add comment column json and spreadsheet parser

Author: HLWeil

src/Json/Table/CompositeHeader.fs

@@ -38,7 +38,7 @@ module CompositeHeader =
       let headerType = get.Required.Field HeaderType Decode.string
       let oa() = get.Required.Field HeaderValues (Decode.index 0 OntologyAnnotation.decoder)
       let io() = get.Required.Field HeaderValues (Decode.index 0 IOType.decoder)
-      let c() = get.Required.Field HeaderValues Decode.string
+      let c() = get.Required.Field HeaderValues (Decode.index 0 Decode.string)
       match headerType with
       | "Characteristic" -> oa() |> CompositeHeader.Characteristic
       | "Parameter" -> oa() |> CompositeHeader.Parameter

src/Spreadsheet/AnnotationTable/ArcTable.fs

@@ -50,6 +50,7 @@ let classifyHeaderOrder (header : CompositeHeader) =
     | CompositeHeader.Characteristic    _
     | CompositeHeader.Factor            _
     | CompositeHeader.Parameter         _ 
+    | CompositeHeader.Comment           _
     | CompositeHeader.FreeText          _ -> ColumnOrder.ParamsClass
 
     | CompositeHeader.Output            _ -> ColumnOrder.OutputClass

tests/Json/ArcTable.Tests.fs

@@ -93,7 +93,7 @@ let private tests = testList "extended" [
 
 let private tests_dataColumns = 
     testList "dataColumns" [
-        testCase "dataColumns" <| fun _ ->
+        testCase "basic WriteRead" <| fun _ ->
             let testTable = ArcTable.init("Test") 
             testTable.AddColumn (CompositeHeader.Input IOType.Data, [|CompositeCell.Data (Data(name="MyInputDataFile.csv"))|])
             testTable.AddColumn (CompositeHeader.Output IOType.Data, [|CompositeCell.Data (Data(name="MyData.csv#row=1",format="text/csv",selectorFormat = "MySelector"))|])
@@ -102,7 +102,27 @@ let private tests_dataColumns =
             let decoded = ArcTable.fromJsonString encoded
             Expect.arcTableEqual decoded testTable "decompressed table should be equal to original table"
     ]
-    
+ 
+let private tests_commentColumns = 
+    testList "commentColumns" [
+        testCase "basic WriteRead" <| fun _ ->
+            let testTable = ArcTable.init("Test") 
+            testTable.AddColumn (CompositeHeader.Input IOType.Source, [|CompositeCell.FreeText "Source"|])
+            testTable.AddColumn (CompositeHeader.Comment "CommentKey", [|CompositeCell.FreeText "CommentValue"|])
+            testTable.AddColumn (CompositeHeader.Output IOType.Sample, [|CompositeCell.FreeText "Sample"|])
+            let encoded = testTable.ToJsonString()
+            let decoded = ArcTable.fromJsonString encoded
+            Expect.arcTableEqual decoded testTable "decoded table should be equal to original table"
+        testCase "compressed WriteRead" <| fun _ ->
+            let testTable = ArcTable.init("Test") 
+            testTable.AddColumn (CompositeHeader.Input IOType.Source, [|CompositeCell.FreeText "Source"|])
+            testTable.AddColumn (CompositeHeader.Comment "CommentKey", [|CompositeCell.FreeText "CommentValue"|])
+            testTable.AddColumn (CompositeHeader.Output IOType.Sample, [|CompositeCell.FreeText "Sample"|])
+            let encoded = testTable.ToCompressedJsonString()
+            let decoded = ArcTable.fromCompressedJsonString encoded
+            Expect.arcTableEqual decoded testTable "decoded table should be equal to original table"
+    ] 
+
 
 let main = testList "ArcTable" [
     tests
@@ -111,4 +131,5 @@ let main = testList "ArcTable" [
     tests_compressedEmpty
     tests_compressedFilled
     tests_dataColumns
+    tests_commentColumns
 ]

tests/Spreadsheet/ArcTableTests.fs

@@ -329,6 +329,54 @@ let private fullDataTable =
         )
     ]
 
+let private commentTable = 
+    testList "commentTable" [
+        let wsName = "MyWorksheet"
+        let ws = 
+                initWorksheet wsName
+                    [
+                        Factor.appendTimeColumn           1
+                        Comment.appendSimpleCommentColumn 1
+                        Comment.appendNiceCommentColumn   1
+                        
+                    ]
+        testCase "Read" (fun () -> 
+                    
+            let table = ArcTable.tryFromFsWorksheet ws        
+        
+            Expect.isSome table "Table was not created"
+            let table = table.Value
+
+            Expect.equal table.Name wsName "Name did not match"
+            Expect.equal table.ColumnCount 3 "Wrong number of columns"
+            Expect.equal table.RowCount 1 "Wrong number of rows"
+
+            let expectedHeaders = 
+                [                      
+                        Factor.timeHeader
+                        Comment.simpleCommentHeader
+                        Comment.niceCommentHeader
+                ]
+            Expect.sequenceEqual table.Headers expectedHeaders "Headers did not match"
+
+            let expectedCells = 
+                [                        
+                        Factor.timeValue
+                        Comment.simpleCommentValue
+                        Comment.niceCommentValue
+                ]
+            Expect.sequenceEqual (table.GetRow(0)) expectedCells "Cells did not match"
+        )
+        testCase "Write" (fun () -> 
+            
+            let table = ArcTable.tryFromFsWorksheet ws        
+            Expect.isSome table "Table was not created"
+            let out = ArcTable.toFsWorksheet table.Value
+            Expect.workSheetEqual out ws "Worksheet was not correctly written"
+           
+        )
+    ]
+
 let private deprecatedColumnTable = 
     testList "deprecatedIOColumnTable" [
         let wsName = "MyWorksheet"
@@ -434,6 +482,7 @@ let main =
         ioTable
         valuelessTable
         fullDataTable
+        commentTable
         deprecatedColumnTable
         writeOrder
         emptyTable

tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.ArcTable.fs

@@ -287,6 +287,40 @@ module Output =
         for i = 2 to l + 1 do  
             t.Cell(FsAddress(i, colCount + 1),c).SetValueAs sampleValueV1
 
+module Comment = 
+    
+    let simpleCommentHeader = 
+        CompositeHeader.Comment "CommentKey"
+
+    let simpleCommentValue = 
+        CompositeCell.FreeText "CommentValue"
+
+    let simpleDataHeaderV1 = "Comment [CommentKey]"
+
+    let simpleDataValueV1 = "CommentValue"
+
+    let appendSimpleCommentColumn l (c : FsCellsCollection) (t : FsTable) = 
+        let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount()
+        t.Cell(FsAddress(1, colCount + 1),c).SetValueAs simpleDataHeaderV1
+        for i = 2 to l + 1 do  
+            t.Cell(FsAddress(i, colCount + 1),c).SetValueAs simpleDataValueV1
+
+    let niceCommentHeader = 
+        CompositeHeader.Comment "NiceComment"
+
+    let niceCommentValue =
+        CompositeCell.FreeText "NiceCommentValue"
+
+    let niceCommentHeaderV1 = "Comment [NiceComment]"
+
+    let niceCommentValueV1 = "NiceCommentValue"
+
+    let appendNiceCommentColumn l (c : FsCellsCollection) (t : FsTable) = 
+        let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount()
+        t.Cell(FsAddress(1, colCount + 1),c).SetValueAs niceCommentHeaderV1
+        for i = 2 to l + 1 do  
+            t.Cell(FsAddress(i, colCount + 1),c).SetValueAs niceCommentValueV1
+
 module Protocol =
     module REF =