Merge pull request #425 from nfdi4plants/fixes

Add  ArcTable cell accession and manipulation functions

src/Core/Table/ArcTable.fs

@@ -1,4 +1,4 @@
-namespace ARCtrl
+namespace ARCtrl
 
 open Fable.Core
 open System.Collections.Generic
@@ -87,6 +87,16 @@ type ArcTable(name: string, headers: ResizeArray<CompositeHeader>, values: Syste
         fun (table:ArcTable) ->
             table.TryGetCellAt(column, row)
 
+    member this.GetCellAt (column: int,row: int) =
+        try 
+            this.Values.[column,row]
+        with
+        | _ -> failwithf "Unable to find cell for index: (%i, %i) in table %s" column row this.Name
+
+    static member getCellAt (column: int,row: int) =
+        fun (table:ArcTable) ->
+            table.GetCellAt(column, row)
+
     member this.IterColumns(action: CompositeColumn -> unit) =
         for columnIndex in 0 .. (this.ColumnCount-1) do
             let column = this.GetColumn columnIndex
@@ -110,19 +120,78 @@ type ArcTable(name: string, headers: ResizeArray<CompositeHeader>, values: Syste
             copy
 
     // - Cell API - //
-    // TODO: And then directly a design question. Is a column with rows containing both CompositeCell.Term and CompositeCell.Unitized allowed?
-    member this.UpdateCellAt(columnIndex, rowIndex,c : CompositeCell) =
-        SanityChecks.validateColumnIndex columnIndex this.ColumnCount false
-        SanityChecks.validateRowIndex rowIndex this.RowCount false
-        SanityChecks.validateColumn <| CompositeColumn.create(this.Headers.[columnIndex],[|c|])
+    /// Update an already existing cell in the table. Fails if cell is outside the column AND row bounds of the table
+    member this.UpdateCellAt(columnIndex, rowIndex,c : CompositeCell, ?skipValidation) =
+        let skipValidation = defaultArg skipValidation false
+        if not(skipValidation) then
+            SanityChecks.validateColumnIndex columnIndex this.ColumnCount false
+            SanityChecks.validateRowIndex rowIndex this.RowCount false
+            c.ValidateAgainstHeader(this.Headers.[columnIndex],raiseException = true) |> ignore
         Unchecked.setCellAt(columnIndex, rowIndex,c) this.Values
 
-    static member updateCellAt(columnIndex: int, rowIndex: int, cell: CompositeCell) =
+    /// Update an already existing cell in the table. Fails if cell is outside the columnd AND row bounds of the table
+    static member updateCellAt(columnIndex: int, rowIndex: int, cell: CompositeCell, ?skipValidation) =
         fun (table:ArcTable) ->
             let newTable = table.Copy()
-            newTable.UpdateCellAt(columnIndex,rowIndex,cell)
+            newTable.UpdateCellAt(columnIndex,rowIndex,cell, ?skipValidation = skipValidation)
             newTable
 
+
+    /// Update an already existing cell in the table, or adds a new cell if the row boundary is exceeded. Fails if cell is outside the column bounds of the table
+    member this.SetCellAt(columnIndex, rowIndex,c : CompositeCell, ?skipValidation) =
+        let skipValidation = defaultArg skipValidation false
+        if not(skipValidation) then
+            SanityChecks.validateColumnIndex columnIndex this.ColumnCount false
+            c.ValidateAgainstHeader(this.Headers.[columnIndex],raiseException = true) |> ignore
+        Unchecked.setCellAt(columnIndex, rowIndex,c) this.Values
+
+    /// Update an already existing cell in the table, or adds a new cell if the row boundary is exceeded. Fails if cell is outside the column bounds of the table
+    static member setCellAt(columnIndex: int, rowIndex: int, cell: CompositeCell, ?skipValidation) =
+        fun (table:ArcTable) ->
+            let newTable = table.Copy()
+            newTable.SetCellAt(columnIndex,rowIndex,cell, ?skipValidation = skipValidation)
+            newTable
+
+
+    /// Update cells in a column by a function.
+    ///
+    /// Inputs of the function are columnIndex, rowIndex, and the current cell.
+    member this.UpdateCellsBy(f : int -> int -> CompositeCell -> CompositeCell, ?skipValidation) =
+        let skipValidation = defaultArg skipValidation false
+        for kv in this.Values do
+            let ci,ri = kv.Key
+            let newCell = f ci ri kv.Value
+            if not(skipValidation) then newCell.ValidateAgainstHeader(this.Headers[ci],raiseException = true) |> ignore
+            Unchecked.setCellAt(ci, ri,newCell) this.Values
+
+    /// Update cells in a column by a function.
+    ///
+    /// Inputs of the function are columnIndex, rowIndex, and the current cell.static member updateCellBy(f : int -> int -> CompositeCell -> CompositeCell) =
+    static member updateCellsBy(f : int -> int -> CompositeCell -> CompositeCell, ?skipValidation) =
+        fun (table:ArcTable) ->
+            let newTable = table.Copy()
+            newTable.UpdateCellsBy(f, ?skipValidation = skipValidation)
+
+    /// Update cells in a column by a function.
+    ///
+    /// Inputs of the function are columnIndex, rowIndex, and the current cell.
+    member this.UpdateCellBy(columnIndex, rowIndex, f : CompositeCell -> CompositeCell, ?skipValidation) =
+        let skipValidation = defaultArg skipValidation false
+        if not(skipValidation) then
+            SanityChecks.validateColumnIndex columnIndex this.ColumnCount false
+            SanityChecks.validateRowIndex rowIndex this.RowCount false
+        let newCell = this.GetCellAt(columnIndex, rowIndex) |> f
+        if not(skipValidation) then newCell.ValidateAgainstHeader(this.Headers.[columnIndex],raiseException = true) |> ignore
+        Unchecked.setCellAt(columnIndex, rowIndex, newCell) this.Values
+
+    /// Update cells in a column by a function.
+    ///
+    /// Inputs of the function are columnIndex, rowIndex, and the current cell.static member updateCellBy(f : int -> int -> CompositeCell -> CompositeCell) =
+    static member updateCellBy(columnIndex, rowIndex, f : CompositeCell -> CompositeCell, ?skipValidation) =
+        fun (table:ArcTable) ->
+            let newTable = table.Copy()
+            newTable.UpdateCellBy(columnIndex, rowIndex, f, ?skipValidation = skipValidation)
+
     // - Header API - //
     member this.UpdateHeader (index:int, newHeader: CompositeHeader, ?forceConvertCells: bool) =
         let forceConvertCells = Option.defaultValue false forceConvertCells

src/Core/Table/CompositeCell.fs

@@ -169,6 +169,29 @@ type CompositeCell =
         | Unitized (v,oa) -> Unitized (v, oa.Copy())
         | Data d -> Data (d.Copy())
 
+    member this.ValidateAgainstHeader(header : CompositeHeader, ?raiseException) =
+        let raiseExeption = Option.defaultValue false raiseException
+        let cell = this
+        match header, cell with
+        // no cell values will be handled later and is no error case
+        | isData when header.IsDataColumn && (cell.isData || cell.isFreeText) -> 
+            true
+        | isData when header.IsDataColumn -> 
+            if raiseExeption then 
+                let msg = $"Invalid combination of header `{header}` and cell `{cell}`, Data header should have either Data or Freetext cells"
+                failwith msg
+            false
+        | isTerm when header.IsTermColumn && (cell.isTerm || cell.isUnitized) -> 
+            true
+        | isNotTerm when (not header.IsTermColumn) && cell.isFreeText -> 
+            true
+        | h, c -> 
+            if raiseExeption then 
+                let msg = $"Invalid combination of header `{h}` and cell `{cell}`"
+                failwith msg
+            // Maybe still return `msg` somehow if `raiseExeption` is false?
+            false
+
 #if FABLE_COMPILER
     //[<CompiledName("Term")>]
     static member term (oa:OntologyAnnotation) = CompositeCell.Term(oa)

src/Core/Table/CompositeColumn.fs

@@ -19,32 +19,9 @@ type CompositeColumn = {
     /// ?raiseExeption: Default false. Set true if this function should raise an exception instead of return false.
     // TODO! Do not only check cells.Head
     member this.Validate(?raiseException: bool) =
-        let raiseExeption = Option.defaultValue false raiseException
-        let header = this.Header
-        let cells = this.Cells
-        match header, cells with
-        // no cell values will be handled later and is no error case
-        | _, emptyCell when cells.Length = 0 -> 
-            true
-        | isData when header.IsDataColumn && (cells.[0].isData || cells.[0].isFreeText) -> 
-            true
-        | isData when header.IsDataColumn -> 
-            if raiseExeption then 
-                let exampleCells = cells.[0]
-                let msg = $"Invalid combination of header `{header}` and cells `{exampleCells}`, Data header should have either Data or Freetext cells"
-                failwith msg
-            false
-        | isTerm when header.IsTermColumn && (cells.[0].isTerm || cells.[0].isUnitized) -> 
-            true
-        | isNotTerm when (not header.IsTermColumn) && cells.[0].isFreeText -> 
-            true
-        | h, c -> 
-            if raiseExeption then 
-                let exampleCells = c.[0]
-                let msg = $"Invalid combination of header `{h}` and cells `{exampleCells}`"
-                failwith msg
-            // Maybe still return `msg` somehow if `raiseExeption` is false?
-            false
+        this.Cells
+        |> Seq.exists (fun c -> c.ValidateAgainstHeader(this.Header, ?raiseException = raiseException) |> not)
+        |> not
 
     /// <summary>
     /// Returns an array of all units found in the cells of this column. Returns None if no units are found.

tests/Core/ArcTable.Tests.fs

@@ -1,4 +1,4 @@
-module ArcTable.Tests
+module ArcTable.Tests
 
 open ARCtrl
 
@@ -303,6 +303,63 @@ let private tests_ArcTableAux =
         ]
     ]
 
+let private tests_GetCellAt =
+    testList "GetCellAt" [
+        testCase "InsideBoundaries" (fun () ->
+            let table = ArcTable.init "MyTable"
+            let c1 = CompositeColumn.create(CompositeHeader.Input IOType.Source, createCells_FreeText "Source" 2)
+            let c2 = CompositeColumn.create(CompositeHeader.Output IOType.Sample, createCells_FreeText "Sample" 2)
+            table.AddColumns([|c1;c2|])
+
+            Expect.equal (table.GetCellAt(0,0)) (CompositeCell.FreeText "Source_0") "Wrong at 0,0"
+            Expect.equal (table.GetCellAt(0,1)) (CompositeCell.FreeText "Source_1") "Wrong at 0,1"
+            Expect.equal (table.GetCellAt(1,0)) (CompositeCell.FreeText "Sample_0") "Wrong at 1,0"
+            Expect.equal (table.GetCellAt(1,1)) (CompositeCell.FreeText "Sample_1") "Wrong at 1,1"       
+        )
+        testCase "Outside Boundaries" (fun () ->
+            let table = ArcTable.init "MyTable"
+            let c1 = CompositeColumn.create(CompositeHeader.Input IOType.Source, createCells_FreeText "Source" 2)
+            let c2 = CompositeColumn.create(CompositeHeader.Output IOType.Sample, createCells_FreeText "Sample" 2)
+            table.AddColumns([|c1;c2|])
+            let f = fun () -> table.GetCellAt(2,0) |> ignore
+
+            Expect.throws f "Should have failed"
+        )       
+    ]
+
+let private tests_TryGetCellAt =
+    testList "TryGetCellAt" [
+        testCase "InsideBoundaries" (fun () ->
+            let table = ArcTable.init "MyTable"
+            let c1 = CompositeColumn.create(CompositeHeader.Input IOType.Source, createCells_FreeText "Source" 2)
+            let c2 = CompositeColumn.create(CompositeHeader.Output IOType.Sample, createCells_FreeText "Sample" 2)
+            table.AddColumns([|c1;c2|])
+
+            let cell1 = Expect.wantSome (table.TryGetCellAt(0,0)) "Should have found cell at 0,0"
+            let cell2 = Expect.wantSome (table.TryGetCellAt(0,1)) "Should have found cell at 0,1"
+            let cell3 = Expect.wantSome (table.TryGetCellAt(1,0)) "Should have found cell at 1,0"
+            let cell4 = Expect.wantSome (table.TryGetCellAt(1,1)) "Should have found cell at 1,1"
+
+            Expect.equal cell1 (CompositeCell.FreeText "Source_0") "Wrong at 0,0"
+            Expect.equal cell2 (CompositeCell.FreeText "Source_1") "Wrong at 0,1"
+            Expect.equal cell3 (CompositeCell.FreeText "Sample_0") "Wrong at 1,0"
+            Expect.equal cell4 (CompositeCell.FreeText "Sample_1") "Wrong at 1,1"
+
+        )
+        testCase "Outside Boundaries" (fun () ->
+            let table = ArcTable.init "MyTable"
+            let c1 = CompositeColumn.create(CompositeHeader.Input IOType.Source, createCells_FreeText "Source" 2)
+            let c2 = CompositeColumn.create(CompositeHeader.Output IOType.Sample, createCells_FreeText "Sample" 2)
+            table.AddColumns([|c1;c2|])
+            let cell = table.TryGetCellAt(2,0)
+            Expect.isNone None "Should have failed"
+        )       
+
+
+
+    ]
+
+
 let private tests_UpdateHeader = 
     testList "UpdateHeader" [
         testCase "ensure test table" (fun () ->
@@ -424,8 +481,8 @@ let private tests_UpdateHeader =
             TestingUtils.Expect.sequenceEqual table.Values table2.Values "equal table values"
     ]
 
-let private tests_UpdateCell =
-    testList "UpdateCell" [
+let private tests_UpdateCellAt =
+    testList "UpdateCellAt" [
         testCase "ensure test table" (fun () ->
             let testTable = create_testTable()
             Expect.equal testTable.RowCount 5 "RowCount"
@@ -473,6 +530,74 @@ let private tests_UpdateCell =
         )
     ]
 
+let private tests_SetCellAt =
+    testList "SetCellAt" [
+        testCase "Valid" (fun () ->
+            let table = ArcTable.init "MyTable"
+            let c1 = CompositeColumn.create(CompositeHeader.Input IOType.Source, createCells_FreeText "Source" 2)
+            let c2 = CompositeColumn.create(CompositeHeader.Output IOType.Sample, createCells_FreeText "Sample" 2)
+            table.AddColumns([|c1;c2|])
+            table.SetCellAt(0,1,CompositeCell.createFreeText "NewCell")
+
+            Expect.equal (table.GetCellAt(0,0)) (CompositeCell.FreeText "Source_0") "Wrong at 0,0"
+            Expect.equal (table.GetCellAt(0,1)) (CompositeCell.FreeText "NewCell") "Wrong at 0,1"
+            Expect.equal (table.GetCellAt(1,0)) (CompositeCell.FreeText "Sample_0") "Wrong at 1,0"
+            Expect.equal (table.GetCellAt(1,1)) (CompositeCell.FreeText "Sample_1") "Wrong at 1,1"       
+        )
+        testCase "Outside Row boundary (Valid)" (fun () ->
+            let table = ArcTable.init "MyTable"
+            let c1 = CompositeColumn.create(CompositeHeader.Input IOType.Source, createCells_FreeText "Source" 2)
+            let c2 = CompositeColumn.create(CompositeHeader.Output IOType.Sample, createCells_FreeText "Sample" 2)
+            table.AddColumns([|c1;c2|])
+            table.SetCellAt(0,3,CompositeCell.createFreeText "NewCell")
+
+            Expect.equal (table.GetCellAt(0,0)) (CompositeCell.FreeText "Source_0") "Wrong at 0,0"
+            Expect.equal (table.GetCellAt(0,1)) (CompositeCell.FreeText "Source_1") "Wrong at 0,1"
+            Expect.equal (table.GetCellAt(1,0)) (CompositeCell.FreeText "Sample_0") "Wrong at 1,0"
+            Expect.equal (table.GetCellAt(1,1)) (CompositeCell.FreeText "Sample_1") "Wrong at 1,1"
+            Expect.equal (table.GetCellAt(0,3)) (CompositeCell.FreeText "NewCell") "Wrong at 0,3"   
+        )
+        testCase "Outside column boundary (Invalid)" (fun () ->
+            let table = ArcTable.init "MyTable"
+            let c1 = CompositeColumn.create(CompositeHeader.Input IOType.Source, createCells_FreeText "Source" 2)
+            let c2 = CompositeColumn.create(CompositeHeader.Output IOType.Sample, createCells_FreeText "Sample" 2)
+            table.AddColumns([|c1;c2|])
+
+            let f = fun () ->table.SetCellAt(3,0,CompositeCell.createFreeText "NewCell")
+
+            Expect.throws f "Should have failed"
+        )
+    ]
+
+let private tests_UpdateCellsBy =
+    testList "UpdateCellsBy" [
+        testCase "InputAndOutput" (fun () ->
+            let table = ArcTable.init "MyTable"
+            let c1 = CompositeColumn.create(CompositeHeader.Input IOType.Source, createCells_FreeText "Source" 2)
+            let c2 = CompositeColumn.create(CompositeHeader.Output IOType.Sample, createCells_FreeText "Sample" 2)
+            table.AddColumns([|c1;c2|])
+            table.UpdateCellsBy(fun _ _ c ->
+                match c with
+                | CompositeCell.FreeText s -> CompositeCell.createFreeText (s + "_new")
+                | _ -> c
+             )
+            Expect.equal (table.GetCellAt(0,0)) (CompositeCell.FreeText "Source_0_new") "Wrong at 0,0"
+            Expect.equal (table.GetCellAt(0,1)) (CompositeCell.FreeText "Source_1_new") "Wrong at 0,1"
+            Expect.equal (table.GetCellAt(1,0)) (CompositeCell.FreeText "Sample_0_new") "Wrong at 1,0"
+            Expect.equal (table.GetCellAt(1,1)) (CompositeCell.FreeText "Sample_1_new") "Wrong at 1,1"           
+        )
+        testCase "Fail For Wrong CellType" (fun () ->
+            let table = ArcTable.init "MyTable"
+            let c1 = CompositeColumn.create(CompositeHeader.Input IOType.Source, createCells_FreeText "Source" 2)
+            table.AddColumns([|c1|])
+            let f = fun () ->
+                table.UpdateCellsBy(fun _ _ c ->
+                    c.ToTermCell()
+                 )
+            Expect.throws f "Should have failed"
+        )
+    ]
+
 let private tests_UpdateColumn = 
     testList "UpdateColumn" [
         testCase "ensure test table" (fun () ->
@@ -2403,8 +2528,12 @@ let main =
         tests_SanityChecks
         tests_ArcTableAux
         tests_member
+        tests_GetCellAt
+        tests_TryGetCellAt
         tests_UpdateHeader
-        tests_UpdateCell
+        tests_UpdateCellAt
+        tests_SetCellAt
+        tests_UpdateCellsBy
         tests_UpdateColumn
         tests_AddColumn_Mutable
         tests_addColumn_Copy