make process conversion more robust against different outputs

src/Core/Conversion.fs

@@ -100,23 +100,32 @@ module JsonTypes =
         let c = MaterialAttribute.create(CharacteristicType = header.ToTerm())
         MaterialAttributeValue.create(Category = c,?Value = v,?Unit = u)
 
+    let composeFreetextMaterialName (headerFT : string) (name : string) =
+        $"{headerFT}={name}"
+
+
     /// Convert a CompositeHeader and Cell tuple to a ISA ProcessInput
     let composeProcessInput (header : CompositeHeader) (value : CompositeCell) : ProcessInput =
         match header with
         | CompositeHeader.Input IOType.Source -> ProcessInput.createSource(value.ToString())
         | CompositeHeader.Input IOType.Sample -> ProcessInput.createSample(value.ToString())
         | CompositeHeader.Input IOType.Material -> ProcessInput.createMaterial(value.ToString())
         | CompositeHeader.Input IOType.Data -> ProcessInput.createRawData(value.ToString())
+        | CompositeHeader.Input (IOType.FreeText ft) ->
+            ProcessInput.createMaterial(composeFreetextMaterialName ft (value.ToString()))
         | _ ->
             failwithf "Could not parse input header %O" header
 
 
     /// Convert a CompositeHeader and Cell tuple to a ISA ProcessOutput
     let composeProcessOutput (header : CompositeHeader) (value : CompositeCell) : ProcessOutput =
         match header with
-        | CompositeHeader.Output IOType.Sample -> ProcessOutput.createSample(value.ToString())
+        | CompositeHeader.Output IOType.Source
+        | CompositeHeader.Output IOType.Sample -> ProcessOutput.createSample(value.ToString())       
         | CompositeHeader.Output IOType.Material -> ProcessOutput.createMaterial(value.ToString())
         | CompositeHeader.Output IOType.Data -> ProcessOutput.createRawData(value.ToString())
+        | CompositeHeader.Output (IOType.FreeText ft) ->
+            ProcessOutput.createMaterial(composeFreetextMaterialName ft (value.ToString()))
         | _ ->
             failwithf "Could not parse output header %O" header
 
@@ -407,8 +416,11 @@ module ProcessParsing =
                         ProcessInput.createSample(input.Name, characteristics = chars)
                         ]
                     else
-                        input
-                        |> ProcessInput.setCharacteristicValues chars
+                        if chars.Length > 0 then
+                            input
+                            |> ProcessInput.setCharacteristicValues chars
+                        else
+                            input                           
                         |> List.singleton
             | None ->
                 fun (matrix : System.Collections.Generic.Dictionary<(int * int),CompositeCell>) i ->
@@ -429,8 +441,11 @@ module ProcessParsing =
                         ProcessOutput.createSample(output.Name, factors = factors)
                         ]
                     else
-                        output
-                        |> ProcessOutput.setFactorValues factors
+                        if factors.Length > 0 then
+                            output
+                            |> ProcessOutput.setFactorValues factors
+                        else
+                            output
                         |> List.singleton
             | None ->
                 fun (matrix : System.Collections.Generic.Dictionary<(int * int),CompositeCell>) i ->

tests/Core/ArcJsonConversion.Tests.fs

@@ -42,6 +42,17 @@ module Helper =
         t.AddColumns(columns)
         t
 
+    let singleRowOutputSource = 
+    /// Input [Source] --> Source_0 .. Source_4
+        let columns = 
+            [|
+            CompositeColumn.create(CompositeHeader.Input IOType.Source, createCells_FreeText "Source" 1)
+            CompositeColumn.create(CompositeHeader.Output IOType.Source, createCells_FreeText "Sample" 1)
+            |]
+        let t = ArcTable.init(tableName1)
+        t.AddColumns(columns)
+        t
+
     let singleRowMixedValues = 
     /// Input [Source] --> Source_0 .. Source_4
         let columns = 
@@ -137,15 +148,19 @@ let private tests_ArcTableProcess =
             let expectedParam = ProtocolParameter.create(ParameterName = oa_species)
             let expectedValue = Value.Ontology oa_chlamy
             let expectedPPV = ProcessParameterValue.create(Category = expectedParam, Value = expectedValue)
+            let expectedInput = Source.create(Name = "Source_0") |> ProcessInput.Source 
+            let expectedOutput = Sample.create(Name = "Sample_0") |> ProcessOutput.Sample
             Expect.equal processes.Length 1 "Should have 1 process"
             let p = processes.[0]
-            Expect.isSome p.ParameterValues "Process should have parameter values"
-            Expect.equal p.ParameterValues.Value.Length 1 "Process should have 1 parameter values"
-            Expect.equal p.ParameterValues.Value.[0] expectedPPV "Param value does not match"
-            Expect.isSome p.Inputs "Process should have inputs"
-            Expect.equal p.Inputs.Value.Length 1 "Process should have 1 input"
-            Expect.isSome p.Outputs "Process should have outputs"
-            Expect.equal p.Outputs.Value.Length 1 "Process should have 1 output"
+            let paramValues = Expect.wantSome p.ParameterValues "Process should have parameter values"
+            Expect.equal paramValues.Length 1 "Process should have 1 parameter values"
+            Expect.equal paramValues.[0] expectedPPV "Param value does not match"
+            let inputs = Expect.wantSome p.Inputs "Process should have inputs"
+            Expect.equal inputs.Length 1 "Process should have 1 input"
+            Expect.equal inputs.[0] expectedInput "Input value does not match"
+            let outputs = Expect.wantSome p.Outputs "Process should have outputs"
+            Expect.equal outputs.Length 1 "Process should have 1 output"
+            Expect.equal outputs.[0] expectedOutput "Output value does not match"
             Expect.isSome p.Name "Process should have name"
             Expect.equal p.Name.Value tableName1 "Process name should match table name"
         )
@@ -156,6 +171,22 @@ let private tests_ArcTableProcess =
             let expectedTable = t
             Expect.arcTableEqual table expectedTable "Table should be equal"
         )
+        testCase "SingleRowOutputSource GetProcesses" (fun () ->
+            let t = singleRowOutputSource.Copy()
+            let processes = t.GetProcesses()           
+            let expectedInput = Source.create(Name = "Source_0") |> ProcessInput.Source 
+            let expectedOutput = Sample.create(Name = "Sample_0") |> ProcessOutput.Sample
+            Expect.equal processes.Length 1 "Should have 1 process"
+            let p = processes.[0]
+            let inputs = Expect.wantSome p.Inputs "Process should have inputs"
+            Expect.equal inputs.Length 1 "Process should have 1 input"
+            Expect.equal inputs.[0] expectedInput "Input value does not match"
+            let outputs = Expect.wantSome p.Outputs "Process should have outputs"
+            Expect.equal outputs.Length 1 "Process should have 1 output"
+            Expect.equal outputs.[0] expectedOutput "Output value does not match"
+            let name = Expect.wantSome p.Name "Process should have name"
+            Expect.equal name tableName1 "Process name should match table name"
+        )
 
         testCase "SingleRowMixedValues GetProcesses" (fun () ->          
             let t = singleRowMixedValues.Copy()