Rework data nodes

src/Core/ARCtrl.Core.fsproj

@@ -46,6 +46,7 @@
     <Compile Include="Table\ArcTableAux.fs" />
     <Compile Include="Table\ArcTable.fs" />
     <Compile Include="Table\ArcTables.fs" />
+    <Compile Include="Table\DataMap.fs" />
     <Compile Include="ArcTypes.fs" />
     <Compile Include="Template.fs" />
     <Compile Include="Templates.fs" />
@@ -60,6 +61,9 @@
     <Content Include="*.fsproj; **\*.fs; **\*.fsi" PackagePath="fable\" />
     <None Include="../../build/logo.png" Pack="true" PackagePath="\" />
   </ItemGroup>
+  <ItemGroup>
+    <PackageReference Update="FSharp.Core" Version="7.0.401" />
+  </ItemGroup>
   <PropertyGroup>
     <Authors>nfdi4plants, Lukas Weil, Kevin Frey, Kevin Schneider, Oliver Maus</Authors>
     <Description>ARC and ISA compliant experimental metadata toolkit in F#. This project is meant as an easy means to open, manipulate and save ISA (Investigation,Study,Assay) metadata files in the dotnet environment.</Description>

src/Core/Conversion.fs

@@ -105,9 +105,7 @@
         | 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.ImageFile -> ProcessInput.createImageFile(value.ToString())
-        | CompositeHeader.Input IOType.RawDataFile ->  ProcessInput.createRawData(value.ToString())
-        | CompositeHeader.Input IOType.DerivedDataFile -> ProcessInput.createDerivedData(value.ToString())
+        | CompositeHeader.Input IOType.Data -> ProcessInput.createRawData(value.ToString())
         | _ ->
             failwithf "Could not parse input header %O" header
 
@@ -117,9 +115,9 @@
         match header with
         | CompositeHeader.Output IOType.Sample -> ProcessOutput.createSample(value.ToString())
         | CompositeHeader.Output IOType.Material -> ProcessOutput.createMaterial(value.ToString())
-        | CompositeHeader.Output IOType.ImageFile -> ProcessOutput.createImageFile(value.ToString())
-        | CompositeHeader.Output IOType.RawDataFile -> ProcessOutput.createRawData(value.ToString())
-        | CompositeHeader.Output IOType.DerivedDataFile -> ProcessOutput.createDerivedData(value.ToString())
+        | CompositeHeader.Output IOType.Data -> ProcessOutput.createImageFile(value.ToString())
+        | CompositeHeader.Output IOType.Data -> ProcessOutput.createRawData(value.ToString())
+        | CompositeHeader.Output IOType.Data -> ProcessOutput.createDerivedData(value.ToString())
         | _ ->
             failwithf "Could not parse output header %O" header
 
@@ -167,9 +165,9 @@
         | ProcessInput.Data d -> 
             let dataType = d.DataType.Value
             match dataType with
-            | DataFile.ImageFile -> CompositeHeader.Input IOType.ImageFile, CompositeCell.FreeText (d.Name |> Option.defaultValue "")
-            | DataFile.RawDataFile -> CompositeHeader.Input IOType.RawDataFile, CompositeCell.FreeText (d.Name |> Option.defaultValue "")
-            | DataFile.DerivedDataFile -> CompositeHeader.Input IOType.DerivedDataFile, CompositeCell.FreeText (d.Name |> Option.defaultValue "")
+            | DataFile.ImageFile -> CompositeHeader.Input IOType.Data, CompositeCell.FreeText (d.Name |> Option.defaultValue "")
+            | DataFile.RawDataFile -> CompositeHeader.Input IOType.Data, CompositeCell.FreeText (d.Name |> Option.defaultValue "")
+            | DataFile.DerivedDataFile -> CompositeHeader.Input IOType.Data, CompositeCell.FreeText (d.Name |> Option.defaultValue "")
 
     /// Convert an ISA ProcessOutput to a CompositeHeader and Cell tuple
     let decomposeProcessOutput (po : ProcessOutput) : CompositeHeader*CompositeCell =
@@ -179,9 +177,9 @@
         | ProcessOutput.Data d -> 
             let dataType = d.DataType.Value
             match dataType with
-            | DataFile.ImageFile -> CompositeHeader.Output IOType.ImageFile, CompositeCell.FreeText (d.Name |> Option.defaultValue "")
-            | DataFile.RawDataFile -> CompositeHeader.Output IOType.RawDataFile, CompositeCell.FreeText (d.Name |> Option.defaultValue "")
-            | DataFile.DerivedDataFile -> CompositeHeader.Output IOType.DerivedDataFile, CompositeCell.FreeText (d.Name |> Option.defaultValue "")
+            | DataFile.ImageFile -> CompositeHeader.Output IOType.Data, CompositeCell.FreeText (d.Name |> Option.defaultValue "")
+            | DataFile.RawDataFile -> CompositeHeader.Output IOType.Data, CompositeCell.FreeText (d.Name |> Option.defaultValue "")
+            | DataFile.DerivedDataFile -> CompositeHeader.Output IOType.Data, CompositeCell.FreeText (d.Name |> Option.defaultValue "")
 
 
     /// This function creates a string containing the name and the ontology short-string of the given ontology annotation term

src/Core/Table/CompositeHeader.fs

@@ -9,9 +9,7 @@ open ARCtrl.Helper
 type IOType =
     | Source
     | Sample
-    | RawDataFile
-    | DerivedDataFile
-    | ImageFile
+    | Data
     | Material
     | FreeText of string
 
@@ -21,9 +19,7 @@ type IOType =
     static member All = [|
         Source
         Sample
-        RawDataFile
-        DerivedDataFile
-        ImageFile
+        Data
         Material
     |]
 
@@ -52,21 +48,8 @@ type IOType =
         | FreeText s1, FreeText s2 when s1 = s2 -> FreeText (s1)
         | FreeText s1, FreeText s2 -> failwith $"FreeText IO column names {s1} and {s2} do differ"
         | FreeText s, _ -> failwith $"FreeText IO column and {other} can not be merged"
-        | ImageFile, Source -> ImageFile
-        | ImageFile, RawDataFile -> ImageFile
-        | ImageFile, DerivedDataFile -> ImageFile
-        | ImageFile, ImageFile -> ImageFile
-        | ImageFile, _ -> failwith $"ImageFile IO column and {other} can not be merged"
-        | DerivedDataFile, Source -> DerivedDataFile
-        | DerivedDataFile, RawDataFile -> DerivedDataFile
-        | DerivedDataFile, DerivedDataFile -> DerivedDataFile
-        | DerivedDataFile, ImageFile -> ImageFile
-        | DerivedDataFile, _ -> failwith $"DerivedDataFile IO column and {other} can not be merged"
-        | RawDataFile, Source -> RawDataFile
-        | RawDataFile, RawDataFile -> RawDataFile
-        | RawDataFile, DerivedDataFile -> DerivedDataFile
-        | RawDataFile, ImageFile -> ImageFile
-        | RawDataFile, _ -> failwith $"RawDataFile IO column and {other} can not be merged"
+        | Data, Source -> Data
+        | Data, _ -> failwith $"Data IO column and {other} can not be merged"
         | Sample, Source -> Sample
         | Sample, Sample -> Sample
         | Sample, _ -> failwith $"Sample IO column and {other} can not be merged"
@@ -79,13 +62,11 @@ type IOType =
 
     override this.ToString() =
         match this with
-        | Source            -> "Source Name" 
-        | Sample            -> "Sample Name" 
-        | RawDataFile       -> "Raw Data File"
-        | DerivedDataFile   -> "Derived Data File"
-        | ImageFile         -> "Image File"
-        | Material          -> "Material" 
-        | FreeText s        -> s
+        | Source     -> "Source Name" 
+        | Sample     -> "Sample Name" 
+        | Data       -> "Data"
+        | Material   -> "Material" 
+        | FreeText s -> s
 
     /// Used to match only(!) IOType string to IOType (without Input/Output). This matching is case sensitive.
     ///
@@ -96,9 +77,10 @@ type IOType =
         match str with
         | "Source" | "Source Name"                  -> Source
         | "Sample" | "Sample Name"                  -> Sample
-        | "RawDataFile" | "Raw Data File"           -> RawDataFile
-        | "DerivedDataFile" | "Derived Data File"   -> DerivedDataFile
-        | "ImageFile" | "Image File"                -> ImageFile
+        | "RawDataFile" | "Raw Data File"           
+        | "DerivedDataFile" | "Derived Data File"  
+        | "ImageFile" | "Image File"                
+        | "Data"                                    -> Data
         | "Material"                                -> Material
         | _                                         -> FreeText str // use str to not store `str.ToLower()`
 
@@ -118,29 +100,24 @@ type IOType =
             "The source value must be a unique identifier for an organism or a sample." 
         | U2.Case1 Sample | U2.Case2 "Sample" -> 
             "The Sample Name column describes specifc laboratory samples with a unique identifier." 
-        | U2.Case1 RawDataFile | U2.Case2 "RawDataFile" -> 
+        | U2.Case1 Data | U2.Case2 "RawDataFile" -> 
             "The Raw Data File column defines untransformed and unprocessed data files."
-        | U2.Case1 DerivedDataFile | U2.Case2 "DerivedDataFile" -> 
+        | U2.Case1 Data | U2.Case2 "DerivedDataFile" -> 
             "The Derived Data File column defines transformed and/or processed data files."
-        | U2.Case1 ImageFile | U2.Case2 "ImageFile" -> 
+        | U2.Case1 Data | U2.Case2 "ImageFile" -> 
             "Placeholder"
         | U2.Case1 Material | U2.Case2 "Material" -> 
             "Placeholder" 
         | U2.Case1 (FreeText _) | U2.Case2 "FreeText" -> 
             "Placeholder"
         | _ -> failwith $"Unable to parse combination to existing IOType: `{iotype}`"
-
 #if FABLE_COMPILER
 
     static member source() = IOType.Source
 
     static member sample() = IOType.Sample
 
-    static member rawDataFile() = IOType.RawDataFile
-
-    static member derivedDataFile() = IOType.DerivedDataFile
-
-    static member imageFile() = IOType.ImageFile
+    static member data() = IOType.Data
 
     static member material() = IOType.Material
 

src/Core/Table/DataMap.fs

@@ -0,0 +1,25 @@
+namespace ARCtrl
+
+open System.Collections.Generic
+open ARCtrl.Helper 
+open ARCtrl
+
+module DataMapAux = 
+
+    [<Literal>]
+    let dataMapName = "DataMap"
+
+    let explicationHeader = CompositeHeader.Parameter
+
+    let allowedHeaders = 1
+
+    let validate (headers : ResizeArray<CompositeHeader>) (values : System.Collections.Generic.Dictionary<int*int,CompositeCell>) = 
+
+        1
+
+type DataMap(headers: ResizeArray<CompositeHeader>, values: System.Collections.Generic.Dictionary<int*int,CompositeCell>) = 
+
+    let _ = DataMapAux.validate headers values
+
+    let table = ArcTable(DataMapAux.dataMapName, headers, values)
+

tests/ARCtrl/ARCtrl.Tests.fs

@@ -427,17 +427,17 @@ let private ``payload_file_filters`` =
 
         let assay = ArcAssay("registered_assay")
         let assayTable = assay.InitTable("MyAssayTable")
-        assayTable.AppendColumn(CompositeHeader.Input (IOType.RawDataFile), [|CompositeCell.createFreeText "registered_assay_input.txt"|])
+        assayTable.AppendColumn(CompositeHeader.Input (IOType.Data), [|CompositeCell.createFreeText "registered_assay_input.txt"|])
         assayTable.AppendColumn(CompositeHeader.ProtocolREF, [|CompositeCell.createFreeText "assay_protocol.rtf"|])
-        assayTable.AppendColumn(CompositeHeader.Output (IOType.DerivedDataFile), [|CompositeCell.createFreeText "registered_assay_output.txt"|])
+        assayTable.AppendColumn(CompositeHeader.Output (IOType.Data), [|CompositeCell.createFreeText "registered_assay_output.txt"|])
 
         let study = ArcStudy("registered_study")
         inv.AddRegisteredStudy(study)
         let studyTable = study.InitTable("MyStudyTable")
         studyTable.AppendColumn(CompositeHeader.Input (IOType.Sample), [|CompositeCell.createFreeText "some_study_input_material"|])
         studyTable.AppendColumn(CompositeHeader.FreeText "Some File", [|CompositeCell.createFreeText "xd/some_file_that_lies_in_slashxd.txt"|])
         studyTable.AppendColumn(CompositeHeader.ProtocolREF, [|CompositeCell.createFreeText "study_protocol.pdf"|])
-        studyTable.AppendColumn(CompositeHeader.Output (IOType.RawDataFile), [|CompositeCell.createFreeText "registered_study_output.txt"|])
+        studyTable.AppendColumn(CompositeHeader.Output (IOType.Data), [|CompositeCell.createFreeText "registered_study_output.txt"|])
         study.AddRegisteredAssay(assay)
 
 

tests/ARCtrl/ARCtrl.Tests.fsproj

@@ -18,6 +18,6 @@
     <ProjectReference Include="..\TestingUtils\TestingUtils.fsproj" />
   </ItemGroup>
   <ItemGroup>
-    <PackageReference Update="FSharp.Core" Version="7.0.401" />
+    <PackageReference Update="FSharp.Core" Version="8.0.200" />
   </ItemGroup>
 </Project>

tests/Core/ArcInvestigation.Tests.fs

@@ -627,7 +627,7 @@ let tests_UpdateIOTypeByEntityIDTypes = testList "UpdateIOTypeByEntityIDType" [
                 CompositeColumn.create (CompositeHeader.Output IOType.Sample, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample %i" i)))
             |]
             t2.AddColumns [|
-                CompositeColumn.create (CompositeHeader.Input IOType.DerivedDataFile, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample %i" i)))
+                CompositeColumn.create (CompositeHeader.Input IOType.Data, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample %i" i)))
                 CompositeColumn.create (CompositeHeader.Output IOType.Sample, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample_Alt %i" i)))
             |]
             Expect.throws (fun () -> i.UpdateIOTypeByEntityID()) "Update should fail as sample and data can not be updated against each other."
@@ -680,7 +680,7 @@ let tests_UpdateIOTypeByEntityIDTypes = testList "UpdateIOTypeByEntityIDType" [
                 CompositeColumn.create (CompositeHeader.Output IOType.Sample, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample %i" i)))
             |]
             t2.AddColumns [|
-                CompositeColumn.create (CompositeHeader.Input IOType.DerivedDataFile, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample %i" i)))
+                CompositeColumn.create (CompositeHeader.Input IOType.Data, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample %i" i)))
                 CompositeColumn.create (CompositeHeader.Output IOType.Sample, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample_Alt %i" i)))
             |]
             Expect.throws (fun () -> i.UpdateIOTypeByEntityID()) "Update should fail as sample and data can not be updated against each other."

tests/Core/ArcJsonConversion.Tests.fs

@@ -60,9 +60,9 @@ module Helper =
     let singleRowDataInputWithCharacteristic = 
         let columns = 
             [|
-            CompositeColumn.create(CompositeHeader.Input IOType.RawDataFile, createCells_FreeText "RData" 1)
+            CompositeColumn.create(CompositeHeader.Input IOType.Data, createCells_FreeText "RData" 1)
             CompositeColumn.create(CompositeHeader.Characteristic oa_species, createCells_chlamy 1)
-            CompositeColumn.create(CompositeHeader.Output IOType.DerivedDataFile, createCells_FreeText "DData" 1)
+            CompositeColumn.create(CompositeHeader.Output IOType.Data, createCells_FreeText "DData" 1)
             |]
         let t = ArcTable.init(tableName1)
         t.AddColumns(columns)
@@ -71,9 +71,9 @@ module Helper =
     let singleRowDataOutputWithFactor = 
         let columns = 
             [|
-            CompositeColumn.create(CompositeHeader.Input IOType.RawDataFile, createCells_FreeText "RData" 1)
+            CompositeColumn.create(CompositeHeader.Input IOType.Data, createCells_FreeText "RData" 1)
             CompositeColumn.create(CompositeHeader.Factor oa_temperature, createCells_DegreeCelsius 1)
-            CompositeColumn.create(CompositeHeader.Output IOType.DerivedDataFile, createCells_FreeText "DData" 1)
+            CompositeColumn.create(CompositeHeader.Output IOType.Data, createCells_FreeText "DData" 1)
             |]
         let t = ArcTable.init(tableName1)
         t.AddColumns(columns)