Merge branch 'stable_ids' of https://code-repo.d4science.org/D-Net/dnet-hadoop into stable_ids

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

@@ -31,7 +31,7 @@
         </property>
         <property>
             <name>sparkExecutorMemory</name>
-            <value>2G</value>
+            <value>4G</value>
             <description>memory for individual executor</description>
         </property>
         <property>
@@ -190,6 +190,14 @@
             <arg>-o</arg><arg>downloads/updated_works</arg>
             <arg>-t</arg><arg>${token}</arg>
         </spark>
+        <ok to="ResetNewAuthors"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="ResetNewAuthors">
+        <fs>
+            <delete path='${workingPath}/orcid_dataset/new_authors'/>
+        </fs>
         <ok to="UpdateOrcidAuthors"/>
         <error to="Kill"/>
     </action>
@@ -217,6 +225,14 @@
             <arg>-o</arg><arg>-</arg>
             <arg>-t</arg><arg>-</arg>
         </spark>
+        <ok to="ResetNewWorks"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="ResetNewWorks">
+        <fs>
+            <delete path='${workingPath}/orcid_dataset/new_works'/>
+        </fs>
         <ok to="UpdateOrcidWorks"/>
         <error to="Kill"/>
     </action>
@@ -270,15 +286,6 @@
             <arg>${workingPath}/orcid_dataset/new_works/*</arg>
             <arg>${workingPath}/orcid_dataset/works</arg>
         </distcp>
-        <ok to="CleanWorkingPath"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="CleanWorkingPath">
-        <fs>
-            <delete path='${workingPath}/orcid_dataset/new_authors'/>
-            <delete path='${workingPath}/orcid_dataset/new_works'/>
-        </fs>
         <ok to="updateLastOrcidAuthorsDataset"/>
         <error to="Kill"/>
     </action>
@@ -309,5 +316,5 @@
         <error to="Kill"/>
     </action>
 
-   <end name="End"/>
+    <end name="End"/>
 </workflow-app>

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/sx/pangaea/PangaeaUtils.scala

@@ -1,6 +1,5 @@
 package eu.dnetlib.sx.pangaea
 
-
 import org.apache.spark.sql.expressions.Aggregator
 import org.apache.spark.sql.{Encoder, Encoders}
 import org.json4s
@@ -9,11 +8,13 @@ import org.json4s.jackson.JsonMethods.parse
 
 import java.text.SimpleDateFormat
 import java.util.Date
+import java.util.regex.Pattern
+import scala.language.postfixOps
+import scala.xml.{Elem, Node, XML}
 
-
+case class PangaeaDataModel(identifier:String, title:List[String], objectType:List[String], creator:List[String],
-case class PangaeaDataModel(datestamp:String, identifier:String, xml:String) {}
+                            publisher:List[String], dataCenter :List[String],subject :List[String], language:String,
-
+                            rights:String, parent:String,relation :List[String],linkage:List[(String,String)] ) {}
-
 
 object PangaeaUtils {
 
@@ -21,14 +22,46 @@ object PangaeaUtils {
   def toDataset(input:String):PangaeaDataModel = {
     implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
     lazy val json: json4s.JValue = parse(input)
-
-    val  d = new Date()
-    val s:String =  s"${new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS")format(d)}Z"
-
-    val ds = (json \ "internal-datestamp").extractOrElse[String](s)
-    val identifier= (json \ "metadatalink").extractOrElse[String]("")
     val xml= (json \ "xml").extract[String]
-    PangaeaDataModel(ds, identifier,xml)
+    parseXml(xml)
+  }
+
+  def findDOIInRelation( input:List[String]):List[String] = {
+    val pattern = Pattern.compile("\\b(10[.][0-9]{4,}(?:[.][0-9]+)*\\/(?:(?![\"&\\'<>])\\S)+)\\b")
+    input.map(i => {
+      val matcher = pattern.matcher(i)
+      if (matcher.find())
+        matcher.group(0)
+      else
+        null
+    }).filter(i => i!= null)
+  }
+
+  def attributeOpt(attribute: String, node:Node): Option[String] =
+    node.attribute(attribute) flatMap (_.headOption) map (_.text)
+
+  def extractLinkage(node:Elem):List[(String, String)] = {
+    (node \ "linkage").map(n =>(attributeOpt("type",n), n.text)).filter(t => t._1.isDefined).map(t=> (t._1.get, t._2))(collection.breakOut)
+  }
+
+  def parseXml(input:String):PangaeaDataModel = {
+    val xml = XML.loadString(input)
+
+    val identifier = (xml \ "identifier").text
+    val title :List[String] = (xml \ "title").map(n => n.text)(collection.breakOut)
+    val pType :List[String] = (xml \ "type").map(n => n.text)(collection.breakOut)
+    val creators:List[String] = (xml \ "creator").map(n => n.text)(collection.breakOut)
+    val publisher :List[String] = (xml \ "publisher").map(n => n.text)(collection.breakOut)
+    val dataCenter :List[String] = (xml \ "dataCenter").map(n => n.text)(collection.breakOut)
+    val subject :List[String] = (xml \ "subject").map(n => n.text)(collection.breakOut)
+    val language= (xml \ "language").text
+    val rights= (xml \ "rights").text
+    val parentIdentifier= (xml \ "parentIdentifier").text
+    val relation :List[String] = (xml \ "relation").map(n => n.text)(collection.breakOut)
+    val relationFiltered = findDOIInRelation(relation)
+    val linkage:List[(String,String)] = extractLinkage(xml)
+
+    PangaeaDataModel(identifier,title, pType, creators,publisher, dataCenter, subject, language, rights, parentIdentifier, relationFiltered, linkage)
   }
 
 
@@ -44,11 +77,9 @@ object PangaeaUtils {
           if (a == null)
             b
           else {
-            val ts1 = b.datestamp
+            if (b.title != null && b.title.nonEmpty)
-            val ts2 = a._2.datestamp
-            if (ts1 > ts2)
               b
-            else
+              else
               a._2
 
           }
@@ -62,9 +93,7 @@ object PangaeaUtils {
           if (b2 == null)
             b1
           else {
-            val ts1 = b1.datestamp
+            if (b1.title != null && b1.title.nonEmpty)
-            val ts2 = b2.datestamp
-            if (ts1 > ts2)
               b1
             else
               b2

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/sx/pangaea/SparkGeneratePanagaeaDataset.scala

@@ -42,7 +42,7 @@ object SparkGeneratePanagaeaDataset {
        .groupByKey(_._1)(Encoders.STRING)
       .agg(PangaeaUtils.getDatasetAggregator().toColumn)
       .map(s => s._2)
-      .write.mode(SaveMode.Overwrite).save(s"$workingPath/dataset_updated")
+      .write.mode(SaveMode.Overwrite).save(s"$workingPath/dataset")
 
   }
 

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/pangaea/PangaeaTransformTest.scala

@@ -1,9 +1,12 @@
 package eu.dnetlib.dhp.sx.pangaea
 
+import eu.dnetlib.sx.pangaea.PangaeaUtils
 import org.junit.jupiter.api.Test
+
 import java.util.TimeZone
 import java.text.SimpleDateFormat
 import java.util.Date
+import scala.io.Source
 class PangaeaTransformTest {
 
 
@@ -15,11 +18,12 @@ class PangaeaTransformTest {
 
     val  d = new Date()
 
-    val s:String =  s"${new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS")format(d)}Z"
+    val s:String =  s"${new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS")format d}Z"
-
-
     println(s)
 
+
+    val xml = Source.fromInputStream(getClass.getResourceAsStream("input.xml")).mkString
+    println(PangaeaUtils.parseXml(xml))
   }
 
 }

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/pangaea/input.xml

@@ -0,0 +1,91 @@
+<dataset xmlns="urn:pangaea.de:dataportals" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <dc:title>The inorganic carbon system measured and calculated on Cibicidoides cf. wuellerstorfi of sediment core PS75/100-1</dc:title>
+    <dc:creator>Kersten, Franziska</dc:creator>
+    <dc:creator>Tiedemann, Ralf</dc:creator>
+    <dc:creator>Fietzke, Jan</dc:creator>
+    <dc:creator>Frische, Matthias</dc:creator>
+    <principalInvestigator>Tiedemann, Ralf</principalInvestigator>
+    <dc:publisher>PANGAEA</dc:publisher>
+    <dataCenter>PANGAEA: Data Publisher for Earth &amp; Environmental Science</dataCenter>
+    <dc:date>2013-10-21</dc:date>
+    <dc:type>Dataset</dc:type>
+    <dc:format>text/tab-separated-values, 8 data points</dc:format>
+    <dc:identifier>https://doi.org/10.1594/PANGAEA.820647</dc:identifier>
+    <parentIdentifier>https://doi.org/10.1594/PANGAEA.821013</parentIdentifier>
+    <dc:language>en</dc:language>
+    <dc:rights>CC-BY-3.0: Creative Commons Attribution 3.0 Unported</dc:rights>
+    <dc:relation>Kersten, Franziska (2013): Last Glacial to Holocene changes of deep and intermediate water carbonate ion concentrations in the Southern Ocean: constraints from foraminiferal Boron/Calcium ratios. PhD Thesis, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven</dc:relation>
+    <dc:relation>Kersten, Franziska; Tiedemann, Ralf; Fietzke, Jan; Frische, Matthias (2013): The B/Ca proxy for past seawater carbonate chemistry reconstructions-laser ablation based calibrations for C. mundulus, C. wuellerstorfi and its morphotype C. cf. wuellerstorfi. Climate of the Past Discussions, 9(4), 4425-4448, https://doi.org/10.5194/cpd-9-4425-2013</dc:relation>
+    <dc:relation>Kersten, Franziska (2013): CO2sys Input variables estimated from nearby GLODAP sites. hdl:10013/epic.42543.d001</dc:relation>
+    <dc:subject type="parameter" xsi:type="SubjectType">DEPTH, sediment/rock</dc:subject>
+    <dc:subject type="parameter" xsi:type="SubjectType">Cibicidoides cf. wuellerstorfi, Boron/Calcium ratio</dc:subject>
+    <dc:subject type="parameter" xsi:type="SubjectType">Cibicidoides cf. wuellerstorfi, Boron/Calcium standard deviation</dc:subject>
+    <dc:subject type="parameter" xsi:type="SubjectType">Δ carbonate ion content</dc:subject>
+    <dc:subject type="parameter" xsi:type="SubjectType">Carbonate ion</dc:subject>
+    <dc:subject type="method" xsi:type="SubjectType">LA-ICP-MS, Laser-ablation inductively coupled plasma mass spectrometer</dc:subject>
+    <dc:subject type="method" xsi:type="SubjectType">Calculated</dc:subject>
+    <dc:subject type="project" xsi:type="SubjectType">AWI_Paleo: Paleoenvironmental Reconstructions from Marine Sediments @ AWI</dc:subject>
+    <dc:subject type="platform" xsi:type="SubjectType">Polarstern</dc:subject>
+    <dc:subject type="sensor" xsi:type="SubjectType">MultiCorer</dc:subject>
+    <dc:subject type="sensor" xsi:type="SubjectType">MUC</dc:subject>
+    <dc:subject type="feature" xsi:type="SubjectType">PS75/100-1</dc:subject>
+    <dc:subject type="feature" xsi:type="SubjectType">ANT-XXVI/2</dc:subject>
+    <dc:subject type="feature" xsi:type="SubjectType">PS75 BIPOMAC</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">citable</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">deNBIchemical</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">author20400</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">author32978</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">author49036</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">author49445</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">basis1</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">campaign33969</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">event2584362</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">geocode1</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">geocode1599</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">geocode1600</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">geocode1601</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">geocode8128</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">inst32</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">journal16751</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">license101</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">method10668</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">method4872</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">method50</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">param131203</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">param131204</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">param7034</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">param82364</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">pi20400</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">project1</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">ref60902</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">ref60959</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">ref61047</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">term1045260</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">term1073131</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">term19836</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">term21005</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">term2663825</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">term33871</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">term37764</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">term38263</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">term38520</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">term41056</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">term43863</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">term44030</dc:subject>
+    <dc:subject type="pangaea-tech-keyword" xsi:type="SubjectType">topotype3</dc:subject>
+    <dc:coverage xsi:type="CoverageType">
+        <northBoundLatitude>-45.75757</northBoundLatitude>
+        <westBoundLongitude>177.14887</westBoundLongitude>
+        <southBoundLatitude>-45.75757</southBoundLatitude>
+        <eastBoundLongitude>177.14887</eastBoundLongitude>
+        <location>South Pacific Ocean</location>
+        <minElevation>0.0 m (DEPTH, sediment/rock)</minElevation>
+        <maxElevation>0.01 m (DEPTH, sediment/rock)</maxElevation>
+        <startDate>2010-01-22</startDate>
+        <endDate>2010-01-22</endDate>
+    </dc:coverage>
+    <linkage type="metadata">https://doi.pangaea.de/10.1594/PANGAEA.820647</linkage>
+    <linkage type="data">https://doi.pangaea.de/10.1594/PANGAEA.820647?format=textfile</linkage>
+    <additionalContent>7x(14-22)</additionalContent>
+    <additionalContent>Reconstruction equation: B/Ca = 2.27(D[CO32-]) + 152.5 (R2= 0.76)</additionalContent>
+</dataset>