small adjustments to updateIOType functionality according to PR request

nfdi4plants · Oct 16, 2023 · 32d9898 · 32d9898
1 parent a4c6c7f
commit 32d9898
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Showing 3 changed files with 34 additions and 29 deletions.
diff --git a/src/ISA/ISA/ArcTypes/ArcTable.fs b/src/ISA/ISA/ArcTypes/ArcTable.fs
@@ -268,14 +268,6 @@ type ArcTable(name: string, headers: ResizeArray<CompositeHeader>, values: Syste
         fun (table:ArcTable) ->
             table.GetColumn(index)
 
-    member this.GetColumnByHeader (header:CompositeHeader) =
-        let index = this.Headers |> Seq.findIndex (fun x -> x = header)
-        this.GetColumn(index)
-
-    static member getColumnByHeader (header:CompositeHeader) =
-        fun (table:ArcTable) ->
-            table.GetColumnByHeader(header)
-
     member this.TryGetColumnByHeader (header:CompositeHeader) =
         let index = this.Headers |> Seq.tryFindIndex (fun x -> x = header)
         index
@@ -285,13 +277,14 @@ type ArcTable(name: string, headers: ResizeArray<CompositeHeader>, values: Syste
         fun (table:ArcTable) ->
             table.TryGetColumnByHeader(header)
 
-    member this.GetInputColumn() =
-        let index = this.Headers |> Seq.findIndex (fun x -> x.isInput)
-        this.GetColumn(index)
+    member this.GetColumnByHeader (header:CompositeHeader) =
+        match this.TryGetColumnByHeader(header) with
+        | Some c -> c
+        | None -> failwithf "Unable to find column with header in table %s: %O" this.Name header
 
-    static member getInputColumn () =
+    static member getColumnByHeader (header:CompositeHeader) =
         fun (table:ArcTable) ->
-            table.GetInputColumn()
+            table.GetColumnByHeader(header)
 
     member this.TryGetInputColumn() =
         let index = this.Headers |> Seq.tryFindIndex (fun x -> x.isInput)
@@ -302,13 +295,14 @@ type ArcTable(name: string, headers: ResizeArray<CompositeHeader>, values: Syste
         fun (table:ArcTable) ->
             table.TryGetInputColumn()
 
-    member this.GetOutputColumn() =
-        let index = this.Headers |> Seq.findIndex (fun x -> x.isOutput)
-        this.GetColumn(index)
+    member this.GetInputColumn() =
+        match this.TryGetInputColumn() with
+        | Some c -> c
+        | None -> failwithf "Unable to find input column in table %s" this.Name
 
-    static member getOutputColumn () =
+    static member getInputColumn () =
         fun (table:ArcTable) ->
-            table.GetOutputColumn()
+            table.GetInputColumn()
 
     member this.TryGetOutputColumn() =
         let index = this.Headers |> Seq.tryFindIndex (fun x -> x.isOutput)
@@ -319,6 +313,15 @@ type ArcTable(name: string, headers: ResizeArray<CompositeHeader>, values: Syste
         fun (table:ArcTable) ->
             table.TryGetOutputColumn()
 
+    member this.GetOutputColumn() =
+        match this.TryGetOutputColumn() with
+        | Some c -> c
+        | None -> failwithf "Unable to find output column in table %s" this.Name
+
+    static member getOutputColumn () =
+        fun (table:ArcTable) ->
+            table.GetOutputColumn()
+
     // - Row API - //
     member this.AddRow (?cells: CompositeCell [], ?index: int) : unit = 
         let index = defaultArg index this.RowCount

diff --git a/src/ISA/ISA/ArcTypes/ArcTypes.fs b/src/ISA/ISA/ArcTypes/ArcTypes.fs
@@ -1684,14 +1684,16 @@ type ArcInvestigation(identifier : string, ?title : string, ?description : strin
             copy.DeregisterMissingAssays()
             copy
 
-    /// Updates the IOtypes of the IO columns across all tables in the investigation if possible.
+    /// Updates the IOtypes of the IO columns (Input, Output) across all tables in the investigation if possible.
     ///
-    /// If an entity with the same name as an entity with a higher IOType specifity is found, the IOType of the entity with the lower IOType specificity is updated.
+    /// If an entity (Row Value of IO Column) with the same name as an entity with a higher IOType specifity is found, the IOType of the entity with the lower IOType specificity is updated.
+    ///
+    /// E.g. In Table1, there is a column "Output [Sample Name]" with an entity "Sample1". In Table2, there is a column "Input [Source Name]" with the same entity "Sample1". By equality of the entities, the IOType of the Input column in Table2 is inferred to be Sample, resulting in "Input [Sample Name]".
     ///
     /// E.g. RawDataFile is more specific than Source, but less specific than DerivedDataFile.
     ///
     /// E.g. Sample is equally specific to RawDataFile.
-    member this.UpdateIO() =
+    member this.UpdateIOTypeByEntityID() =
         let ioMap = 
             [
                 for study in this.Studies do

diff --git a/tests/ISA/ISA.Tests/ArcInvestigation.Tests.fs b/tests/ISA/ISA.Tests/ArcInvestigation.Tests.fs
@@ -541,7 +541,7 @@ let tests_Assay = testList "CRUD Assay" [
     ]
 ]
 
-let tests_UpdateIOTypes = testList "UpdateIOType" [
+let tests_UpdateIOTypeByEntityIDTypes = testList "UpdateIOTypeByEntityIDType" [
     testList "SameAssay" [ 
         testCase "nothingToUpdate" <| fun _ ->
             let i = ArcInvestigation.init("MyInvestigation")
@@ -557,7 +557,7 @@ let tests_UpdateIOTypes = testList "UpdateIOType" [
                 CompositeColumn.create (CompositeHeader.Output IOType.Sample, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample_Alt %i" i)))
             |]
             let a_Copy = a.Copy()
-            i.UpdateIO()
+            i.UpdateIOTypeByEntityID()
             Expect.sequenceEqual a.Tables a_Copy.Tables "Tables should be unchanged"
         testCase "updateOutputByNextInput" <| fun _ ->
             let i = ArcInvestigation.init("MyInvestigation")
@@ -572,7 +572,7 @@ let tests_UpdateIOTypes = testList "UpdateIOType" [
                 CompositeColumn.create (CompositeHeader.Input IOType.Source, 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)))
             |]
-            i.UpdateIO()
+            i.UpdateIOTypeByEntityID()
             Expect.sequenceEqual t1.Headers [CompositeHeader.Input IOType.Source; CompositeHeader.Output IOType.Sample] "Headers should be updated"
             Expect.sequenceEqual t2.Headers [CompositeHeader.Input IOType.Sample; CompositeHeader.Output IOType.Sample] "Headers should be updated"
         testCase "failBecauseClashing" <| fun _ ->
@@ -588,7 +588,7 @@ let tests_UpdateIOTypes = testList "UpdateIOType" [
                 CompositeColumn.create (CompositeHeader.Input IOType.DerivedDataFile, 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.UpdateIO()) "Update should fail as sample and data can not be updated against each other."
+            Expect.throws (fun () -> i.UpdateIOTypeByEntityID()) "Update should fail as sample and data can not be updated against each other."
     ]
     testList "AssayAndStudy" [ 
         testCase "nothingToUpdate" <| fun _ ->
@@ -607,7 +607,7 @@ let tests_UpdateIOTypes = testList "UpdateIOType" [
             |]
             let a_Copy = a.Copy()
             let s_Copy = s.Copy()
-            i.UpdateIO()
+            i.UpdateIOTypeByEntityID()
             Expect.sequenceEqual a.Tables a_Copy.Tables "Tables should be unchanged"
             Expect.sequenceEqual s.Tables s_Copy.Tables "Tables should be unchanged"
         testCase "updateOutputByNextInput" <| fun _ ->
@@ -624,7 +624,7 @@ let tests_UpdateIOTypes = testList "UpdateIOType" [
                 CompositeColumn.create (CompositeHeader.Input IOType.Source, 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)))
             |]
-            i.UpdateIO()
+            i.UpdateIOTypeByEntityID()
             Expect.sequenceEqual t1.Headers [CompositeHeader.Input IOType.Source; CompositeHeader.Output IOType.Sample] "Headers should be updated"
             Expect.sequenceEqual t2.Headers [CompositeHeader.Input IOType.Sample; CompositeHeader.Output IOType.Sample] "Headers should be updated"
         testCase "failBecauseClashing" <| fun _ ->
@@ -641,7 +641,7 @@ let tests_UpdateIOTypes = testList "UpdateIOType" [
                 CompositeColumn.create (CompositeHeader.Input IOType.DerivedDataFile, 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.UpdateIO()) "Update should fail as sample and data can not be updated against each other."
+            Expect.throws (fun () -> i.UpdateIOTypeByEntityID()) "Update should fail as sample and data can not be updated against each other."
     ]
 ]
 
@@ -805,6 +805,6 @@ let main =
         tests_Study
         tests_Assay
         tests_GetHashCode
-        tests_UpdateIOTypes
+        tests_UpdateIOTypeByEntityIDTypes
         // tests_UpdateBy
     ]