com/vor"))) + assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("CLOSED"))) + assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == null)) + + + + + } + + @Test + def testLicenseOpen() :Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_open.json")).mkString + + + assertNotNull(json) + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + + val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result] + + assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html"))) + assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("OPEN"))) + assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == OpenAccessRoute.hybrid)) + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + println(mapper.writeValueAsString(item)) + + } + + @Test + def testLicenseEmbargoOpen() :Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo_open.json")).mkString + + + assertNotNull(json) + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + + val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result] + + assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model"))) + assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("OPEN"))) + assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == OpenAccessRoute.hybrid)) + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + println(mapper.writeValueAsString(item)) + + } + + @Test + def testLicenseEmbargo() :Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo.json")).mkString + + + assertNotNull(json) + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + + val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result] + + assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model"))) + assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("EMBARGO"))) + assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == null)) + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + println(mapper.writeValueAsString(item)) + + } + + + @Test + def testLicenseEmbargoDateTime() :Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo_datetime.json")).mkString + + + assertNotNull(json) + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + + val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result] + + assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model"))) + assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("EMBARGO"))) + assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == null)) + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + println(mapper.writeValueAsString(item)) + + } + } diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json new file mode 100644 index 000000000..47ca55f34 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json @@ -0,0 +1,1537 @@ +{ +"indexed": { +"date-parts": [ +[ +2021, +7, +2 +] +], +"date-time": "2021-07-02T07:30:10Z", +"timestamp": 1625211010708 +}, +"reference-count": 83, +"publisher": "Springer Science and Business Media LLC", +"issue": "5", +"license": [ +{ +"URL": "https://www.springer.com/tdm", +"start": { +"date-parts": [ +[ +2021, +2, +22 +] +], +"date-time": "2021-02-22T00:00:00Z", +"timestamp": 1613952000000 +}, +"delay-in-days": 0, +"content-version": "tdm" +}, +{ +"URL": "https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model", +"start": { +"date-parts": [ +[ +2021, +2, +22 +] +], +"date-time": "2021-02-22T00:00:00Z", +"timestamp": 1613952000000 +}, +"delay-in-days": 0, +"content-version": "vor" +} +], +"content-domain": { +"domain": [ +"link.springer.com" +], +"crossmark-restriction": false +}, +"short-container-title": [ +"Nat Astron" +], +"published-print": { +"date-parts": [ +[ +2021, +5 +] +] +}, +"DOI": "10.1038/s41550-020-01295-8", +"type": "journal-article", +"created": { +"date-parts": [ +[ +2021, +2, +22 +] +], +"date-time": "2021-02-22T17:03:42Z", +"timestamp": 1614013422000 +}, +"page": "510-518", +"update-policy": "http://dx.doi.org/10.1007/springer_crossmark_policy", +"source": "Crossref", +"is-referenced-by-count": 6, +"title": [ +"A tidal disruption event coincident with a high-energy neutrino" +], +"prefix": "10.1038", +"volume": "5", +"author": [ +{ +"ORCID": "http://orcid.org/0000-0003-2434-0387", +"authenticated-orcid": false, +"given": "Robert", +"family": "Stein", +"sequence": "first", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-3859-8074", +"authenticated-orcid": false, +"given": "Sjoert van", +"family": "Velzen", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0001-8594-8666", +"authenticated-orcid": false, +"given": "Marek", +"family": "Kowalski", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Anna", +"family": "Franckowiak", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0003-3703-5154", +"authenticated-orcid": false, +"given": "Suvi", +"family": "Gezari", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0003-3124-2814", +"authenticated-orcid": false, +"given": "James C. A.", +"family": "Miller-Jones", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Sara", +"family": "Frederick", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0003-0466-3779", +"authenticated-orcid": false, +"given": "Itai", +"family": "Sfaradi", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Michael F.", +"family": "Bietenholz", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-5936-1156", +"authenticated-orcid": false, +"given": "Assaf", +"family": "Horesh", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Rob", +"family": "Fender", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0003-2403-4582", +"authenticated-orcid": false, +"given": "Simone", +"family": "Garrappa", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-2184-6430", +"authenticated-orcid": false, +"given": "Tomás", +"family": "Ahumada", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Igor", +"family": "Andreoni", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Justin", +"family": "Belicki", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0001-8018-5348", +"authenticated-orcid": false, +"given": "Eric C.", +"family": "Bellm", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Markus", +"family": "Böttcher", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Valery", +"family": "Brinnel", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Rick", +"family": "Burruss", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0003-1673-970X", +"authenticated-orcid": false, +"given": "S. Bradley", +"family": "Cenko", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-8262-2924", +"authenticated-orcid": false, +"given": "Michael W.", +"family": "Coughlin", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0003-2292-0441", +"authenticated-orcid": false, +"given": "Virginia", +"family": "Cunningham", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Andrew", +"family": "Drake", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Glennys R.", +"family": "Farrar", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Michael", +"family": "Feeney", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Ryan J.", +"family": "Foley", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-3653-5598", +"authenticated-orcid": false, +"given": "Avishay", +"family": "Gal-Yam", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "V. Zach", +"family": "Golkhou", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-4163-4996", +"authenticated-orcid": false, +"given": "Ariel", +"family": "Goobar", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-3168-0139", +"authenticated-orcid": false, +"given": "Matthew J.", +"family": "Graham", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Erica", +"family": "Hammerstein", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0003-3367-3415", +"authenticated-orcid": false, +"given": "George", +"family": "Helou", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-9878-7889", +"authenticated-orcid": false, +"given": "Tiara", +"family": "Hung", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Mansi M.", +"family": "Kasliwal", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-5740-7747", +"authenticated-orcid": false, +"given": "Charles D.", +"family": "Kilpatrick", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-5105-344X", +"authenticated-orcid": false, +"given": "Albert K. H.", +"family": "Kong", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-6540-1484", +"authenticated-orcid": false, +"given": "Thomas", +"family": "Kupfer", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0003-2451-5482", +"authenticated-orcid": false, +"given": "Russ R.", +"family": "Laher", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0003-2242-0244", +"authenticated-orcid": false, +"given": "Ashish A.", +"family": "Mahabal", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-8532-9395", +"authenticated-orcid": false, +"given": "Frank J.", +"family": "Masci", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0003-0280-7484", +"authenticated-orcid": false, +"given": "Jannis", +"family": "Necker", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0001-8342-6274", +"authenticated-orcid": false, +"given": "Jakob", +"family": "Nordin", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Daniel A.", +"family": "Perley", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-8121-2560", +"authenticated-orcid": false, +"given": "Mickael", +"family": "Rigault", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-7788-628X", +"authenticated-orcid": false, +"given": "Simeon", +"family": "Reusch", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Hector", +"family": "Rodriguez", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0002-7559-315X", +"authenticated-orcid": false, +"given": "César", +"family": "Rojas-Bravo", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0001-7648-4142", +"authenticated-orcid": false, +"given": "Ben", +"family": "Rusholme", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0003-4401-0430", +"authenticated-orcid": false, +"given": "David L.", +"family": "Shupe", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0001-9898-5597", +"authenticated-orcid": false, +"given": "Leo P.", +"family": "Singer", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0003-1546-6615", +"authenticated-orcid": false, +"given": "Jesper", +"family": "Sollerman", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Maayane T.", +"family": "Soumagnac", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Daniel", +"family": "Stern", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Kirsty", +"family": "Taggart", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Jakob", +"family": "van Santen", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Charlotte", +"family": "Ward", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"given": "Patrick", +"family": "Woudt", +"sequence": "additional", +"affiliation": [ + +] +}, +{ +"ORCID": "http://orcid.org/0000-0001-6747-8509", +"authenticated-orcid": false, +"given": "Yuhan", +"family": "Yao", +"sequence": "additional", +"affiliation": [ + +] +} +], +"member": "297", +"published-online": { +"date-parts": [ +[ +2021, +2, +22 +] +] +}, +"reference": [ +{ +"key": "1295_CR1", +"doi-asserted-by": "crossref", +"first-page": "P03012", +"DOI": "10.1088/1748-0221/12/03/P03012", +"volume": "12", +"author": "MG Aartsen", +"year": "2017", +"unstructured": "Aartsen, M. G. et al. The IceCube Neutrino Observatory: instrumentation and online systems. J. Instrum. 12, P03012 (2017).", +"journal-title": "J. Instrum." +}, +{ +"key": "1295_CR2", +"unstructured": "Stein, R. IceCube-191001A—IceCube observation of a high-energy neutrino candidate event. GCN Circ. 25913 (2019)." +}, +{ +"key": "1295_CR3", +"doi-asserted-by": "crossref", +"first-page": "018002", +"DOI": "10.1088/1538-3873/aaecbe", +"volume": "131", +"author": "EC Bellm", +"year": "2019", +"unstructured": "Bellm, E. C. et al. The Zwicky Transient Facility: system overview, performance, and first results. Publ. Astron. Soc. Pac. 131, 018002 (2019).", +"journal-title": "Publ. Astron. Soc. Pac." +}, +{ +"key": "1295_CR4", +"doi-asserted-by": "crossref", +"first-page": "533", +"DOI": "10.1016/j.astropartphys.2007.03.005", +"volume": "27", +"author": "M Kowalski", +"year": "2007", +"unstructured": "Kowalski, M. & Mohr, A. Detecting neutrino transients with optical follow-up observations. Astropart. Phys. 27, 533–538 (2007).", +"journal-title": "Astropart. Phys." +}, +{ +"key": "1295_CR5", +"doi-asserted-by": "crossref", +"first-page": "329", +"DOI": "10.1088/0004-637X/693/1/329", +"volume": "693", +"author": "GR Farrar", +"year": "2009", +"unstructured": "Farrar, G. R. & Gruzinov, A. Giant AGN flares and cosmic ray bursts. Astrophys. J. 693, 329–332 (2009).", +"journal-title": "Astrophys. J." +}, +{ +"key": "1295_CR6", +"doi-asserted-by": "crossref", +"first-page": "1354", +"DOI": "10.1093/mnras/stx863", +"volume": "469", +"author": "L Dai", +"year": "2017", +"unstructured": "Dai, L. & Fang, K. Can tidal disruption events produce the IceCube neutrinos? Mon. Not. R. Astron. Soc. 469, 1354–1359 (2017).", +"journal-title": "Mon. Not. R. Astron. Soc." +}, +{ +"key": "1295_CR7", +"doi-asserted-by": "crossref", +"first-page": "114", +"DOI": "10.3847/1538-4357/ab44ca", +"volume": "886", +"author": "K Hayasaki", +"year": "2019", +"unstructured": "Hayasaki, K. & Yamazaki, R. Neutrino emissions from tidal disruption remnants. Astrophys. J. 886, 114 (2019).", +"journal-title": "Astrophys. J." +}, +{ +"key": "1295_CR8", +"unstructured": "Farrar, G. R. & Piran, T. Tidal disruption jets as the source of Ultra-High Energy Cosmic Rays. Preprint at https://arxiv.org/abs/1411.0704 (2014)." +}, +{ +"key": "1295_CR9", +"doi-asserted-by": "crossref", +"first-page": "3", +"DOI": "10.3847/1538-4357/aa6344", +"volume": "838", +"author": "N Senno", +"year": "2017", +"unstructured": "Senno, N., Murase, K. & Mészáros, P. High-energy neutrino flares from X-ray bright and dark tidal disruption events. Astrophys. J. 838, 3 (2017).", +"journal-title": "Astrophys. J." +}, +{ +"key": "1295_CR10", +"doi-asserted-by": "crossref", +"first-page": "083005", +"DOI": "10.1103/PhysRevD.93.083005", +"volume": "93", +"author": "XY Wang", +"year": "2016", +"unstructured": "Wang, X. Y. & Liu, R. Y. Tidal disruption jets of supermassive black holes as hidden sources of cosmic rays: explaining the IceCube TeV–PeV neutrinos. Phys. Rev. D 93, 083005 (2016).", +"journal-title": "Phys. Rev. D" +}, +{ +"key": "1295_CR11", +"doi-asserted-by": "crossref", +"first-page": "123001", +"DOI": "10.1103/PhysRevD.95.123001", +"volume": "95", +"author": "C Lunardini", +"year": "2017", +"unstructured": "Lunardini, C. & Winter, W. High energy neutrinos from the tidal disruption of stars. Phys. Rev. D 95, 123001 (2017).", +"journal-title": "Phys. Rev. D" +}, +{ +"key": "1295_CR12", +"unstructured": "Stein, R., Franckowiak, A., Necker, J., Gezari, S. & Velzen, S. V. Candidate counterparts to IceCube-191001A with ZTF. Astron. Telegr. 13160 (2019)." +}, +{ +"key": "1295_CR13", +"doi-asserted-by": "crossref", +"first-page": "078001", +"DOI": "10.1088/1538-3873/ab006c", +"volume": "131", +"author": "MJ Graham", +"year": "2019", +"unstructured": "Graham, M. J. et al. The Zwicky Transient Facility: science objectives. Publ. Astron. Soc. Pac. 131, 078001 (2019).", +"journal-title": "Publ. Astron. Soc. Pac." +}, +{ +"key": "1295_CR14", +"unstructured": "Nordin, J. et al. TNS Astronomical Transient Report 33340 (2019)." +}, +{ +"key": "1295_CR15", +"unstructured": "Nicholl, M. et al. ePESSTO+ classification of optical transients. Astron. Telegr. 12752 (2019)." +}, +{ +"key": "1295_CR16", +"unstructured": "van Velzen, S. et al. Seventeen tidal disruption events from the first half of ZTF survey observations: entering a new era of population studies. Preprint at https://arxiv.org/abs/2001.01409 (2020)." +}, +{ +"key": "1295_CR17", +"doi-asserted-by": "crossref", +"first-page": "82", +"DOI": "10.3847/1538-4357/ab1844", +"volume": "878", +"author": "S van Velzen", +"year": "2019", +"unstructured": "van Velzen, S. et al. Late-time UV observations of tidal disruption flares reveal unobscured, compact accretion disks. Astrophys. 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Pac." +}, +{ +"key": "1295_CR81", +"doi-asserted-by": "crossref", +"first-page": "6", +"DOI": "10.3847/1538-4365/aab761", +"volume": "236", +"author": "J Guillochon", +"year": "2018", +"unstructured": "Guillochon, J. et al. MOSFiT: Modular Open Source Fitter for Transients. Astrophys. J. Suppl. Ser. 236, 6 (2018).", +"journal-title": "Astrophys. J. Suppl. Ser." +}, +{ +"key": "1295_CR82", +"doi-asserted-by": "crossref", +"first-page": "e008", +"DOI": "10.1017/pasa.2013.44", +"volume": "31", +"author": "J Granot", +"year": "2014", +"unstructured": "Granot, J. & van der Horst, A. J. Gamma-ray burst jets and their radio observations. Publ. Astron. Soc. Aust. 31, e008 (2014).", +"journal-title": "Publ. Astron. Soc. Aust." +}, +{ +"key": "1295_CR83", +"doi-asserted-by": "crossref", +"first-page": "102", +"DOI": "10.1088/0004-637X/815/2/102", +"volume": "815", +"author": "W Fong", +"year": "2015", +"unstructured": "Fong, W., Berger, E., Margutti, R. & Zauderer, B. A. A decade of short-duration gamma-ray burst broadband afterglows: energetics, circumburst densities, and jet opening angles. Astrophys. J. 815, 102 (2015).", +"journal-title": "Astrophys. J." +} +], +"container-title": [ +"Nature Astronomy" +], +"original-title": [ + +], +"language": "en", +"link": [ +{ +"URL": "http://www.nature.com/articles/s41550-020-01295-8.pdf", +"content-type": "application/pdf", +"content-version": "vor", +"intended-application": "text-mining" +}, +{ +"URL": "http://www.nature.com/articles/s41550-020-01295-8", +"content-type": "text/html", +"content-version": "vor", +"intended-application": "text-mining" +}, +{ +"URL": "http://www.nature.com/articles/s41550-020-01295-8.pdf", +"content-type": "application/pdf", +"content-version": "vor", +"intended-application": "similarity-checking" +} +], +"deposited": { +"date-parts": [ +[ +2021, +5, +17 +] +], +"date-time": "2021-05-17T15:08:12Z", +"timestamp": 1621264092000 +}, +"score": 1.0, +"subtitle": [ + +], +"short-title": [ + +], +"issued": { +"date-parts": [ +[ +2021, +2, +22 +] +] +}, +"references-count": 83, +"journal-issue": { +"published-print": { +"date-parts": [ +[ +2021, +5 +] +] +}, +"issue": "5" +}, +"alternative-id": [ +"1295" +], +"URL": "http://dx.doi.org/10.1038/s41550-020-01295-8", +"relation": { +"cites": [ + +] +}, +"ISSN": [ +"2397-3366" +], +"issn-type": [ +{ +"value": "2397-3366", +"type": "electronic" +} +], +"assertion": [ +{ +"value": "21 July 2020", +"order": 1, +"name": "received", +"label": "Received", +"group": { +"name": "ArticleHistory", +"label": "Article History" +} +}, +{ +"value": "16 December 2020", +"order": 2, +"name": "accepted", +"label": "Accepted", +"group": { +"name": "ArticleHistory", +"label": "Article History" +} +}, +{ +"value": "22 February 2021", +"order": 3, +"name": "first_online", +"label": "First Online", +"group": { +"name": "ArticleHistory", +"label": "Article History" +} +}, +{ +"value": "The authors declare no competing interests.", +"order": 1, +"name": "Ethics", +"group": { +"name": "EthicsHeading", +"label": "Competing interests" +} +} +] +} +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 1e80dfd46..03c3eeb3c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -71,6 +71,8 @@ public abstract class AbstractMdRecordToOafMapper { private final boolean shouldHashId; + private final boolean forceOriginalId; + protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4"; protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; @@ -98,11 +100,20 @@ public abstract class AbstractMdRecordToOafMapper { nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); } + protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, + final boolean shouldHashId, final boolean forceOriginalId) { + this.vocs = vocs; + this.invisible = invisible; + this.shouldHashId = shouldHashId; + this.forceOriginalId = forceOriginalId; + } + protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId) { this.vocs = vocs; this.invisible = invisible; this.shouldHashId = shouldHashId; + this.forceOriginalId = false; } public List processMdRecord(final String xml) { @@ -190,10 +201,16 @@ public abstract class AbstractMdRecordToOafMapper { final long lastUpdateTimestamp) { final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); - final String id = IdentifierFactory.createIdentifier(entity, shouldHashId); - if (!id.equals(entity.getId())) { - entity.getOriginalId().add(entity.getId()); - entity.setId(id); + + final Set originalId = Sets.newHashSet(entity.getOriginalId()); + originalId.add(entity.getId()); + entity.setOriginalId(Lists.newArrayList(originalId)); + + if (!forceOriginalId) { + final String id = IdentifierFactory.createIdentifier(entity, shouldHashId); + if (!id.equals(entity.getId())) { + entity.setId(id); + } } final List oafs = Lists.newArrayList(entity); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index fcd6f459a..bbfb7429f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -163,11 +163,13 @@ public class GenerateEntitiesApplication { switch (type.toLowerCase()) { case "oaf-store-cleaned": - case "oaf-store-claim": return new OafToOafMapper(vocs, false, shouldHashId).processMdRecord(s); + case "oaf-store-claim": + return new OafToOafMapper(vocs, false, shouldHashId, true).processMdRecord(s); case "odf-store-cleaned": - case "odf-store-claim": return new OdfToOafMapper(vocs, false, shouldHashId).processMdRecord(s); + case "odf-store-claim": + return new OdfToOafMapper(vocs, false, shouldHashId, true).processMdRecord(s); case "oaf-store-intersection": return new OafToOafMapper(vocs, true, shouldHashId).processMdRecord(s); case "odf-store-intersection": diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 06aeab345..d753cddeb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -27,6 +27,11 @@ import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; public class OafToOafMapper extends AbstractMdRecordToOafMapper { + public OafToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId, + final boolean forceOrginalId) { + super(vocs, invisible, shouldHashId, forceOrginalId); + } + public OafToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId) { super(vocs, invisible, shouldHashId); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index b7400873b..7925a7826 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -22,6 +22,11 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { public static final String HTTP_DX_DOI_PREIFX = "http://dx.doi.org/"; + public OdfToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId, + final boolean forceOrginalId) { + super(vocs, invisible, shouldHashId, forceOrginalId); + } + public OdfToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId) { super(vocs, invisible, shouldHashId); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java new file mode 100644 index 000000000..5523863ff --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java @@ -0,0 +1,127 @@ + +package eu.dnetlib.dhp.oa.graph.raw; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.FileNotFoundException; +import java.util.Objects; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping; +import eu.dnetlib.dhp.schema.oaf.Relation; +import scala.Tuple2; + +public class PatchRelationsApplication { + + private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Optional + .ofNullable( + PatchRelationsApplication.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json")) + .orElseThrow(FileNotFoundException::new))); + parser.parseArgument(args); + + final Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String graphBasePath = parser.get("graphBasePath"); + log.info("graphBasePath: {}", graphBasePath); + + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); + + final String idMappingPath = parser.get("idMappingPath"); + log.info("idMappingPath: {}", idMappingPath); + + final SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath)); + } + + /** + * Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the + * mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location. + * + * @param spark the SparkSession + * @param graphBasePath base graph path providing the set of relations to patch + * @param workingDir intermediate storage location + * @param idMappingPath dataset providing the old -> new identifier mapping + */ + private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir, + final String idMappingPath) { + + final String relationPath = graphBasePath + "/relation"; + + final Dataset rels = Utils.readPath(spark, relationPath, Relation.class); + final Dataset idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class); + + log.info("relations: {}", rels.count()); + log.info("idMapping: {}", idMapping.count()); + + final Dataset bySource = rels + .joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left") + .map((MapFunction, Relation>) t -> { + final Relation r = t._1(); + Optional + .ofNullable(t._2()) + .map(RelationIdMapping::getNewId) + .ifPresent(r::setSource); + return r; + }, Encoders.bean(Relation.class)); + + bySource + .joinWith(idMapping, bySource.col("target").equalTo(idMapping.col("oldId")), "left") + .map((MapFunction, Relation>) t -> { + final Relation r = t._1(); + Optional + .ofNullable(t._2()) + .map(RelationIdMapping::getNewId) + .ifPresent(r::setTarget); + return r; + }, Encoders.bean(Relation.class)) + .map( + (MapFunction) OBJECT_MAPPER::writeValueAsString, + Encoders.STRING()) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .text(workingDir); + + spark + .read() + .textFile(workingDir) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .text(relationPath); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java new file mode 100644 index 000000000..d5852ab70 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.raw.common; + +public class RelationIdMapping { + + private String oldId; + + private String newId; + + public String getOldId() { + return oldId; + } + + public void setOldId(final String oldId) { + this.oldId = oldId; + } + + public String getNewId() { + return newId; + } + + public void setNewId(final String newId) { + this.newId = newId; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertDatasetToJsonRDD.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertDatasetToJsonRDD.scala new file mode 100644 index 000000000..3ee0c7dd6 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertDatasetToJsonRDD.scala @@ -0,0 +1,42 @@ +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 org.apache.commons.io.IOUtils +import org.apache.hadoop.io.compress.GzipCodec +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Encoder, Encoders, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +object SparkConvertDatasetToJsonRDD { + + + def main(args: Array[String]): Unit = { + val log: Logger = LoggerFactory.getLogger(getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json"))) + 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 -> $targetPath") + + val resultObject = List("publication","dataset","software", "otherResearchProduct") + val mapper = new ObjectMapper() + implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + + + resultObject.foreach{item => + spark.read.load(s"$sourcePath/$item").as[Result].map(r=> mapper.writeValueAsString(r))(Encoders.STRING).rdd.saveAsTextFile(s"$targetPath/${item.toLowerCase}", classOf[GzipCodec]) + } + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala new file mode 100644 index 000000000..cb41d6134 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -0,0 +1,67 @@ +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 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 = { + + + val log: Logger = LoggerFactory.getLogger(getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json"))) + 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 t = parser.get("targetPath") + log.info(s"targetPath -> $t") + + val entityPath = s"$t/entities" + val relPath = s"$t/relation" + val mapper = new ObjectMapper() + implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset]) + implicit val publicationEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication]) + implicit val relationEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation]) + implicit val orpEncoder: Encoder[OtherResearchProduct] = Encoders.kryo(classOf[OtherResearchProduct]) + implicit val softwareEncoder: Encoder[Software] = Encoders.kryo(classOf[Software]) + + + log.info("Converting dataset") + val rddDataset =spark.sparkContext.textFile(s"$sourcePath/dataset").map(s => mapper.readValue(s, classOf[OafDataset])) + spark.createDataset(rddDataset).as[OafDataset].write.mode(SaveMode.Overwrite).save(s"$entityPath/dataset") + + + log.info("Converting publication") + val rddPublication =spark.sparkContext.textFile(s"$sourcePath/publication").map(s => mapper.readValue(s, classOf[Publication])) + spark.createDataset(rddPublication).as[Publication].write.mode(SaveMode.Overwrite).save(s"$entityPath/publication") + + log.info("Converting software") + val rddSoftware =spark.sparkContext.textFile(s"$sourcePath/software").map(s => mapper.readValue(s, classOf[Software])) + spark.createDataset(rddSoftware).as[Software].write.mode(SaveMode.Overwrite).save(s"$entityPath/software") + + log.info("Converting otherresearchproduct") + val rddOtherResearchProduct =spark.sparkContext.textFile(s"$sourcePath/otherresearchproduct").map(s => mapper.readValue(s, classOf[OtherResearchProduct])) + spark.createDataset(rddOtherResearchProduct).as[OtherResearchProduct].write.mode(SaveMode.Overwrite).save(s"$entityPath/otherresearchproduct") + + + log.info("Converting Relation") + + + val rddRelation =spark.sparkContext.textFile(s"$sourcePath/relation").map(s => mapper.readValue(s, classOf[Relation])) + spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala index a37dd2132..350b00c5e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala @@ -70,7 +70,7 @@ object SparkCreateInputGraph { resultObject.foreach { r => log.info(s"Make ${r._1} unique") - makeDatasetUnique(s"$targetPath/extracted/${r._1}",s"$targetPath/dedup/${r._1}",spark, r._2) + makeDatasetUnique(s"$targetPath/extracted/${r._1}",s"$targetPath/preprocess/${r._1}",spark, r._2) } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala index ba483bfb2..0a7fc18fb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala @@ -42,6 +42,7 @@ object SparkCreateScholix { val relationDS: Dataset[(String, Relation)] = spark.read.load(relationPath).as[Relation] + .filter(r => (r.getDataInfo== null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge")) .map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relEncoder)) val summaryDS: Dataset[(String, ScholixSummary)] = spark.read.load(summaryPath).as[ScholixSummary] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateSummaryObject.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateSummaryObject.scala index a66da3e6d..0970375f5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateSummaryObject.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateSummaryObject.scala @@ -1,7 +1,7 @@ package eu.dnetlib.dhp.sx.graph import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.Result +import eu.dnetlib.dhp.schema.oaf.{Oaf, Result} import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils import org.apache.commons.io.IOUtils @@ -29,11 +29,12 @@ object SparkCreateSummaryObject { log.info(s"targetPath -> $targetPath") implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result] + implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf] implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] - val ds:Dataset[Result] = spark.read.load(s"$sourcePath/*").as[Result] + val ds:Dataset[Result] = spark.read.load(s"$sourcePath/*").as[Result].filter(r=>r.getDataInfo== null || r.getDataInfo.getDeletedbyinference== false) ds.repartition(6000).map(r => ScholixUtils.resultToSummary(r)).filter(s => s!= null).write.mode(SaveMode.Overwrite).save(targetPath) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkResolveRelation.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkResolveRelation.scala index 6ee575e2a..b2fddec20 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkResolveRelation.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkResolveRelation.scala @@ -1,10 +1,17 @@ package eu.dnetlib.dhp.sx.graph +import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.{Relation, Result} import org.apache.commons.io.IOUtils +import org.apache.hadoop.io.compress.GzipCodec import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD import org.apache.spark.sql._ +import org.json4s +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse import org.slf4j.{Logger, LoggerFactory} import scala.collection.JavaConverters._ @@ -25,60 +32,109 @@ object SparkResolveRelation { val relationPath = parser.get("relationPath") log.info(s"sourcePath -> $relationPath") val entityPath = parser.get("entityPath") - log.info(s"targetPath -> $entityPath") + log.info(s"entityPath -> $entityPath") val workingPath = parser.get("workingPath") log.info(s"workingPath -> $workingPath") - - implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation]) import spark.implicits._ - val entities:Dataset[Result] = spark.read.load(s"$entityPath/*").as[Result] - entities.flatMap(e => e.getPid.asScala - .map(p => - convertPidToDNETIdentifier(p.getValue, p.getQualifier.getClassid)) - .filter(s => s!= null) - .map(s => (s,e.getId)) - ).groupByKey(_._1) - .reduceGroups((x,y) => if (x._2.startsWith("50|doi") || x._2.startsWith("50|pmid")) x else y) - .map(s =>s._2) - .write - .mode(SaveMode.Overwrite) - .save(s"$workingPath/resolvedPid") - val rPid:Dataset[(String,String)] = spark.read.load(s"$workingPath/resolvedPid").as[(String,String)] + extractPidResolvedTableFromJsonRDD(spark, entityPath, workingPath) + + val mappper = new ObjectMapper() + + val rPid:Dataset[(String,String)] = spark.read.load(s"$workingPath/relationResolvedPid").as[(String,String)] val relationDs:Dataset[(String,Relation)] = spark.read.load(relationPath).as[Relation].map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) - relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_1")), "left").map{ + relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_2")), "left").map{ m => val sourceResolved = m._2 val currentRelation = m._1._2 - if (sourceResolved!=null && sourceResolved._2.nonEmpty) - currentRelation.setSource(sourceResolved._2) + if (sourceResolved!=null && sourceResolved._1!=null && sourceResolved._1.nonEmpty) + currentRelation.setSource(sourceResolved._1) currentRelation }.write .mode(SaveMode.Overwrite) - .save(s"$workingPath/resolvedSource") + .save(s"$workingPath/relationResolvedSource") - val relationSourceResolved:Dataset[(String,Relation)] = spark.read.load(s"$workingPath/resolvedSource").as[Relation].map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) - relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_1")), "left").map{ + val relationSourceResolved:Dataset[(String,Relation)] = spark.read.load(s"$workingPath/relationResolvedSource").as[Relation].map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) + relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_2")), "left").map{ m => val targetResolved = m._2 val currentRelation = m._1._2 - if (targetResolved!=null && targetResolved._2.nonEmpty) - currentRelation.setTarget(targetResolved._2) + if (targetResolved!=null && targetResolved._1.nonEmpty) + currentRelation.setTarget(targetResolved._1) currentRelation }.filter(r => r.getSource.startsWith("50")&& r.getTarget.startsWith("50")) .write .mode(SaveMode.Overwrite) - .save(s"$workingPath/resolvedRelation") + .save(s"$workingPath/relation_resolved") + + spark.read.load(s"$workingPath/relation_resolved").as[Relation] + .map(r => mappper.writeValueAsString(r)) + .rdd.saveAsTextFile(s"$workingPath/relation", classOf[GzipCodec]) + } + private def extractPidsFromRecord(input:String):(String,List[(String,String)]) = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: json4s.JValue = parse(input) + val id:String = (json \ "id").extract[String] + val result: List[(String,String)] = for { + JObject(pids) <- json \ "pid" + JField("value", JString(pidValue)) <- pids + JField("qualifier", JObject(qualifier)) <- pids + JField("classname", JString(pidType)) <- qualifier + } yield (pidValue, pidType) + (id,result) + } + private def extractPidResolvedTableFromJsonRDD(spark: SparkSession, entityPath: String, workingPath: String) = { + import spark.implicits._ + + val d: RDD[(String,String)] = spark.sparkContext.textFile(s"$entityPath/*") + .map(i => extractPidsFromRecord(i)) + .filter(s => s != null && s._1!= null && s._2!=null && s._2.nonEmpty) + .flatMap{ p => + p._2.map(pid => + (p._1, convertPidToDNETIdentifier(pid._1, pid._2)) + ) + }.filter(r =>r._1 != null || r._2 != null) + + spark.createDataset(d) + .groupByKey(_._2) + .reduceGroups((x, y) => if (x._1.startsWith("50|doi") || x._1.startsWith("50|pmid")) x else y) + .map(s => s._2) + .write + .mode(SaveMode.Overwrite) + .save(s"$workingPath/relationResolvedPid") + } + + + /* + This method should be used once we finally convert everythings in Kryo dataset + instead of using rdd of json + */ + private def extractPidResolvedTableFromKryo(spark: SparkSession, entityPath: String, workingPath: String) = { + import spark.implicits._ + implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + val entities: Dataset[Result] = spark.read.load(s"$entityPath/*").as[Result] + entities.flatMap(e => e.getPid.asScala + .map(p => + convertPidToDNETIdentifier(p.getValue, p.getQualifier.getClassid)) + .filter(s => s != null) + .map(s => (s, e.getId)) + ).groupByKey(_._1) + .reduceGroups((x, y) => if (x._2.startsWith("50|doi") || x._2.startsWith("50|pmid")) x else y) + .map(s => s._2) + .write + .mode(SaveMode.Overwrite) + .save(s"$workingPath/relationResolvedPid") + } def convertPidToDNETIdentifier(pid:String, pidType: String):String = { if (pid==null || pid.isEmpty || pidType== null || pidType.isEmpty) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala index a19c6fb12..90b65c8f7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala @@ -199,7 +199,7 @@ object BioDBToOAF { d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO)) } val relevant_dates: List[StructuredProperty] = dates.filter(d => !d.date_info.contains("entry version")) - .map(date => OafMapperUtils.structuredProperty(date.date, "UNKNOWN", "UNKNOWN", ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO)) + .map(date => OafMapperUtils.structuredProperty(date.date, ModelConstants.UNKNOWN, ModelConstants.UNKNOWN, ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO)) if (relevant_dates != null && relevant_dates.nonEmpty) d.setRelevantdate(relevant_dates.asJava) d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO)) @@ -218,12 +218,12 @@ object BioDBToOAF { if (references_pmid != null && references_pmid.nonEmpty) { - val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if (i_date.isDefined) i_date.get.date else null) + val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null) rel.getCollectedfrom List(d, rel) } else if (references_doi != null && references_doi.nonEmpty) { - val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if (i_date.isDefined) i_date.get.date else null) + val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null) List(d, rel) } else @@ -243,7 +243,7 @@ object BioDBToOAF { rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava) rel.setDataInfo(DATA_INFO) - rel.setRelType("resultResult") + rel.setRelType(ModelConstants.RESULT_RESULT) rel.setSubRelType(subRelType) rel.setRelClass(relClass) @@ -263,7 +263,7 @@ object BioDBToOAF { def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date:String): Relation = { - createRelation(pid,pidType,sourceId,collectedFrom, "supplement","IsSupplementTo", date) + createRelation(pid,pidType,sourceId,collectedFrom, ModelConstants.SUPPLEMENT, ModelConstants.IS_SUPPLEMENT_TO, date) } @@ -392,6 +392,6 @@ object BioDBToOAF { i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO)) d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO)) - List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"),"relationship", "isRelatedTo", GraphCleaningFunctions.cleanDate(input.date))) + List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, GraphCleaningFunctions.cleanDate(input.date))) } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala index ae4a72062..9a49deebc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala @@ -16,7 +16,7 @@ object PubMedToOaf { ) def createResult(cobjQualifier: Qualifier, vocabularies: VocabularyGroup): Result = { - val result_typologies = getVocabularyTerm("dnet:result_typologies", vocabularies, cobjQualifier.getClassid) + val result_typologies = getVocabularyTerm(ModelConstants.DNET_RESULT_TYPOLOGIES, vocabularies, cobjQualifier.getClassid) result_typologies.getClassid match { case "dataset" => new Dataset case "publication" => new Publication @@ -68,11 +68,11 @@ object PubMedToOaf { //else We have to find a terms that match the vocabulary otherwise we discard it val ja = article.getPublicationTypes.asScala.find(s => "Journal Article".equalsIgnoreCase(s.getValue)) if (ja.isDefined) { - val cojbCategory = getVocabularyTerm("dnet:publication_resource", vocabularies, ja.get.getValue) + val cojbCategory = getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, ja.get.getValue) i.setInstancetype(cojbCategory) } else { val i_type = article.getPublicationTypes.asScala - .map(s => getVocabularyTerm("dnet:publication_resource", vocabularies, s.getValue)) + .map(s => getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue)) .find(q => q != null) if (i_type.isDefined) i.setInstancetype(i_type.get) @@ -112,7 +112,7 @@ object PubMedToOaf { if (article.getLanguage != null) { - val term = vocabularies.getSynonymAsQualifier("dnet:languages", article.getLanguage) + val term = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_LANGUAGES, article.getLanguage) if (term != null) result.setLanguage(term) } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json new file mode 100644 index 000000000..178c2d69b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "g", + "paramLongName": "graphBasePath", + "paramDescription": "base graph path providing the set of relations to patch", + "paramRequired": true + }, + { + "paramName": "w", + "paramLongName": "workingDir", + "paramDescription": "intermediate storage location", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "idMappingPath", + "paramDescription": "dataset providing the old -> new identifier mapping", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml index 7f1ecb39f..321ca4090 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -100,6 +100,16 @@ a blacklist of nsprefixes (comma separeted) + + shouldPatchRelations + false + activates the relation patching phase, driven by the content in ${idMappingPath} + + + idMappingPath + + path pointing to the relations identifiers mapping dataset + sparkDriverMemory memory for driver process @@ -551,7 +561,6 @@ - yarn @@ -760,7 +769,42 @@ - + + + + + + ${(shouldPatchRelations eq "true") and + (fs:exists(concat(concat(wf:conf('nameNode'),'/'),wf:conf('idMappingPath'))) eq "true")} + + + + + + + + yarn + cluster + PatchRelations + eu.dnetlib.dhp.oa.graph.raw.PatchRelationsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --graphBasePath${graphOutputPath} + --workingDir${workingDir}/patch_relations + --idMappingPath${idMappingPath} + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json new file mode 100644 index 000000000..8bfdde5b0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json @@ -0,0 +1,5 @@ +[ + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/extractEntities/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/extractEntities/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/extractEntities/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/extractEntities/oozie_app/workflow.xml new file mode 100644 index 000000000..685976ce6 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/extractEntities/oozie_app/workflow.xml @@ -0,0 +1,85 @@ + + + + sourcePath + the working dir base path + + + targetPath + the graph Raw base path + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Extract entities in raw graph + eu.dnetlib.dhp.sx.graph.SparkCreateInputGraph + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=2000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${sourcePath} + --targetPath${targetPath} + + + + + + + + + + + + + + + + + yarn + cluster + Generate Input Graph for deduplication + eu.dnetlib.dhp.sx.graph.SparkConvertDatasetToJsonRDD + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=3000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${targetPath}/preprocess + --targetPath${targetPath}/dedup + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/workflow.xml similarity index 78% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/workflow.xml index 3ea4e9d30..d8eb1fc80 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/workflow.xml @@ -1,4 +1,4 @@ - + sourcePath @@ -6,48 +6,22 @@ targetPath - the graph Raw base path + the final graph path - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + yarn cluster - Extract entities in raw graph - eu.dnetlib.dhp.sx.graph.SparkCreateInputGraph - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn - --sourcePath${sourcePath} - --targetPath${targetPath} - - - - - - - - - yarn - cluster - Resolve Relations in raw graph - eu.dnetlib.dhp.sx.graph.SparkResolveRelation + Import JSONRDD to Dataset kryo + eu.dnetlib.dhp.sx.graph.SparkConvertRDDtoDataset dhp-graph-mapper-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} @@ -60,9 +34,8 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --masteryarn - --relationPath${targetPath}/extracted/relation - --workingPath${targetPath}/resolved/ - --entityPath${targetPath}/dedup + --sourcePath${sourcePath} + --targetPath${targetPath} @@ -87,7 +60,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --masteryarn - --sourcePath${targetPath}/dedup + --sourcePath${targetPath}/entities --targetPath${targetPath}/provision/summaries @@ -114,7 +87,7 @@ --masteryarn --summaryPath${targetPath}/provision/summaries --targetPath${targetPath}/provision/scholix - --relationPath${targetPath}/resolved/resolvedRelation + --relationPath${targetPath}/relation @@ -182,9 +155,5 @@ - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step3/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step3/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/workflow.xml new file mode 100644 index 000000000..7683ff94c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/workflow.xml @@ -0,0 +1,62 @@ + + + + entityPath + the path of deduplicate Entities + + + relationPath + the path of relation unresolved + + + targetPath + the path of relation unresolved + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + + yarn + cluster + Resolve Relations in raw graph + eu.dnetlib.dhp.sx.graph.SparkResolveRelation + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=3000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --relationPath${relationPath} + --workingPath${targetPath} + --entityPath${entityPath} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml deleted file mode 100644 index 9d06c42d6..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml +++ /dev/null @@ -1,120 +0,0 @@ - - - - workingPath - the working path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - ${jobTracker} - ${nameNode} - yarn-cluster - cluster - Extract DLI Entities (Publication) - eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory ${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=5000 - ${sparkExtraOPT} - - -mt yarn-cluster - --workingPath${workingPath} - -epublication - - - - - - - - ${jobTracker} - ${nameNode} - yarn-cluster - cluster - Extract DLI Entities (Dataset) - eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory ${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=5000 - ${sparkExtraOPT} - - -mt yarn-cluster - --workingPath${workingPath} - -edataset - - - - - - - - ${jobTracker} - ${nameNode} - yarn-cluster - cluster - Extract DLI Entities (Unknown) - eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory ${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=5000 - ${sparkExtraOPT} - - -mt yarn-cluster - --workingPath${workingPath} - -eunknown - - - - - - - - ${jobTracker} - ${nameNode} - yarn-cluster - cluster - Extract DLI Entities (Relation) - eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory ${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=5000 - ${sparkExtraOPT} - - -mt yarn-cluster - --workingPath${workingPath} - -erelation - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step3/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step3/oozie_app/workflow.xml deleted file mode 100644 index 4d54b2afb..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step3/oozie_app/workflow.xml +++ /dev/null @@ -1,61 +0,0 @@ - - - - sourcePath - the source path - - - targetPath - the source path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - entity - the entity to be merged - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - ${jobTracker} - ${nameNode} - yarn-cluster - cluster - Merge ${entity} - eu.dnetlib.dhp.sx.graph.SparkScholexplorerCreateRawGraphJob - dhp-graph-mapper-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} - -mt yarn-cluster - --sourcePath${sourcePath}/${entity} - --targetPath${targetPath}/${entity} - --entity${entity} - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 5b229a625..60970f4d6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -1,11 +1,9 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertFalse; -import static org.junit.jupiter.api.Assertions.assertNotNull; -import static org.junit.jupiter.api.Assertions.assertNull; -import static org.junit.jupiter.api.Assertions.assertTrue; +import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.cleanup; +import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.fixVocabularyNames; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.lenient; import java.io.IOException; @@ -25,15 +23,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.PidType; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -74,7 +64,7 @@ public class MappersTest { assertValidId(p.getId()); - assertEquals(1, p.getOriginalId().size()); + assertEquals(2, p.getOriginalId().size()); assertTrue(p.getOriginalId().contains("10.3897/oneeco.2.e13718")); assertValidId(p.getCollectedfrom().get(0).getKey()); @@ -261,8 +251,8 @@ public class MappersTest { final Relation r2 = (Relation) list.get(2); assertValidId(d.getId()); - assertEquals(1, d.getOriginalId().size()); - assertTrue(d.getOriginalId().contains("oai:zenodo.org:3234526")); + assertEquals(2, d.getOriginalId().size()); + assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526"))); assertValidId(d.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); assertTrue(d.getAuthor().size() > 0); @@ -351,8 +341,11 @@ public class MappersTest { final Publication p = (Publication) list.get(0); assertValidId(p.getId()); - assertTrue(p.getOriginalId().size() == 1); - assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0)); + assertEquals(2, p.getOriginalId().size()); + + assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:pub.uni-bielefeld.de:2949739"))); + // assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0)); + assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(p.getAuthor().size() > 0); @@ -413,7 +406,8 @@ public class MappersTest { assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, d.getDataInfo().getProvenanceaction().getSchemename()); assertValidId(d.getId()); - assertTrue(d.getOriginalId().size() == 1); + assertEquals(2, d.getOriginalId().size()); + assertEquals("feabb67c-1fd1-423b-aec6-606d04ce53c6", d.getOriginalId().get(0)); assertValidId(d.getCollectedfrom().get(0).getKey()); @@ -567,6 +561,31 @@ public class MappersTest { assertNotNull(d.getInstance().get(0).getUrl()); } + @Test + void testEnermaps() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("enermaps.xml")); + final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Dataset); + + final Dataset d = (Dataset) list.get(0); + + assertValidId(d.getId()); + assertValidId(d.getCollectedfrom().get(0).getKey()); + assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); + assertEquals(1, d.getAuthor().size()); + assertEquals(1, d.getInstance().size()); + assertNotNull(d.getInstance().get(0).getUrl()); + assertNotNull(d.getContext()); + assertTrue(StringUtils.isNotBlank(d.getContext().get(0).getId())); + assertEquals("enermaps::selection::tgs00004", d.getContext().get(0).getId()); + } + @Test void testClaimFromCrossref() throws IOException { final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_crossref.xml")); @@ -648,6 +667,30 @@ public class MappersTest { System.out.println(p.getTitle().get(0).getValue()); } + @Test + void testJairo() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_jairo.xml")); + final List list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + + final Publication p = (Publication) list.get(0); + assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); + + assertNotNull(p.getTitle()); + assertFalse(p.getTitle().isEmpty()); + assertTrue(p.getTitle().size() == 1); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + + final Publication p_cleaned = cleanup(fixVocabularyNames(p)); + + assertNotNull(p_cleaned.getTitle()); + assertFalse(p_cleaned.getTitle().isEmpty()); + } + @Test void testOdfFromHdfs() throws IOException { final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_from_hdfs.xml")); @@ -663,8 +706,8 @@ public class MappersTest { final Dataset p = (Dataset) list.get(0); assertValidId(p.getId()); - assertTrue(p.getOriginalId().size() == 1); - assertEquals("df76e73f-0483-49a4-a9bb-63f2f985574a", p.getOriginalId().get(0)); + assertEquals(2, p.getOriginalId().size()); + assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("df76e73f-0483-49a4-a9bb-63f2f985574a"))); assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(p.getAuthor().size() > 0); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java new file mode 100644 index 000000000..3fd365416 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java @@ -0,0 +1,115 @@ + +package eu.dnetlib.dhp.oa.graph.raw; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.Relation; + +public class PatchRelationApplicationTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static final String ID_MAPPING_PATH = "map/id_mapping.json"; + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(PatchRelationApplicationTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(PatchRelationApplicationTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(PatchRelationApplicationTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(PatchRelationApplicationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + + FileUtils + .copyInputStreamToFile( + PatchRelationApplicationTest.class.getResourceAsStream("id_mapping.json"), + workingDir.resolve(ID_MAPPING_PATH).toFile()); + + FileUtils + .copyInputStreamToFile( + PatchRelationApplicationTest.class.getResourceAsStream("relations_to_patch.json"), + workingDir.resolve("graphBasePath/relation/rels.json").toFile()); + + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testPatchRelationApplication() throws Exception { + + final String graphBasePath = workingDir.toString() + "/graphBasePath"; + PatchRelationsApplication.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-graphBasePath", graphBasePath, + "-workingDir", workingDir.toString() + "/workingDir", + "-idMappingPath", workingDir.toString() + "/" + ID_MAPPING_PATH + }); + + final List rels = spark + .read() + .textFile(graphBasePath + "/relation") + .map( + (MapFunction) s -> OBJECT_MAPPER.readValue(s, Relation.class), + Encoders.bean(Relation.class)) + .collectAsList(); + + assertEquals(6, rels.size()); + + assertEquals(0, getCount(rels, "1a"), "should be patched to 1b"); + assertEquals(0, getCount(rels, "2a"), "should be patched to 2b"); + + assertEquals(2, getCount(rels, "10a"), "not included in patching"); + assertEquals(2, getCount(rels, "20a"), "not included in patching"); + + assertEquals(2, getCount(rels, "15a"), "not included in patching"); + assertEquals(2, getCount(rels, "25a"), "not included in patching"); + + assertEquals(2, getCount(rels, "1b"), "patched from 1a"); + assertEquals(2, getCount(rels, "2b"), "patched from 2a"); + } + + private long getCount(List rels, final String id) { + return rels.stream().filter(r -> r.getSource().equals(id) || r.getTarget().equals(id)).count(); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/enermaps.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/enermaps.xml new file mode 100644 index 000000000..362b40c85 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/enermaps.xml @@ -0,0 +1,72 @@ + + + + enermaps____::04149ee428d07360314c2cb3ba95d41e + tgs00004 + 2021-07-20T18:43:12.096+02:00 + enermaps____ + + + + https://ec.europa.eu/eurostat/web/products-datasets/-/tgs00004 + + + Statistical Office of the European Union (Eurostat) + + + + + Regional GDP + + + Statistical Office of the European Union (Eurostat) + 2020 + + 2020-10-07 + + + + OPEN + Creative Commons Attribution 4.0 International + + + GDP expressed in PPS (purchasing power standards) eliminates differences in price levels between countries. Calculations on a per inhabitant basis allow for the comparison of economies and regions significantly different in absolute size. GDP per inhabitant in PPS is the key variable for determining the eligibility of NUTS 2 regions in the framework of the European Unions structural policy. + + 0021 + 2020-10-07 + OPEN + Creative Commons Attribution 4.0 International + + + + + + + + + https%3A%2F%2Flab.idiap.ch%2Fenermaps%2Fapi%2Fdatacite + + + + + + + false + false + 0.9 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/id_mapping.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/id_mapping.json new file mode 100644 index 000000000..640d042b1 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/id_mapping.json @@ -0,0 +1,5 @@ +{"oldId": "1a", "newId": "1b"} +{"oldId": "2a", "newId": "2b"} +{"oldId": "3a", "newId": "3b"} +{"oldId": "4a", "newId": "4b"} +{"oldId": "5a", "newId": "5b"} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml new file mode 100644 index 000000000..9ec696256 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml @@ -0,0 +1,70 @@ + + +
+ jairo_______::000012e58ed836576ef2a0d38b0f726f + oai:irdb.nii.ac.jp:01221:0000010198 + + + + + + 2021-05-10T11:31:09.424Z + 2021-06-03T01:45:42.536Z + jairo_______ +
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We first unravel misconceptions as perceived on different continents and subsequently present a revised interpretation of the identity and typification of three European taxa at species level: Ruppia maritima L., Ruppia spiralis L. ex Dumortier, and Ruppia cirrhosa (Petagna) Grande. To do this, historical specimens, illustrations and original descriptions were studied. We supersede a previous choice of the figure of Buccaferrea maritima, foliis minus acutis Micheli (1729) as the lectotype of R. maritima and type species of the genus Ruppia owing to a serious conflict with the protologue. Based on a meticulous interpretation of protologues and figures in a historical context, we reject the recent view of assigning R. cirrhosa and its proposed lectotype (iconotype) as a homotypic synonym of R. maritima. We agree with an earlier lectotypification of R. spiralis, though for another reason than the above-mentioned abused homotypy. 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(ISSCC)","issnPrinted":null,"issnOnline":null,"issnLinking":null,"ep":null,"iss":null,"sp":null,"vol":null,"edition":null,"conferenceplace":null,"conferencedate":null,"dataInfo":null}} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index c279436d7..e402d0600 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -9,6 +9,41 @@ dhp-graph-provision + + + + net.alchim31.maven + scala-maven-plugin + 4.0.1 + + + scala-compile-first + initialize + + add-source + compile + + + + scala-test-compile + process-test-resources + + testCompile + + + + + + -Xmax-classfile-name + 200 + + ${scala.version} + + + + + + diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java index 7d53d3554..b3f785492 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java @@ -10,6 +10,7 @@ import java.util.Set; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -81,6 +82,7 @@ public class PrepareRelationsJob { Set relationFilter = Optional .ofNullable(parser.get("relationFilter")) + .map(String::toLowerCase) .map(s -> Sets.newHashSet(Splitter.on(",").split(s))) .orElse(new HashSet<>()); log.info("relationFilter: {}", relationFilter); @@ -130,7 +132,7 @@ public class PrepareRelationsJob { JavaRDD rels = readPathRelationRDD(spark, inputRelationsPath) .filter(rel -> rel.getDataInfo().getDeletedbyinference() == false) - .filter(rel -> relationFilter.contains(rel.getRelClass()) == false); + .filter(rel -> relationFilter.contains(StringUtils.lowerCase(rel.getRelClass())) == false); JavaRDD pruned = pruneRels( pruneRels( diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 86bbae99e..2c8240290 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -42,6 +42,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; public class XmlRecordFactory implements Serializable { @@ -183,6 +184,7 @@ public class XmlRecordFactory implements Serializable { .getOriginalId() .stream() .filter(Objects::nonNull) + .filter(id -> !id.matches("^\\d{2}" + IdentifierFactory.ID_PREFIX_SEPARATOR)) .map(s -> XmlSerializationUtils.asXmlElement("originalId", s)) .collect(Collectors.toList())); } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/sx/provision/DropAndCreateESIndex.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/sx/provision/DropAndCreateESIndex.java index f96a64a27..ffeb0995d 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/sx/provision/DropAndCreateESIndex.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/sx/provision/DropAndCreateESIndex.java @@ -71,6 +71,9 @@ public class DropAndCreateESIndex { log.info(STATUS_CODE_TEXT, response.getStatusLine()); } + log.info("Sleeping 60 seconds to avoid to lost the creation of index request"); + Thread.sleep(60000); + try (CloseableHttpClient client = HttpClients.createDefault()) { final String summaryConf = IOUtils diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 6631cb4da..221049f90 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -21,8 +21,10 @@ import com.google.common.collect.Lists; 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.oa.provision.utils.ContextDef; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; +import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -131,4 +133,32 @@ public class XmlRecordFactoryTest { System.out.println(doc.asXML()); assertEquals("", doc.valueOf("//rel/validated")); } + + @Test + public void testEnermapsRecord() throws IOException, DocumentException { + + String contextmap = "" + + + "" + + "" + + ""; + + ContextMapper contextMapper = ContextMapper.fromXml(contextmap); + XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, + otherDsTypeId); + + Dataset d = OBJECT_MAPPER + .readValue(IOUtils.toString(getClass().getResourceAsStream("enermaps.json")), Dataset.class); + + JoinedEntity je = new JoinedEntity<>(d); + + String xml = xmlRecordFactory.build(je); + + assertNotNull(xml); + + Document doc = new SAXReader().read(new StringReader(xml)); + assertNotNull(doc); + System.out.println(doc.asXML()); + assertEquals("enermaps::selection::tgs00004", doc.valueOf("//concept/@id")); + } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/enermaps.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/enermaps.json new file mode 100644 index 000000000..dcd4c2ee1 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/enermaps.json @@ -0,0 +1 @@ +{"collectedfrom":[{"key":"10|enermaps____::d77d5e503ad1439f585ac494268b351b","value":"Enermaps","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626800904248,"id":"50|enermaps____::04149ee428d07360314c2cb3ba95d41e","originalId":["50|enermaps____::04149ee428d07360314c2cb3ba95d41e","tgs00004"],"pid":[],"dateofcollection":"2021-07-20T18:43:12.096+02:00","dateoftransformation":"","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2021-07-20T18:43:12.096+02:00","altered":true,"baseURL":"https%3A%2F%2Flab.idiap.ch%2Fenermaps%2Fapi%2Fdatacite","identifier":"","datestamp":"","metadataNamespace":""}},"measures":null,"author":[{"fullname":"Statistical Office of the European Union (Eurostat)","name":"","surname":"","rank":1,"pid":[],"affiliation":[]}],"resulttype":{"classid":"dataset","classname":"dataset","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[],"title":[{"value":"\n Regional GDP\n ","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[{"value":"2020-10-07","qualifier":{"classid":"Issued","classname":"Issued","schemeid":"dnet:dataCite_date","schemename":"dnet:dataCite_date"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"description":[{"value":"GDP expressed in PPS (purchasing power standards) eliminates differences in price levels between countries. Calculations on a per inhabitant basis allow for the comparison of economies and regions significantly different in absolute size. GDP per inhabitant in PPS is the key variable for determining the eligibility of NUTS 2 regions in the framework of the European Unions structural policy.","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2020-10-07","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":{"value":"Statistical Office of the European Union (Eurostat)","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"coverage":[],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[{"id":"enermaps::selection::tgs00004","dataInfo":[{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}]}],"externalReference":[],"instance":[{"license":{"value":"Creative Commons Attribution 4.0 International","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes","openAccessRoute":null},"instancetype":{"classid":"0021","classname":"Dataset","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository","dataInfo":null},"url":["https://ec.europa.eu/eurostat/web/products-datasets/-/tgs00004"],"distributionlocation":null,"collectedfrom":{"key":"10|enermaps____::d77d5e503ad1439f585ac494268b351b","value":"Enermaps","dataInfo":null},"pid":[],"alternateIdentifier":[],"dateofacceptance":{"value":"2020-10-07","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"}}],"storagedate":{"value":"2020-10-07","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"device":null,"size":null,"version":null,"lastmetadataupdate":null,"metadataversionnumber":null,"geolocation":[]} diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/indicators.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/indicators.sh index d5aa207d1..fb944f4ff 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/indicators.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/indicators.sh @@ -13,7 +13,7 @@ echo "Getting file from " $SCRIPT_PATH hdfs dfs -copyToLocal $SCRIPT_PATH echo "Creating indicators" -impala-shell -d ${TARGET} -q "invalidate metadata" +impala-shell -q "invalidate metadata" impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/^\(.*\)/compute stats ${TARGET}.\1;/" | impala-shell -c -f - cat step16_7-createIndicatorsTables.sql | impala-shell -d $TARGET -f - echo "Indicators created" \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql index d79396b3b..e4e81175c 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql @@ -57,12 +57,14 @@ UNION ALL SELECT * FROM ${stats_db_name}.software_sources UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; --- --- ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_sources COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_sources COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file + + +create table ${stats_db_name}.result_orcid as +select distinct res.id, regexp_replace(res.orcid, 'http://orcid.org/' ,'') as orcid +from ( + SELECT substr(res.id, 4) as id, auth_pid.value as orcid + FROM ${openaire_db_name}.result res + LATERAL VIEW explode(author) a as auth + LATERAL VIEW explode(auth.pid) ap as auth_pid + LATERAL VIEW explode(auth.pid.qualifier.classid) apt as author_pid_type + WHERE res.datainfo.deletedbyinference = FALSE and res.datainfo.invisible = FALSE and author_pid_type = 'orcid') as res \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql index 8f364d747..8e66e05c0 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql @@ -33,13 +33,4 @@ select * from ${stats_db_name}.dataset_refereed union all select * from ${stats_db_name}.software_refereed union all -select * from ${stats_db_name}.otherresearchproduct_refereed; --- --- ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_refereed COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_refereed COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +select * from ${stats_db_name}.otherresearchproduct_refereed; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_7-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_7-createIndicatorsTables.sql index 8998cb9fc..f1ebf0d87 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_7-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_7-createIndicatorsTables.sql @@ -39,4 +39,198 @@ from publication p join result_instance ri on ri.id = p.id join datasource on datasource.id = ri.hostedby where datasource.id like '%doajarticles%') tmp -on p.id= tmp.id; \ No newline at end of file +on p.id= tmp.id; + +create table indi_project_pubs_count stored as parquet as +select pr.id id, count(p.id) total_pubs from project_results pr +join publication p on p.id=pr.result +group by pr.id; + +create table indi_project_datasets_count stored as parquet as +select pr.id id, count(d.id) total_datasets from project_results pr +join dataset d on d.id=pr.result +group by pr.id; + +create table indi_project_software_count stored as parquet as +select pr.id id, count(s.id) total_software from project_results pr +join software s on s.id=pr.result +group by pr.id; + +create table indi_project_otherresearch_count stored as parquet as +select pr.id id, count(o.id) total_other from project_results pr +join otherresearchproduct o on o.id=pr.result +group by pr.id; + +create table indi_pub_avg_year_country_oa stored as parquet as +select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, +round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA + from + (SELECT year, country, SUM(CASE + WHEN bestlicence='Open Access' THEN 1 + ELSE 0 + END) AS OpenAccess, SUM(CASE + WHEN bestlicence<>'Open Access' THEN 1 + ELSE 0 + END) AS NonOpenAccess + FROM publication p + join result_organization ro on p.id=ro.id + join organization o on o.id=ro.organization + where cast(year as int)>=2003 and cast(year as int)<=2021 + group by year, country) tmp; + +create table indi_dataset_avg_year_country_oa stored as parquet as +select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, +round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA + from + (SELECT year, country, SUM(CASE + WHEN bestlicence='Open Access' THEN 1 + ELSE 0 + END) AS OpenAccess, SUM(CASE + WHEN bestlicence<>'Open Access' THEN 1 + ELSE 0 + END) AS NonOpenAccess + FROM dataset d + join result_organization ro on d.id=ro.id + join organization o on o.id=ro.organization + where cast(year as int)>=2003 and cast(year as int)<=2021 + group by year, country) tmp; + +create table indi_software_avg_year_country_oa stored as parquet as +select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, +round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA + from + (SELECT year, country, SUM(CASE + WHEN bestlicence='Open Access' THEN 1 + ELSE 0 + END) AS OpenAccess, SUM(CASE + WHEN bestlicence<>'Open Access' THEN 1 + ELSE 0 + END) AS NonOpenAccess + FROM software s + join result_organization ro on s.id=ro.id + join SOURCER.organization o on o.id=ro.organization + where cast(year as int)>=2003 and cast(year as int)<=2021 + group by year, country) tmp; + + +create table indi_other_avg_year_country_oa stored as parquet as +select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, +round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA + from + (SELECT year, country, SUM(CASE + WHEN bestlicence='Open Access' THEN 1 + ELSE 0 + END) AS OpenAccess, SUM(CASE + WHEN bestlicence<>'Open Access' THEN 1 + ELSE 0 + END) AS NonOpenAccess + FROM otherresearchproduct orp + join result_organization ro on orp.id=ro.id + join organization o on o.id=ro.organization + where cast(year as int)>=2003 and cast(year as int)<=2021 + group by year, country) tmp; + +create table indi_pub_avg_year_context_oa stored as parquet as +with total as +(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from publication_concepts pc +join context c on pc.concept like concat('%',c.id,'%') +join publication p on p.id=pc.id +where cast(year as int)>=2003 and cast(year as int)<=2021 +group by c.name, year ) +select year, name, round(no_of_pubs/total*100,3) averageofpubs +from total; + +create table indi_dataset_avg_year_context_oa stored as parquet as +with total as +(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from dataset_concepts pc +join context c on pc.concept like concat('%',c.id,'%') +join dataset p on p.id=pc.id +where cast(year as int)>=2003 and cast(year as int)<=2021 +group by c.name, year ) +select year, name, round(no_of_pubs/total*100,3) averageofdataset +from total; + +create table indi_software_avg_year_context_oa stored as parquet as +with total as +(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from software_concepts pc +join context c on pc.concept like concat('%',c.id,'%') +join software p on p.id=pc.id +where cast(year as int)>=2003 and cast(year as int)<=2021 +group by c.name, year ) +select year, name, round(no_of_pubs/total*100,3) averageofsoftware +from total; + +create table indi_other_avg_year_context_oa stored as parquet as +with total as +(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from otherresearchproduct_concepts pc +join context c on pc.concept like concat('%',c.id,'%') +join otherresearchproduct p on p.id=pc.id +where cast(year as int)>=2003 and cast(year as int)<=2021 +group by c.name, year ) +select year, name, round(no_of_pubs/total*100,3) averageofother +from total; + +create table indi_other_avg_year_content_oa stored as parquet as +with total as +(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total +from otherresearchproduct_datasources pd +join datasource d on datasource=d.id +join otherresearchproduct p on p.id=pd.id +where cast(year as int)>=2003 and cast(year as int)<=2021 +group by d.type, year) +select year, type, round(no_of_pubs/total*100,3) averageOfOtherresearchproduct +from total; + +create table indi_software_avg_year_content_oa stored as parquet as +with total as +(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total +from software_datasources pd +join datasource d on datasource=d.id +join software p on p.id=pd.id +where cast(year as int)>=2003 and cast(year as int)<=2021 +group by d.type, year) +select year, type, round(no_of_pubs/total*100,3) averageOfSoftware +from total; + +create table indi_dataset_avg_year_content_oa stored as parquet as +with total as +(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total +from dataset_datasources pd +join datasource d on datasource=d.id +join dataset p on p.id=pd.id +where cast(year as int)>=2003 and cast(year as int)<=2021 +group by d.type, year) +select year, type, round(no_of_pubs/total*100,3) averageOfDatasets +from total; + +create table indi_pub_avg_year_content_oa stored as parquet as +with total as +(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total +from publication_datasources pd +join datasource d on datasource=d.id +join publication p on p.id=pd.id +where cast(year as int)>=2003 and cast(year as int)<=2021 +group by d.type, year) +select year, type, round(no_of_pubs/total*100,3) averageOfPubs +from total; + +create table indi_pub_has_cc_licence stored as parquet as +select distinct p.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license +from publication p +left outer join (select p.id, license.type as lic from publication p +join publication_licenses as license on license.id = p.id +where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp +on p.id= tmp.id; + +create table indi_pub_has_cc_licence_url stored as parquet as +select distinct p.id, (case when lic_host='' or lic_host is null then 0 else 1 end) as has_cc_license_url +from publication p +left outer join (select p.id, lower(parse_url(license.type, "HOST")) as lic_host +from publication p +join publication_licenses as license on license.id = p.id +WHERE lower(parse_url(license.type, 'HOST')) = 'creativecommons.org') tmp +on p.id= tmp.id; + +create table indi_pub_has_abstract stored as parquet as +select distinct publication.id, coalesce(abstract, 1) has_abstract +from publication; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql index 75b24b189..bb0d0ac6c 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql @@ -90,27 +90,8 @@ FROM ${openaire_db_name}.publication p where p.datainfo.deletedbyinference = false; CREATE TABLE ${stats_db_name}.publication_citations AS -SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS result +SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.publication p lateral view explode(p.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" - and p.datainfo.deletedbyinference = false; - --- ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.publication_classifications COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.publication_classifications COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.publication_concepts COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.publication_concepts COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.publication_datasources COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.publication_datasources COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.publication_languages COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.publication_languages COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.publication_oids COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.publication_oids COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.publication_pids COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.publication_pids COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.publication_topics COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.publication_topics COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.publication_citations COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.publication_citations COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file + and p.datainfo.deletedbyinference = false; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 7442b7c10..5da028304 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -116,6 +116,13 @@ compute stats TARGET.indi_pub_doi_from_crossref; create table TARGET.indi_pub_gold_oa as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_gold_oa; +create view TARGET.indi_dataset_avg_year_country_oa as select * from SOURCE.indi_dataset_avg_year_country_oa orig; +create view TARGET.indi_project_datasets_count as select * from SOURCE.indi_project_datasets_count orig; +create view TARGET.indi_project_otherresearch_count as select * from SOURCE.indi_project_otherresearch_count orig; +create view TARGET.indi_project_pubs_count as select * from SOURCE.indi_project_pubs_count orig; +create view TARGET.indi_project_software_count as select * from SOURCE.indi_project_software_count orig; +create view TARGET.indi_pub_avg_year_country_oa as select * from SOURCE.indi_pub_avg_year_country_oa orig; + --denorm alter table TARGET.result rename to TARGET.res_tmp; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql index 540cc03a5..953eaad6a 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql @@ -41,7 +41,7 @@ FROM ${openaire_db_name}.dataset d WHERE d.datainfo.deletedbyinference = FALSE; CREATE TABLE ${stats_db_name}.dataset_citations AS -SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS result +SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.dataset d LATERAL VIEW explode(d.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" @@ -95,21 +95,4 @@ CREATE TABLE ${stats_db_name}.dataset_topics AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.subject) subjects AS subject -where p.datainfo.deletedbyinference = false; --- --- ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.dataset_classifications COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.dataset_classifications COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.dataset_concepts COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.dataset_concepts COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.dataset_datasources COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.dataset_datasources COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.dataset_languages COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.dataset_languages COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.dataset_oids COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.dataset_oids COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.dataset_pids COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.dataset_pids COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.dataset_topics COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.dataset_topics COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +where p.datainfo.deletedbyinference = false; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql index 54345e074..0210dc8cb 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql @@ -41,7 +41,7 @@ from ${openaire_db_name}.software s where s.datainfo.deletedbyinference = false; CREATE TABLE ${stats_db_name}.software_citations AS -SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS RESULT +SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.software s LATERAL VIEW explode(s.extrainfo) citations as citation where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" @@ -95,21 +95,4 @@ CREATE TABLE ${stats_db_name}.software_topics AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.subject) subjects AS subject -where p.datainfo.deletedbyinference = false; --- --- ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.software_classifications COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.software_classifications COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.software_concepts COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.software_concepts COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.software_datasources COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.software_datasources COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.software_languages COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.software_languages COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.software_oids COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.software_oids COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.software_pids COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.software_pids COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.software_topics COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.software_topics COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +where p.datainfo.deletedbyinference = false; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql index 36ad5d92a..f7b302186 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql @@ -41,7 +41,7 @@ WHERE o.datainfo.deletedbyinference = FALSE; -- Otherresearchproduct_citations CREATE TABLE ${stats_db_name}.otherresearchproduct_citations AS -SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS RESULT +SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" and o.datainfo.deletedbyinference = false; @@ -86,21 +86,4 @@ where p.datainfo.deletedbyinference = false; CREATE TABLE ${stats_db_name}.otherresearchproduct_topics AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject -where p.datainfo.deletedbyinference = false; - --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_classifications COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_classifications COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_concepts COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_concepts COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_datasources COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_datasources COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_languages COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_languages COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_oids COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_oids COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_pids COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_pids COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_topics COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_topics COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +where p.datainfo.deletedbyinference = false; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index 5d81e97bb..378e0f17b 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -13,11 +13,17 @@ WHERE r.reltype = 'projectOrganization' and r.datainfo.deletedbyinference = false; CREATE TABLE ${stats_db_name}.project_results AS -SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result +SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance FROM ${openaire_db_name}.relation r WHERE r.reltype = 'resultProject' and r.datainfo.deletedbyinference = false; +create table ${stats_db_name}.project_classification as +select substr(p.id, 4) as id, class.h2020programme.code, class.level1, class.level2, class.level3 +from ${openaire_db_name}.project p + lateral view explode(p.h2020classification) classifs as class +where p.datainfo.deletedbyinference=false and class.h2020programme is not null; + CREATE TABLE ${stats_db_name}.project_tmp ( id STRING, diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index ae540b9b2..b3cbc9b41 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -130,12 +130,7 @@ WHERE r.reltype = 'resultOrganization' and r.datainfo.deletedbyinference = false; CREATE TABLE ${stats_db_name}.result_projects AS -select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend +select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance FROM ${stats_db_name}.result r JOIN ${stats_db_name}.project_results pr ON r.id = pr.result - JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; - --- ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.result_projects COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.result_projects COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file + JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index de0fedd7e..76d31eb5e 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -17,7 +17,9 @@ CREATE TABLE ${stats_db_name}.datasource_tmp `latitude` STRING, `longitude` STRING, `websiteurl` STRING, - `compatibility` STRING + `compatibility` STRING, + issn_printed STRING, + issn_online STRING ) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); -- Insert statement that takes into account the piwik_id of the openAIRE graph @@ -32,7 +34,9 @@ SELECT substr(d1.id, 4) AS id, d1.latitude.value AS latitude, d1.longitude.value AS longitude, d1.websiteurl.value AS websiteurl, - d1.openairecompatibility.classid AS compatibility + d1.openairecompatibility.classid AS compatibility, + d1.journal.issnprinted AS issn_printed, + d1.journal.issnonline AS issn_online FROM ${openaire_db_name}.datasource d1 LEFT OUTER JOIN (SELECT id, split(originalidd, '\\:')[1] as piwik_id @@ -51,7 +55,7 @@ CREATE TABLE ${stats_db_name}.dual INSERT INTO ${stats_db_name}.dual VALUES ('X'); INSERT INTO ${stats_db_name}.datasource_tmp (`id`, `name`, `type`, `dateofvalidation`, `yearofvalidation`, `harvested`, - `piwik_id`, `latitude`, `longitude`, `websiteurl`, `compatibility`) + `piwik_id`, `latitude`, `longitude`, `websiteurl`, `compatibility`, `issn_printed`, `issn_online`) SELECT 'other', 'Other', 'Repository', @@ -62,7 +66,9 @@ SELECT 'other', NULL, NULL, NULL, - 'unknown' + 'unknown', + null, + null FROM ${stats_db_name}.dual WHERE 'other' not in (SELECT id FROM ${stats_db_name}.datasource_tmp WHERE name = 'Unknown Repository'); DROP TABLE ${stats_db_name}.dual; @@ -97,13 +103,4 @@ where d.datainfo.deletedbyinference = false; CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS SELECT datasource AS id, id AS result -FROM ${stats_db_name}.result_datasources; - --- ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.datasource_languages COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.datasource_languages COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.datasource_oids COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.datasource_oids COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.datasource_organizations COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.datasource_organizations COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +FROM ${stats_db_name}.result_datasources; \ No newline at end of file diff --git a/pom.xml b/pom.xml index 6e4526e41..433c88093 100644 --- a/pom.xml +++ b/pom.xml @@ -205,6 +205,11 @@ dateparser 1.0.7 + + me.xuender + unidecode + 0.0.7 + com.google.guava @@ -736,7 +741,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.7.14] + [2.7.15] [4.0.3] [6.0.5] [3.1.6]