test and fix ro-crate propertyValue parsing

Author: HLWeil

src/Core/OntologyAnnotation.fs

@@ -55,13 +55,14 @@ type OntologyAnnotation(?name,?tsr,?tan, ?comments) =
         $"{Url.OntobeeOboPurl}{termSourceRef}_{localTAN}"
 
     /// Will always be created without `OntologyAnnotion.Name`
-    static member fromTermAnnotation (tan : string) =
+    static member fromTermAnnotation (tan : string, ?name) =
+        let name = Option.defaultValue "" name
         tan
         |> Regex.tryParseTermAnnotation
         |> Option.get 
         |> fun r ->
             let accession = r.IDSpace + ":" + r.LocalID
-            OntologyAnnotation.create ("", r.IDSpace, accession)
+            OntologyAnnotation.create (name, r.IDSpace, accession)
 
     /// Parses any value in `TermAccessionString` to term accession format "termsourceref:localtan". Exmp.: "MS:000001".
     ///

src/Json/Process/PropertyValue.fs

@@ -57,17 +57,21 @@ module PropertyValue =
                 let category =
                     let name = get.Optional.Field "category" Decode.string
                     let code = get.Optional.Field "categoryCode" Decode.string
-                    if name.IsNone && code.IsNone then None
-                    else Some(OntologyAnnotation.create(?name = name, ?tan = code))
+                    match name, code with
+                    | None, None -> None
+                    | _, None -> Some(OntologyAnnotation.create(?name = name))
+                    | _, Some code -> Some(OntologyAnnotation.fromTermAnnotation(code, ?name = name))
                 let value = 
-                    let value = get.Optional.Field "value" Decode.string
+                    let value = get.Optional.Field "value" AnnotationValue.decoder
                     let code = get.Optional.Field "valueCode" Decode.string
                     if value.IsNone && code.IsNone then None
                     else Value.fromOptions value None code
                 let unit = 
                     let name = get.Optional.Field "unit" Decode.string
                     let code = get.Optional.Field "unitCode" Decode.string
-                    if name.IsNone && code.IsNone then None
-                    else Some(OntologyAnnotation.create(?name = name, ?tan = code))
+                    match name, code with
+                    | None, None -> None
+                    | _, None -> Some(OntologyAnnotation.create(?name = name))
+                    | _, Some code -> Some(OntologyAnnotation.fromTermAnnotation(code, ?name = name))
                 create category value unit 
             )

src/Json/Study.fs

@@ -170,7 +170,7 @@ module Study =
         /// <param name="assays"></param>
         let encoder (assays: ArcAssay list option) (s : ArcStudy) = 
             let study = s.Copy(true)
-            let fileName = Identifier.Assay.fileNameFromIdentifier study.Identifier
+            let fileName = Identifier.Study.fileNameFromIdentifier study.Identifier
             let assaysRaw = Helper.getAssayInformation assays study
             let assays = 
                 let n = ResizeArray()

tests/Json/ARCtrl.Json.Tests.fsproj

@@ -26,6 +26,7 @@
     <Compile Include="Assay.Tests.fs" />
     <Compile Include="Study.Tests.fs" />
     <Compile Include="Investigation.Tests.fs" />
+    <Compile Include="Process\ProcessParameterValue.fs" />
     <Compile Include="Process\ProcessInput.Tests.fs" />
     <Compile Include="Process\Protocol.Tests.fs" />
     <Compile Include="Process\Process.Tests.fs" />

tests/Json/Main.fs

@@ -16,6 +16,7 @@ let all = testSequenced <| testList "Json" [
     Tests.Study.main
     Tests.Investigation.main
     Tests.Template.main
+    Tests.Process.ProcessParameterValue.main
     Tests.Process.ProcessInput.main
     Tests.Process.Protocol.main
     Tests.Process.Process.main

tests/Json/Process/ProcessParameterValue.fs

@@ -0,0 +1,40 @@
+module Tests.Process.ProcessParameterValue
+
+open ARCtrl
+open ARCtrl.Process
+open ARCtrl.Json
+open TestingUtils
+open TestObjects.Json
+
+let private tests_roCrate =
+    testList "RO-Crate" [
+        testCase "ReadWriteIntegerValue" (fun () -> 
+            let pp = ProtocolParameter.create(ParameterName = OntologyAnnotation("temperature","NCIT","http://purl.obolibrary.org/obo/NCIT_0000029"))
+            let value = Value.Int 25
+            let unit = OntologyAnnotation("degree Celsius","UO","http://purl.obolibrary.org/obo/UO_0000185")
+            let ppv = ProcessParameterValue.create(pp,value,unit)
+
+            let roCrate = ProcessParameterValue.toROCrateJsonString() ppv
+            let ppv2 = ProcessParameterValue.fromROCrateJsonString roCrate
+
+            Expect.equal ppv ppv2 "RO-Crate roundtrip failed"
+        )
+        testCase "ReadWriteOntologyValue" (fun () -> 
+            let pp = ProtocolParameter.create(ParameterName = OntologyAnnotation("organism","NCIT","http://purl.obolibrary.org/obo/NCIT_0000029"))
+            let value = Value.Ontology (OntologyAnnotation(
+                "chlamydomonas reinhardtii",
+                 "NCIT",
+                 "http://purl.obolibrary.org/obo/NCIT_0000030"
+            ))
+            let ppv = ProcessParameterValue.create(pp,value)
+
+            let roCrate = ProcessParameterValue.toROCrateJsonString() ppv
+            let ppv2 = ProcessParameterValue.fromROCrateJsonString roCrate
+
+            Expect.equal ppv ppv2 "RO-Crate roundtrip failed"
+        )
+    ]
+
+let main = testList "ProcessParameterValue" [
+    tests_roCrate
+]