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nfdi4plants · Nov 15, 2023 · f8a4ceb · f8a4ceb
1 parent 996b465
commit f8a4ceb
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Showing 7 changed files with 67 additions and 49 deletions.
diff --git a/src/ISA/ISA/ARCtrl.ISA.fsproj b/src/ISA/ISA/ARCtrl.ISA.fsproj
@@ -54,6 +54,7 @@
     <Compile Include="ArcTypes\ArcTables.fs" />
     <Compile Include="ArcTypes\ArcTypes.fs" />
     <Compile Include="ArcTypes\IdentifierSetters.fs" />
+    <Compile Include="UIHelper.fs" />
     <Compile Include="Builder\Types.fs" />
     <Compile Include="Builder\ProcessBuilder.fs" />
     <Compile Include="Builder\AssayBuilder.fs" />
@@ -63,9 +64,7 @@
   <ItemGroup>
     <ProjectReference Include="..\..\FileSystem\ARCtrl.FileSystem.fsproj" />
   </ItemGroup>
-  <ItemGroup>
-  	<Content Include="*.fsproj; **\*.fs; **\*.fsi" PackagePath="fable\" />
-  </ItemGroup>
+  <ItemGroup />
   <PropertyGroup>
     <Authors>nfdi4plants, Lukas Weil, Kevin Frey, Kevin Schneider, Oliver Muas</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>

diff --git a/src/ISA/ISA/ArcTypes/ArcTable.fs b/src/ISA/ISA/ArcTypes/ArcTable.fs
@@ -81,15 +81,27 @@ type ArcTable(name: string, headers: ResizeArray<CompositeHeader>, values: Syste
         fun (table:ArcTable) ->
             table.TryGetCellAt(column, row)
 
-    member this.IterColumns(mapping: CompositeColumn -> unit) =
+    member this.IterColumns(action: CompositeColumn -> unit) =
         for columnIndex in 0 .. (this.ColumnCount-1) do
             let column = this.GetColumn columnIndex
-            mapping column
+            action column
 
-    member this.IteriColumns(mapping: int -> CompositeColumn -> unit) =
+    static member iterColumns(action: CompositeColumn -> unit) =
+        fun (table:ArcTable) ->
+            let copy = table.Copy()
+            copy.IterColumns(action)
+            copy
+
+    member this.IteriColumns(action: int -> CompositeColumn -> unit) =
         for columnIndex in 0 .. (this.ColumnCount-1) do
             let column = this.GetColumn columnIndex
-            mapping columnIndex column
+            action columnIndex column
+
+    static member iteriColumns(action: int -> CompositeColumn -> unit) =
+        fun (table:ArcTable) ->
+            let copy = table.Copy()
+            copy.IteriColumns(action)
+            copy
 
     // - Cell API - //
     // TODO: And then directly a design question. Is a column with rows containing both CompositeCell.Term and CompositeCell.Unitized allowed?

diff --git a/src/ISA/ISA/ArcTypes/CompositeCell.fs b/src/ISA/ISA/ArcTypes/CompositeCell.fs
@@ -35,19 +35,6 @@ type CompositeCell =
     member this.isTerm = match this with | Term _ -> true | _ -> false
     member this.isFreeText = match this with | FreeText _ -> true | _ -> false
 
-    /// <summary>
-    /// Updates current CompositeCell with information from OntologyAnnotation.
-    ///
-    /// For `Term`, OntologyAnnotation (oa) is fully set. For `Unitized`, oa is set as unit while value is untouched.
-    /// For `FreeText` oa.NameText is set.
-    /// </summary>
-    /// <param name="oa"></param>
-    member this.UpdateWithOA(oa:OntologyAnnotation) =
-        match this with
-        | CompositeCell.Term _ -> CompositeCell.createTerm oa
-        | CompositeCell.Unitized (v,_) -> CompositeCell.createUnitized (v,oa)
-        | CompositeCell.FreeText _ -> CompositeCell.createFreeText oa.NameText
-
     /// <summary>
     /// This returns the default empty cell from an existing CompositeCell.
     /// </summary>

diff --git a/src/ISA/ISA/ArcTypes/CompositeColumn.fs b/src/ISA/ISA/ArcTypes/CompositeColumn.fs
@@ -52,8 +52,10 @@ type CompositeColumn = {
 
     /// <summary>
     /// Simple predictor for empty default cells.
+    ///
+    /// Currently uses majority vote for the column to decide cell type.
     /// </summary>
-    member this.PredictNewColumnCell() =
+    member this.GetDefaultEmptyCell() =
             if not this.Header.IsTermColumn then
                 CompositeCell.emptyFreeText
             else

diff --git a/src/ISA/ISA/ArcTypes/CompositeHeader.fs b/src/ISA/ISA/ArcTypes/CompositeHeader.fs
@@ -211,16 +211,16 @@ type CompositeHeader =
         | Characteristic oa     -> oa
         | Component oa          -> oa
         | ProtocolType          -> OntologyAnnotation.fromString(this.ToString(), tan=this.GetFeaturedColumnAccession) 
-        | ProtocolREF           
-        | ProtocolDescription   
-        | ProtocolUri           
-        | ProtocolVersion       
-        | Performer           
-        | Date                  
-        | Input _              
-        | Output _             
-        | FreeText _          -> 
-            OntologyAnnotation.fromString (this.ToString())
+        | ProtocolREF           -> OntologyAnnotation.fromString (this.ToString())  // use owl ontology in the future
+        | ProtocolDescription   -> OntologyAnnotation.fromString (this.ToString())  // use owl ontology in the future
+        | ProtocolUri           -> OntologyAnnotation.fromString (this.ToString())  // use owl ontology in the future
+        | ProtocolVersion       -> OntologyAnnotation.fromString (this.ToString())  // use owl ontology in the future
+        | Performer             -> OntologyAnnotation.fromString (this.ToString())  // use owl ontology in the future
+        | Date                  -> OntologyAnnotation.fromString (this.ToString())  // use owl ontology in the future
+        | Input _               -> OntologyAnnotation.fromString (this.ToString())  // use owl ontology in the future
+        | Output _              -> OntologyAnnotation.fromString (this.ToString())  // use owl ontology in the future
+        | FreeText _            -> OntologyAnnotation.fromString (this.ToString())  // use owl ontology in the future
+        // owl ontology: https://github.com/nfdi4plants/ARC_ontology/blob/main/ARC_v2.0.owl
 
     /// <summary>
     /// Tries to create a `CompositeHeader` from a given string.

diff --git a/src/ISA/ISA/UIHelper.fs b/src/ISA/ISA/UIHelper.fs
@@ -0,0 +1,16 @@
+module ARCtrl.ISA.UIHelper
+
+module CompositeCell =
+    /// <summary>
+    /// Updates current CompositeCell with information from OntologyAnnotation.
+    ///
+    /// For `Term`, OntologyAnnotation (oa) is fully set. For `Unitized`, oa is set as unit while value is untouched.
+    /// For `FreeText` oa.NameText is set.
+    /// </summary>
+    /// <param name="oa"></param>
+    /// <param name="cell"></param>
+    let updateWithOA (oa:OntologyAnnotation) (cell: CompositeCell) =
+        match cell with
+        | CompositeCell.Term _ -> CompositeCell.createTerm oa
+        | CompositeCell.Unitized (v,_) -> CompositeCell.createUnitized (v,oa)
+        | CompositeCell.FreeText _ -> CompositeCell.createFreeText oa.NameText
diff --git a/tests/ISA/ISA.Tests/CompositeCell.Tests.fs b/tests/ISA/ISA.Tests/CompositeCell.Tests.fs
@@ -154,23 +154,25 @@ let private tests_GetContent = testList "GetContent" [
 
 ]
 
-let private tests_UpdateWithOA = testList "UpdateWithOA" [
-    let testOntologyAnnotation = OntologyAnnotation.fromString("New OA", "NEW", "NEW:00001") 
-    testCase "Term" <| fun _ ->
-        let cc = CompositeCell.createTermFromString("TestTerm", "TEST", "TEST:00001")
-        let actual = cc.UpdateWithOA testOntologyAnnotation
-        let expected = CompositeCell.createTermFromString(testOntologyAnnotation.NameText, testOntologyAnnotation.TermSourceREFString, testOntologyAnnotation.TermAccessionShort)
-        Expect.equal actual expected ""
-    testCase "Unitized" <| fun _ ->
-        let cc = CompositeCell.createUnitizedFromString("12", "TestTerm", "TEST", "TEST:00001")
-        let actual = cc.UpdateWithOA testOntologyAnnotation
-        let expected = CompositeCell.createUnitizedFromString("12", testOntologyAnnotation.NameText, testOntologyAnnotation.TermSourceREFString, testOntologyAnnotation.TermAccessionShort)
-        Expect.equal actual expected ""
-    testCase "FreeText" <| fun _ ->
-        let cc = CompositeCell.createFreeText("TestTerm")
-        let actual = cc.UpdateWithOA testOntologyAnnotation
-        let expected = CompositeCell.createFreeText(testOntologyAnnotation.NameText)
-        Expect.equal actual expected ""
+let private tests_UIHelper = testList "UIHelper" [
+    testList "UpdateWithOA" [
+        let testOntologyAnnotation = OntologyAnnotation.fromString("New OA", "NEW", "NEW:00001") 
+        testCase "Term" <| fun _ ->
+            let cc = CompositeCell.createTermFromString("TestTerm", "TEST", "TEST:00001")
+            let actual = cc |> UIHelper.CompositeCell.updateWithOA testOntologyAnnotation
+            let expected = CompositeCell.createTermFromString(testOntologyAnnotation.NameText, testOntologyAnnotation.TermSourceREFString, testOntologyAnnotation.TermAccessionShort)
+            Expect.equal actual expected ""
+        testCase "Unitized" <| fun _ ->
+            let cc = CompositeCell.createUnitizedFromString("12", "TestTerm", "TEST", "TEST:00001")
+            let actual = cc |> UIHelper.CompositeCell.updateWithOA testOntologyAnnotation
+            let expected = CompositeCell.createUnitizedFromString("12", testOntologyAnnotation.NameText, testOntologyAnnotation.TermSourceREFString, testOntologyAnnotation.TermAccessionShort)
+            Expect.equal actual expected ""
+        testCase "FreeText" <| fun _ ->
+            let cc = CompositeCell.createFreeText("TestTerm")
+            let actual = cc |> UIHelper.CompositeCell.updateWithOA testOntologyAnnotation
+            let expected = CompositeCell.createFreeText(testOntologyAnnotation.NameText)
+            Expect.equal actual expected ""
+    ]
 ]
 
 let main = 
@@ -179,5 +181,5 @@ let main =
         tests_create
         tests_ToString
         tests_GetContent
-        tests_UpdateWithOA
+        tests_UIHelper
     ]