added date of collection, resource type as workflow parameter

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/bioschema/generate_dataset_params.json

@@ -40,5 +40,11 @@
     "paramLongName": "datasourceKey",
     "paramDescription": "the key that identifies the datasource",
     "paramRequired": true
+  },
+  {
+    "paramName": "p",
+    "paramLongName": "profile",
+    "paramDescription": "resource profile",
+    "paramRequired": true
   }
 ]

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

@@ -10,6 +10,11 @@
             <value>ped</value>
             <description>the key that identifies the datasource (eg ped, disprot)</description>
         </property>
+        <property>
+            <name>profile</name>
+            <value>protein</value>
+            <description>resource profile (eg protein, gene)</description>
+        </property>
     </parameters>
 
     <start to="TransformJob"/>
@@ -57,6 +62,7 @@
             <arg>--targetPath</arg><arg>${mainPath}/dataset</arg>
             <arg>--exportLinks</arg><arg>true</arg>
             <arg>--datasourceKey</arg><arg>${datasourceKey}</arg>
+            <arg>--profile</arg><arg>${profile}</arg>
             <arg>--master</arg><arg>yarn-cluster</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/bioschema/BioschemaModelConstants.scala

@@ -1,7 +1,7 @@
 package eu.dnetlib.dhp.bioschema
 
 import eu.dnetlib.dhp.schema.common.ModelConstants
-import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
+import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue, Qualifier}
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
 
 import java.time.format.DateTimeFormatter
@@ -61,6 +61,9 @@ class BioschemaModelConstants extends Serializable {}
 
 object BioschemaModelConstants {
 
+  val PROTEIN_RESOURCETYPE: Qualifier =
+    qualifier("protein", "protein", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)
+
   val DATA_INFO: DataInfo = OafMapperUtils.dataInfo(
     false,
     null,
@@ -273,4 +276,12 @@ object BioschemaModelConstants {
     Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE)
   )
 
+  private def qualifier(classid: String, classname: String, schemeid: String, schemename: String) = {
+    val q = new Qualifier
+    q.setClassid(classid)
+    q.setClassname(classname)
+    q.setSchemeid(schemeid)
+    q.setSchemename(schemename)
+    q
+  }
 }

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/bioschema/BioschemaToOAFTransformation.scala

@@ -11,7 +11,9 @@ import org.json4s.DefaultFormats
 import org.json4s.JsonAST.{JField, JObject, JString}
 import org.json4s.jackson.JsonMethods.parse
 
+import java.text.SimpleDateFormat
 import java.time.LocalDate
+import java.util.{Date, Locale}
 import scala.collection.JavaConverters._
 
 object BioschemaToOAFTransformation {
@@ -46,19 +48,20 @@ object BioschemaToOAFTransformation {
     d
   }
 
-  def getResult(): Result = {
+  def getResult(resourceClassName: String): Result = {
     val i = new Instance
-    i.setInstancetype(
-      OafMapperUtils.qualifier(
-        "0046",
-        "Bioentity",
-        ModelConstants.DNET_PUBLICATION_RESOURCE,
-        ModelConstants.DNET_PUBLICATION_RESOURCE
-      )
-    )
-    val d = new OafDataset
-    d.setInstance(List(i).asJava)
-    return d
+    resourceClassName.toUpperCase() match {
+      case "PROTEIN" =>
+        i.setInstancetype(
+          PROTEIN_RESOURCETYPE
+        )
+        val d = new OafDataset
+        d.setInstance(List(i).asJava)
+        d.setResourcetype(
+          PROTEIN_RESOURCETYPE
+        )
+        return d
+    }
     null
   }
 
@@ -69,19 +72,14 @@ object BioschemaToOAFTransformation {
   def generateOAF(
     input: String,
     exportLinks: Boolean,
-    datasourceKey: String
+    datasourceKey: String,
+    resourceClassName: String
   ): List[Oaf] = {
 
     implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
     lazy val json = parse(input)
 
-    val resourceType = (json \ "types" \ "resourceType").extractOrElse[String](null)
-    val resourceTypeGeneral =
-      (json \ "types" \ "resourceTypeGeneral").extractOrElse[String](null)
-    val schemaOrg = (json \ "types" \ "schemaOrg").extractOrElse[String](null)
-
-    val result = getResult(
-    )
+    val result = getResult(resourceClassName)
     if (result == null)
       return List()
 
@@ -101,7 +99,6 @@ object BioschemaToOAFTransformation {
     )
     result.setId(OafMapperUtils.createOpenaireId(50, s"${datasourceKeyPrefix(datasourceKey)}::$pid", true))
     result.setOriginalId(List(pid).asJava)
-
     result.setDataInfo(dataInfo)
 
     val titles: List[TitleType] = (json \\ "titles").extractOrElse[List[TitleType]](List())
@@ -117,30 +114,15 @@ object BioschemaToOAFTransformation {
     )
 
     val dates = (json \\ "dates").extract[List[DateType]]
-    val publication_year = (json \\ "publicationYear").extractOrElse[String](null)
 
-    val i_date = dates
+    val collected_date = dates
       .filter(d => d.date.isDefined && d.dateType.isDefined)
-      .find(d => d.dateType.get.equalsIgnoreCase("issued"))
-      .map(d => extract_date(d.date.get))
-    val a_date: Option[String] = dates
-      .filter(d => d.date.isDefined && d.dateType.isDefined && d.dateType.get.equalsIgnoreCase("available"))
+      .find(d => d.dateType.get.equalsIgnoreCase("collected"))
       .map(d => extract_date(d.date.get))
       .find(d => d != null && d.isDefined)
       .map(d => d.get)
-
-    if (a_date.isDefined) {
-      result.setEmbargoenddate(OafMapperUtils.field(a_date.get, null))
-    }
-    if (i_date.isDefined && i_date.get.isDefined) {
-      result.setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
-      result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
-    } else if (publication_year != null) {
-      result.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
-      result
-        .getInstance()
-        .get(0)
-        .setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
+    if (collected_date.isDefined) {
+      result.setDateofcollection(collected_date.get)
     }
 
     result.setRelevantdate(
@@ -242,7 +224,7 @@ object BioschemaToOAFTransformation {
       relations = relations ::: generateRelations(
         rels,
         result.getId,
-        if (i_date.isDefined && i_date.get.isDefined) i_date.get.get else null,
+        null,
         pid,
         datasourceKey
       )

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/bioschema/GenerateBioschemaDatasetSpark.scala

@@ -24,6 +24,8 @@ class GenerateBioschemaDatasetSpark(propertyPath: String, args: Array[String], l
     log.info(s"exportLinks is '$exportLinks'")
     val datasourceKey = parser.get("datasourceKey").toLowerCase
     log.info(s"datasourceKey is '$datasourceKey'")
+    val profile = parser.get("profile").toLowerCase
+    log.info(s"profile is '$profile'")
 
 //    val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
 //    log.info(s"mdstoreOutputVersion is '$mdstoreOutputVersion'")
@@ -36,7 +38,7 @@ class GenerateBioschemaDatasetSpark(propertyPath: String, args: Array[String], l
 
     val targetPath = parser.get("targetPath")
 
-    generateBioschemaDataset(sourcePath, exportLinks, targetPath, datasourceKey, spark)
+    generateBioschemaDataset(sourcePath, exportLinks, targetPath, datasourceKey, profile, spark)
 
 //    reportTotalSize(targetPath, outputBasePath)
   }
@@ -66,6 +68,7 @@ class GenerateBioschemaDatasetSpark(propertyPath: String, args: Array[String], l
     exportLinks: Boolean,
     targetPath: String,
     datasourceKey: String,
+    profile: String,
     spark: SparkSession
   ): Unit = {
     require(spark != null)
@@ -75,7 +78,7 @@ class GenerateBioschemaDatasetSpark(propertyPath: String, args: Array[String], l
       spark.createDataset(
         spark.sparkContext
           .textFile(sourcePath)
-          .flatMap(i => BioschemaToOAFTransformation.generateOAF(i, exportLinks, datasourceKey))
+          .flatMap(i => BioschemaToOAFTransformation.generateOAF(i, exportLinks, datasourceKey, profile))
       ),
       targetPath
     )

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/bioschema/BioschemaDataciteToOAFTest.scala

@@ -46,13 +46,13 @@ class BioschemaDataciteToOAFTest {
     val instance = new GenerateBioschemaDatasetSpark(null, null, log)
     val targetPath = s"$workingDir/result"
 
-    instance.generateBioschemaDataset(path, exportLinks = true, targetPath, "ped", spark)
+    instance.generateBioschemaDataset(path, exportLinks = true, targetPath, "ped", "protein", spark)
 
     val total_items = spark.read.text(targetPath).count()
     println(s"total_items: $total_items")
     assertTrue(total_items == 50)
 
-    instance.generateBioschemaDataset(path, exportLinks = false, targetPath, "ped", spark)
+    instance.generateBioschemaDataset(path, exportLinks = false, targetPath, "ped", "protein", spark)
 
     val total_datasets = spark.read.text(targetPath).count()
     println(s"total_datasets: $total_datasets")
@@ -67,7 +67,7 @@ class BioschemaDataciteToOAFTest {
       .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/bioschema/ped_record.json"))
       .mkString
     val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
-    val res: List[Oaf] = BioschemaToOAFTransformation.generateOAF(record, true, "ped")
+    val res: List[Oaf] = BioschemaToOAFTransformation.generateOAF(record, true, "ped", "protein")
     res.foreach(r => {
       println(mapper.writeValueAsString(r))
       println("----------------------------")