enrichment steps #38
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@ -10,10 +10,11 @@ import org.json4s.jackson.JsonMethods._
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import org.slf4j.Logger
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import scala.collection.JavaConverters._
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case class mappingAffiliation(name:String)
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case class mappingAuthor(given: Option[String], family: String, ORCID: Option[String], affiliation:Option[mappingAffiliation]) {}
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case class mappingAffiliation(name: String)
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case class mappingAuthor(given: Option[String], family: String, ORCID: Option[String], affiliation: Option[mappingAffiliation]) {}
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class Crossref2Oaf {
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case object Crossref2Oaf {
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//STATIC STRING
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val MAG = "MAG"
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@ -28,7 +29,6 @@ class Crossref2Oaf {
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val DNET_LANGUAGES = "dnet:languages"
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val PID_TYPES = "dnet:pid_types"
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val mappingCrossrefType = Map(
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"book-section" -> "publication",
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"book" -> "publication",
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@ -84,7 +84,7 @@ class Crossref2Oaf {
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)
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def mappingResult(result: Result, json: JValue, cobjCategory:String): Result = {
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def mappingResult(result: Result, json: JValue, cobjCategory: String): Result = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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//MAPPING Crossref DOI into PID
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@ -111,7 +111,7 @@ class Crossref2Oaf {
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result.setCollectedfrom(List(createCollectedFrom()).asJava)
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// Publisher ( Name of work's publisher mapped into Result/Publisher)
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val publisher = (json \ "publisher").extract[String]
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val publisher = (json \ "publisher").extractOrElse[String](null)
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result.setPublisher(asField(publisher))
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// TITLE
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@ -144,7 +144,7 @@ class Crossref2Oaf {
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//Mapping AUthor
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val authorList:List[mappingAuthor] = (json \ "author").extract[List[mappingAuthor]]
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val authorList: List[mappingAuthor] = (json \ "author").extractOrElse[List[mappingAuthor]](List())
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result.setAuthor(authorList.map(a => generateAuhtor(a.given.orNull, a.family, a.ORCID.orNull)).asJava)
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@ -152,8 +152,8 @@ class Crossref2Oaf {
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val instance = new Instance()
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val license = for {
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JString(lic) <- json \ "license" \ "URL"
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} yield asField(lic)
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JString(lic) <- json \ "license" \ "URL"
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} yield asField(lic)
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val l = license.filter(d => StringUtils.isNotBlank(d.getValue))
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if (l.nonEmpty)
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instance.setLicense(l.head)
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@ -161,24 +161,22 @@ class Crossref2Oaf {
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instance.setAccessright(createQualifier("Restricted", "dnet:access_modes"))
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result.setInstance(List(instance).asJava)
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instance.setInstancetype(createQualifier(cobjCategory.substring(0,4), cobjCategory.substring(5), "dnet:publication_resource", "dnet:publication_resource"))
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instance.setInstancetype(createQualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), "dnet:publication_resource", "dnet:publication_resource"))
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instance.setCollectedfrom(createCollectedFrom())
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if (StringUtils.isNotBlank(issuedDate)) {
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instance.setDateofacceptance(asField(issuedDate))
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}
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val s: String =(json \ "URL").extract[String]
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val links:List[String] = ((for {JString(url) <-json \ "link" \ "URL"} yield url) ::: List(s)).filter(p =>p != null).distinct
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val s: String = (json \ "URL").extract[String]
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val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null).distinct
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if (links.nonEmpty)
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instance.setUrl(links.asJava)
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result
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}
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def generateAuhtor(given:String, family:String, orcid:String):Author = {
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val a =new Author
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def generateAuhtor(given: String, family: String, orcid: String): Author = {
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val a = new Author
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a.setName(given)
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a.setSurname(family)
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a.setFullname(s"${given} ${family}")
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@ -202,30 +200,28 @@ class Crossref2Oaf {
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if (result == null)
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return result
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val cOBJCategory = mappingCrossrefSubType.getOrElse(objectType, mappingCrossrefSubType.getOrElse(objectSubType, "0038 Other literature type"));
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logger.debug(mappingCrossrefType(objectType))
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logger.debug(cOBJCategory)
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// logger.debug(mappingCrossrefType(objectType))
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// logger.debug(cOBJCategory)
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mappingResult(result, json, cOBJCategory)
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result match {
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case publication: Publication => convertPublication(publication)
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case publication: Publication => convertPublication(publication, json, cOBJCategory)
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case dataset: Dataset => convertDataset(dataset)
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}
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result
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}
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def convertDataset(dataset: Dataset): Unit = {
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//TODO probably we need to add relation and other stuff here
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}
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def convertPublication(publication: Publication, json: JValue, cobjCategory:String): Unit = {
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def convertPublication(publication: Publication, json: JValue, cobjCategory: String): Unit = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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val containerTitles = for {JString(ct) <- json \ "container-title"} yield ct
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@ -243,12 +239,44 @@ class Crossref2Oaf {
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publication.setSource(List(asField(source)).asJava)
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}
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} else {
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val issn =
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// Mapping Journal
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val issnInfos = for {JArray(issn_types) <- json \ "issn-type"
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JObject(issn_type) <- issn_types
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JField("type", JString(tp)) <- issn_type
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JField("value", JString(vl)) <- issn_type
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} yield Tuple2(tp, vl)
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val volume = (json \ "volume").extractOrElse[String] (null)
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if (containerTitles.nonEmpty) {
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val journal = new Journal
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journal.setName(containerTitles.head)
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if (issnInfos.nonEmpty) {
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issnInfos.foreach(tp => {
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tp._1 match {
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case "electronic" => journal.setIssnOnline(tp._2)
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case "print" => journal.setIssnPrinted(tp._2)
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}
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})
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}
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journal.setVol(volume)
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val page = (json \ "page").extractOrElse[String] (null)
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if(page!= null ) {
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val pp = page.split("-")
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journal.setSp(pp.head)
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if (pp.size > 1)
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journal.setEp(pp(1))
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}
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publication.setJournal(journal)
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}
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}
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// Mapping other types of publications
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}
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@ -322,7 +350,7 @@ class Crossref2Oaf {
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}
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def createQualifier(clsName: String,clsValue: String, schName: String, schValue: String): Qualifier = {
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def createQualifier(clsName: String, clsValue: String, schName: String, schValue: String): Qualifier = {
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val q = new Qualifier
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q.setClassid(clsName)
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q.setClassname(clsValue)
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@ -1,6 +1,8 @@
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package eu.dnetlib.doiboost.crossref;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import java.io.ByteArrayOutputStream;
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import java.util.zip.Inflater;
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import org.apache.commons.codec.binary.Base64;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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@ -12,30 +14,29 @@ import org.apache.hadoop.io.Text;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.ByteArrayOutputStream;
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import java.util.zip.Inflater;
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public class CrossrefImporter {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(CrossrefImporter.class.getResourceAsStream("/eu/dnetlib/dhp/doiboost/import_from_es.json")));
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final ArgumentApplicationParser parser =
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new ArgumentApplicationParser(
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IOUtils.toString(
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CrossrefImporter.class.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/import_from_es.json")));
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Logger logger = LoggerFactory.getLogger(CrossrefImporter.class);
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parser.parseArgument(args);
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final String hdfsuri = parser.get("namenode");
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logger.info("HDFS URI"+hdfsuri);
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logger.info("HDFS URI" + hdfsuri);
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Path hdfswritepath = new Path(parser.get("targetPath"));
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logger.info("TargetPath: "+hdfsuri);
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logger.info("TargetPath: " + hdfsuri);
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final Long timestamp = StringUtils.isNotBlank(parser.get("timestamp"))?Long.parseLong(parser.get("timestamp")):-1;
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if(timestamp>0)
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logger.info("Timestamp added "+timestamp);
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final Long timestamp =
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StringUtils.isNotBlank(parser.get("timestamp"))
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? Long.parseLong(parser.get("timestamp"))
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: -1;
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if (timestamp > 0) logger.info("Timestamp added " + timestamp);
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// ====== Init HDFS File System Object
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Configuration conf = new Configuration();
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@ -45,16 +46,21 @@ public class CrossrefImporter {
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conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
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conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
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ESClient client =
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timestamp > 0
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? new ESClient(
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"ip-90-147-167-25.ct1.garrservices.it", "crossref", timestamp)
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: new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref");
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ESClient client = timestamp>0?new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref", timestamp):new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref");
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try (SequenceFile.Writer writer = SequenceFile.createWriter(conf,
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SequenceFile.Writer.file(hdfswritepath), SequenceFile.Writer.keyClass(IntWritable.class),
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SequenceFile.Writer.valueClass(Text.class))) {
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try (SequenceFile.Writer writer =
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SequenceFile.createWriter(
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conf,
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SequenceFile.Writer.file(hdfswritepath),
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SequenceFile.Writer.keyClass(IntWritable.class),
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SequenceFile.Writer.valueClass(Text.class))) {
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int i = 0;
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long start= System.currentTimeMillis();
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long start = System.currentTimeMillis();
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long end = 0;
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final IntWritable key = new IntWritable(i);
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final Text value = new Text();
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@ -65,7 +71,10 @@ public class CrossrefImporter {
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if (i % 1000000 == 0) {
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end = System.currentTimeMillis();
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final float time = (end - start) / 1000.0F;
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logger.info(String.format("Imported %d records last 100000 imported in %f seconds", i, time));
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logger.info(
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String.format(
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"Imported %d records last 100000 imported in %f seconds",
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i, time));
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start = System.currentTimeMillis();
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}
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}
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@ -87,7 +96,7 @@ public class CrossrefImporter {
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decompresser.end();
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return new String(unzippeddata);
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} catch (Throwable e) {
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throw new RuntimeException("Wrong record:" + blob,e);
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throw new RuntimeException("Wrong record:" + blob, e);
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}
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}
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}
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@ -1,6 +1,9 @@
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package eu.dnetlib.doiboost.crossref;
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import com.jayway.jsonpath.JsonPath;
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import java.io.IOException;
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import java.util.Iterator;
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import java.util.List;
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import org.apache.commons.io.IOUtils;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpPost;
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@ -10,18 +13,15 @@ import org.apache.http.impl.client.HttpClients;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.IOException;
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import java.util.Iterator;
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import java.util.List;
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public class ESClient implements Iterator<String> {
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private final static Logger logger = LoggerFactory.getLogger(ESClient.class);
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private static final Logger logger = LoggerFactory.getLogger(ESClient.class);
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final static String blobPath = "$.hits[*].hits[*]._source.blob";
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final static String scrollIdPath = "$._scroll_id";
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final static String JSON_NO_TS ="{\"size\":1000}";
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final static String JSON_WITH_TS ="{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}";
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final static String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}";
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static final String blobPath = "$.hits[*].hits[*]._source.blob";
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static final String scrollIdPath = "$._scroll_id";
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static final String JSON_NO_TS = "{\"size\":1000}";
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static final String JSON_WITH_TS =
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"{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}";
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static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}";
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private final String scrollId;
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@ -29,29 +29,34 @@ public class ESClient implements Iterator<String> {
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private final String esHost;
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public ESClient(final String esHost, final String esIndex) throws IOException {
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this.esHost = esHost;
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final String body =getResponse(String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), JSON_NO_TS);
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scrollId= getJPathString(scrollIdPath, body);
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final String body =
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getResponse(
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String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex),
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JSON_NO_TS);
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scrollId = getJPathString(scrollIdPath, body);
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buffer = getBlobs(body);
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}
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public ESClient(final String esHost, final String esIndex, final long timestamp) throws IOException {
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public ESClient(final String esHost, final String esIndex, final long timestamp)
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throws IOException {
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this.esHost = esHost;
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final String body =getResponse(String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), String.format(JSON_WITH_TS, timestamp));
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scrollId= getJPathString(scrollIdPath, body);
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final String body =
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getResponse(
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String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex),
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String.format(JSON_WITH_TS, timestamp));
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scrollId = getJPathString(scrollIdPath, body);
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buffer = getBlobs(body);
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}
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private String getResponse(final String url,final String json ) {
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private String getResponse(final String url, final String json) {
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CloseableHttpClient client = HttpClients.createDefault();
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try {
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HttpPost httpPost = new HttpPost(url);
|
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if (json!= null) {
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if (json != null) {
|
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StringEntity entity = new StringEntity(json);
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httpPost.setEntity(entity);
|
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httpPost.setHeader("Accept", "application/json");
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|
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@ -61,22 +66,20 @@ public class ESClient implements Iterator<String> {
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|
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return IOUtils.toString(response.getEntity().getContent());
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} catch (Throwable e) {
|
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throw new RuntimeException("Error on executing request ",e);
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throw new RuntimeException("Error on executing request ", e);
|
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} finally {
|
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try {
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client.close();
|
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} catch (IOException e) {
|
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throw new RuntimeException("Unable to close client ",e);
|
||||
throw new RuntimeException("Unable to close client ", e);
|
||||
}
|
||||
}
|
||||
|
||||
}
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private String getJPathString(final String jsonPath, final String json) {
|
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private String getJPathString(final String jsonPath, final String json) {
|
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try {
|
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Object o = JsonPath.read(json, jsonPath);
|
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if (o instanceof String)
|
||||
return (String) o;
|
||||
if (o instanceof String) return (String) o;
|
||||
return null;
|
||||
} catch (Exception e) {
|
||||
return "";
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||||
|
|
@ -84,14 +87,13 @@ public class ESClient implements Iterator<String> {
|
|||
}
|
||||
|
||||
private List<String> getBlobs(final String body) {
|
||||
final List<String > res = JsonPath.read(body, "$.hits.hits[*]._source.blob");
|
||||
final List<String> res = JsonPath.read(body, "$.hits.hits[*]._source.blob");
|
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return res;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean hasNext() {
|
||||
return (buffer!= null && !buffer.isEmpty());
|
||||
|
||||
return (buffer != null && !buffer.isEmpty());
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
@ -100,11 +102,12 @@ public class ESClient implements Iterator<String> {
|
|||
if (buffer.isEmpty()) {
|
||||
|
||||
final String json_param = String.format(JSON_SCROLL, scrollId);
|
||||
final String body =getResponse(String.format("http://%s:9200/_search/scroll", esHost), json_param);
|
||||
final String body =
|
||||
getResponse(String.format("http://%s:9200/_search/scroll", esHost), json_param);
|
||||
try {
|
||||
buffer = getBlobs(body);
|
||||
} catch (Throwable e) {
|
||||
logger.error("Error on get next page: body:"+body);
|
||||
logger.error("Error on get next page: body:" + body);
|
||||
}
|
||||
}
|
||||
return nextItem;
|
||||
|
|
|
|||
|
|
@ -1,22 +1,22 @@
|
|||
package eu.dnetlib.doiboost.crossref
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.io.{IntWritable, Text}
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.SparkSession
|
||||
import org.apache.spark.sql.{Dataset, Encoders, SaveMode, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
|
||||
|
||||
case class Reference(author:String, firstPage:String) {}
|
||||
case class Reference(author: String, firstPage: String) {}
|
||||
|
||||
object SparkMapDumpIntoOAF {
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
||||
|
||||
val logger:Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
|
||||
val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
|
||||
val conf: SparkConf = new SparkConf()
|
||||
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkMapDumpIntoOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json")))
|
||||
parser.parseArgument(args)
|
||||
|
|
@ -26,33 +26,42 @@ object SparkMapDumpIntoOAF {
|
|||
.config(conf)
|
||||
.appName(SparkMapDumpIntoOAF.getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
import spark.implicits._
|
||||
implicit val mapEncoder = Encoders.bean(classOf[Publication])
|
||||
|
||||
val sc = spark.sparkContext
|
||||
val x: String = sc.sequenceFile(parser.get("sourcePath"), classOf[IntWritable], classOf[Text])
|
||||
.map(k => k._2.toString).first()
|
||||
|
||||
val item =CrossrefImporter.decompressBlob(x)
|
||||
val total = sc.sequenceFile(parser.get("sourcePath"), classOf[IntWritable], classOf[Text])
|
||||
.map(k => k._2.toString).map(CrossrefImporter.decompressBlob)
|
||||
.map(k => Crossref2Oaf.convert(k, logger))
|
||||
.filter(k => k != null && k.isInstanceOf[Publication])
|
||||
.map(k => k.asInstanceOf[Publication])
|
||||
|
||||
|
||||
logger.info(item)
|
||||
val ds: Dataset[Publication] = spark.createDataset(total)
|
||||
val targetPath = parser.get("targetPath")
|
||||
ds.write.mode(SaveMode.Overwrite).save(s"${targetPath}/publication")
|
||||
|
||||
// lazy val json: json4s.JValue = parse(item)
|
||||
//
|
||||
//
|
||||
// val references = for {
|
||||
// JArray(references) <- json \\ "reference"
|
||||
// JObject(reference) <- references
|
||||
// JField("first-page", JString(firstPage)) <- reference
|
||||
// JField("author", JString(author)) <- reference
|
||||
// } yield Reference(author, firstPage)
|
||||
//
|
||||
//
|
||||
//
|
||||
//
|
||||
// logger.info((json \ "created" \ "timestamp").extractOrElse("missing"))
|
||||
// logger.info(references.toString())
|
||||
//
|
||||
// logger.info((json \ "type").extractOrElse("missing"))
|
||||
|
||||
logger.info(s"total Item :${total}")
|
||||
|
||||
// lazy val json: json4s.JValue = parse(item)
|
||||
//
|
||||
//
|
||||
// val references = for {
|
||||
// JArray(references) <- json \\ "reference"
|
||||
// JObject(reference) <- references
|
||||
// JField("first-page", JString(firstPage)) <- reference
|
||||
// JField("author", JString(author)) <- reference
|
||||
// } yield Reference(author, firstPage)
|
||||
//
|
||||
//
|
||||
//
|
||||
//
|
||||
// logger.info((json \ "created" \ "timestamp").extractOrElse("missing"))
|
||||
// logger.info(references.toString())
|
||||
//
|
||||
// logger.info((json \ "type").extractOrElse("missing"))
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,20 +1,18 @@
|
|||
package eu.dnetlib.doiboost.orcid.json;
|
||||
|
||||
import com.google.gson.JsonObject;
|
||||
|
||||
import eu.dnetlib.doiboost.orcid.model.AuthorData;
|
||||
|
||||
|
||||
public class JsonWriter {
|
||||
|
||||
public static String create(AuthorData authorData) {
|
||||
JsonObject author = new JsonObject();
|
||||
author.addProperty("oid", authorData.getOid());
|
||||
author.addProperty("name", authorData.getName());
|
||||
author.addProperty("surname", authorData.getSurname());
|
||||
if (authorData.getCreditName()!=null) {
|
||||
author.addProperty("creditname", authorData.getCreditName());
|
||||
}
|
||||
return author.toString();
|
||||
}
|
||||
public static String create(AuthorData authorData) {
|
||||
JsonObject author = new JsonObject();
|
||||
author.addProperty("oid", authorData.getOid());
|
||||
author.addProperty("name", authorData.getName());
|
||||
author.addProperty("surname", authorData.getSurname());
|
||||
if (authorData.getCreditName() != null) {
|
||||
author.addProperty("creditname", authorData.getCreditName());
|
||||
}
|
||||
return author.toString();
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,40 +2,49 @@ package eu.dnetlib.doiboost.orcid.model;
|
|||
|
||||
public class AuthorData {
|
||||
|
||||
private String oid;
|
||||
private String name;
|
||||
private String surname;
|
||||
private String creditName;
|
||||
private String errorCode;
|
||||
|
||||
public String getErrorCode() {
|
||||
return errorCode;
|
||||
}
|
||||
public void setErrorCode(String errorCode) {
|
||||
this.errorCode = errorCode;
|
||||
}
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
public void setName(String name) {
|
||||
this.name = name;
|
||||
}
|
||||
public String getSurname() {
|
||||
return surname;
|
||||
}
|
||||
public void setSurname(String surname) {
|
||||
this.surname = surname;
|
||||
}
|
||||
public String getCreditName() {
|
||||
return creditName;
|
||||
}
|
||||
public void setCreditName(String creditName) {
|
||||
this.creditName = creditName;
|
||||
}
|
||||
public String getOid() {
|
||||
return oid;
|
||||
}
|
||||
public void setOid(String oid) {
|
||||
this.oid = oid;
|
||||
}
|
||||
private String oid;
|
||||
private String name;
|
||||
private String surname;
|
||||
private String creditName;
|
||||
private String errorCode;
|
||||
|
||||
public String getErrorCode() {
|
||||
return errorCode;
|
||||
}
|
||||
|
||||
public void setErrorCode(String errorCode) {
|
||||
this.errorCode = errorCode;
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
public void setName(String name) {
|
||||
this.name = name;
|
||||
}
|
||||
|
||||
public String getSurname() {
|
||||
return surname;
|
||||
}
|
||||
|
||||
public void setSurname(String surname) {
|
||||
this.surname = surname;
|
||||
}
|
||||
|
||||
public String getCreditName() {
|
||||
return creditName;
|
||||
}
|
||||
|
||||
public void setCreditName(String creditName) {
|
||||
this.creditName = creditName;
|
||||
}
|
||||
|
||||
public String getOid() {
|
||||
return oid;
|
||||
}
|
||||
|
||||
public void setOid(String oid) {
|
||||
this.oid = oid;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,5 +1,6 @@
|
|||
[
|
||||
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
|
||||
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true},
|
||||
{"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true}
|
||||
|
||||
]
|
||||
|
|
@ -26,18 +26,98 @@ public class DoiBoostTest {
|
|||
// CrossrefImporter.main("-n file:///tmp -t file:///tmp/p.seq -ts 1586110000749".split("
|
||||
// "));
|
||||
SparkMapDumpIntoOAF.main(
|
||||
"-m local[*] -s file:///data/doiboost/crossref_dump.seq".split(" "));
|
||||
"-m local[*] -s file:///data/doiboost/crossref_dump.seq -t /data/doiboost"
|
||||
.split(" "));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testConvertDatasetCrossRef2Oaf() throws IOException {
|
||||
final String json = IOUtils.toString(getClass().getResourceAsStream("dataset.json"));
|
||||
ObjectMapper mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT);
|
||||
assertNotNull(json);
|
||||
assertFalse(StringUtils.isBlank(json));
|
||||
final Result result = Crossref2Oaf.convert(json, logger);
|
||||
|
||||
logger.info(mapper.writeValueAsString(result));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testConvertPreprintCrossRef2Oaf() throws IOException {
|
||||
|
||||
final String json = IOUtils.toString(getClass().getResourceAsStream("article.json"));
|
||||
final String json = IOUtils.toString(getClass().getResourceAsStream("preprint.json"));
|
||||
ObjectMapper mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT);
|
||||
assertNotNull(json);
|
||||
assertFalse(StringUtils.isBlank(json));
|
||||
Crossref2Oaf cf = new Crossref2Oaf();
|
||||
final Result result = cf.convert(json, logger);
|
||||
|
||||
final Result result = Crossref2Oaf.convert(json, logger);
|
||||
assertNotNull(result);
|
||||
|
||||
assertNotNull(result.getDataInfo(), "Datainfo test not null Failed");
|
||||
assertNotNull(
|
||||
result.getDataInfo().getProvenanceaction(),
|
||||
"DataInfo/Provenance test not null Failed");
|
||||
assertFalse(
|
||||
StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getClassid()),
|
||||
"DataInfo/Provenance/classId test not null Failed");
|
||||
assertFalse(
|
||||
StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getClassname()),
|
||||
"DataInfo/Provenance/className test not null Failed");
|
||||
assertFalse(
|
||||
StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getSchemeid()),
|
||||
"DataInfo/Provenance/SchemeId test not null Failed");
|
||||
assertFalse(
|
||||
StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getSchemename()),
|
||||
"DataInfo/Provenance/SchemeName test not null Failed");
|
||||
|
||||
assertNotNull(result.getCollectedfrom(), "CollectedFrom test not null Failed");
|
||||
assertTrue(result.getCollectedfrom().size() > 0);
|
||||
assertTrue(
|
||||
result.getCollectedfrom().stream()
|
||||
.anyMatch(
|
||||
c ->
|
||||
c.getKey()
|
||||
.equalsIgnoreCase(
|
||||
"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")));
|
||||
assertTrue(
|
||||
result.getCollectedfrom().stream()
|
||||
.anyMatch(c -> c.getValue().equalsIgnoreCase("crossref")));
|
||||
|
||||
assertTrue(
|
||||
result.getRelevantdate().stream()
|
||||
.anyMatch(d -> d.getQualifier().getClassid().equalsIgnoreCase("created")));
|
||||
assertTrue(
|
||||
result.getRelevantdate().stream()
|
||||
.anyMatch(
|
||||
d -> d.getQualifier().getClassid().equalsIgnoreCase("available")));
|
||||
assertTrue(
|
||||
result.getRelevantdate().stream()
|
||||
.anyMatch(d -> d.getQualifier().getClassid().equalsIgnoreCase("accepted")));
|
||||
assertTrue(
|
||||
result.getRelevantdate().stream()
|
||||
.anyMatch(
|
||||
d ->
|
||||
d.getQualifier()
|
||||
.getClassid()
|
||||
.equalsIgnoreCase("published-online")));
|
||||
assertTrue(
|
||||
result.getRelevantdate().stream()
|
||||
.anyMatch(
|
||||
d ->
|
||||
d.getQualifier()
|
||||
.getClassid()
|
||||
.equalsIgnoreCase("published-print")));
|
||||
|
||||
logger.info(mapper.writeValueAsString(result));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testConvertArticleCrossRef2Oaf() throws IOException {
|
||||
|
||||
final String json = IOUtils.toString(getClass().getResourceAsStream("article.json"));
|
||||
ObjectMapper mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT);
|
||||
assertNotNull(json);
|
||||
assertFalse(StringUtils.isBlank(json));
|
||||
final Result result = Crossref2Oaf.convert(json, logger);
|
||||
assertNotNull(result);
|
||||
|
||||
assertNotNull(result.getDataInfo(), "Datainfo test not null Failed");
|
||||
|
|
@ -73,15 +153,6 @@ public class DoiBoostTest {
|
|||
assertTrue(
|
||||
result.getRelevantdate().stream()
|
||||
.anyMatch(d -> d.getQualifier().getClassid().equalsIgnoreCase("created")));
|
||||
// assertTrue(
|
||||
// result.getRelevantdate().stream()
|
||||
// .anyMatch(
|
||||
// d ->
|
||||
// d.getQualifier().getClassid().equalsIgnoreCase("available")));
|
||||
// assertTrue(
|
||||
// result.getRelevantdate().stream()
|
||||
// .anyMatch(d ->
|
||||
// d.getQualifier().getClassid().equalsIgnoreCase("accepted")));
|
||||
assertTrue(
|
||||
result.getRelevantdate().stream()
|
||||
.anyMatch(
|
||||
|
|
@ -107,8 +178,7 @@ public class DoiBoostTest {
|
|||
ObjectMapper mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT);
|
||||
assertNotNull(json);
|
||||
assertFalse(StringUtils.isBlank(json));
|
||||
Crossref2Oaf cf = new Crossref2Oaf();
|
||||
final Result result = cf.convert(json, logger);
|
||||
final Result result = Crossref2Oaf.convert(json, logger);
|
||||
assertNotNull(result);
|
||||
logger.info(mapper.writeValueAsString(result));
|
||||
|
||||
|
|
|
|||
|
|
@ -170,5 +170,5 @@
|
|||
"container-title": [
|
||||
"Ecl\u00e9tica Qu\u00edmica Journal"
|
||||
],
|
||||
"page": "41"
|
||||
"page": "41-50"
|
||||
}
|
||||
|
|
@ -0,0 +1,105 @@
|
|||
{
|
||||
"DOI": "10.1037/e522512014-096",
|
||||
"subtitle": [
|
||||
"(522512014-096)"
|
||||
],
|
||||
"issued": {
|
||||
"date-parts": [
|
||||
[
|
||||
2012
|
||||
]
|
||||
]
|
||||
},
|
||||
"prefix": "10.1037",
|
||||
"author": [
|
||||
{
|
||||
"affiliation": [],
|
||||
"given": "Jessica",
|
||||
"family": "Trudeau",
|
||||
"sequence": "first"
|
||||
},
|
||||
{
|
||||
"affiliation": [],
|
||||
"given": "Amy",
|
||||
"family": "McShane",
|
||||
"sequence": "additional"
|
||||
},
|
||||
{
|
||||
"affiliation": [],
|
||||
"given": "Renee",
|
||||
"family": "McDonald",
|
||||
"sequence": "additional"
|
||||
}
|
||||
],
|
||||
"reference-count": 0,
|
||||
"member": "15",
|
||||
"source": "Crossref",
|
||||
"score": 1.0,
|
||||
"deposited": {
|
||||
"timestamp": 1413827035000,
|
||||
"date-parts": [
|
||||
[
|
||||
2014,
|
||||
10,
|
||||
20
|
||||
]
|
||||
],
|
||||
"date-time": "2014-10-20T17:43:55Z"
|
||||
},
|
||||
"indexed": {
|
||||
"timestamp": 1550142454710,
|
||||
"date-parts": [
|
||||
[
|
||||
2019,
|
||||
2,
|
||||
14
|
||||
]
|
||||
],
|
||||
"date-time": "2019-02-14T11:07:34Z"
|
||||
},
|
||||
"type": "dataset",
|
||||
"URL": "http://dx.doi.org/10.1037/e522512014-096",
|
||||
"is-referenced-by-count": 0,
|
||||
"published-print": {
|
||||
"date-parts": [
|
||||
[
|
||||
2012
|
||||
]
|
||||
]
|
||||
},
|
||||
"references-count": 0,
|
||||
"institution": {
|
||||
"acronym": [
|
||||
"APA"
|
||||
],
|
||||
"place": [
|
||||
"-"
|
||||
],
|
||||
"name": "American Psychological Association"
|
||||
},
|
||||
"publisher": "American Psychological Association (APA)",
|
||||
"content-domain": {
|
||||
"domain": [],
|
||||
"crossmark-restriction": false
|
||||
},
|
||||
"created": {
|
||||
"timestamp": 1413826121000,
|
||||
"date-parts": [
|
||||
[
|
||||
2014,
|
||||
10,
|
||||
20
|
||||
]
|
||||
],
|
||||
"date-time": "2014-10-20T17:28:41Z"
|
||||
},
|
||||
"title": [
|
||||
"Project Support: A Randomized Control Study to Evaluate the Translation of an Evidence- Based Program"
|
||||
],
|
||||
"alternative-id": [
|
||||
"522512014-096"
|
||||
],
|
||||
"container-title": [
|
||||
"PsycEXTRA Dataset"
|
||||
]
|
||||
}
|
||||
|
|
@ -10,19 +10,6 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance;
|
|||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
|
||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.Date;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.DocumentFactory;
|
||||
import org.dom4j.DocumentHelper;
|
||||
import org.dom4j.Node;
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.raw.common.MigrationConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Author;
|
||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||
|
|
@ -41,388 +28,439 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
|
|||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.oaf.Software;
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.Date;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.DocumentFactory;
|
||||
import org.dom4j.DocumentHelper;
|
||||
import org.dom4j.Node;
|
||||
|
||||
public abstract class AbstractMdRecordToOafMapper {
|
||||
|
||||
protected final Map<String, String> code2name;
|
||||
|
||||
protected static final Qualifier MAIN_TITLE_QUALIFIER =
|
||||
qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
|
||||
|
||||
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
|
||||
this.code2name = code2name;
|
||||
}
|
||||
|
||||
public List<Oaf> processMdRecord(final String xml) {
|
||||
try {
|
||||
final Map<String, String> nsContext = new HashMap<>();
|
||||
nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
|
||||
nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
|
||||
nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
|
||||
nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
|
||||
nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
|
||||
nsContext.put("dc", "http://purl.org/dc/elements/1.1/");
|
||||
nsContext.put("datacite", "http://datacite.org/schema/kernel-3");
|
||||
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
|
||||
|
||||
final Document doc =
|
||||
DocumentHelper.parseText(xml.replaceAll("http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3"));
|
||||
|
||||
final String type = doc.valueOf("//dr:CobjCategory/@type");
|
||||
final KeyValue collectedFrom =
|
||||
keyValue(createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true), doc.valueOf("//oaf:collectedFrom/@name"));
|
||||
final KeyValue hostedBy =
|
||||
StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
|
||||
? collectedFrom
|
||||
: keyValue(createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), doc.valueOf("//oaf:hostedBy/@name"));
|
||||
|
||||
final DataInfo info = prepareDataInfo(doc);
|
||||
final long lastUpdateTimestamp = new Date().getTime();
|
||||
|
||||
return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
} catch (final Exception e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
protected List<Oaf> createOafs(
|
||||
final Document doc,
|
||||
final String type,
|
||||
final KeyValue collectedFrom,
|
||||
final KeyValue hostedBy,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp) {
|
||||
|
||||
final List<Oaf> oafs = new ArrayList<>();
|
||||
|
||||
switch (type.toLowerCase()) {
|
||||
case "":
|
||||
case "publication":
|
||||
final Publication p = new Publication();
|
||||
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
p.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER);
|
||||
p.setJournal(prepareJournal(doc, info));
|
||||
oafs.add(p);
|
||||
break;
|
||||
case "dataset":
|
||||
final Dataset d = new Dataset();
|
||||
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
d.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER);
|
||||
d.setStoragedate(prepareDatasetStorageDate(doc, info));
|
||||
d.setDevice(prepareDatasetDevice(doc, info));
|
||||
d.setSize(prepareDatasetSize(doc, info));
|
||||
d.setVersion(prepareDatasetVersion(doc, info));
|
||||
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
|
||||
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
|
||||
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
|
||||
oafs.add(d);
|
||||
break;
|
||||
case "software":
|
||||
final Software s = new Software();
|
||||
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
s.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER);
|
||||
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
|
||||
s.setLicense(prepareSoftwareLicenses(doc, info));
|
||||
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
|
||||
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
|
||||
oafs.add(s);
|
||||
break;
|
||||
case "otherresearchproducts":
|
||||
default:
|
||||
final OtherResearchProduct o = new OtherResearchProduct();
|
||||
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
o.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER);
|
||||
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
|
||||
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
|
||||
o.setTool(prepareOtherResearchProductTools(doc, info));
|
||||
oafs.add(o);
|
||||
break;
|
||||
}
|
||||
|
||||
if (!oafs.isEmpty()) {
|
||||
oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp));
|
||||
oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp));
|
||||
}
|
||||
|
||||
return oafs;
|
||||
}
|
||||
|
||||
private List<Oaf> addProjectRels(
|
||||
final Document doc,
|
||||
final KeyValue collectedFrom,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp) {
|
||||
|
||||
final List<Oaf> res = new ArrayList<>();
|
||||
|
||||
final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false);
|
||||
|
||||
for (final Object o : doc.selectNodes("//oaf:projectid")) {
|
||||
final String projectId = createOpenaireId(40, ((Node) o).getText(), true);
|
||||
|
||||
final Relation r1 = new Relation();
|
||||
r1.setRelType("resultProject");
|
||||
r1.setSubRelType("outcome");
|
||||
r1.setRelClass("isProducedBy");
|
||||
r1.setSource(docId);
|
||||
r1.setTarget(projectId);
|
||||
r1.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||
r1.setDataInfo(info);
|
||||
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||
res.add(r1);
|
||||
|
||||
final Relation r2 = new Relation();
|
||||
r2.setRelType("resultProject");
|
||||
r2.setSubRelType("outcome");
|
||||
r2.setRelClass("produces");
|
||||
r2.setSource(projectId);
|
||||
r2.setTarget(docId);
|
||||
r2.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||
r2.setDataInfo(info);
|
||||
r2.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||
res.add(r2);
|
||||
}
|
||||
|
||||
return res;
|
||||
}
|
||||
|
||||
protected abstract List<Oaf> addOtherResultRels(
|
||||
final Document doc,
|
||||
final KeyValue collectedFrom,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp);
|
||||
|
||||
private void populateResultFields(
|
||||
final Result r,
|
||||
final Document doc,
|
||||
final KeyValue collectedFrom,
|
||||
final KeyValue hostedBy,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp) {
|
||||
r.setDataInfo(info);
|
||||
r.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
|
||||
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
|
||||
r.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||
r.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
|
||||
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
|
||||
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
|
||||
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setOaiprovenance(prepareOAIprovenance(doc));
|
||||
r.setAuthor(prepareAuthors(doc, info));
|
||||
r.setLanguage(prepareLanguages(doc));
|
||||
r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setSubject(prepareSubjects(doc, info));
|
||||
r.setTitle(prepareTitles(doc, info));
|
||||
r.setRelevantdate(prepareRelevantDates(doc, info));
|
||||
r.setDescription(prepareDescriptions(doc, info));
|
||||
r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info));
|
||||
r.setPublisher(preparePublisher(doc, info));
|
||||
r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info));
|
||||
r.setSource(prepareSources(doc, info));
|
||||
r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setFormat(prepareFormats(doc, info));
|
||||
r.setContributor(prepareContributors(doc, info));
|
||||
r.setResourcetype(prepareResourceType(doc, info));
|
||||
r.setCoverage(prepareCoverages(doc, info));
|
||||
r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
|
||||
}
|
||||
|
||||
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Instance> prepareInstances(
|
||||
Document doc,
|
||||
DataInfo info,
|
||||
KeyValue collectedfrom,
|
||||
KeyValue hostedby);
|
||||
|
||||
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<StructuredProperty> prepareRelevantDates(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareCoverages(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareContributors(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareFormats(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> preparePublisher(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareDescriptions(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Qualifier prepareLanguages(Document doc);
|
||||
|
||||
protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareOtherResearchProductTools(
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
|
||||
protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<StructuredProperty> prepareSoftwareLicenses(
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
|
||||
protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetMetadataVersionNumber(
|
||||
Document doc,
|
||||
DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetVersion(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetSize(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetDevice(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
|
||||
|
||||
private Journal prepareJournal(final Document doc, final DataInfo info) {
|
||||
final Node n = doc.selectSingleNode("//oaf:journal");
|
||||
if (n != null) {
|
||||
final String name = n.getText();
|
||||
final String issnPrinted = n.valueOf("@issn");
|
||||
final String issnOnline = n.valueOf("@eissn");
|
||||
final String issnLinking = n.valueOf("@lissn");
|
||||
final String ep = n.valueOf("@ep");
|
||||
final String iss = n.valueOf("@iss");
|
||||
final String sp = n.valueOf("@sp");
|
||||
final String vol = n.valueOf("@vol");
|
||||
final String edition = n.valueOf("@edition");
|
||||
if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); }
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
protected Qualifier prepareQualifier(
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final String schemeId,
|
||||
final String schemeName) {
|
||||
final String classId = node.valueOf(xpath);
|
||||
final String className = code2name.get(classId);
|
||||
return qualifier(classId, className, schemeId, schemeName);
|
||||
}
|
||||
|
||||
protected List<StructuredProperty> prepareListStructProps(
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final String xpathClassId,
|
||||
final String schemeId,
|
||||
final String schemeName,
|
||||
final DataInfo info) {
|
||||
final List<StructuredProperty> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final Node n = (Node) o;
|
||||
final String classId = n.valueOf(xpathClassId);
|
||||
final String className = code2name.get(classId);
|
||||
res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info));
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
protected List<StructuredProperty> prepareListStructProps(
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final Qualifier qualifier,
|
||||
final DataInfo info) {
|
||||
final List<StructuredProperty> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final Node n = (Node) o;
|
||||
res.add(structuredProperty(n.getText(), qualifier, info));
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
protected List<StructuredProperty> prepareListStructProps(
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final DataInfo info) {
|
||||
final List<StructuredProperty> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final Node n = (Node) o;
|
||||
res.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info));
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
protected OAIProvenance prepareOAIprovenance(final Document doc) {
|
||||
final Node n =
|
||||
doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
|
||||
|
||||
if (n == null) { return null; }
|
||||
|
||||
final String identifier = n.valueOf("./*[local-name()='identifier']");
|
||||
final String baseURL = n.valueOf("./*[local-name()='baseURL']");;
|
||||
final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");;
|
||||
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
|
||||
final String datestamp = n.valueOf("./*[local-name()='datestamp']");;
|
||||
final String harvestDate = n.valueOf("@harvestDate");;
|
||||
|
||||
return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
|
||||
}
|
||||
|
||||
protected DataInfo prepareDataInfo(final Document doc) {
|
||||
final Node n = doc.selectSingleNode("//oaf:datainfo");
|
||||
|
||||
if (n == null) { return dataInfo(false, null, false, false, MigrationConstants.REPOSITORY_PROVENANCE_ACTIONS, "0.9"); }
|
||||
|
||||
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
|
||||
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
|
||||
final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");
|
||||
final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename");
|
||||
|
||||
final boolean deletedbyinference =
|
||||
Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference"));
|
||||
final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance");
|
||||
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
|
||||
final String trust = n.valueOf("./oaf:trust");
|
||||
|
||||
return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
|
||||
}
|
||||
|
||||
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
|
||||
return field(node.valueOf(xpath), info);
|
||||
}
|
||||
|
||||
protected List<Field<String>> prepareListFields(
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final DataInfo info) {
|
||||
return listFields(info, prepareListString(node, xpath));
|
||||
}
|
||||
|
||||
protected List<String> prepareListString(final Node node, final String xpath) {
|
||||
final List<String> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final String s = ((Node) o).getText().trim();
|
||||
if (StringUtils.isNotBlank(s)) {
|
||||
res.add(s);
|
||||
}
|
||||
}
|
||||
return res;
|
||||
}
|
||||
protected final Map<String, String> code2name;
|
||||
|
||||
protected static final Qualifier MAIN_TITLE_QUALIFIER =
|
||||
qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
|
||||
|
||||
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
|
||||
this.code2name = code2name;
|
||||
}
|
||||
|
||||
public List<Oaf> processMdRecord(final String xml) {
|
||||
try {
|
||||
final Map<String, String> nsContext = new HashMap<>();
|
||||
nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
|
||||
nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
|
||||
nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
|
||||
nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
|
||||
nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
|
||||
nsContext.put("dc", "http://purl.org/dc/elements/1.1/");
|
||||
nsContext.put("datacite", "http://datacite.org/schema/kernel-3");
|
||||
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
|
||||
|
||||
final Document doc =
|
||||
DocumentHelper.parseText(
|
||||
xml.replaceAll(
|
||||
"http://datacite.org/schema/kernel-4",
|
||||
"http://datacite.org/schema/kernel-3"));
|
||||
|
||||
final String type = doc.valueOf("//dr:CobjCategory/@type");
|
||||
final KeyValue collectedFrom =
|
||||
keyValue(
|
||||
createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true),
|
||||
doc.valueOf("//oaf:collectedFrom/@name"));
|
||||
final KeyValue hostedBy =
|
||||
StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
|
||||
? collectedFrom
|
||||
: keyValue(
|
||||
createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true),
|
||||
doc.valueOf("//oaf:hostedBy/@name"));
|
||||
|
||||
final DataInfo info = prepareDataInfo(doc);
|
||||
final long lastUpdateTimestamp = new Date().getTime();
|
||||
|
||||
return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
} catch (final Exception e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
protected List<Oaf> createOafs(
|
||||
final Document doc,
|
||||
final String type,
|
||||
final KeyValue collectedFrom,
|
||||
final KeyValue hostedBy,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp) {
|
||||
|
||||
final List<Oaf> oafs = new ArrayList<>();
|
||||
|
||||
switch (type.toLowerCase()) {
|
||||
case "":
|
||||
case "publication":
|
||||
final Publication p = new Publication();
|
||||
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
p.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER);
|
||||
p.setJournal(prepareJournal(doc, info));
|
||||
oafs.add(p);
|
||||
break;
|
||||
case "dataset":
|
||||
final Dataset d = new Dataset();
|
||||
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
d.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER);
|
||||
d.setStoragedate(prepareDatasetStorageDate(doc, info));
|
||||
d.setDevice(prepareDatasetDevice(doc, info));
|
||||
d.setSize(prepareDatasetSize(doc, info));
|
||||
d.setVersion(prepareDatasetVersion(doc, info));
|
||||
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
|
||||
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
|
||||
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
|
||||
oafs.add(d);
|
||||
break;
|
||||
case "software":
|
||||
final Software s = new Software();
|
||||
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
s.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER);
|
||||
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
|
||||
s.setLicense(prepareSoftwareLicenses(doc, info));
|
||||
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
|
||||
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
|
||||
oafs.add(s);
|
||||
break;
|
||||
case "otherresearchproducts":
|
||||
default:
|
||||
final OtherResearchProduct o = new OtherResearchProduct();
|
||||
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
o.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER);
|
||||
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
|
||||
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
|
||||
o.setTool(prepareOtherResearchProductTools(doc, info));
|
||||
oafs.add(o);
|
||||
break;
|
||||
}
|
||||
|
||||
if (!oafs.isEmpty()) {
|
||||
oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp));
|
||||
oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp));
|
||||
}
|
||||
|
||||
return oafs;
|
||||
}
|
||||
|
||||
private List<Oaf> addProjectRels(
|
||||
final Document doc,
|
||||
final KeyValue collectedFrom,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp) {
|
||||
|
||||
final List<Oaf> res = new ArrayList<>();
|
||||
|
||||
final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false);
|
||||
|
||||
for (final Object o : doc.selectNodes("//oaf:projectid")) {
|
||||
final String projectId = createOpenaireId(40, ((Node) o).getText(), true);
|
||||
|
||||
final Relation r1 = new Relation();
|
||||
r1.setRelType("resultProject");
|
||||
r1.setSubRelType("outcome");
|
||||
r1.setRelClass("isProducedBy");
|
||||
r1.setSource(docId);
|
||||
r1.setTarget(projectId);
|
||||
r1.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||
r1.setDataInfo(info);
|
||||
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||
res.add(r1);
|
||||
|
||||
final Relation r2 = new Relation();
|
||||
r2.setRelType("resultProject");
|
||||
r2.setSubRelType("outcome");
|
||||
r2.setRelClass("produces");
|
||||
r2.setSource(projectId);
|
||||
r2.setTarget(docId);
|
||||
r2.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||
r2.setDataInfo(info);
|
||||
r2.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||
res.add(r2);
|
||||
}
|
||||
|
||||
return res;
|
||||
}
|
||||
|
||||
protected abstract List<Oaf> addOtherResultRels(
|
||||
final Document doc,
|
||||
final KeyValue collectedFrom,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp);
|
||||
|
||||
private void populateResultFields(
|
||||
final Result r,
|
||||
final Document doc,
|
||||
final KeyValue collectedFrom,
|
||||
final KeyValue hostedBy,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp) {
|
||||
r.setDataInfo(info);
|
||||
r.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
|
||||
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
|
||||
r.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||
r.setPid(
|
||||
prepareListStructProps(
|
||||
doc,
|
||||
"//oaf:identifier",
|
||||
"@identifierType",
|
||||
"dnet:pid_types",
|
||||
"dnet:pid_types",
|
||||
info));
|
||||
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
|
||||
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
|
||||
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setOaiprovenance(prepareOAIprovenance(doc));
|
||||
r.setAuthor(prepareAuthors(doc, info));
|
||||
r.setLanguage(prepareLanguages(doc));
|
||||
r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setSubject(prepareSubjects(doc, info));
|
||||
r.setTitle(prepareTitles(doc, info));
|
||||
r.setRelevantdate(prepareRelevantDates(doc, info));
|
||||
r.setDescription(prepareDescriptions(doc, info));
|
||||
r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info));
|
||||
r.setPublisher(preparePublisher(doc, info));
|
||||
r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info));
|
||||
r.setSource(prepareSources(doc, info));
|
||||
r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setFormat(prepareFormats(doc, info));
|
||||
r.setContributor(prepareContributors(doc, info));
|
||||
r.setResourcetype(prepareResourceType(doc, info));
|
||||
r.setCoverage(prepareCoverages(doc, info));
|
||||
r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
|
||||
}
|
||||
|
||||
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Instance> prepareInstances(
|
||||
Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby);
|
||||
|
||||
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<StructuredProperty> prepareRelevantDates(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareCoverages(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareContributors(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareFormats(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> preparePublisher(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareDescriptions(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Qualifier prepareLanguages(Document doc);
|
||||
|
||||
protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareOtherResearchProductTools(
|
||||
Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
|
||||
Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
|
||||
Document doc, DataInfo info);
|
||||
|
||||
protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<StructuredProperty> prepareSoftwareLicenses(
|
||||
Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
|
||||
Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetMetadataVersionNumber(
|
||||
Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetVersion(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetSize(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetDevice(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
|
||||
|
||||
private Journal prepareJournal(final Document doc, final DataInfo info) {
|
||||
final Node n = doc.selectSingleNode("//oaf:journal");
|
||||
if (n != null) {
|
||||
final String name = n.getText();
|
||||
final String issnPrinted = n.valueOf("@issn");
|
||||
final String issnOnline = n.valueOf("@eissn");
|
||||
final String issnLinking = n.valueOf("@lissn");
|
||||
final String ep = n.valueOf("@ep");
|
||||
final String iss = n.valueOf("@iss");
|
||||
final String sp = n.valueOf("@sp");
|
||||
final String vol = n.valueOf("@vol");
|
||||
final String edition = n.valueOf("@edition");
|
||||
if (StringUtils.isNotBlank(name)) {
|
||||
return journal(
|
||||
name,
|
||||
issnPrinted,
|
||||
issnOnline,
|
||||
issnLinking,
|
||||
ep,
|
||||
iss,
|
||||
sp,
|
||||
vol,
|
||||
edition,
|
||||
null,
|
||||
null,
|
||||
info);
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
protected Qualifier prepareQualifier(
|
||||
final Node node, final String xpath, final String schemeId, final String schemeName) {
|
||||
final String classId = node.valueOf(xpath);
|
||||
final String className = code2name.get(classId);
|
||||
return qualifier(classId, className, schemeId, schemeName);
|
||||
}
|
||||
|
||||
protected List<StructuredProperty> prepareListStructProps(
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final String xpathClassId,
|
||||
final String schemeId,
|
||||
final String schemeName,
|
||||
final DataInfo info) {
|
||||
final List<StructuredProperty> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final Node n = (Node) o;
|
||||
final String classId = n.valueOf(xpathClassId);
|
||||
final String className = code2name.get(classId);
|
||||
res.add(
|
||||
structuredProperty(
|
||||
n.getText(), classId, className, schemeId, schemeName, info));
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
protected List<StructuredProperty> prepareListStructProps(
|
||||
final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) {
|
||||
final List<StructuredProperty> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final Node n = (Node) o;
|
||||
res.add(structuredProperty(n.getText(), qualifier, info));
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
protected List<StructuredProperty> prepareListStructProps(
|
||||
final Node node, final String xpath, final DataInfo info) {
|
||||
final List<StructuredProperty> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final Node n = (Node) o;
|
||||
res.add(
|
||||
structuredProperty(
|
||||
n.getText(),
|
||||
n.valueOf("@classid"),
|
||||
n.valueOf("@classname"),
|
||||
n.valueOf("@schemeid"),
|
||||
n.valueOf("@schemename"),
|
||||
info));
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
protected OAIProvenance prepareOAIprovenance(final Document doc) {
|
||||
final Node n =
|
||||
doc.selectSingleNode(
|
||||
"//*[local-name()='provenance']/*[local-name()='originDescription']");
|
||||
|
||||
if (n == null) {
|
||||
return null;
|
||||
}
|
||||
|
||||
final String identifier = n.valueOf("./*[local-name()='identifier']");
|
||||
final String baseURL = n.valueOf("./*[local-name()='baseURL']");
|
||||
;
|
||||
final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");
|
||||
;
|
||||
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
|
||||
final String datestamp = n.valueOf("./*[local-name()='datestamp']");
|
||||
;
|
||||
final String harvestDate = n.valueOf("@harvestDate");
|
||||
;
|
||||
|
||||
return oaiIProvenance(
|
||||
identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
|
||||
}
|
||||
|
||||
protected DataInfo prepareDataInfo(final Document doc) {
|
||||
final Node n = doc.selectSingleNode("//oaf:datainfo");
|
||||
|
||||
if (n == null) {
|
||||
return dataInfo(
|
||||
false,
|
||||
null,
|
||||
false,
|
||||
false,
|
||||
MigrationConstants.REPOSITORY_PROVENANCE_ACTIONS,
|
||||
"0.9");
|
||||
}
|
||||
|
||||
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
|
||||
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
|
||||
final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");
|
||||
final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename");
|
||||
|
||||
final boolean deletedbyinference =
|
||||
Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference"));
|
||||
final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance");
|
||||
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
|
||||
final String trust = n.valueOf("./oaf:trust");
|
||||
|
||||
return dataInfo(
|
||||
deletedbyinference,
|
||||
inferenceprovenance,
|
||||
inferred,
|
||||
false,
|
||||
qualifier(paClassId, paClassName, paSchemeId, paSchemeName),
|
||||
trust);
|
||||
}
|
||||
|
||||
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
|
||||
return field(node.valueOf(xpath), info);
|
||||
}
|
||||
|
||||
protected List<Field<String>> prepareListFields(
|
||||
final Node node, final String xpath, final DataInfo info) {
|
||||
return listFields(info, prepareListString(node, xpath));
|
||||
}
|
||||
|
||||
protected List<String> prepareListString(final Node node, final String xpath) {
|
||||
final List<String> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final String s = ((Node) o).getText().trim();
|
||||
if (StringUtils.isNotBlank(s)) {
|
||||
res.add(s);
|
||||
}
|
||||
}
|
||||
return res;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -6,17 +6,28 @@ import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
|||
|
||||
public class MigrationConstants {
|
||||
|
||||
public static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
|
||||
qualifier("publication", "publication", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier DATASET_RESULTTYPE_QUALIFIER =
|
||||
qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER =
|
||||
qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier OTHER_RESULTTYPE_QUALIFIER =
|
||||
qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier REPOSITORY_PROVENANCE_ACTIONS =
|
||||
qualifier("sysimport:crosswalk:repository", "sysimport:crosswalk:repository", "dnet:provenanceActions", "dnet:provenanceActions");
|
||||
public static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION =
|
||||
qualifier("sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", "dnet:provenanceActions", "dnet:provenanceActions");
|
||||
|
||||
public static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
|
||||
qualifier(
|
||||
"publication",
|
||||
"publication",
|
||||
"dnet:result_typologies",
|
||||
"dnet:result_typologies");
|
||||
public static final Qualifier DATASET_RESULTTYPE_QUALIFIER =
|
||||
qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER =
|
||||
qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier OTHER_RESULTTYPE_QUALIFIER =
|
||||
qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier REPOSITORY_PROVENANCE_ACTIONS =
|
||||
qualifier(
|
||||
"sysimport:crosswalk:repository",
|
||||
"sysimport:crosswalk:repository",
|
||||
"dnet:provenanceActions",
|
||||
"dnet:provenanceActions");
|
||||
public static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION =
|
||||
qualifier(
|
||||
"sysimport:crosswalk:entityregistry",
|
||||
"sysimport:crosswalk:entityregistry",
|
||||
"dnet:provenanceActions",
|
||||
"dnet:provenanceActions");
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue