added ped test with doi citation; fix pmid pid type

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

@@ -2,12 +2,12 @@
     <parameters>
         <property>
             <name>mainPath</name>
-            <value>/data/bioschema/mobidb</value>
+            <value>/data/bioschema/ped</value>
             <description>the working path of Bioschema stores</description>
         </property>
         <property>
             <name>datasourceKey</name>
-            <value>mobidb</value>
+            <value>ped</value>
             <description>the key that identifies the datasource (eg ped, disprot, mobidb)</description>
         </property>
         <property>

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

@@ -62,7 +62,7 @@ class BioschemaModelConstants extends Serializable {}
 object BioschemaModelConstants {
 
   val PROTEIN_RESOURCETYPE: Qualifier =
-    qualifier("protein", "protein", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)
+    qualifier("0047", "Protein", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)
 
   val DATA_INFO: DataInfo = OafMapperUtils.dataInfo(
     false,
@@ -73,35 +73,35 @@ object BioschemaModelConstants {
     "0.9"
   )
 
-  val PED_PREFIX: String = "ped_________"
+  val PED_PREFIX: String = "fsh_____3595"
-  val DISPROT_PREFIX: String = "disprot_____"
+  val DISPROT_PREFIX: String = "fsh_____1904"
-  val MOBIDB_PREFIX: String = "mobidb______"
+  val MOBIDB_PREFIX: String = "fsh_____2176"
 
   val resolvedURLPattern: Map[String, String] = Map(
-    "https://identifiers.org/pubmed:"  -> "pubmed",
+    "https://identifiers.org/pubmed:"  -> "pmid",
     "http://purl.uniprot.org/uniprot/" -> "uniprot",
     "https://identifiers.org/uniprot:" -> "uniprot",
     "https://identifiers.org/disprot:" -> "disprot",
-    "https://identifiers.org/mobidb:"  -> "mobidb"
+    "https://identifiers.org/mobidb:"  -> "mobidb",
+    "https://doi.org/"                 -> "doi"
   )
 
-  //TODO create DatasourceId and update those value
   val collectedFromMap: Map[String, KeyValue] = {
     val PEDCollectedFrom: KeyValue = OafMapperUtils.keyValue(
-      "10|ped_________::pedDatasourceId",
+      "10|fairsharing_::c0e8517b1fe0b5270f3f41d4b56d6118",
       "Protein Ensemble Database"
     )
     PEDCollectedFrom.setDataInfo(DATA_INFO)
 
     val DISPROTCollectedFrom: KeyValue = OafMapperUtils.keyValue(
-      "10|disprot_____::disprotDatasourceId",
+      "10|fairsharing_::c91591a8d461c2869b9f535ded3e213e",
-      "DisProt, the database of intrinsically disordered proteins"
+      "Database of Protein Disorder"
     )
     DISPROTCollectedFrom.setDataInfo(DATA_INFO)
 
     val MOBIDBCollectedFrom: KeyValue = OafMapperUtils.keyValue(
-      "10|mobidb______::mobidbDatasourceId",
+      "10|fairsharing_::0234c510bc6d908b28c70ff313743079",
-      "MobiDB, a database of protein disorder and mobility annotations"
+      "MobiDB"
     )
     MOBIDBCollectedFrom.setDataInfo(DATA_INFO)
 

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/bioschema/ped_doi_citation.json

@@ -0,0 +1,80 @@
+{
+  "id": "PED00180#Q9KPH3_A_0",
+  "types": {
+    "resourceType": "Protein",
+    "resourceTypeGeneral": "Dataset"
+  },
+  "creators": [],
+  "identifiers": [
+    {
+      "identifier": "https://proteinensemble.org/PED00180#Q9KPH3_A_0",
+      "identifierType": "URL"
+    }
+  ],
+  "relatedIdentifiers": [
+    {
+      "relationType": "IsCitedBy",
+      "relatedIdentifier": "https://doi.org/10.1016/j.jsb.2020.107573",
+      "relatedIdentifierType": "URL"
+    },
+    {
+      "relationType": "IsIdenticalTo",
+      "relatedIdentifier": "http://purl.uniprot.org/uniprot/Q9KPH3",
+      "relatedIdentifierType": "URL"
+    }
+  ],
+  "alternateIdentifiers": [
+    {
+      "alternateIdentifier": "https://identifiers.org/uniprot:Q9KPH3"
+    }
+  ],
+  "descriptions": [],
+  "titles": [
+    {
+      "title": "PED00180#Q9KPH3_A_0 - Structural ensemble of protein DciA from Vibrio cholerae (1-157) "
+    }
+  ],
+  "dates": [
+    {
+      "date": "2022-05-10T18:03:43",
+      "dateType": "Collected"
+    }
+  ],
+  "subjects": [
+    {
+      "schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00120",
+      "value": "NMR",
+      "subjectScheme": "IDPO:00120"
+    },
+    {
+      "schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00125",
+      "value": "SAXS",
+      "subjectScheme": "IDPO:00125"
+    },
+    {
+      "schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00224",
+      "value": "GROMACS",
+      "subjectScheme": "IDPO:00224"
+    },
+    {
+      "schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00228",
+      "value": "AMBER",
+      "subjectScheme": "IDPO:00228"
+    },
+    {
+      "schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl:00185",
+      "value": "FM",
+      "subjectScheme": "IDPO:00185"
+    },
+    {
+      "schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl:00213",
+      "value": "EOM",
+      "subjectScheme": "IDPO:00213"
+    },
+    {
+      "schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl:00214",
+      "value": "GAJOE",
+      "subjectScheme": "IDPO:00214"
+    }
+  ]
+}

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

@@ -99,4 +99,17 @@ class BioschemaDataciteToOAFTest {
       println("----------------------------")
     })
   }
+
+  @Test
+  def testPEDDoiCitationMapping(): Unit = {
+    val record = Source
+      .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/bioschema/ped_doi_citation.json"))
+      .mkString
+    val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
+    val res: List[Oaf] = BioschemaToOAFTransformation.generateOAF(record, true, "ped", "protein")
+    res.foreach(r => {
+      println(mapper.writeValueAsString(r))
+      println("----------------------------")
+    })
+  }
 }