completed mapping of UnpayWall and ORCID

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala

@@ -7,6 +7,7 @@ object DoiBoostMappingUtil {
 
   //STATIC STRING
   val MAG = "microsoft"
+  val MAG_NAME= "Microsoft Academic Graph"
   val ORCID = "ORCID"
   val CROSSREF = "Crossref"
   val UNPAYWALL = "UnpayWall"
@@ -56,11 +57,32 @@ object DoiBoostMappingUtil {
 
     val cf = new KeyValue
     cf.setValue(CROSSREF)
-    cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5("crossref"))
+    cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(CROSSREF.toLowerCase))
     cf
 
   }
 
+
+  def createUnpayWallCollectedFrom(): KeyValue = {
+
+    val cf = new KeyValue
+    cf.setValue(UNPAYWALL)
+    cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(UNPAYWALL.toLowerCase))
+    cf
+
+  }
+
+  def createORIDCollectedFrom(): KeyValue = {
+
+    val cf = new KeyValue
+    cf.setValue(ORCID)
+    cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(ORCID.toLowerCase))
+    cf
+
+  }
+
+
+
   def generateIdentifier(oaf: Result, doi: String): String = {
     val id = DHPUtils.md5(doi.toLowerCase)
     if (oaf.isInstanceOf[Dataset])

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala

@@ -0,0 +1,63 @@
+package eu.dnetlib.doiboost
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser
+import eu.dnetlib.dhp.schema.oaf.{Publication, Dataset => OafDataset}
+import org.apache.commons.io.IOUtils
+import org.apache.spark.SparkConf
+import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
+import org.slf4j.{Logger, LoggerFactory}
+
+object SparkGenerateDoiBoost {
+
+  def main(args: Array[String]): Unit = {
+
+    val logger: Logger = LoggerFactory.getLogger(getClass)
+    val conf: SparkConf = new SparkConf()
+    val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json")))
+    parser.parseArgument(args)
+    val spark: SparkSession =
+      SparkSession
+        .builder()
+        .config(conf)
+        .appName(getClass.getSimpleName)
+        .master(parser.get("master")).getOrCreate()
+
+
+
+    val crossrefPublicationPath =parser.get("crossrefPublicationPath")
+    val crossrefDatasetPath     =parser.get("crossrefDatasetPath")
+    val uwPublicationPath       =parser.get("uwPublicationPath")
+    val magPublicationPath      =parser.get("magPublicationPath")
+    val orcidPublicationPath    =parser.get("orcidPublicationPath")
+    val workingDirPath          =parser.get("workingDirPath")
+
+
+    logger.info("Phase 1) repartition and move all the dataset in a same working folder")
+    spark.read.load(crossrefPublicationPath).as(Encoders.bean(classOf[Publication])).map(s=>s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefPublication")
+    spark.read.load(crossrefDatasetPath).as(Encoders.bean(classOf[OafDataset])).map(s=>s)(Encoders.kryo[OafDataset]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefDataset")
+    spark.read.load(uwPublicationPath).as(Encoders.bean(classOf[Publication])).map(s=>s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/uwPublication")
+    spark.read.load(orcidPublicationPath).as(Encoders.bean(classOf[Publication])).map(s=>s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/orcidPublication")
+    spark.read.load(magPublicationPath).as(Encoders.bean(classOf[Publication])).map(s=>s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/magPublication")
+
+    implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
+    implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
+    implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub)
+
+    logger.info("Phase 2) Join Crossref with UnpayWall")
+
+    val crossrefPublication:Dataset[(String,Publication)] = spark.read.load(s"$workingDirPath/crossrefPublication").as[Publication].map(p =>(p.getId, p) )
+    val uwPublication:Dataset[(String,Publication)] = spark.read.load(s"$workingDirPath/crossrefPublication").as[Publication].map(p =>(p.getId, p) )
+
+    crossrefPublication.joinWith(uwPublication, crossrefPublication("_1").equalTo(uwPublication("_1")),"left").map(item => {
+      val crossrefPub = item._1._2
+      val unpayWallPub = item._1._2
+      if(unpayWallPub!= null) {
+        crossrefPub.mergeFrom(unpayWallPub)
+      }
+      crossrefPub
+    }).write.save(s"$workingDirPath/firstJoin")
+
+
+  }
+
+}

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala

@@ -165,6 +165,13 @@ case object Crossref2Oaf {
     if (l.nonEmpty)
       instance.setLicense(l.head)
 
+
+    val has_review = (json \ "relation" \"has-review" \ "id")
+
+    if(has_review != JNothing)
+      instance.setRefereed(asField("peerReviewed"))
+
+
     instance.setAccessright(createQualifier("Restricted", "dnet:access_modes"))
 
     result.setInstance(List(instance).asJava)
@@ -186,7 +193,7 @@ case object Crossref2Oaf {
     val a = new Author
     a.setName(given)
     a.setSurname(family)
-    a.setFullname(s"${given} ${family}")
+    a.setFullname(s"$given $family")
     if (StringUtils.isNotBlank(orcid))
       a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava)
 

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala

@@ -38,7 +38,9 @@ case class MagPaperAuthorDenormalized(PaperId: Long, author: MagAuthor, affiliat
 
 case class MagPaperUrl(PaperId: Long, SourceType: Option[Int], SourceUrl: Option[String], LanguageCode: Option[String]) {}
 
-case class MagUrl(PaperId: Long, instances: List[String])
+case class MagUrlInstance(SourceUrl:String){}
+
+case class MagUrl(PaperId: Long, instances: List[MagUrlInstance])
 
 case class MagSubject(FieldOfStudyId:Long, DisplayName:String, MainType:Option[String], Score:Float){}
 
@@ -47,6 +49,8 @@ case class MagFieldOfStudy(PaperId:Long, subjects:List[MagSubject]) {}
 case class MagJournal(JournalId: Long, Rank: Option[Int], NormalizedName: Option[String], DisplayName: Option[String], Issn: Option[String], Publisher: Option[String], Webpage: Option[String], PaperCount: Option[Long], CitationCount: Option[Long], CreatedDate: Option[java.sql.Timestamp]) {}
 
 
+case class MagConferenceInstance(ci:Long, DisplayName:Option[String], Location:Option[String], StartDate:Option[java.sql.Timestamp],   EndDate:Option[java.sql.Timestamp],  PaperId:Long){}
+
 case object ConversionUtil {
 
   def extractMagIdentifier(pids:mutable.Buffer[String]) :String ={
@@ -70,7 +74,7 @@ case object ConversionUtil {
 
     if (urls!= null) {
 
-      val l:List[String] = urls.instances.filter(k=>k.nonEmpty):::List(s"https://academic.microsoft.com/#/detail/${extractMagIdentifier(pub.getOriginalId.asScala)}")
+      val l:List[String] = urls.instances.filter(k=>k.SourceUrl.nonEmpty).map(k=>k.SourceUrl):::List(s"https://academic.microsoft.com/#/detail/${extractMagIdentifier(pub.getOriginalId.asScala)}")
 
       i.setUrl(l.asJava)
     }
@@ -133,7 +137,7 @@ case object ConversionUtil {
       j.setSp(paper.FirstPage)
       j.setEp(paper.LastPage)
       if (journal.Publisher.isDefined)
-        j.setEdition(journal.Publisher.get)
+        pub.setPublisher(asField(journal.Publisher.get))
       if (journal.Issn.isDefined)
         j.setIssnPrinted(journal.Issn.get)
       pub.setJournal(j)

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala

@@ -1,7 +1,7 @@
 package eu.dnetlib.doiboost.mag
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.schema.oaf.{Publication, StructuredProperty}
+import eu.dnetlib.dhp.schema.oaf.{Journal, Publication, StructuredProperty}
 import eu.dnetlib.doiboost.DoiBoostMappingUtil
 import eu.dnetlib.doiboost.DoiBoostMappingUtil.{asField, createSP}
 import org.apache.commons.io.IOUtils
@@ -10,6 +10,7 @@ import org.apache.spark.rdd.RDD
 import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
 import org.slf4j.{Logger, LoggerFactory}
 import org.apache.spark.sql.functions._
+
 import scala.collection.JavaConverters._
 
 object SparkPreProcessMAG {
@@ -51,7 +52,6 @@ object SparkPreProcessMAG {
     }.map(_._2)
 
 
-
     val distinctPaper: Dataset[MagPapers] = spark.createDataset(result)
     distinctPaper.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/Papers_distinct")
     logger.info(s"Total number of element: ${result.count()}")
@@ -90,6 +90,36 @@ object SparkPreProcessMAG {
 
     var magPubs: Dataset[(String, Publication)] = spark.read.load(s"${parser.get("targetPath")}/merge_step_2").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
 
+
+    val conference = spark.read.load(s"$sourcePath/ConferenceInstances").select($"ConferenceInstanceId".as("ci"), $"DisplayName", $"Location", $"StartDate",$"EndDate" )
+    val conferenceInstance = conference.joinWith(papers, papers("ConferenceInstanceId").equalTo(conference("ci"))).select($"_1.ci", $"_1.DisplayName", $"_1.Location", $"_1.StartDate",$"_1.EndDate", $"_2.PaperId").as[MagConferenceInstance]
+
+
+    magPubs.joinWith(conferenceInstance, col("_1").equalTo(conferenceInstance("PaperId")), "left")
+      .map(p => {
+        val publication:Publication= p._1._2
+        val ci:MagConferenceInstance = p._2
+
+        if (ci!= null){
+
+          val j:Journal = new Journal
+          if (ci.Location.isDefined)
+            j.setConferenceplace(ci.Location.get)
+          j.setName(ci.DisplayName.get)
+          if (ci.StartDate.isDefined && ci.EndDate.isDefined)
+            {
+              j.setConferencedate(s"${ci.StartDate.get.toString} - ${ci.EndDate.get.toString}")
+            }
+
+          publication.setJournal(j)
+        }
+        publication
+
+      }).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_2_conference")
+
+
+    magPubs= spark.read.load(s"${parser.get("targetPath")}/merge_step_2_conference").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
+
     val paperUrlDataset = spark.read.load(s"$sourcePath/PaperUrls").as[MagPaperUrl].groupBy("PaperId").agg(collect_list(struct("sourceUrl")).as("instances")).as[MagUrl]
 
 

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala

@@ -0,0 +1,104 @@
+package eu.dnetlib.doiboost.orcid
+
+import java.io.IOException
+
+import eu.dnetlib.dhp.schema.oaf.{Author, Publication}
+import eu.dnetlib.doiboost.DoiBoostMappingUtil
+import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier}
+import eu.dnetlib.doiboost.crossref.Crossref2Oaf
+import org.apache.commons.lang.StringUtils
+import org.codehaus.jackson.map.ObjectMapper
+import org.json4s
+import org.json4s.DefaultFormats
+import org.json4s.jackson.JsonMethods.parse
+import org.slf4j.{Logger, LoggerFactory}
+
+import scala.collection.JavaConverters._
+
+
+case class ORCIDItem(oid:String,name:String,surname:String,creditName:String,errorCode:String){}
+object ORCIDToOAF {
+  val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
+  val mapper = new ObjectMapper
+
+  def isJsonValid(inputStr: String): Boolean = {
+    import java.io.IOException
+    try {
+      mapper.readTree(inputStr)
+      true
+    } catch {
+      case e: IOException =>
+        false
+    }
+  }
+
+  def extractValueFromInputString(input: String): (String, String) = {
+    val i = input.indexOf('[')
+    if (i <5) {
+      return null
+    }
+    val orcidList = input.substring(i, input.length - 1)
+    val doi = input.substring(1, i - 1)
+    if (isJsonValid(orcidList)) {
+      (doi, orcidList)
+    } else null
+  }
+
+
+  def convertTOOAF(input:String) :Publication = {
+    implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
+
+    val item:(String, String) = extractValueFromInputString(input)
+
+    if (item== null) {
+      return  null
+    }
+
+    val json_str = item._2
+    lazy val json: json4s.JValue = parse(json_str)
+
+    val doi = item._1
+
+    val pub:Publication = new Publication
+    pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
+    pub.setDataInfo(generateDataInfo())
+    pub.setId(generateIdentifier(pub, doi.toLowerCase))
+
+
+
+
+    try{
+      val authorList:List[ORCIDItem] = json.extract[List[ORCIDItem]]
+
+
+      pub.setAuthor(authorList.map(a=> {
+        generateAuhtor(a.name, a.surname, a.creditName, a.oid)
+      }).asJava)
+
+
+      pub.setCollectedfrom(List(DoiBoostMappingUtil.createORIDCollectedFrom()).asJava)
+      pub
+    } catch {
+      case e: Throwable =>
+        logger.info(s"ERROR ON GENERATE Publication from $input")
+        null
+    }
+
+  }
+
+  def generateAuhtor(given: String, family: String, fullName:String, orcid: String): Author = {
+    val a = new Author
+    a.setName(given)
+    a.setSurname(family)
+    if (fullName!= null && fullName.nonEmpty)
+      a.setFullname(fullName)
+    else
+      a.setFullname(s"$given $family")
+    if (StringUtils.isNotBlank(orcid))
+      a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava)
+
+    a
+  }
+
+
+}

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala

@@ -0,0 +1,41 @@
+package eu.dnetlib.doiboost.orcid
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser
+import eu.dnetlib.dhp.schema.oaf.Publication
+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.slf4j.{Logger, LoggerFactory}
+
+object SparkConvertORCIDToOAF {
+
+
+
+  def main(args: Array[String]): Unit = {
+
+    val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
+    val conf: SparkConf = new SparkConf()
+    val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json")))
+    parser.parseArgument(args)
+    val spark: SparkSession =
+      SparkSession
+        .builder()
+        .config(conf)
+        .appName(getClass.getSimpleName)
+        .master(parser.get("master")).getOrCreate()
+
+    implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication])
+
+    val sourcePath = parser.get("sourcePath")
+    val targetPath = parser.get("targetPath")
+    val inputRDD:RDD[String] = spark.sparkContext.textFile(s"$sourcePath")
+
+    println(s"SourcePath is $sourcePath, targetPath is $targetPath master is ${parser.get("master")} ")
+
+    logger.info("Converting ORCID to OAF")
+    val d:Dataset[Publication] = spark.createDataset(inputRDD.map(ORCIDToOAF.convertTOOAF).filter(p=>p!=null)).as[Publication]
+    d.write.mode(SaveMode.Overwrite).save(targetPath)
+  }
+
+}

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala

@@ -0,0 +1,42 @@
+package eu.dnetlib.doiboost.uw
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser
+
+import eu.dnetlib.dhp.schema.oaf.Publication
+import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF
+import org.apache.commons.io.IOUtils
+import org.apache.spark.SparkConf
+import org.apache.spark.rdd.RDD
+import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
+import org.slf4j.{Logger, LoggerFactory}
+
+
+object SparkMapUnpayWallToOAF {
+
+  def main(args: Array[String]): Unit = {
+
+
+    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)
+    val spark: SparkSession =
+      SparkSession
+        .builder()
+        .config(conf)
+        .appName(getClass.getSimpleName)
+        .master(parser.get("master")).getOrCreate()
+
+    implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication])
+
+
+    val sourcePath = parser.get("sourcePath")
+    val targetPath = parser.get("targetPath")
+    val inputRDD:RDD[String] = spark.sparkContext.textFile(s"$sourcePath")
+
+    logger.info("Converting UnpayWall to OAF")
+    val d:Dataset[Publication] = spark.createDataset(inputRDD.repartition(1000).map(UnpayWallToOAF.convertToOAF).filter(p=>p!=null)).as[Publication]
+    d.write.mode(SaveMode.Overwrite).save(targetPath)
+  }
+
+}

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala

@@ -0,0 +1,63 @@
+package eu.dnetlib.doiboost.uw
+
+import eu.dnetlib.dhp.schema.oaf.{Instance, Publication}
+import org.json4s
+import org.json4s.DefaultFormats
+import org.json4s.jackson.JsonMethods.parse
+import org.slf4j.{Logger, LoggerFactory}
+
+import scala.collection.JavaConverters._
+import eu.dnetlib.doiboost.DoiBoostMappingUtil._
+
+
+
+case class OALocation(evidence:Option[String], host_type:Option[String], is_best:Option[Boolean], license: Option[String], pmh_id:Option[String], updated:Option[String],
+                      url:Option[String], url_for_landing_page:Option[String], url_for_pdf:Option[String], version:Option[String]) {}
+
+
+
+
+object UnpayWallToOAF {
+  val logger: Logger = LoggerFactory.getLogger(getClass)
+
+  def convertToOAF(input:String):Publication = {
+    val pub = new Publication
+
+    implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
+    lazy val json: json4s.JValue = parse(input)
+
+    val doi = (json \"doi").extract[String]
+
+
+    val is_oa = (json\ "is_oa").extract[Boolean]
+
+    val oaLocation:OALocation = (json \ "best_oa_location").extractOrElse[OALocation](null)
+    pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
+    pub.setId(generateIdentifier(pub, doi.toLowerCase))
+
+    pub.setCollectedfrom(List(createUnpayWallCollectedFrom()).asJava)
+    pub.setDataInfo(generateDataInfo())
+
+    if (!is_oa)
+      return null
+
+    if(oaLocation== null || oaLocation.url.isEmpty)
+      return  null
+    val i :Instance= new Instance()
+
+    i.setCollectedfrom(createUnpayWallCollectedFrom())
+    i.setAccessright(createQualifier("Open", "dnet:access_modes"))
+    i.setUrl(List(oaLocation.url.get).asJava)
+
+    if (oaLocation.license.isDefined)
+      i.setLicense(asField(oaLocation.license.get))
+    pub.setInstance(List(i).asJava)
+
+    pub
+
+  }
+
+
+
+
+}

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml

@@ -63,8 +63,8 @@
                 --driver-memory=${sparkDriverMemory}
                 ${sparkExtraOPT}
             </spark-opts>
-            <arg>--sourcePath</arg><arg>${workingPath}/index_dump</arg>
+            <arg>--sourcePath</arg><arg>${workingPath}/crossref/index_dump</arg>
-            <arg>--targetPath</arg><arg>${workingPath}</arg>
+            <arg>--targetPath</arg><arg>${workingPath}/input/crossref</arg>
             <arg>--master</arg><arg>yarn-cluster</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json

@@ -0,0 +1,9 @@
+[
+  {"paramName": "m",    "paramLongName":"master",                    "paramDescription": "the master name",                "paramRequired": true},
+  {"paramName": "cp",   "paramLongName":"crossrefPublicationPath",   "paramDescription": "the Crossref Publication Path",  "paramRequired": true},
+  {"paramName": "cd",   "paramLongName":"crossrefDatasetPath",       "paramDescription": "the Crossref Dataset Path",      "paramRequired": true},
+  {"paramName": "up",   "paramLongName":"uwPublicationPath",         "paramDescription": "the UnpayWall Publication Path", "paramRequired": true},
+  {"paramName": "mp",   "paramLongName":"magPublicationPath",        "paramDescription": "the MAG Publication Path",       "paramRequired": true},
+  {"paramName": "op",   "paramLongName":"orcidPublicationPath",      "paramDescription": "the ORCID Publication Path",     "paramRequired": true},
+  {"paramName": "w",    "paramLongName":"workingDirPath",            "paramDescription": "the Working Path",               "paramRequired": true}
+]

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml

@@ -22,7 +22,7 @@
         </property>
     </parameters>
 
-    <start to="PreprocessMag"/>
+    <start to="ResetWorkingPath"/>
 
 
     <kill name="Kill">

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml

@@ -0,0 +1,38 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+    <property>
+        <name>hive_metastore_uris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>spark2YarnHistoryServerAddress</name>
+        <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
+    <property>
+        <name>spark2ExtraListeners</name>
+        <value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
+    </property>
+</configuration>

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml

@@ -0,0 +1,110 @@
+<workflow-app name="import MAG into HDFS" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>crossrefPublicationPath</name>
+            <description>the Crossref Publication Path</description>
+        </property>
+        <property>
+            <name>crossrefDatasetPath</name>
+            <description>the Crossref Dataset Path</description>
+        </property>
+        <property>
+            <name>uwPublicationPath</name>
+            <description>the UnpayWall Publication Path</description>
+        </property>
+        <property>
+            <name>magPublicationPath</name>
+            <description>the MAG Publication Path</description>
+        </property>
+        <property>
+            <name>orcidPublicationPath</name>
+            <description>the ORCID Publication Path</description>
+        </property>
+        <property>
+            <name>workingDirPath</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="ResetWorkingPath"/>
+
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="ResetWorkingPath">
+        <fs>
+            <delete path='${workingDirPath}'/>
+            <mkdir path='${workingDirPath}'/>
+        </fs>
+        <ok to="CreateDOIBoost"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="CreateDOIBoost">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Create DOIBoost Infospace</name>
+            <class>eu.dnetlib.doiboost.SparkGenerateDoiBoost</class>
+            <jar>dhp-doiboost-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=3840
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>--crossrefPublicationPath</arg><arg>${crossrefPublicationPath}</arg>
+            <arg>--crossrefDatasetPath</arg><arg>${crossrefDatasetPath}</arg>
+            <arg>--uwPublicationPath</arg><arg>${uwPublicationPath}</arg>
+            <arg>--magPublicationPath</arg><arg>${magPublicationPath}</arg>
+            <arg>--orcidPublicationPath</arg><arg>${orcidPublicationPath}</arg>
+            <arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
+            <arg>--master</arg><arg>yarn-cluster</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+
+
+<!--    <action name="PreprocessMag">-->
+<!--        <spark xmlns="uri:oozie:spark-action:0.2">-->
+<!--            <master>yarn-cluster</master>-->
+<!--            <mode>cluster</mode>-->
+<!--            <name>Convert Mag to Dataset</name>-->
+<!--            <class>eu.dnetlib.doiboost.mag.SparkPreProcessMAG</class>-->
+<!--            <jar>dhp-doiboost-${projectVersion}.jar</jar>-->
+<!--            <spark-opts>-->
+<!--                &#45;&#45;executor-memory=${sparkExecutorMemory}-->
+<!--                &#45;&#45;executor-cores=${sparkExecutorCores}-->
+<!--                &#45;&#45;driver-memory=${sparkDriverMemory}-->
+<!--                &#45;&#45;conf spark.sql.shuffle.partitions=3840-->
+<!--                ${sparkExtraOPT}-->
+<!--            </spark-opts>-->
+<!--            <arg>&#45;&#45;sourcePath</arg><arg>${sourcePath}</arg>-->
+<!--            <arg>&#45;&#45;targetPath</arg><arg>${targetPath}</arg>-->
+<!--            <arg>&#45;&#45;master</arg><arg>yarn-cluster</arg>-->
+<!--        </spark>-->
+<!--        <ok to="End"/>-->
+<!--        <error to="Kill"/>-->
+<!--    </action>-->
+
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/config-default.xml

@@ -0,0 +1,38 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+    <property>
+        <name>hive_metastore_uris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>spark2YarnHistoryServerAddress</name>
+        <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
+    <property>
+        <name>spark2ExtraListeners</name>
+        <value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
+    </property>
+</configuration>

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml

@@ -0,0 +1,55 @@
+<workflow-app name="import ORCID into HDFS" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>sourcePath</name>
+            <description>the working dir base path</description>
+        </property>
+        <property>
+            <name>targetPath</name>
+            <description>the working dir base 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="PreprocessORCID"/>
+
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="PreprocessORCID">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Convert ORCID to Dataset</name>
+            <class>eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF</class>
+            <jar>dhp-doiboost-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=3840
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${sourcePath}</arg>
+            <arg>--targetPath</arg><arg>${targetPath}</arg>
+            <arg>--master</arg><arg>yarn-cluster</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml

@@ -0,0 +1,38 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+    <property>
+        <name>hive_metastore_uris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>spark2YarnHistoryServerAddress</name>
+        <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
+    <property>
+        <name>spark2ExtraListeners</name>
+        <value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
+    </property>
+</configuration>

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml

@@ -0,0 +1,55 @@
+<workflow-app name="import UnpayWall into HDFS" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>sourcePath</name>
+            <description>the working dir base path</description>
+        </property>
+        <property>
+            <name>targetPath</name>
+            <description>the working dir base 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="PreprocessUW"/>
+
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="PreprocessUW">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Convert UnpayWall to Dataset</name>
+            <class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</class>
+            <jar>dhp-doiboost-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=3840
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${sourcePath}/json.gz</arg>
+            <arg>--targetPath</arg><arg>${targetPath}</arg>
+            <arg>--master</arg><arg>yarn-cluster</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala

@@ -1,9 +1,8 @@
-package eu.dnetlib.doiboost
+package eu.dnetlib.doiboost.crossref
 
 import eu.dnetlib.dhp.schema.oaf._
 import eu.dnetlib.dhp.utils.DHPUtils
-import eu.dnetlib.doiboost.crossref.Crossref2Oaf
+import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
-import org.codehaus.jackson.map.ObjectMapper
 import org.junit.jupiter.api.Assertions._
 import org.junit.jupiter.api.Test
 import org.slf4j.{Logger, LoggerFactory}
@@ -56,6 +55,29 @@ class CrossrefMappingTest {
 
     })
 
+  }
+
+
+  @Test
+  def testPeerReviewed(): Unit = {
+    val json = Source.fromInputStream(getClass.getResourceAsStream("prwTest.json")).mkString
+    mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
+
+    assertNotNull(json)
+    assertFalse(json.isEmpty);
+
+    val resultList: List[Oaf] = Crossref2Oaf.convert(json)
+
+    assertTrue(resultList.nonEmpty)
+
+    val items = resultList.filter(p => p.isInstanceOf[Result])
+
+
+    items.foreach(p => logger.info(mapper.writeValueAsString(p)))
+
+
+
+
   }
 
   def extractECAward(award: String): String = {

dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala

@@ -0,0 +1,52 @@
+package eu.dnetlib.doiboost.orcid
+
+import eu.dnetlib.dhp.schema.oaf.Publication
+import eu.dnetlib.doiboost.crossref.Crossref2Oaf
+import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
+import org.junit.jupiter.api.Test
+import org.slf4j.{Logger, LoggerFactory}
+import org.junit.jupiter.api.Assertions._
+
+import scala.io.Source
+
+class MappingORCIDToOAFTest {
+  val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
+  val mapper = new ObjectMapper()
+
+  @Test
+  def testExtractData():Unit ={
+    val json = Source.fromInputStream(getClass.getResourceAsStream("dataOutput")).mkString
+    assertNotNull(json)
+    assertFalse(json.isEmpty)
+    json.lines.foreach(s => {
+      assertNotNull(ORCIDToOAF.extractValueFromInputString(s))
+    })
+  }
+
+
+  @Test
+  def testConvertOrcidToOAF():Unit ={
+    val json = Source.fromInputStream(getClass.getResourceAsStream("dataOutput")).mkString
+    mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
+
+    assertNotNull(json)
+    assertFalse(json.isEmpty)
+//    json.lines.foreach(s => {
+//
+//    })
+
+
+    val p :Publication = ORCIDToOAF.convertTOOAF(json.lines.next())
+
+
+    logger.info(mapper.writeValueAsString(p))
+  }
+
+
+
+
+
+
+
+
+}

dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala

@@ -0,0 +1,49 @@
+package eu.dnetlib.doiboost.uw
+
+import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
+import org.junit.jupiter.api.Test
+
+import scala.io.Source
+import org.junit.jupiter.api.Assertions._
+import org.slf4j.{Logger, LoggerFactory}
+
+class UnpayWallMappingTest {
+
+  val logger: Logger = LoggerFactory.getLogger(getClass)
+  val mapper = new ObjectMapper()
+
+
+  @Test
+  def testMappingToOAF():Unit ={
+
+    val Ilist = Source.fromInputStream(getClass.getResourceAsStream("input.json")).mkString
+
+
+    for (line <-Ilist.lines) {
+
+
+      val p = UnpayWallToOAF.convertToOAF(line)
+
+      if(p!= null) {
+        assertTrue(p.getPid.size()==1)
+        logger.info(p.getId)
+      }
+      assertNotNull(line)
+      assertTrue(line.nonEmpty)
+    }
+    mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
+
+
+     val l = Ilist.lines.next()
+
+    logger.info(mapper.writeValueAsString(UnpayWallToOAF.convertToOAF(l)))
+
+
+
+
+
+
+
+  }
+
+}

dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/dataOutput

@@ -0,0 +1,309 @@
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+(10.1016/j.mjafi.2016.05.007,[{"oid":"0000-0002-4342-6656","name":"Anoop","surname":"Sharma","creditName":null,"errorCode":null}])
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