Merge branch 'beta' into beta_solr_config
This commit is contained in:
commit
14fbf92ad6
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@ -60,14 +60,10 @@ object SparkCreateActionset {
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val entities: Dataset[(String, Result)] = spark.read.load(s"$sourcePath/entities/*").as[Result].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING, resultEncoders))
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entities.filter(r => r.isInstanceOf[Result]).map(r => r.asInstanceOf[Result])
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entities
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.joinWith(idRelation, entities("_1").equalTo(idRelation("value")))
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.map(p => p._1._2)
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.write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
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}
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}
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@ -1,14 +1,12 @@
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package eu.dnetlib.dhp.sx.graph.bio
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package eu.dnetllib.dhp.sx.bio
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, OafMapperUtils}
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import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, Instance, KeyValue, Oaf, Relation, StructuredProperty}
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import eu.dnetlib.dhp.schema.oaf._
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import org.json4s.DefaultFormats
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import org.json4s.JsonAST.{JField, JObject, JString}
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import org.json4s.jackson.JsonMethods.{compact, parse, render}
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import scala.collection.JavaConverters._
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import collection.JavaConverters._
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object BioDBToOAF {
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case class EBILinkItem(id: Long, links: String) {}
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@ -17,23 +15,23 @@ object BioDBToOAF {
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case class UniprotDate(date: String, date_info: String) {}
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case class ScholixResolved(pid:String, pidType:String, typology:String, tilte:List[String], datasource:List[String], date:List[String], authors:List[String]){}
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case class ScholixResolved(pid: String, pidType: String, typology: String, tilte: List[String], datasource: List[String], date: List[String], authors: List[String]) {}
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val DATA_INFO: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9")
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val SUBJ_CLASS = "Keywords"
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val DATE_RELATION_KEY = "RelationDate"
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val resolvedURL:Map[String,String] = Map(
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"genbank"-> "https://www.ncbi.nlm.nih.gov/nuccore/",
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"ncbi-n" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
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"ncbi-wgs" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
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"ncbi-p" -> "https://www.ncbi.nlm.nih.gov/protein/",
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"ena" -> "https://www.ebi.ac.uk/ena/browser/view/",
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"clinicaltrials.gov"-> "https://clinicaltrials.gov/ct2/show/",
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"onim"-> "https://omim.org/entry/",
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"refseq"-> "https://www.ncbi.nlm.nih.gov/nuccore/",
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"geo"-> "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="
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val resolvedURL: Map[String, String] = Map(
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"genbank" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
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"ncbi-n" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
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"ncbi-wgs" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
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"ncbi-p" -> "https://www.ncbi.nlm.nih.gov/protein/",
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"ena" -> "https://www.ebi.ac.uk/ena/browser/view/",
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"clinicaltrials.gov" -> "https://clinicaltrials.gov/ct2/show/",
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"onim" -> "https://omim.org/entry/",
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"refseq" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
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"geo" -> "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="
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)
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@ -45,7 +43,7 @@ object BioDBToOAF {
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val ElsevierCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|openaire____::8f87e10869299a5fe80b315695296b88", "Elsevier")
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val springerNatureCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|openaire____::6e380d9cf51138baec8480f5a0ce3a2e", "Springer Nature")
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val EBICollectedFrom: KeyValue = OafMapperUtils.keyValue("10|opendoar____::83e60e09c222f206c725385f53d7e567c", "EMBL-EBIs Protein Data Bank in Europe (PDBe)")
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val pubmedCollectedFrom:KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
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val pubmedCollectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
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UNIPROTCollectedFrom.setDataInfo(DATA_INFO)
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PDBCollectedFrom.setDataInfo(DATA_INFO)
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@ -58,9 +56,9 @@ object BioDBToOAF {
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Map(
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"uniprot" -> UNIPROTCollectedFrom,
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"pdb"-> PDBCollectedFrom,
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"elsevier" ->ElsevierCollectedFrom,
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"ebi" ->EBICollectedFrom,
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"pdb" -> PDBCollectedFrom,
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"elsevier" -> ElsevierCollectedFrom,
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"ebi" -> EBICollectedFrom,
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"Springer Nature" -> springerNatureCollectedFrom,
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"NCBI Nucleotide" -> ncbiCollectedFrom,
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"European Nucleotide Archive" -> enaCollectedFrom,
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@ -68,7 +66,7 @@ object BioDBToOAF {
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)
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}
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def crossrefLinksToOaf(input:String):Oaf = {
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def crossrefLinksToOaf(input: String): Oaf = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json = parse(input)
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val source_pid = (json \ "Source" \ "Identifier" \ "ID").extract[String].toLowerCase
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@ -77,16 +75,16 @@ object BioDBToOAF {
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val target_pid = (json \ "Target" \ "Identifier" \ "ID").extract[String].toLowerCase
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val target_pid_type = (json \ "Target" \ "Identifier" \ "IDScheme").extract[String].toLowerCase
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val relation_semantic= (json \ "RelationshipType" \ "Name").extract[String]
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val relation_semantic = (json \ "RelationshipType" \ "Name").extract[String]
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val date = GraphCleaningFunctions.cleanDate((json \ "LinkedPublicationDate").extract[String])
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createRelation(target_pid, target_pid_type, generate_unresolved_id(source_pid, source_pid_type),collectedFromMap("elsevier"),"relationship", relation_semantic, date)
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createRelation(target_pid, target_pid_type, generate_unresolved_id(source_pid, source_pid_type), collectedFromMap("elsevier"), "relationship", relation_semantic, date)
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}
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def scholixResolvedToOAF(input:ScholixResolved):Oaf = {
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def scholixResolvedToOAF(input: ScholixResolved): Oaf = {
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val d = new Dataset
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@ -127,18 +125,18 @@ object BioDBToOAF {
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d.setInstance(List(i).asJava)
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if (input.authors != null && input.authors.nonEmpty) {
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val authors = input.authors.map(a =>{
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val authors = input.authors.map(a => {
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val authorOAF = new Author
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authorOAF.setFullname(a)
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authorOAF
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})
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d.setAuthor(authors.asJava)
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}
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if (input.date!= null && input.date.nonEmpty) {
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val dt = input.date.head
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i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
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d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
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}
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if (input.date != null && input.date.nonEmpty) {
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val dt = input.date.head
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i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
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d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
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}
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d
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}
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@ -190,7 +188,7 @@ object BioDBToOAF {
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OafMapperUtils.structuredProperty(s, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, null)
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).asJava)
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}
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var i_date:Option[UniprotDate] = None
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var i_date: Option[UniprotDate] = None
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if (dates.nonEmpty) {
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i_date = dates.find(d => d.date_info.contains("entry version"))
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@ -218,12 +216,12 @@ object BioDBToOAF {
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if (references_pmid != null && references_pmid.nonEmpty) {
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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)
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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)
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rel.getCollectedfrom
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List(d, rel)
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}
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else if (references_doi != null && references_doi.nonEmpty) {
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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)
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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)
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List(d, rel)
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}
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else
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@ -231,13 +229,12 @@ object BioDBToOAF {
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}
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def generate_unresolved_id(pid:String, pidType:String) :String = {
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def generate_unresolved_id(pid: String, pidType: String): String = {
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s"unresolved::$pid::$pidType"
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}
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|
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def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType:String, relClass:String, date:String):Relation = {
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def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType: String, relClass: String, date: String): Relation = {
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val rel = new Relation
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rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava)
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@ -251,7 +248,7 @@ object BioDBToOAF {
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rel.setTarget(s"unresolved::$pid::$pidType")
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val dateProps:KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
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val dateProps: KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
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rel.setProperties(List(dateProps).asJava)
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@ -262,8 +259,8 @@ object BioDBToOAF {
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}
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|
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def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date:String): Relation = {
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createRelation(pid,pidType,sourceId,collectedFrom, ModelConstants.SUPPLEMENT, ModelConstants.IS_SUPPLEMENT_TO, date)
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def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date: String): Relation = {
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createRelation(pid, pidType, sourceId, collectedFrom, ModelConstants.SUPPLEMENT, ModelConstants.IS_SUPPLEMENT_TO, date)
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}
|
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|
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|
||||
|
|
@ -338,7 +335,7 @@ object BioDBToOAF {
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|||
|
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def EBITargetLinksFilter(input: EBILinks): Boolean = {
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|
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input.targetPidType.equalsIgnoreCase("ena") || input.targetPidType.equalsIgnoreCase("pdb") || input.targetPidType.equalsIgnoreCase("uniprot")
|
||||
input.targetPidType.equalsIgnoreCase("ena") || input.targetPidType.equalsIgnoreCase("pdb") || input.targetPidType.equalsIgnoreCase("uniprot")
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -1,8 +1,8 @@
|
|||
package eu.dnetlib.dhp.sx.graph.bio
|
||||
package eu.dnetllib.dhp.sx.bio
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
|
||||
import BioDBToOAF.ScholixResolved
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||
import eu.dnetllib.dhp.sx.bio.BioDBToOAF.ScholixResolved
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
|
|
@ -31,17 +31,16 @@ object SparkTransformBioDatabaseToOAF {
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|||
.master(parser.get("master")).getOrCreate()
|
||||
val sc = spark.sparkContext
|
||||
|
||||
implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
|
||||
import spark.implicits._
|
||||
|
||||
implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
|
||||
import spark.implicits._
|
||||
database.toUpperCase() match {
|
||||
case "UNIPROT" =>
|
||||
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).write.mode(SaveMode.Overwrite).save(targetPath)
|
||||
case "PDB"=>
|
||||
case "PDB" =>
|
||||
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).write.mode(SaveMode.Overwrite).save(targetPath)
|
||||
case "SCHOLIX" =>
|
||||
spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).write.mode(SaveMode.Overwrite).save(targetPath)
|
||||
case "CROSSREF_LINKS"=>
|
||||
case "CROSSREF_LINKS" =>
|
||||
spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).write.mode(SaveMode.Overwrite).save(targetPath)
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,200 @@
|
|||
package eu.dnetllib.dhp.sx.bio.ebi
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||
import eu.dnetlib.dhp.schema.oaf.Result
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory
|
||||
import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.conf.Configuration
|
||||
import org.apache.hadoop.fs.{FSDataOutputStream, FileSystem, Path}
|
||||
import org.apache.http.client.config.RequestConfig
|
||||
import org.apache.http.client.methods.HttpGet
|
||||
import org.apache.http.impl.client.HttpClientBuilder
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql.expressions.Aggregator
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import java.io.InputStream
|
||||
import scala.io.Source
|
||||
import scala.xml.pull.XMLEventReader
|
||||
|
||||
object SparkCreateBaselineDataFrame {
|
||||
|
||||
|
||||
def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = {
|
||||
val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
|
||||
|
||||
val result = data.lines.filter(l => l.startsWith("<a href=")).map { l =>
|
||||
val end = l.lastIndexOf("\">")
|
||||
val start = l.indexOf("<a href=\"")
|
||||
|
||||
if (start >= 0 && end > start)
|
||||
l.substring(start + 9, end - start)
|
||||
else
|
||||
""
|
||||
}.filter(s => s.endsWith(".gz")).filter(s => s > maxFile).map(s => (s, s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s")).toList
|
||||
|
||||
result
|
||||
}
|
||||
|
||||
|
||||
def downloadBaselinePart(url: String): InputStream = {
|
||||
val r = new HttpGet(url)
|
||||
val timeout = 60; // seconds
|
||||
val config = RequestConfig.custom()
|
||||
.setConnectTimeout(timeout * 1000)
|
||||
.setConnectionRequestTimeout(timeout * 1000)
|
||||
.setSocketTimeout(timeout * 1000).build()
|
||||
val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
|
||||
val response = client.execute(r)
|
||||
println(s"get response with status${response.getStatusLine.getStatusCode}")
|
||||
response.getEntity.getContent
|
||||
|
||||
}
|
||||
|
||||
def requestPage(url: String): String = {
|
||||
val r = new HttpGet(url)
|
||||
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()
|
||||
try {
|
||||
var tries = 4
|
||||
while (tries > 0) {
|
||||
println(s"requesting ${r.getURI}")
|
||||
try {
|
||||
val response = client.execute(r)
|
||||
println(s"get response with status${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 ${r.getURI}")
|
||||
e.printStackTrace()
|
||||
tries -= 1
|
||||
}
|
||||
}
|
||||
""
|
||||
} finally {
|
||||
if (client != null)
|
||||
client.close()
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
def downloadBaseLineUpdate(baselinePath: String, hdfsServerUri: String): Unit = {
|
||||
|
||||
|
||||
val conf = new Configuration
|
||||
conf.set("fs.defaultFS", hdfsServerUri)
|
||||
val fs = FileSystem.get(conf)
|
||||
val p = new Path(baselinePath)
|
||||
val files = fs.listFiles(p, false)
|
||||
var max_file = ""
|
||||
while (files.hasNext) {
|
||||
val c = files.next()
|
||||
val data = c.getPath.toString
|
||||
val fileName = data.substring(data.lastIndexOf("/") + 1)
|
||||
|
||||
if (fileName > max_file)
|
||||
max_file = fileName
|
||||
}
|
||||
|
||||
val files_to_download = requestBaseLineUpdatePage(max_file)
|
||||
|
||||
files_to_download.foreach { u =>
|
||||
val hdfsWritePath: Path = new Path(s"$baselinePath/${u._1}")
|
||||
val fsDataOutputStream: FSDataOutputStream = fs.create(hdfsWritePath, true)
|
||||
val i = downloadBaselinePart(u._2)
|
||||
IOUtils.copy(i, fsDataOutputStream)
|
||||
println(s"Downloaded ${u._2} into $baselinePath/${u._1}")
|
||||
fsDataOutputStream.close()
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
val pmArticleAggregator: Aggregator[(String, PMArticle), PMArticle, PMArticle] = new Aggregator[(String, PMArticle), PMArticle, PMArticle] with Serializable {
|
||||
override def zero: PMArticle = new PMArticle
|
||||
|
||||
override def reduce(b: PMArticle, a: (String, PMArticle)): PMArticle = {
|
||||
if (b != null && b.getPmid != null) b else a._2
|
||||
}
|
||||
|
||||
override def merge(b1: PMArticle, b2: PMArticle): PMArticle = {
|
||||
if (b1 != null && b1.getPmid != null) b1 else b2
|
||||
|
||||
}
|
||||
|
||||
override def finish(reduction: PMArticle): PMArticle = reduction
|
||||
|
||||
override def bufferEncoder: Encoder[PMArticle] = Encoders.kryo[PMArticle]
|
||||
|
||||
override def outputEncoder: Encoder[PMArticle] = Encoders.kryo[PMArticle]
|
||||
}
|
||||
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
val conf: SparkConf = new SparkConf()
|
||||
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json")))
|
||||
parser.parseArgument(args)
|
||||
val isLookupUrl: String = parser.get("isLookupUrl")
|
||||
log.info("isLookupUrl: {}", isLookupUrl)
|
||||
val workingPath = parser.get("workingPath")
|
||||
log.info("workingPath: {}", workingPath)
|
||||
|
||||
val targetPath = parser.get("targetPath")
|
||||
log.info("targetPath: {}", targetPath)
|
||||
|
||||
val hdfsServerUri = parser.get("hdfsServerUri")
|
||||
log.info("hdfsServerUri: {}", targetPath)
|
||||
|
||||
val skipUpdate = parser.get("skipUpdate")
|
||||
log.info("skipUpdate: {}", skipUpdate)
|
||||
|
||||
|
||||
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
|
||||
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
|
||||
val spark: SparkSession =
|
||||
SparkSession
|
||||
.builder()
|
||||
.config(conf)
|
||||
.appName(SparkEBILinksToOaf.getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
|
||||
val sc = spark.sparkContext
|
||||
import spark.implicits._
|
||||
|
||||
implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
|
||||
implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
|
||||
implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor])
|
||||
implicit val resultEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||
|
||||
if (!"true".equalsIgnoreCase(skipUpdate)) {
|
||||
downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri)
|
||||
val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline", 2000)
|
||||
val ds: Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i => {
|
||||
val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
|
||||
new PMParser(xml)
|
||||
}))
|
||||
ds.map(p => (p.getPmid, p))(Encoders.tuple(Encoders.STRING, PMEncoder)).groupByKey(_._1)
|
||||
.agg(pmArticleAggregator.toColumn)
|
||||
.map(p => p._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_dataset")
|
||||
}
|
||||
|
||||
val exported_dataset = spark.read.load(s"$workingPath/baseline_dataset").as[PMArticle]
|
||||
exported_dataset
|
||||
.map(a => PubMedToOaf.convert(a, vocabularies)).as[Result]
|
||||
.filter(p => p != null)
|
||||
.write.mode(SaveMode.Overwrite).save(targetPath)
|
||||
}
|
||||
}
|
||||
|
|
@ -1,33 +1,28 @@
|
|||
package eu.dnetlib.dhp.sx.graph.ebi
|
||||
package eu.dnetllib.dhp.sx.bio.ebi
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.EBILinkItem
|
||||
import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
|
||||
import eu.dnetllib.dhp.sx.bio.BioDBToOAF.EBILinkItem
|
||||
import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.conf.Configuration
|
||||
import org.apache.hadoop.fs.{FileSystem, Path}
|
||||
import org.apache.http.client.config.RequestConfig
|
||||
import org.apache.http.client.methods.{HttpGet, HttpUriRequest}
|
||||
import org.apache.http.client.methods.HttpGet
|
||||
import org.apache.http.impl.client.HttpClientBuilder
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.expressions.Aggregator
|
||||
import org.apache.spark.sql.functions.max
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkDownloadEBILinks {
|
||||
|
||||
|
||||
def createEBILinks(pmid:Long):EBILinkItem = {
|
||||
def createEBILinks(pmid: Long): EBILinkItem = {
|
||||
|
||||
val res = requestLinks(pmid)
|
||||
if (res!=null)
|
||||
if (res != null)
|
||||
return EBILinkItem(pmid, res)
|
||||
null
|
||||
}
|
||||
|
||||
|
||||
def requestPage(url:String):String = {
|
||||
def requestPage(url: String): String = {
|
||||
val r = new HttpGet(url)
|
||||
val timeout = 60; // seconds
|
||||
val config = RequestConfig.custom()
|
||||
|
|
@ -61,46 +56,11 @@ object SparkDownloadEBILinks {
|
|||
}
|
||||
}
|
||||
|
||||
|
||||
def requestBaseLineUpdatePage():List[String] = {
|
||||
val data =requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
|
||||
|
||||
val result =data.lines.filter(l => l.startsWith("<a href=")).map{l =>
|
||||
val end = l.lastIndexOf("\">")
|
||||
val start = l.indexOf("<a href=\"")
|
||||
|
||||
if (start>= 0 && end >start)
|
||||
l.substring(start+9, (end-start))
|
||||
else
|
||||
""
|
||||
}.filter(s =>s.endsWith(".gz") ).map(s => s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s").toList
|
||||
|
||||
result
|
||||
}
|
||||
|
||||
def downloadBaseLineUpdate(baselinePath:String, hdfsServerUri:String ):Unit = {
|
||||
|
||||
|
||||
val conf = new Configuration
|
||||
conf.set("fs.defaultFS", hdfsServerUri)
|
||||
val fs = FileSystem.get(conf)
|
||||
val p = new Path((baselinePath))
|
||||
val files = fs.listFiles(p,false)
|
||||
|
||||
while (files.hasNext) {
|
||||
val c = files.next()
|
||||
c.getPath
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
def requestLinks(PMID:Long):String = {
|
||||
def requestLinks(PMID: Long): String = {
|
||||
requestPage(s"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/$PMID/datalinks?format=json")
|
||||
|
||||
}
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
||||
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||
|
|
@ -117,9 +77,9 @@ object SparkDownloadEBILinks {
|
|||
|
||||
import spark.implicits._
|
||||
|
||||
implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
|
||||
implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
|
||||
implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor])
|
||||
implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
|
||||
implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
|
||||
implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor])
|
||||
|
||||
val sourcePath = parser.get("sourcePath")
|
||||
log.info(s"sourcePath -> $sourcePath")
|
||||
|
|
@ -127,29 +87,29 @@ object SparkDownloadEBILinks {
|
|||
log.info(s"workingPath -> $workingPath")
|
||||
|
||||
log.info("Getting max pubmedId where the links have been requested")
|
||||
val links:Dataset[EBILinkItem] = spark.read.load(s"$sourcePath/ebi_links_dataset").as[EBILinkItem]
|
||||
val lastPMIDRequested =links.map(l => l.id).select(max("value")).first.getLong(0)
|
||||
val links: Dataset[EBILinkItem] = spark.read.load(s"$sourcePath/ebi_links_dataset").as[EBILinkItem]
|
||||
val lastPMIDRequested = links.map(l => l.id).select(max("value")).first.getLong(0)
|
||||
|
||||
log.info("Retrieving PMID to request links")
|
||||
val pubmed = spark.read.load(s"$sourcePath/baseline_dataset").as[PMArticle]
|
||||
pubmed.map(p => p.getPmid.toLong).where(s"value > $lastPMIDRequested").write.mode(SaveMode.Overwrite).save(s"$workingPath/id_to_request")
|
||||
|
||||
val pmidToReq:Dataset[Long] = spark.read.load(s"$workingPath/id_to_request").as[Long]
|
||||
val pmidToReq: Dataset[Long] = spark.read.load(s"$workingPath/id_to_request").as[Long]
|
||||
|
||||
val total = pmidToReq.count()
|
||||
|
||||
spark.createDataset(pmidToReq.rdd.repartition((total/MAX_ITEM_PER_PARTITION).toInt).map(pmid =>createEBILinks(pmid)).filter(l => l!= null)).write.mode(SaveMode.Overwrite).save(s"$workingPath/links_update")
|
||||
spark.createDataset(pmidToReq.rdd.repartition((total / MAX_ITEM_PER_PARTITION).toInt).map(pmid => createEBILinks(pmid)).filter(l => l != null)).write.mode(SaveMode.Overwrite).save(s"$workingPath/links_update")
|
||||
|
||||
val updates:Dataset[EBILinkItem] =spark.read.load(s"$workingPath/links_update").as[EBILinkItem]
|
||||
val updates: Dataset[EBILinkItem] = spark.read.load(s"$workingPath/links_update").as[EBILinkItem]
|
||||
|
||||
links.union(updates).groupByKey(_.id)
|
||||
.reduceGroups{(x,y) =>
|
||||
if (x == null || x.links ==null)
|
||||
.reduceGroups { (x, y) =>
|
||||
if (x == null || x.links == null)
|
||||
y
|
||||
if (y ==null || y.links ==null)
|
||||
if (y == null || y.links == null)
|
||||
x
|
||||
if (x.links.length > y.links.length)
|
||||
x
|
||||
x
|
||||
else
|
||||
y
|
||||
}.map(_._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/links_final")
|
||||
|
|
@ -1,15 +1,14 @@
|
|||
package eu.dnetlib.dhp.sx.graph.ebi
|
||||
package eu.dnetllib.dhp.sx.bio.ebi
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||
import eu.dnetlib.dhp.sx.graph.bio
|
||||
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF
|
||||
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.EBILinkItem
|
||||
import eu.dnetllib.dhp.sx.bio.BioDBToOAF
|
||||
import eu.dnetllib.dhp.sx.bio.BioDBToOAF.EBILinkItem
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkEBILinksToOaf {
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
|
@ -24,17 +23,17 @@ object SparkEBILinksToOaf {
|
|||
.appName(SparkEBILinksToOaf.getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
|
||||
|
||||
import spark.implicits._
|
||||
val sourcePath = parser.get("sourcePath")
|
||||
log.info(s"sourcePath -> $sourcePath")
|
||||
val targetPath = parser.get("targetPath")
|
||||
log.info(s"targetPath -> $targetPath")
|
||||
implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
|
||||
|
||||
import spark.implicits._
|
||||
implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
|
||||
val ebLinks: Dataset[EBILinkItem] = spark.read.load(s"${sourcePath}_dataset").as[EBILinkItem].filter(l => l.links != null)
|
||||
|
||||
val ebLinks:Dataset[EBILinkItem] = spark.read.load(s"${sourcePath}_dataset").as[EBILinkItem].filter(l => l.links!= null)
|
||||
|
||||
ebLinks.flatMap(j =>BioDBToOAF.parse_ebi_links(j.links))
|
||||
ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
|
||||
.filter(p => BioDBToOAF.EBITargetLinksFilter(p))
|
||||
.flatMap(p => BioDBToOAF.convertEBILinksToOaf(p))
|
||||
.write.mode(SaveMode.Overwrite).save(targetPath)
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.ArrayList;
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed;
|
||||
|
||||
public class PMGrant {
|
||||
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
package eu.dnetlib.dhp.sx.graph.bio.pubmed
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed
|
||||
|
||||
import scala.xml.MetaData
|
||||
import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed;
|
||||
|
||||
public class PMSubject {
|
||||
private String value;
|
||||
|
|
@ -1,11 +1,12 @@
|
|||
package eu.dnetlib.dhp.sx.graph.bio.pubmed
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed
|
||||
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf._
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType}
|
||||
import eu.dnetlib.dhp.schema.oaf._
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
import java.util.regex.Pattern
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
object PubMedToOaf {
|
||||
|
||||
|
|
@ -15,7 +16,7 @@ object PubMedToOaf {
|
|||
"doi" -> "https://dx.doi.org/"
|
||||
)
|
||||
|
||||
def cleanDoi(doi:String):String = {
|
||||
def cleanDoi(doi: String): String = {
|
||||
|
||||
val regex = "^10.\\d{4,9}\\/[\\[\\]\\-\\<\\>._;()\\/:A-Z0-9]+$"
|
||||
|
||||
|
|
@ -71,14 +72,14 @@ object PubMedToOaf {
|
|||
if (article.getPublicationTypes == null)
|
||||
return null
|
||||
val i = new Instance
|
||||
var pidList: List[StructuredProperty] = List(OafMapperUtils.structuredProperty(article.getPmid, PidType.pmid.toString, PidType.pmid.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo))
|
||||
val pidList: List[StructuredProperty] = List(OafMapperUtils.structuredProperty(article.getPmid, PidType.pmid.toString, PidType.pmid.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo))
|
||||
if (pidList == null)
|
||||
return null
|
||||
|
||||
var alternateIdentifier :StructuredProperty = null
|
||||
var alternateIdentifier: StructuredProperty = null
|
||||
if (article.getDoi != null) {
|
||||
val normalizedPid = cleanDoi(article.getDoi)
|
||||
if (normalizedPid!= null)
|
||||
if (normalizedPid != null)
|
||||
alternateIdentifier = OafMapperUtils.structuredProperty(normalizedPid, PidType.doi.toString, PidType.doi.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo)
|
||||
}
|
||||
|
||||
|
|
@ -102,10 +103,10 @@ object PubMedToOaf {
|
|||
return result
|
||||
result.setDataInfo(dataInfo)
|
||||
i.setPid(pidList.asJava)
|
||||
if (alternateIdentifier!= null)
|
||||
if (alternateIdentifier != null)
|
||||
i.setAlternateIdentifier(List(alternateIdentifier).asJava)
|
||||
result.setInstance(List(i).asJava)
|
||||
i.getPid.asScala.filter(p => "pmid".equalsIgnoreCase(p.getQualifier.getClassid)).map(p => p.getValue)(collection breakOut)
|
||||
i.getPid.asScala.filter(p => "pmid".equalsIgnoreCase(p.getQualifier.getClassid)).map(p => p.getValue)(collection.breakOut)
|
||||
val urlLists: List[String] = pidList
|
||||
.map(s => (urlMap.getOrElse(s.getQualifier.getClassid, ""), s.getValue))
|
||||
.filter(t => t._1.nonEmpty)
|
||||
|
|
@ -136,7 +137,7 @@ object PubMedToOaf {
|
|||
}
|
||||
|
||||
|
||||
val subjects: List[StructuredProperty] = article.getSubjects.asScala.map(s => OafMapperUtils.structuredProperty(s.getValue, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, dataInfo))(collection breakOut)
|
||||
val subjects: List[StructuredProperty] = article.getSubjects.asScala.map(s => OafMapperUtils.structuredProperty(s.getValue, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, dataInfo))(collection.breakOut)
|
||||
if (subjects != null)
|
||||
result.setSubject(subjects.asJava)
|
||||
|
||||
|
|
@ -148,7 +149,7 @@ object PubMedToOaf {
|
|||
author.setFullname(a.getFullName)
|
||||
author.setRank(index + 1)
|
||||
author
|
||||
}(collection breakOut)
|
||||
}(collection.breakOut)
|
||||
|
||||
|
||||
if (authors != null && authors.nonEmpty)
|
||||
|
|
@ -0,0 +1,8 @@
|
|||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"i", "paramLongName":"isLookupUrl", "paramDescription": "isLookupUrl", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
|
||||
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the oaf path ", "paramRequired": true},
|
||||
{"paramName":"s", "paramLongName":"skipUpdate", "paramDescription": "skip update ", "paramRequired": false},
|
||||
{"paramName":"h", "paramLongName":"hdfsServerUri", "paramDescription": "the working path ", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -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":"w", "paramLongName":"workingPath", "paramDescription": "the working path ", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -1,17 +1,22 @@
|
|||
<workflow-app name="Transform_Pubmed_Workflow" xmlns="uri:oozie:workflow:0.5">
|
||||
<workflow-app name="Download_Transform_Pubmed_Workflow" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>baselineWorkingPath</name>
|
||||
<description>the Baseline Working Path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>the Target Path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>isLookupUrl</name>
|
||||
<description>The IS lookUp service endopoint</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>The target path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>skipUpdate</name>
|
||||
<value>false</value>
|
||||
<description>The request block size</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="ConvertDataset"/>
|
||||
|
|
@ -24,9 +29,9 @@
|
|||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert Baseline to Dataset</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.ebi.SparkCreateBaselineDataFrame</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<name>Convert Baseline to OAF Dataset</name>
|
||||
<class>eu.dnetllib.dhp.sx.bio.ebi.SparkCreateBaselineDataFrame</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
|
|
@ -41,6 +46,8 @@
|
|||
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
|
||||
<arg>--skipUpdate</arg><arg>${skipUpdate}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
|
|
@ -1,13 +1,10 @@
|
|||
package eu.dnetlib.dhp.sx.graph.bio.pubmed
|
||||
package eu.dnetllib.dhp.sx.bio
|
||||
|
||||
import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature}
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.{CleaningFunctions, OafMapperUtils, PidType}
|
||||
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
|
||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
|
||||
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.ScholixResolved
|
||||
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF
|
||||
import eu.dnetlib.dhp.sx.graph.bio.pubmed.PubMedToOaf.dataInfo
|
||||
import eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks
|
||||
import eu.dnetllib.dhp.sx.bio.BioDBToOAF.ScholixResolved
|
||||
import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf}
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
|
|
@ -51,16 +48,11 @@ class BioScholixTest extends AbstractVocabularyTest{
|
|||
}
|
||||
|
||||
|
||||
@Test
|
||||
def testDownloadEBIUpdate() = {
|
||||
val data = SparkDownloadEBILinks.requestBaseLineUpdatePage()
|
||||
println(data)
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Test
|
||||
def testEBIData() = {
|
||||
val inputXML = Source.fromInputStream(getClass.getResourceAsStream("pubmed.xml")).mkString
|
||||
val inputXML = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml")).mkString
|
||||
val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes()))
|
||||
new PMParser(xml).foreach(s =>println(mapper.writeValueAsString(s)))
|
||||
}
|
||||
|
|
@ -70,7 +62,7 @@ class BioScholixTest extends AbstractVocabularyTest{
|
|||
def testPubmedToOaf(): Unit = {
|
||||
assertNotNull(vocabularies)
|
||||
assertTrue(vocabularies.vocabularyExists("dnet:publication_resource"))
|
||||
val records:String =Source.fromInputStream(getClass.getResourceAsStream("pubmed_dump")).mkString
|
||||
val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump")).mkString
|
||||
val r:List[Oaf] = records.lines.toList.map(s=>mapper.readValue(s, classOf[PMArticle])).map(a => PubMedToOaf.convert(a, vocabularies))
|
||||
assertEquals(10, r.size)
|
||||
assertTrue(r.map(p => p.asInstanceOf[Result]).flatMap(p => p.getInstance().asScala.map(i => i.getInstancetype.getClassid)).exists(p => "0037".equalsIgnoreCase(p)))
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -1,3 +1,4 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.dedup;
|
||||
|
||||
import java.io.IOException;
|
||||
|
|
@ -5,10 +6,7 @@ import java.util.Optional;
|
|||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaPairRDD;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.api.java.function.PairFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
|
|
@ -21,7 +19,6 @@ import org.slf4j.LoggerFactory;
|
|||
import org.xml.sax.SAXException;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.dedup.model.Block;
|
||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
|
|
@ -31,121 +28,127 @@ import eu.dnetlib.pace.config.DedupConfig;
|
|||
import eu.dnetlib.pace.model.MapDocument;
|
||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||
import scala.Tuple2;
|
||||
import scala.Tuple3;
|
||||
|
||||
public class SparkWhitelistSimRels extends AbstractSparkAction {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
|
||||
|
||||
private static final String WHITELIST_SEPARATOR = "####";
|
||||
private static final String WHITELIST_SEPARATOR = "####";
|
||||
|
||||
public SparkWhitelistSimRels(ArgumentApplicationParser parser, SparkSession spark) {
|
||||
super(parser, spark);
|
||||
}
|
||||
public SparkWhitelistSimRels(ArgumentApplicationParser parser, SparkSession spark) {
|
||||
super(parser, spark);
|
||||
}
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateSimRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
public static void main(String[] args) throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateSimRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
new SparkWhitelistSimRels(parser, getSparkSession(conf))
|
||||
.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
|
||||
}
|
||||
SparkConf conf = new SparkConf();
|
||||
new SparkWhitelistSimRels(parser, getSparkSession(conf))
|
||||
.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
|
||||
}
|
||||
|
||||
@Override
|
||||
public void run(ISLookUpService isLookUpService)
|
||||
throws DocumentException, IOException, ISLookUpException, SAXException {
|
||||
@Override
|
||||
public void run(ISLookUpService isLookUpService)
|
||||
throws DocumentException, IOException, ISLookUpException, SAXException {
|
||||
|
||||
// read oozie parameters
|
||||
final String graphBasePath = parser.get("graphBasePath");
|
||||
final String isLookUpUrl = parser.get("isLookUpUrl");
|
||||
final String actionSetId = parser.get("actionSetId");
|
||||
final String workingPath = parser.get("workingPath");
|
||||
final int numPartitions = Optional
|
||||
.ofNullable(parser.get("numPartitions"))
|
||||
.map(Integer::valueOf)
|
||||
.orElse(NUM_PARTITIONS);
|
||||
final String whiteListPath = parser.get("whiteListPath");
|
||||
// read oozie parameters
|
||||
final String graphBasePath = parser.get("graphBasePath");
|
||||
final String isLookUpUrl = parser.get("isLookUpUrl");
|
||||
final String actionSetId = parser.get("actionSetId");
|
||||
final String workingPath = parser.get("workingPath");
|
||||
final int numPartitions = Optional
|
||||
.ofNullable(parser.get("numPartitions"))
|
||||
.map(Integer::valueOf)
|
||||
.orElse(NUM_PARTITIONS);
|
||||
final String whiteListPath = parser.get("whiteListPath");
|
||||
|
||||
log.info("numPartitions: '{}'", numPartitions);
|
||||
log.info("graphBasePath: '{}'", graphBasePath);
|
||||
log.info("isLookUpUrl: '{}'", isLookUpUrl);
|
||||
log.info("actionSetId: '{}'", actionSetId);
|
||||
log.info("workingPath: '{}'", workingPath);
|
||||
log.info("whiteListPath: '{}'", whiteListPath);
|
||||
log.info("numPartitions: '{}'", numPartitions);
|
||||
log.info("graphBasePath: '{}'", graphBasePath);
|
||||
log.info("isLookUpUrl: '{}'", isLookUpUrl);
|
||||
log.info("actionSetId: '{}'", actionSetId);
|
||||
log.info("workingPath: '{}'", workingPath);
|
||||
log.info("whiteListPath: '{}'", whiteListPath);
|
||||
|
||||
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
//file format: source####target
|
||||
Dataset<Tuple2<String, String>> whiteListRels = spark.createDataset(sc
|
||||
.textFile(whiteListPath)
|
||||
//check if the line is in the correct format: id1####id2
|
||||
.filter(s -> s.contains(WHITELIST_SEPARATOR) && s.split(WHITELIST_SEPARATOR).length == 2)
|
||||
.map(s -> new Tuple2<>(s.split(WHITELIST_SEPARATOR)[0], s.split(WHITELIST_SEPARATOR)[1]))
|
||||
.rdd(),
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
// file format: source####target
|
||||
Dataset<Tuple2<String, String>> whiteListRels = spark
|
||||
.createDataset(
|
||||
sc
|
||||
.textFile(whiteListPath)
|
||||
// check if the line is in the correct format: id1####id2
|
||||
.filter(s -> s.contains(WHITELIST_SEPARATOR) && s.split(WHITELIST_SEPARATOR).length == 2)
|
||||
.map(s -> new Tuple2<>(s.split(WHITELIST_SEPARATOR)[0], s.split(WHITELIST_SEPARATOR)[1]))
|
||||
.rdd(),
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
|
||||
// for each dedup configuration
|
||||
for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
|
||||
// for each dedup configuration
|
||||
for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
|
||||
|
||||
final String entity = dedupConf.getWf().getEntityType();
|
||||
final String subEntity = dedupConf.getWf().getSubEntityValue();
|
||||
log.info("Adding whitelist simrels for: '{}'", subEntity);
|
||||
final String entity = dedupConf.getWf().getEntityType();
|
||||
final String subEntity = dedupConf.getWf().getSubEntityValue();
|
||||
log.info("Adding whitelist simrels for: '{}'", subEntity);
|
||||
|
||||
final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity);
|
||||
final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity);
|
||||
|
||||
Dataset<Tuple2<String, String>> entities = spark.createDataset(sc
|
||||
.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
|
||||
.repartition(numPartitions)
|
||||
.mapToPair(
|
||||
(PairFunction<String, String, String>) s -> {
|
||||
MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
|
||||
return new Tuple2<>(d.getIdentifier(), "present");
|
||||
})
|
||||
.rdd(),
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
Dataset<Tuple2<String, String>> entities = spark
|
||||
.createDataset(
|
||||
sc
|
||||
.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
|
||||
.repartition(numPartitions)
|
||||
.mapToPair(
|
||||
(PairFunction<String, String, String>) s -> {
|
||||
MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
|
||||
return new Tuple2<>(d.getIdentifier(), "present");
|
||||
})
|
||||
.rdd(),
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
|
||||
Dataset<Tuple2<String, String>> whiteListRels1 = whiteListRels
|
||||
.joinWith(entities, whiteListRels.col("_1").equalTo(entities.col("_1")), "inner")
|
||||
.map((MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, String>>, Tuple2<String, String>>) Tuple2::_1, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
Dataset<Tuple2<String, String>> whiteListRels1 = whiteListRels
|
||||
.joinWith(entities, whiteListRels.col("_1").equalTo(entities.col("_1")), "inner")
|
||||
.map(
|
||||
(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, String>>, Tuple2<String, String>>) Tuple2::_1,
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
|
||||
Dataset<Tuple2<String, String>> whiteListRels2 = whiteListRels1
|
||||
.joinWith(entities, whiteListRels1.col("_2").equalTo(entities.col("_1")), "inner")
|
||||
.map((MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, String>>, Tuple2<String, String>>) Tuple2::_1, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
Dataset<Tuple2<String, String>> whiteListRels2 = whiteListRels1
|
||||
.joinWith(entities, whiteListRels1.col("_2").equalTo(entities.col("_1")), "inner")
|
||||
.map(
|
||||
(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, String>>, Tuple2<String, String>>) Tuple2::_1,
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
|
||||
Dataset<Relation> whiteListSimRels = whiteListRels2
|
||||
.map((MapFunction<Tuple2<String, String>, Relation>)
|
||||
r -> createSimRel(r._1(), r._2(), entity),
|
||||
Encoders.bean(Relation.class)
|
||||
);
|
||||
Dataset<Relation> whiteListSimRels = whiteListRels2
|
||||
.map(
|
||||
(MapFunction<Tuple2<String, String>, Relation>) r -> createSimRel(r._1(), r._2(), entity),
|
||||
Encoders.bean(Relation.class));
|
||||
|
||||
saveParquet(whiteListSimRels, outputPath, SaveMode.Append);
|
||||
}
|
||||
}
|
||||
saveParquet(whiteListSimRels, outputPath, SaveMode.Append);
|
||||
}
|
||||
}
|
||||
|
||||
private Relation createSimRel(String source, String target, String entity) {
|
||||
final Relation r = new Relation();
|
||||
r.setSource(source);
|
||||
r.setTarget(target);
|
||||
r.setSubRelType("dedupSimilarity");
|
||||
r.setRelClass("isSimilarTo");
|
||||
r.setDataInfo(new DataInfo());
|
||||
private Relation createSimRel(String source, String target, String entity) {
|
||||
final Relation r = new Relation();
|
||||
r.setSource(source);
|
||||
r.setTarget(target);
|
||||
r.setSubRelType("dedupSimilarity");
|
||||
r.setRelClass("isSimilarTo");
|
||||
r.setDataInfo(new DataInfo());
|
||||
|
||||
switch (entity) {
|
||||
case "result":
|
||||
r.setRelType("resultResult");
|
||||
break;
|
||||
case "organization":
|
||||
r.setRelType("organizationOrganization");
|
||||
break;
|
||||
default:
|
||||
throw new IllegalArgumentException("unmanaged entity type: " + entity);
|
||||
}
|
||||
return r;
|
||||
}
|
||||
switch (entity) {
|
||||
case "result":
|
||||
r.setRelType("resultResult");
|
||||
break;
|
||||
case "organization":
|
||||
r.setRelType("organizationOrganization");
|
||||
break;
|
||||
default:
|
||||
throw new IllegalArgumentException("unmanaged entity type: " + entity);
|
||||
}
|
||||
return r;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,117 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.dedup;
|
||||
|
||||
import java.util.concurrent.TimeUnit;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
import org.apache.http.impl.client.CloseableHttpClient;
|
||||
import org.apache.http.impl.client.HttpClients;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
|
||||
public class UpdateOpenorgsJob {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(UpdateOpenorgsJob.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateSimRels.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateOpenorgsJob_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
final String apiUrl = parser.get("apiUrl");
|
||||
final int delay = Integer.parseInt(parser.get("delay"));
|
||||
|
||||
log.info("apiUrl: '{}'", apiUrl);
|
||||
log.info("delay: '{}'", delay);
|
||||
|
||||
APIResponse res = httpCall(apiUrl);
|
||||
while (res != null && res.getStatus().equals(ImportStatus.RUNNING)) {
|
||||
TimeUnit.MINUTES.sleep(delay);
|
||||
res = httpCall(apiUrl + "/status");
|
||||
}
|
||||
|
||||
if (res == null) {
|
||||
log.error("Openorgs Update FAILED: No response");
|
||||
throw new RuntimeException("Openorgs Update FAILED: No response");
|
||||
}
|
||||
|
||||
if (res.getStatus() == null || !res.getStatus().equals(ImportStatus.SUCCESS)) {
|
||||
log.error("Openorgs Update FAILED: '{}' - '{}'", res.getStatus(), res.getMessage());
|
||||
throw new RuntimeException(res.getMessage());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private static APIResponse httpCall(final String url) throws Exception {
|
||||
final HttpGet req = new HttpGet(url);
|
||||
|
||||
try (final CloseableHttpClient client = HttpClients.createDefault()) {
|
||||
try (final CloseableHttpResponse response = client.execute(req)) {
|
||||
final String s = IOUtils.toString(response.getEntity().getContent());
|
||||
return (new ObjectMapper()).readValue(s, APIResponse.class);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
class APIResponse {
|
||||
private String id;
|
||||
private Long dateStart;
|
||||
private Long dateEnd;
|
||||
private ImportStatus status;
|
||||
private String message;
|
||||
|
||||
public String getId() {
|
||||
return id;
|
||||
}
|
||||
|
||||
public void setId(String id) {
|
||||
this.id = id;
|
||||
}
|
||||
|
||||
public Long getDateStart() {
|
||||
return dateStart;
|
||||
}
|
||||
|
||||
public void setDateStart(Long dateStart) {
|
||||
this.dateStart = dateStart;
|
||||
}
|
||||
|
||||
public Long getDateEnd() {
|
||||
return dateEnd;
|
||||
}
|
||||
|
||||
public void setDateEnd(Long dateEnd) {
|
||||
this.dateEnd = dateEnd;
|
||||
}
|
||||
|
||||
public ImportStatus getStatus() {
|
||||
return status;
|
||||
}
|
||||
|
||||
public void setStatus(ImportStatus status) {
|
||||
this.status = status;
|
||||
}
|
||||
|
||||
public String getMessage() {
|
||||
return message;
|
||||
}
|
||||
|
||||
public void setMessage(String message) {
|
||||
this.message = message;
|
||||
}
|
||||
}
|
||||
|
||||
enum ImportStatus {
|
||||
SUCCESS, FAILED, RUNNING, NOT_LAUNCHED, NOT_YET_STARTED
|
||||
}
|
||||
|
|
@ -28,6 +28,11 @@
|
|||
<name>dbPwd</name>
|
||||
<description>password to access the OpenOrgs database</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>dbConnections</name>
|
||||
<value>10</value>
|
||||
<description>number of connections to the postgres db</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>workingPath</name>
|
||||
<description>path for the working directory</description>
|
||||
|
|
@ -223,7 +228,7 @@
|
|||
<arg>--dbTable</arg><arg>${dbTable}</arg>
|
||||
<arg>--dbUser</arg><arg>${dbUser}</arg>
|
||||
<arg>--dbPwd</arg><arg>${dbPwd}</arg>
|
||||
<arg>--numConnections</arg><arg>20</arg>
|
||||
<arg>--numConnections</arg><arg>${dbConnections}</arg>
|
||||
</spark>
|
||||
<ok to="PrepareNewOrgs"/>
|
||||
<error to="Kill"/>
|
||||
|
|
@ -254,19 +259,24 @@
|
|||
<arg>--dbTable</arg><arg>${dbTable}</arg>
|
||||
<arg>--dbUser</arg><arg>${dbUser}</arg>
|
||||
<arg>--dbPwd</arg><arg>${dbPwd}</arg>
|
||||
<arg>--numConnections</arg><arg>20</arg>
|
||||
<arg>--numConnections</arg><arg>${dbConnections}</arg>
|
||||
</spark>
|
||||
<ok to="update_openorgs"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="update_openorgs">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>/usr/bin/curl</exec>
|
||||
<argument>${apiUrl}</argument>
|
||||
</shell>
|
||||
<java>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
</configuration>
|
||||
<main-class>eu.dnetlib.dhp.oa.dedup.UpdateOpenorgsJob</main-class>
|
||||
<arg>--apiUrl</arg><arg>${apiUrl}</arg>
|
||||
<arg>--delay</arg><arg>5</arg>
|
||||
</java>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,14 @@
|
|||
[
|
||||
{
|
||||
"paramName": "api",
|
||||
"paramLongName": "apiUrl",
|
||||
"paramDescription": "the url of the API",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "d",
|
||||
"paramLongName": "delay",
|
||||
"paramDescription": "delay for the HTTP call in minutes",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -208,7 +208,7 @@ object SparkGenerateDoiBoost {
|
|||
(r.getTarget,r)
|
||||
else
|
||||
("resolved", r)
|
||||
})
|
||||
})(Encoders.tuple(Encoders.STRING, mapEncoderRel))
|
||||
|
||||
val openaireOrganization:Dataset[(String,String)] = spark.read.text(openaireOrganizationPath).as[String].flatMap(s => extractIdGRID(s)).groupByKey(_._2).reduceGroups((x,y) => if (x != null) x else y ).map(_._2)
|
||||
|
||||
|
|
@ -222,7 +222,7 @@ object SparkGenerateDoiBoost {
|
|||
else
|
||||
currentRels.setTarget(currentOrgs._1)
|
||||
currentRels
|
||||
}.write.save(s"$workingDirPath/doiBoostPublicationAffiliation")
|
||||
}.filter(r=> !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved")).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation")
|
||||
|
||||
magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).map( item => {
|
||||
val affiliation = item._2
|
||||
|
|
|
|||
|
|
@ -48,7 +48,7 @@
|
|||
<!-- MAG Parameters -->
|
||||
<property>
|
||||
<name>inputPathMAG</name>
|
||||
<description>the MAG working path</description>
|
||||
<description>the MAG input path</description>
|
||||
</property>
|
||||
|
||||
|
||||
|
|
@ -138,7 +138,7 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${inputPathMAG}/dataset</arg>
|
||||
<arg>--workingPath</arg><arg>${inputPathMAG}/process_p</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}/MAG</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
|
|
|
|||
|
|
@ -69,7 +69,7 @@ public class PropagationConstant {
|
|||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_COUNTRY_INSTREPO_CLASS_ID,
|
||||
PROPAGATION_COUNTRY_INSTREPO_CLASS_NAME,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS));
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS));
|
||||
return nc;
|
||||
}
|
||||
|
||||
|
|
@ -84,7 +84,8 @@ public class PropagationConstant {
|
|||
return di;
|
||||
}
|
||||
|
||||
public static Qualifier getQualifier(String inference_class_id, String inference_class_name, String qualifierSchema) {
|
||||
public static Qualifier getQualifier(String inference_class_id, String inference_class_name,
|
||||
String qualifierSchema) {
|
||||
Qualifier pa = new Qualifier();
|
||||
pa.setClassid(inference_class_id);
|
||||
pa.setClassname(inference_class_name);
|
||||
|
|
@ -108,7 +109,11 @@ public class PropagationConstant {
|
|||
r.setRelClass(rel_class);
|
||||
r.setRelType(rel_type);
|
||||
r.setSubRelType(subrel_type);
|
||||
r.setDataInfo(getDataInfo(inference_provenance, inference_class_id, inference_class_name, ModelConstants.DNET_PROVENANCE_ACTIONS));
|
||||
r
|
||||
.setDataInfo(
|
||||
getDataInfo(
|
||||
inference_provenance, inference_class_id, inference_class_name,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS));
|
||||
return r;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -173,14 +173,17 @@ public class SparkOrcidToResultFromSemRelJob {
|
|||
if (toaddpid) {
|
||||
StructuredProperty p = new StructuredProperty();
|
||||
p.setValue(autoritative_author.getOrcid());
|
||||
p.setQualifier(getQualifier(ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, ModelConstants.DNET_PID_TYPES));
|
||||
p
|
||||
.setQualifier(
|
||||
getQualifier(
|
||||
ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, ModelConstants.DNET_PID_TYPES));
|
||||
p
|
||||
.setDataInfo(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID,
|
||||
PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS));
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS));
|
||||
|
||||
Optional<List<StructuredProperty>> authorPid = Optional.ofNullable(author.getPid());
|
||||
if (authorPid.isPresent()) {
|
||||
|
|
|
|||
|
|
@ -10,7 +10,6 @@ import java.util.List;
|
|||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
|
|
@ -22,6 +21,7 @@ import org.slf4j.Logger;
|
|||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Context;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import scala.Tuple2;
|
||||
|
|
@ -130,7 +130,7 @@ public class SparkResultToCommunityFromOrganizationJob {
|
|||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS)));
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS)));
|
||||
propagatedContexts.add(newContext);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
|||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
|
|
@ -20,6 +19,7 @@ import org.slf4j.LoggerFactory;
|
|||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import scala.Tuple2;
|
||||
|
||||
|
|
@ -126,7 +126,7 @@ public class SparkResultToCommunityThroughSemRelJob {
|
|||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
|
||||
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS)));
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS)));
|
||||
return newContext;
|
||||
}
|
||||
return null;
|
||||
|
|
|
|||
|
|
@ -1,93 +0,0 @@
|
|||
package eu.dnetlib.dhp.sx.graph.ebi
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||
import eu.dnetlib.dhp.schema.oaf.Result
|
||||
import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql.expressions.Aggregator
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.io.Source
|
||||
import scala.xml.pull.XMLEventReader
|
||||
|
||||
object SparkCreateBaselineDataFrame {
|
||||
|
||||
|
||||
val pmArticleAggregator: Aggregator[(String, PMArticle), PMArticle, PMArticle] = new Aggregator[(String, PMArticle), PMArticle, PMArticle] with Serializable {
|
||||
override def zero: PMArticle = new PMArticle
|
||||
|
||||
override def reduce(b: PMArticle, a: (String, PMArticle)): PMArticle = {
|
||||
if (b != null && b.getPmid!= null) b else a._2
|
||||
}
|
||||
|
||||
override def merge(b1: PMArticle, b2: PMArticle): PMArticle = {
|
||||
if (b1 != null && b1.getPmid!= null) b1 else b2
|
||||
|
||||
}
|
||||
|
||||
override def finish(reduction: PMArticle): PMArticle = reduction
|
||||
|
||||
override def bufferEncoder: Encoder[PMArticle] = Encoders.kryo[PMArticle]
|
||||
|
||||
override def outputEncoder: Encoder[PMArticle] = Encoders.kryo[PMArticle]
|
||||
}
|
||||
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
val conf: SparkConf = new SparkConf()
|
||||
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json")))
|
||||
parser.parseArgument(args)
|
||||
val isLookupUrl: String = parser.get("isLookupUrl")
|
||||
log.info("isLookupUrl: {}", isLookupUrl)
|
||||
val workingPath = parser.get("workingPath")
|
||||
log.info("workingPath: {}", workingPath)
|
||||
|
||||
val targetPath = parser.get("targetPath")
|
||||
log.info("targetPath: {}", targetPath)
|
||||
|
||||
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
|
||||
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
|
||||
val spark: SparkSession =
|
||||
SparkSession
|
||||
.builder()
|
||||
.config(conf)
|
||||
.appName(SparkEBILinksToOaf.getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
import spark.implicits._
|
||||
|
||||
|
||||
val sc = spark.sparkContext
|
||||
|
||||
|
||||
|
||||
implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
|
||||
implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
|
||||
implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor])
|
||||
implicit val resultEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||
|
||||
val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline",2000)
|
||||
val ds:Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i =>{
|
||||
val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
|
||||
new PMParser(xml)
|
||||
|
||||
} ))
|
||||
|
||||
ds.map(p => (p.getPmid,p))(Encoders.tuple(Encoders.STRING, PMEncoder)).groupByKey(_._1)
|
||||
.agg(pmArticleAggregator.toColumn)
|
||||
.map(p => p._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_dataset")
|
||||
|
||||
val exported_dataset = spark.read.load(s"$workingPath/baseline_dataset").as[PMArticle]
|
||||
exported_dataset
|
||||
.map(a => PubMedToOaf.convert(a, vocabularies)).as[Result]
|
||||
.filter(p => p!= null)
|
||||
.write.mode(SaveMode.Overwrite).save(targetPath)
|
||||
|
||||
//s"$workingPath/oaf/baseline_oaf"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,7 +1,6 @@
|
|||
package eu.dnetlib.dhp.sx.graph.pangaea
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.sx.graph.ebi.SparkEBILinksToOaf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.{SparkConf, SparkContext}
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
|
|
|
|||
|
|
@ -1,6 +0,0 @@
|
|||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"i", "paramLongName":"isLookupUrl","paramDescription": "isLookupUrl", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workingPath","paramDescription": "the path of the sequencial file to read", "paramRequired": true},
|
||||
{"paramName":"t", "paramLongName":"targetPath","paramDescription": "the oaf path ", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"s", "paramLongName":"sourcePath","paramDescription": "the source Path", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workingPath","paramDescription": "the working path ", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -25,7 +25,6 @@
|
|||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
|
||||
<action name="GenerateBaselineDataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
|
|
@ -43,6 +42,7 @@
|
|||
</spark-opts>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
|||
|
|
@ -1,59 +1,67 @@
|
|||
<workflow-app name="Create EBI Dataset" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sourcePath</name>
|
||||
<description>the Working Path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>workingPath</name>
|
||||
<description>the Working Path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
</parameters>
|
||||
<workflow-app name="Create EBI Dataset" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sourcePath</name>
|
||||
<description>the Working Path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>workingPath</name>
|
||||
<description>the Working Path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="DownloadEBILinks"/>
|
||||
<start to="DownloadEBILinks"/>
|
||||
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
|
||||
<action name="DownloadEBILinks">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Incremental Download EBI Links</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--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}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
<action name="DownloadEBILinks">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Incremental Download EBI Links</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${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}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
</spark>
|
||||
<ok to="OverrideFolders"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<action name="OverrideFolders">
|
||||
<fs>
|
||||
<delete path="${sourcePath}/ebi_links_dataset_old"/>
|
||||
<move source="${sourcePath}/ebi_links_dataset" target="${sourcePath}/ebi_links_dataset_old"/>
|
||||
<move source="${workingPath}/links_final" target="${sourcePath}/ebi_links_dataset"/>
|
||||
</fs>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -84,7 +84,28 @@ public class IndexRecordTransformerTest {
|
|||
|
||||
@Test
|
||||
public void testForEOSCFutureTraining() throws IOException, TransformerException {
|
||||
final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/training-notebooks-seadatanet.xml"));
|
||||
final String record = IOUtils
|
||||
.toString(getClass().getResourceAsStream("eosc-future/training-notebooks-seadatanet.xml"));
|
||||
testRecordTransformation(record);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testForEOSCFutureAirQualityCopernicus() throws IOException, TransformerException {
|
||||
final String record = IOUtils
|
||||
.toString(getClass().getResourceAsStream("eosc-future/air-quality-copernicus.xml"));
|
||||
testRecordTransformation(record);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testForEOSCFutureB2SharePlotSw() throws IOException, TransformerException {
|
||||
final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/b2share-plot-sw.xml"));
|
||||
testRecordTransformation(record);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testForEOSCFutureB2SharePlotRelatedORP() throws IOException, TransformerException {
|
||||
final String record = IOUtils
|
||||
.toString(getClass().getResourceAsStream("eosc-future/b2share-plot-related-orp.xml"));
|
||||
testRecordTransformation(record);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,114 @@
|
|||
<record>
|
||||
<result xmlns:dri="http://www.driver-repository.eu/namespace/dri"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<header>
|
||||
<dri:objIdentifier>r37b0ad08687::a8df7db30ae0e4e0b875a098df7b652f</dri:objIdentifier>
|
||||
<dri:dateOfCollection>2021-10-07T01:56:56Z</dri:dateOfCollection>
|
||||
<dri:status>under curation</dri:status>
|
||||
<counters/>
|
||||
</header>
|
||||
<metadata>
|
||||
<oaf:entity xmlns:oaf="http://namespace.openaire.eu/oaf"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://namespace.openaire.eu/oaf http://namespace.openaire.eu/oaf http://www.openaire.eu/schema/0.2/oaf-0.2.xsd">
|
||||
|
||||
<oaf:result>
|
||||
<title classid="main title" classname="main title" schemeid="dnet:dataCite_title"
|
||||
schemename="dnet:dataCite_title">Using CAMS European air quality analysis from Copernicus
|
||||
Atmosphere Monitoring with RELIANCE services
|
||||
</title>
|
||||
<creator rank="1" name="Simone" surname="Mantovani" orcid_pending="0000-0003-3979-3645">Simone Mantovani</creator>
|
||||
<dateofacceptance>2021-10-07</dateofacceptance>
|
||||
<resulttype classid="software" classname="software" schemeid="dnet:result_typologies"
|
||||
schemename="dnet:result_typologies"/>
|
||||
<language classid="" classname="" schemeid="dnet:languages" schemename="dnet:languages"/>
|
||||
<description>
|
||||
This notebook shows how to discover and access the Copernicus Atmosphere Monitoring products available in the RELIANCE datacube resources.
|
||||
The process is structured in 6 steps, including example of data analysis and visualization with the Python libraries installed in the Jupyter environment
|
||||
</description>
|
||||
<country classid="" classname="" schemeid="" schemename=""/>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">EOSC Jupyter Notebook
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">RELIANCE
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">Copernicus
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">Air quality
|
||||
</subject>
|
||||
|
||||
<relevantdate classid="" classname="" schemeid="" schemename=""/>
|
||||
<publisher>Zenodo</publisher>
|
||||
<embargoenddate/>
|
||||
<journal issn="" eissn="" lissn="" ep="" iss="" sp="" vol=""/>
|
||||
<source/>
|
||||
<fulltext/>
|
||||
<format/>
|
||||
<storagedate/>
|
||||
<resourcetype classid="" classname="" schemeid="" schemename=""/>
|
||||
<device/>
|
||||
<size/>
|
||||
<version/>
|
||||
<lastmetadataupdate/>
|
||||
<metadataversionnumber/>
|
||||
<documentationUrl/>
|
||||
<codeRepositoryUrl/>
|
||||
<programmingLanguage classid="" classname="" schemeid="" schemename=""/>
|
||||
<contactperson/>
|
||||
<contactgroup/>
|
||||
<tool/>
|
||||
<originalId>oai:zenodo.org:5554786</originalId>
|
||||
<collectedfrom name="Zenodo" id="re3data_____::7b0ad08687b2c960d5aeef06f811d5e6"/>
|
||||
<pid classid="oai" classname="Open Archives Initiative" schemeid="dnet:pid_types"
|
||||
schemename="dnet:pid_types">oai:zenodo.org:5554786
|
||||
</pid>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types"
|
||||
schemename="dnet:pid_types">10.5281/zenodo.5554786
|
||||
</pid>
|
||||
<bestaccessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes"
|
||||
schemename="dnet:access_modes"/>
|
||||
<datainfo>
|
||||
<inferred>false</inferred>
|
||||
<deletedbyinference>false</deletedbyinference>
|
||||
<trust>0.9</trust>
|
||||
<inferenceprovenance/>
|
||||
<provenanceaction classid="user:insert" classname="user:insert"
|
||||
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
|
||||
</datainfo>
|
||||
<rels>
|
||||
<rel inferred="false" trust="0.9" inferenceprovenance="" provenanceaction="user:claim">
|
||||
<to class="isProducedBy" scheme="dnet:result_project_relations" type="project">
|
||||
corda__h2020::8771f523c34e38902d4921037d545ef8
|
||||
</to>
|
||||
<title>REsearch LIfecycle mAnagemeNt for Earth Science Communities and CopErnicus users in EOSC</title>
|
||||
<code>101017501</code>
|
||||
<acronym>RELIANCE</acronym>
|
||||
<funding>
|
||||
<funder id="ec__________::EC" shortname="EC" name="European Commission" jurisdiction="EU" />
|
||||
<funding_level_0 name="H2020">ec__________::EC::H2020</funding_level_0>
|
||||
<funding_level_1 name="RIA">ec__________::EC::H2020::RIA</funding_level_1>
|
||||
</funding>
|
||||
</rel>
|
||||
</rels>
|
||||
<children>
|
||||
<instance id="r37b0ad08687::a8df7db30ae0e4e0b875a098df7b652f">
|
||||
<instancetype classid="0029" classname="Software" schemeid="dnet:publication_resource"
|
||||
schemename="dnet:publication_resource"/>
|
||||
<collectedfrom name="Zenodo" id="re3data_____::7b0ad08687b2c960d5aeef06f811d5e6"/>
|
||||
<hostedby name="Zenodo" id="re3data_____::7b0ad08687b2c960d5aeef06f811d5e6"/>
|
||||
<accessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes"
|
||||
schemename="dnet:access_modes"/>
|
||||
<dateofacceptance/>
|
||||
<webresource>
|
||||
<url>https://zenodo.org/record/5554786</url>
|
||||
</webresource>
|
||||
</instance>
|
||||
</children>
|
||||
</oaf:result>
|
||||
</oaf:entity>
|
||||
</metadata>
|
||||
</result>
|
||||
</record>
|
||||
|
|
@ -0,0 +1,288 @@
|
|||
<record>
|
||||
<result xmlns:dri="http://www.driver-repository.eu/namespace/dri"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<header>
|
||||
<dri:objIdentifier>doi_dedup___::44fd8a9b5b79adb0783ac245b21e3127</dri:objIdentifier>
|
||||
<dri:dateOfCollection>2019-09-19T07:43:31+0000</dri:dateOfCollection>
|
||||
<dri:dateOfTransformation>2019-09-19T07:43:31+0000</dri:dateOfTransformation>
|
||||
</header>
|
||||
<metadata>
|
||||
<oaf:entity xmlns:oaf="http://namespace.openaire.eu/oaf"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://namespace.openaire.eu/oaf http://namespace.openaire.eu/oaf http://www.openaire.eu/schema/0.2/oaf-0.2.xsd">
|
||||
|
||||
<oaf:result>
|
||||
<collectedfrom name="Datacite" id="openaire____::9e3be59865b2c1c335d32dae2fe7b254"/>
|
||||
<collectedfrom name="B2FIND" id="re3data_____::730f562f9efe8a3b3742d2da510d4335"/>
|
||||
<originalId>10.23728/b2share.ebcd2972c5fb44199f8b3fdf9f6413c6</originalId>
|
||||
<originalId>10.23728/b2share.a69a7b2dcc22449e8734552dde4d3906</originalId>
|
||||
<originalId>6a93c069-a167-44cb-bfe8-74c275637347</originalId>
|
||||
<originalId>50|r3730f562f9e::9b434fedc00d568b8e00611a7fa19f41</originalId>
|
||||
<originalId>10.23728/b2share.7c8655b6f25348358b4e6fece7ab6016</originalId>
|
||||
<originalId>ada23067-496a-494f-bd82-6ffe3cf4f0fb</originalId>
|
||||
<originalId>50|r3730f562f9e::b9cd774e8126b6902d56f9a4aa03e1dc</originalId>
|
||||
<originalId>f3bd1041-422c-439d-8e68-c1d0711d130d</originalId>
|
||||
<originalId>50|r3730f562f9e::b847821a0ca5365b0d971dd89dea6bf1</originalId>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types"
|
||||
schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:actionset"
|
||||
trust="0.9">10.23728/b2share.ebcd2972c5fb44199f8b3fdf9f6413c6
|
||||
</pid>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types"
|
||||
schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:actionset"
|
||||
trust="0.9">10.23728/b2share.a69a7b2dcc22449e8734552dde4d3906
|
||||
</pid>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types"
|
||||
schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:actionset"
|
||||
trust="0.9">10.23728/b2share.7c8655b6f25348358b4e6fece7ab6016
|
||||
</pid>
|
||||
<title classid="main title" classname="main title" schemeid="dnet:dataCite_title"
|
||||
schemename="dnet:dataCite_title">HCG16 L-band VLA C+D array final data
|
||||
</title>
|
||||
<bestaccessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes"
|
||||
schemename="dnet:access_modes"/>
|
||||
<creator rank="1" name="Michael G." surname="Jones">Jones, Michael G.</creator>
|
||||
<dateofacceptance>2019-01-01</dateofacceptance>
|
||||
<description>These are the reduced final data associated with the paper Jones et al. 2019 submitted
|
||||
to Astronomy & Astrophysics. They are used by a mybinder (https://gke.mybinder.org/)
|
||||
executable environment to generate the final plots of that paper. The link for this environment
|
||||
is https://mybinder.org/v2/gh/AMIGA-IAA/hcg-16/master. The raw VLA D and C array data of HCG 16
|
||||
were collected by the Very Large Array (http://www.vla.nrao.edu/) in 1989 and 1999, under PI
|
||||
projects of Barbara Williams. The project numbers are AW234 and AW500 respectively. The file
|
||||
also includes a grz colour image and r-band image from DECaLS DR8
|
||||
(http://legacysurvey.org/decamls/), a GBT HI spectrum published in Borthakur et al. 2010 (ApJ
|
||||
710, 385), an HI data cube from HIPASS (https://www.atnf.csiro.au/research/multibeam/release/),
|
||||
and a source mask (and associated parameters file) for the HIPASS cube generated using SoFiA
|
||||
(https://github.com/SoFiA-Admin/SoFiA-2).
|
||||
</description>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">3.5.2.1.1 → Observational astronomy →
|
||||
Radio astronomy
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">HI
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">VLA
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">HCG16
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies" inferred="false"
|
||||
provenanceaction="sysimport:crosswalk:repository" trust="0.9">Various
|
||||
</subject>
|
||||
<language classid="und" classname="Undetermined" schemeid="dnet:languages"
|
||||
schemename="dnet:languages"/>
|
||||
<relevantdate classid="issued" classname="issued" schemeid="dnet:dataCite_date"
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||||
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trust="0.9">10.23728/b2share.7c8655b6f25348358b4e6fece7ab6016
|
||||
</pid>
|
||||
<collectedfrom name="Datacite" id="openaire____::9e3be59865b2c1c335d32dae2fe7b254"/>
|
||||
<collectedfrom name="B2FIND" id="re3data_____::730f562f9efe8a3b3742d2da510d4335"/>
|
||||
</rel>
|
||||
</rels>
|
||||
<children>
|
||||
<instance id="userclaim___::ee29372a239b79db3ac4c5debe44d6e6">
|
||||
<instancetype classid="0029" classname="Software" schemeid="dnet:publication_resource"
|
||||
schemename="dnet:publication_resource"/>
|
||||
<collectedfrom name="B2FIND" id="re3data_____::730f562f9efe8a3b3742d2da510d4335"/>
|
||||
<hostedby name="B2SHARE" id="re3data_____::ad3609c351bd520edf6f10f5e0d9b877"/>
|
||||
<accessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes"
|
||||
schemename="dnet:access_modes"/>
|
||||
<dateofacceptance>2021-09-30</dateofacceptance>
|
||||
<webresource>
|
||||
<url>http://dx.doi.org/10.23728/b2share.adf6e2e942b04561a8640c449b48c14a</url>
|
||||
</webresource>
|
||||
</instance>
|
||||
</children>
|
||||
</oaf:result>
|
||||
</oaf:entity>
|
||||
</metadata>
|
||||
</result>
|
||||
</record>
|
||||
|
|
@ -1,26 +1,25 @@
|
|||
<record>
|
||||
<result xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<header>
|
||||
<dri:objIdentifier>r37b0ad08687::dec0d8520e726f2adda9a51280ac7299</dri:objIdentifier>
|
||||
<dri:dateOfCollection>2021-09-22T08:53:16Z</dri:dateOfCollection>
|
||||
<dri:status>under curation</dri:status>
|
||||
<counters />
|
||||
<dri:objIdentifier>doi_dedup___::ab57f086011a9ae23d1165211dc6e04b</dri:objIdentifier>
|
||||
<dri:dateOfCollection>2020-11-03T05:39:50+0000</dri:dateOfCollection>
|
||||
<dri:dateOfTransformation>2020-11-03T05:39:50+0000</dri:dateOfTransformation>
|
||||
</header>
|
||||
<metadata>
|
||||
<oaf:entity xmlns:oaf="http://namespace.openaire.eu/oaf"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://namespace.openaire.eu/oaf http://namespace.openaire.eu/oaf http://www.openaire.eu/schema/0.2/oaf-0.2.xsd">
|
||||
<oaf:result>
|
||||
<title classid="main title" classname="main title" schemeid="dnet:dataCite_title" schemename="dnet:dataCite_title">EGI-Foundation/data-transfer-pilot: Include libraries in environment.yml</title>
|
||||
<creator rank="1" name="" surname="">Giuseppe La Rocca</creator>
|
||||
<creator rank="2" name="" surname="">Enol Fernández</creator>
|
||||
<creator rank="3" name="" surname="">Andrea Manzi</creator>
|
||||
<dateofacceptance />
|
||||
<creator rank="1" name="Giuseppe" surname="La Rocca">Giuseppe La Rocca</creator>
|
||||
<creator rank="2" name="Enol" surname="Fernández">Enol Fernández</creator>
|
||||
<creator rank="3" name="Andrea" surname="Manzi">Andrea Manzi</creator>
|
||||
<dateofacceptance>2020-11-03</dateofacceptance>
|
||||
<resulttype classid="software" classname="software" schemeid="dnet:result_typologies" schemename="dnet:result_typologies" />
|
||||
<language classid="" classname="" schemeid="dnet:languages" schemename="dnet:languages" />
|
||||
<description>This notebook is used to demonstrate how a scientist from one of the PaNOSC RIs can use the resources provided by EGI to perform analysis on the data sets obtained during an expirement.</description>
|
||||
<country classid="" classname="" schemeid="" schemename="" />
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">EOSC Jupyter Notebook</subject>
|
||||
<relevantdate classid="" classname="" schemeid="" schemename="" />
|
||||
<relevantdate classid="issued" classname="issued" schemeid="dnet:dataCite_date" schemename="dnet:dataCite_date">2020-11-03</relevantdate>
|
||||
<publisher>Zenodo</publisher>
|
||||
<embargoenddate />
|
||||
<journal issn="" eissn="" lissn="" ep="" iss="" sp="" vol="" />
|
||||
|
|
@ -43,8 +42,8 @@
|
|||
<originalId>oai:zenodo.org:4218562</originalId>
|
||||
<collectedfrom name="Zenodo" id="re3data_____::7b0ad08687b2c960d5aeef06f811d5e6" />
|
||||
<pid classid="oai" classname="Open Archives Initiative" schemeid="dnet:pid_types" schemename="dnet:pid_types">oai:zenodo.org:4218562</pid>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types" schemename="dnet:pid_types">10.5281/zenodo.4218562</pid>
|
||||
<bestaccessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes" schemename="dnet:access_modes" />
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types" schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:actionset" trust="0.9">10.5281/zenodo.4195418</pid>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types" schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:actionset" trust="0.9">10.5281/zenodo.4218562</pid><bestaccessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes" schemename="dnet:access_modes" />
|
||||
<datainfo>
|
||||
<inferred>false</inferred>
|
||||
<deletedbyinference>false</deletedbyinference>
|
||||
|
|
@ -59,7 +58,7 @@
|
|||
<collectedfrom name="Zenodo" id="re3data_____::7b0ad08687b2c960d5aeef06f811d5e6" />
|
||||
<hostedby name="Zenodo" id="re3data_____::7b0ad08687b2c960d5aeef06f811d5e6" />
|
||||
<accessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes" schemename="dnet:access_modes" />
|
||||
<dateofacceptance />
|
||||
<dateofacceptance>2020-11-03</dateofacceptance>
|
||||
<webresource>
|
||||
<url>https://zenodo.org/record/4218562</url>
|
||||
</webresource>
|
||||
|
|
|
|||
|
|
@ -1,10 +1,8 @@
|
|||
<record>
|
||||
<result xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<header>
|
||||
<dri:objIdentifier>r37b0ad08687::eb430fb7438e1533ba95d6aa50a477eb</dri:objIdentifier>
|
||||
<dri:objIdentifier>doi_dedup___::8539a8de8996e01350f0de8ca4899b7f</dri:objIdentifier>
|
||||
<dri:dateOfCollection>2021-09-22T08:53:13Z</dri:dateOfCollection>
|
||||
<dri:status>under curation</dri:status>
|
||||
<counters />
|
||||
</header>
|
||||
<metadata>
|
||||
<oaf:entity xmlns:oaf="http://namespace.openaire.eu/oaf"
|
||||
|
|
@ -13,10 +11,10 @@
|
|||
<oaf:result>
|
||||
<title classid="main title" classname="main title" schemeid="dnet:dataCite_title" schemename="dnet:dataCite_title">EGI-Foundation/training-notebooks-seadatanet: Version 0.4</title>
|
||||
<creator rank="1" name="" surname="">Enol Fernández</creator>
|
||||
<dateofacceptance />
|
||||
<dateofacceptance>2019-12-04</dateofacceptance>
|
||||
<resulttype classid="software" classname="software" schemeid="dnet:result_typologies" schemename="dnet:result_typologies" />
|
||||
<language classid="" classname="" schemeid="dnet:languages" schemename="dnet:languages" />
|
||||
<description>A sample notebook using SeaDataNet data to plot a map that shows surface temperature of Black Sea, Arctic Sea and Baltic Sea. The data is available at EGI DataHub with PID http://hdl.handle.net/21.T15999/qVk6JWQ (run at EGI Notebooks service for easy access to data).This release updates the PID for the data.</description>
|
||||
<description>A sample notebook using SeaDataNet data to plot a map that shows surface temperature of Black Sea, Arctic Sea and Baltic Sea. The data is available at EGI DataHub with PID http://hdl.handle.net/21.T15999/3Byz9Cw (run at EGI Notebooks service for easy access to data). This release uses the correct path of the data share from the EGI DataHub.</description>
|
||||
<country classid="" classname="" schemeid="" schemename="" />
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">EOSC Jupyter Notebook</subject>
|
||||
<relevantdate classid="" classname="" schemeid="" schemename="" />
|
||||
|
|
@ -43,6 +41,9 @@
|
|||
<collectedfrom name="Zenodo" id="re3data_____::7b0ad08687b2c960d5aeef06f811d5e6" />
|
||||
<pid classid="oai" classname="Open Archives Initiative" schemeid="dnet:pid_types" schemename="dnet:pid_types">oai:zenodo.org:3561323</pid>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types" schemename="dnet:pid_types">10.5281/zenodo.3561323</pid>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types" schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:actionset" trust="0.9">10.5281/zenodo.3443996</pid>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types" schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:actionset" trust="0.9">10.5281/zenodo.3475539</pid>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types" schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:actionset" trust="0.9">10.5281/zenodo.3475785</pid>
|
||||
<bestaccessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes" schemename="dnet:access_modes" />
|
||||
<datainfo>
|
||||
<inferred>false</inferred>
|
||||
|
|
|
|||
|
|
@ -11,9 +11,13 @@ TARGET_DB=$2
|
|||
|
||||
TMP=/tmp/stats-update-`tr -dc A-Za-z0-9 </dev/urandom | head -c 6`
|
||||
|
||||
echo "Downloading context data"
|
||||
echo "Downloading context ids"
|
||||
curl -L ${CONTEXT_API}/contexts/?type=ri,community -H "accept: application/json" | /usr/local/sbin/jq -r '.[] | "\(.id),\(.label)"' > contexts.csv
|
||||
|
||||
echo "Downloading categories data"
|
||||
cat contexts.csv | cut -d , -f1 | xargs -I {} curl -L ${CONTEXT_API}/context/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split(":")[0]),\(.id),\(.label)"' > categories.csv
|
||||
|
||||
echo "Downloading concepts data"
|
||||
cat categories.csv | cut -d , -f2 | sed 's/:/%3A/g'| xargs -I {} curl -L ${CONTEXT_API}/context/category/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split("::")[0])::\(.id|split("::")[1]),\(.id),\(.label)"' > concepts.csv
|
||||
cat contexts.csv | sed 's/^\(.*\),\(.*\)/\1,\1::other,\2/' >> categories.csv
|
||||
cat categories.csv | sed 's/^.*,\(.*\),\(.*\)/\1,\1::other,\2/' >> concepts.csv
|
||||
|
|
|
|||
2
pom.xml
2
pom.xml
|
|
@ -753,7 +753,7 @@
|
|||
<mockito-core.version>3.3.3</mockito-core.version>
|
||||
<mongodb.driver.version>3.4.2</mongodb.driver.version>
|
||||
<vtd.version>[2.12,3.0)</vtd.version>
|
||||
<dhp-schemas.version>[2.7.18]</dhp-schemas.version>
|
||||
<dhp-schemas.version>[2.8.20]</dhp-schemas.version>
|
||||
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
|
||||
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
|
||||
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
|
||||
|
|
|
|||
Loading…
Reference in New Issue