Merge pull request #463 from nfdi4plants/templateCopy

Template copy and test+fix deepcopying of ArcTable

src/Core/ArcTypes.fs

@@ -381,10 +381,7 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno
         assay
 
     member this.Copy() : ArcAssay =
-        let nextTables = ResizeArray()
-        for table in this.Tables do
-            let copy = table.Copy()
-            nextTables.Add(copy)
+        let nextTables = this.Tables |> ResizeArray.map (fun c -> c.Copy())
         let nextComments = this.Comments |> ResizeArray.map (fun c -> c.Copy())
         let nextDataMap = this.DataMap |> Option.map (fun d -> d.Copy())
         let nextPerformers = this.Performers |> ResizeArray.map (fun c -> c.Copy())

src/Core/Table/ArcTable.fs

@@ -73,11 +73,18 @@ type ArcTable(name: string, headers: ResizeArray<CompositeHeader>, values: Syste
     member this.Columns 
         with get() = [|for i = 0 to this.ColumnCount - 1 do this.GetColumn(i)|] 
 
-    member this.Copy() : ArcTable = 
+    member this.Copy() : ArcTable =
+        let nextHeaders = this.Headers |> ResizeArray.map (fun h -> h.Copy())
+        let nextValues = Dictionary<int*int,CompositeCell>()
+        this.Values.Keys
+        |> Seq.iter (fun (ci,ri) -> 
+            let newCell = this.Values.[ci,ri].Copy()
+            nextValues.Add((ci,ri),newCell)
+        )
         ArcTable.create(
             this.Name,
-            ResizeArray(this.Headers), 
-            Dictionary(this.Values)
+            nextHeaders, 
+            nextValues
         )
 
     /// Returns a cell at given position if it exists, else returns None.

src/Core/Table/CompositeHeader.fs

@@ -432,6 +432,15 @@ type CompositeHeader =
         | ProtocolType | ProtocolREF | ProtocolDescription | ProtocolUri | ProtocolVersion | Performer | Date | Input _ | Output _ -> true
         | _ -> false
 
+    member this.Copy() =
+        match this with
+        | Parameter oa -> Parameter (oa.Copy())
+        | Factor oa -> Factor (oa.Copy())
+        | Characteristic oa -> Characteristic (oa.Copy())
+        | Component oa -> Component (oa.Copy())
+        | _ -> this
+
+
 #if FABLE_COMPILER
 
     [<CompiledName("component")>]
@@ -465,4 +474,4 @@ type CompositeHeader =
 
     static member comment(s:string) = Comment s
 
-#endif
+#endif

src/Core/Template.fs

@@ -1,4 +1,4 @@
-namespace ARCtrl
+namespace ARCtrl
 
 open Fable.Core
 open ARCtrl.Helper
@@ -68,6 +68,23 @@ type Template(id: System.Guid, table: ArcTable, ?name: string, ?description, ?or
     member this.StructurallyEquals (other: Template) =
         this.GetHashCode() = other.GetHashCode()
 
+    member this.Copy() : Template =
+        let nextAuthors = this.Authors |> ResizeArray.map (fun c -> c.Copy())
+        let nextRepos = this.EndpointRepositories |> ResizeArray.map (fun c -> c.Copy())
+        let nextTags = this.Tags |> ResizeArray.map (fun c -> c.Copy())
+        Template.create(
+            this.Id,
+            this.Table.Copy(),
+            this.Name,
+            this.Description,
+            this.Organisation,
+            this.Version,
+            nextAuthors,
+            nextRepos,
+            nextTags,
+            this.LastUpdated
+        )
+
     // custom check
     override this.Equals other =
         match other with

tests/Core/ArcTable.Tests.fs

@@ -926,7 +926,7 @@ let private tests_AddColumn_Mutable =
     ]
 
 /// Exemplary tests to check non mutable implementation of mutability bases member function.
-let private tests_addColumn_Copy =
+let private tests_addColumn =
     let header_input = CompositeHeader.Input IOType.Source
     let header_chara = CompositeHeader.Characteristic oa_species
     let createCells_chara (count) = Array.init count (fun _ -> CompositeCell.createTerm oa_chlamy)
@@ -2539,6 +2539,131 @@ let private tests_equality = testList "equality" [
     ]
 ]
 
+let private tests_copy = testList "Copy" [
+    testCase "DefaultEquality"<| fun _ ->
+        let table = create_testTable()
+        let copy = table.Copy()
+        Expect.equal table copy "Tables should be equal"
+    testCase "StructuralEquality" <| fun _ ->
+        let table = create_testTable()
+        let copy = table.Copy()
+        let equals = table.StructurallyEquals(copy)
+        Expect.isTrue equals "Structural equality should be true"
+    testCase "ReferenceEquality" <| fun _ ->
+        let table = create_testTable()
+        let copy = table.Copy()
+        let equals = table.ReferenceEquals(copy)
+        Expect.isFalse equals "Reference equality should be false"
+    testCase "UpdateInputHeader" <| fun _ ->
+        let table = ArcTable.init("NewTable")
+        table.AddColumn(CompositeHeader.Input IOType.Sample)
+        let copy = table.Copy()
+        Expect.equal copy table "Should be equal before change"
+        copy.UpdateHeader(0,CompositeHeader.Input IOType.Data)
+        Expect.equal (table.Headers.[0]) (CompositeHeader.Input IOType.Sample) "Header of old table should stay as is"
+        Expect.notEqual copy table "Should not be equal after change"
+    testCase "UpdateParameterHeader" <| fun _ ->
+        let table = ArcTable.init("NewTable")
+        table.AddColumn(CompositeHeader.Parameter (OntologyAnnotation("OldAnnotation")))
+        let copy = table.Copy()
+        Expect.equal copy table "Should be equal before change"
+        copy.UpdateHeader(0,CompositeHeader.Parameter (OntologyAnnotation("NewAnnotation")))
+        Expect.equal (table.Headers.[0]) (CompositeHeader.Parameter (OntologyAnnotation("OldAnnotation"))) "Header of old table should stay as is"
+        Expect.notEqual copy table "Should not be equal after change"
+    testCase "UpdateAnnotationOfParameterHeader" <| fun _ ->
+        let table = ArcTable.init("NewTable")
+        table.AddColumn(CompositeHeader.Parameter (OntologyAnnotation("OldAnnotation")))
+        let copy = table.Copy()
+        Expect.equal copy table "Should be equal before change"
+        match copy.Headers.[0] with
+        | CompositeHeader.Parameter oa -> oa.Name <- Some "NewAnnotation"
+        | _ -> Expect.isTrue false "Header not parameter?"
+        Expect.equal (table.Headers.[0]) (CompositeHeader.Parameter (OntologyAnnotation("OldAnnotation"))) "Header of old table should stay as is"
+        Expect.notEqual copy table "Should not be equal after change"
+    testCase "UpdateFreetextCell" <| fun _ ->
+        let table = ArcTable.init("NewTable")
+        table.AddColumn(
+            CompositeHeader.Input IOType.Sample,
+            [|CompositeCell.FreeText "OldFreetext"|]
+            )
+        let copy = table.Copy()
+        Expect.equal copy table "Should be equal before change"
+        copy.SetCellAt(0,0,CompositeCell.FreeText "NewFreetext")
+        Expect.equal (table.GetCellAt(0,0)) (CompositeCell.FreeText "OldFreetext") "Cell of old table should stay as is"
+        Expect.notEqual copy table "Should not be equal after change"
+    testCase "UpdateDataCell" <| fun _ ->
+        let table = ArcTable.init("NewTable")
+        table.AddColumn(
+            CompositeHeader.Input IOType.Data,
+            [|CompositeCell.Data (Data(name = "OldData"))|]
+            )
+        let copy = table.Copy()
+        Expect.equal copy table "Should be equal before change"
+        copy.SetCellAt(0,0,CompositeCell.Data (Data(name = "NewData")))
+        Expect.equal (table.GetCellAt(0,0)) (CompositeCell.Data (Data(name = "OldData"))) "Cell of old table should stay as is"
+        Expect.notEqual copy table "Should not be equal after change"
+    testCase "UpdateNameOfDataCell" <| fun _ ->
+        let table = ArcTable.init("NewTable")
+        table.AddColumn(
+            CompositeHeader.Input IOType.Data,
+            [|CompositeCell.Data (Data(name = "OldData"))|]
+            )
+        let copy = table.Copy()
+        Expect.equal copy table "Should be equal before change"
+        match copy.GetCellAt(0,0) with
+        | CompositeCell.Data d -> d.Name <- Some "NewData"
+        | _ -> Expect.isTrue false "Cell not data?"
+        Expect.equal (table.GetCellAt(0,0)) (CompositeCell.Data (Data(name = "OldData"))) "Cell of old table should stay as is"
+        Expect.notEqual copy table "Should not be equal after change"
+    testCase "UpdateTermCell" <| fun _ ->
+        let table = ArcTable.init("NewTable")
+        table.AddColumn(
+            CompositeHeader.Parameter (OntologyAnnotation("MyParameter")),
+            [|CompositeCell.createTerm (OntologyAnnotation("OldAnnotation"))|]
+            )
+        let copy = table.Copy()
+        Expect.equal copy table "Should be equal before change"
+        copy.SetCellAt(0,0,CompositeCell.createTerm (OntologyAnnotation("NewAnnotation")))
+        Expect.equal (table.GetCellAt(0,0)) (CompositeCell.createTerm (OntologyAnnotation("OldAnnotation"))) "Cell of old table should stay as is"
+        Expect.notEqual copy table "Should not be equal after change"
+    testCase "UpdateAnnotationOfTermCell" <| fun _ ->
+        let table = ArcTable.init("NewTable")
+        table.AddColumn(
+            CompositeHeader.Parameter (OntologyAnnotation("MyParameter")),
+            [|CompositeCell.createTerm (OntologyAnnotation("OldAnnotation"))|]
+            )
+        let copy = table.Copy()
+        Expect.equal copy table "Should be equal before change"
+        match copy.GetCellAt(0,0) with
+        | CompositeCell.Term oa -> oa.Name <- Some "NewAnnotation"
+        | _ -> Expect.isTrue false "Cell not term?"
+        Expect.equal (table.GetCellAt(0,0)) (CompositeCell.createTerm (OntologyAnnotation("OldAnnotation"))) "Cell of old table should stay as is"
+        Expect.notEqual copy table "Should not be equal after change"
+    testCase "UpdateUnitCell" <| fun _ ->
+        let table = ArcTable.init("NewTable")
+        table.AddColumn(
+            CompositeHeader.Parameter (OntologyAnnotation("MyParameter")),
+            [|CompositeCell.createUnitized("OldValue",(OntologyAnnotation("OldAnnotation")))|]
+            )
+        let copy = table.Copy()
+        Expect.equal copy table "Should be equal before change"
+        copy.SetCellAt(0,0,CompositeCell.createUnitized("NewValue",(OntologyAnnotation("NewAnnotation"))))
+        Expect.equal (table.GetCellAt(0,0)) (CompositeCell.createUnitized("OldValue",(OntologyAnnotation("OldAnnotation")))) "Cell of old table should stay as is"
+        Expect.notEqual copy table "Should not be equal after change"
+    testCase "UpdateAnnotationOfUnitCell" <| fun _ ->
+        let table = ArcTable.init("NewTable")
+        table.AddColumn(
+            CompositeHeader.Parameter (OntologyAnnotation("MyParameter")),
+            [|CompositeCell.createUnitized("OldValue",(OntologyAnnotation("OldAnnotation")))|]
+            )
+        let copy = table.Copy()
+        Expect.equal copy table "Should be equal before change"
+        match copy.GetCellAt(0,0) with
+        | CompositeCell.Unitized (v,oa) -> oa.Name <- Some "NewAnnotation"
+        | _ -> Expect.isTrue false "Cell not unit?"
+        Expect.equal (table.GetCellAt(0,0)) (CompositeCell.createUnitized("OldValue",(OntologyAnnotation("OldAnnotation")))) "Cell of old table should stay as is"
+        Expect.notEqual copy table "Should not be equal after change"
+]
 
 let private tests_fillMissing = testList "fillMissing" [
         testCase "OntologyAnnotationCopied" <| fun _ ->
@@ -2574,7 +2699,7 @@ let main =
         tests_UpdateCellsBy
         tests_UpdateColumn
         tests_AddColumn_Mutable
-        tests_addColumn_Copy
+        tests_addColumn
         tests_AddColumns
         tests_AddColumnFill
         tests_RemoveColumn
@@ -2591,5 +2716,6 @@ let main =
         tests_IterColumns
         tests_GetHashCode
         tests_equality
+        tests_copy
         tests_fillMissing
     ]

tests/Core/Template.Tests.fs

@@ -1,4 +1,4 @@
-module Template.Tests
+module Template.Tests
 
 open Thoth.Json.Core
 
@@ -182,8 +182,40 @@ let private tests_filters = testList "filters" [
     ]
 ]
 
+let private tests_copy = testList "Copy" [
+    testCase "DefaultEquality"<| fun _ ->
+        let template = create_TestTemplate()
+        let copy = template.Copy()
+        Expect.equal template copy "Templates should be equal"
+    testCase "StructuralEquality" <| fun _ ->
+        let template = create_TestTemplate()
+        let copy = template.Copy()
+        let equals = template.StructurallyEquals(copy)
+        Expect.isTrue equals "Structural equality should be true"
+    testCase "ReferenceEquality" <| fun _ ->
+        let template = create_TestTemplate()
+        let copy = template.Copy()
+        let equals = template.ReferenceEquals(copy)
+        Expect.isFalse equals "Reference equality should be false"
+    testCase "UpdatePerson" <| fun _ ->
+        let template = create_TestTemplate()
+        let copy = template.Copy()
+        Expect.equal template copy "Templates should be equal before change"
+        copy.Authors.[0].FirstName <- Some "Jane"
+        Expect.equal template.Authors.[0].FirstName (Some "John") "Name should not have been updated"
+        Expect.notEqual copy template "Templates should not be equal after change"
+    testCase "AddTableColumn" <| fun _ ->
+        let template = create_TestTemplate()
+        let copy = template.Copy()
+        Expect.equal template copy "Templates should be equal before change"
+        copy.Table.AddColumn(CompositeHeader.Parameter (OntologyAnnotation("VeryImportant")))
+        Expect.notEqual copy template "Templates should not be equal after change"
+]
+
+
 let main = testList "Templates" [
     tests_equality
     tests_HashCode
     tests_filters
+    tests_copy
 ]