fix multi annotationTable writing and unify API

#423

src/ARCtrl/ARC.fs

@@ -329,7 +329,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
         let workbooks = System.Collections.Generic.Dictionary<string, DTOType*FsWorkbook>()
         match this.ISA with
         | Some inv -> 
-            let investigationConverter = Spreadsheet.ArcInvestigation.toFsWorkbook
+            let investigationConverter = ArcInvestigation.toFsWorkbook
             workbooks.Add (InvestigationFileName, (DTOType.ISA_Investigation, investigationConverter inv))
             inv.StaticHash <- inv.GetLightHashCode()
             inv.Studies
@@ -365,7 +365,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
 
         | None -> 
             //printfn "ARC contains no ISA part."
-            workbooks.Add (InvestigationFileName, (DTOType.ISA_Investigation, Spreadsheet.ArcInvestigation.toFsWorkbook (ArcInvestigation.create(Identifier.MISSING_IDENTIFIER))))
+            workbooks.Add (InvestigationFileName, (DTOType.ISA_Investigation, ArcInvestigation.toFsWorkbook (ArcInvestigation.create(Identifier.MISSING_IDENTIFIER))))
 
         // Iterates over filesystem and creates a write contract for every file. If possible, include DTO.       
         _fs.Tree.ToFilePaths(true)

src/Spreadsheet/AnnotationTable/ArcTable.fs

@@ -1,4 +1,4 @@
-module ARCtrl.Spreadsheet.ArcTable
+module ARCtrl.Spreadsheet.ArcTable
 
 open ARCtrl
 open ARCtrl.Helper
@@ -121,7 +121,7 @@ let tryFromFsWorksheet (sheet : FsWorksheet) =
     | err -> failwithf "Could not parse table with name \"%s\":\n%s" sheet.Name err.Message
 
 
-let toFsWorksheet (table : ArcTable) =
+let toFsWorksheet (index : int option) (table : ArcTable) =
     /// This dictionary is used to add spaces at the end of duplicate headers.
     let stringCount = System.Collections.Generic.Dictionary<string,string>()
     let ws = FsWorksheet(table.Name)
@@ -137,7 +137,11 @@ let toFsWorksheet (table : ArcTable) =
         |> List.collect CompositeColumn.toStringCellColumns
     let maxRow = columns.Head.Length
     let maxCol = columns.Length
-    let fsTable = ws.Table("annotationTable",FsRangeAddress(FsAddress(1,1),FsAddress(maxRow,maxCol)))
+    let name =
+        match index with
+        | Some i -> $"{annotationTablePrefix}{i}"
+        | None -> annotationTablePrefix
+    let fsTable = ws.Table(name,FsRangeAddress(FsAddress(1,1),FsAddress(maxRow,maxCol)))
     columns
     |> List.iteri (fun colI col ->         
         col

src/Spreadsheet/ArcAssay.fs

@@ -133,6 +133,12 @@ module ArcAssayExtensions =
                 |> Option.iter (DataMapTable.toFsWorksheet >> doc.AddWorksheet)
 
             assay.Tables
-            |> Seq.iter (ArcTable.toFsWorksheet >> doc.AddWorksheet)
+            |> Seq.iteri (fun i -> ArcTable.toFsWorksheet (Some i) >> doc.AddWorksheet)
 
-            doc
+            doc
+
+        /// Write an assay to a spreadsheet
+        ///
+        /// If datamapSheet is true, the datamap will be written to a worksheet inside assay workbook.
+        member this.ToFsWorkbook (?datamapSheet: bool) =
+            ArcAssay.toFsWorkbook (this, ?datamapSheet = datamapSheet)

src/Spreadsheet/ArcInvestigation.fs

@@ -24,8 +24,8 @@ module ArcInvestigation =
     let [<Literal>] publicationsLabelPrefix = "Investigation Publication"
     let [<Literal>] contactsLabelPrefix = "Investigation Person"
 
-    let [<Literal>] metaDataSheetName = "isa_investigation"
-    let [<Literal>] metaDataSheetName_deprecated = "Investigation"
+    let [<Literal>] metadataSheetName = "isa_investigation"
+    let [<Literal>] obsoleteMetadataSheetName = "Investigation"
 
 
     type InvestigationInfo =
@@ -202,28 +202,45 @@ module ArcInvestigation =
         |> insertRemarks (List.ofSeq investigation.Remarks)
         |> seq
 
-    let fromFsWorkbook (doc:FsWorkbook) =  
-        try
-            match doc.TryGetWorksheetByName metaDataSheetName with
-            | Some sheet -> sheet
-            | None -> 
-                match doc.TryGetWorksheetByName metaDataSheetName_deprecated with
+    let isMetadataSheetName (name : string) =
+        name = metadataSheetName || name = obsoleteMetadataSheetName
+
+    let isMetadataSheet (sheet : FsWorksheet) =
+        isMetadataSheetName sheet.Name
+
+    let tryGetMetadataSheet (doc:FsWorkbook) =
+        doc.GetWorksheets()
+        |> Seq.tryFind isMetadataSheet
+
+
+[<AutoOpen>]
+module ArcInvestigationExtensions =
+
+    open ArcInvestigation
+
+    type ArcInvestigation with
+
+        static member fromFsWorkbook (doc:FsWorkbook) =  
+            try
+                match ArcInvestigation.tryGetMetadataSheet doc with
                 | Some sheet -> sheet
                 | None -> failwith "Could not find metadata sheet with sheetname \"isa_investigation\" or deprecated sheetname \"Investigation\""
-            |> FsWorksheet.getRows
-            |> Seq.map SparseRow.fromFsRow
-            |> fromRows 
-        with
-        | err -> failwithf "Could not read investigation from spreadsheet: %s" err.Message
-
-    let toFsWorkbook (investigation:ArcInvestigation) : FsWorkbook =           
-        try
-            let wb = new FsWorkbook()
-            let sheet = FsWorksheet(metaDataSheetName)
-            investigation
-            |> toRows
-            |> Seq.iteri (fun rowI r -> SparseRow.writeToSheet (rowI + 1) r sheet)                     
-            wb.AddWorksheet(sheet)
-            wb
-        with
-        | err -> failwithf "Could not write investigation to spreadsheet: %s" err.Message
+                |> FsWorksheet.getRows
+                |> Seq.map SparseRow.fromFsRow
+                |> fromRows 
+            with
+            | err -> failwithf "Could not read investigation from spreadsheet: %s" err.Message
+
+        static member toFsWorkbook (investigation:ArcInvestigation) : FsWorkbook =           
+            try
+                let wb = new FsWorkbook()
+                let sheet = FsWorksheet(metadataSheetName)
+                investigation
+                |> toRows
+                |> Seq.iteri (fun rowI r -> SparseRow.writeToSheet (rowI + 1) r sheet)                     
+                wb.AddWorksheet(sheet)
+                wb
+            with
+            | err -> failwithf "Could not write investigation to spreadsheet: %s" err.Message
+
+        member this.ToFsWorkbook() = ArcInvestigation.toFsWorkbook this

src/Spreadsheet/ArcStudy.fs

@@ -108,6 +108,9 @@ module ArcStudyExtensions =
                 |> Option.iter (DataMapTable.toFsWorksheet >> doc.AddWorksheet)
 
             study.Tables
-            |> ResizeArray.iter (ArcTable.toFsWorksheet >> doc.AddWorksheet)
+            |> Seq.iteri (fun i -> ArcTable.toFsWorksheet (Some i) >> doc.AddWorksheet)
 
-            doc
+            doc
+
+        member this.ToFsWorkbook (?assays : ArcAssay list, ?datamapSheet: bool) =
+            ArcStudy.toFsWorkbook (this, ?assays = assays, ?datamapSheet = datamapSheet)

src/Spreadsheet/Template.fs

@@ -1,4 +1,4 @@
-namespace ARCtrl.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
 open FsSpreadsheet
 open ARCtrl.Helper
@@ -300,7 +300,7 @@ module Template =
         doc.AddWorksheet metaDataSheet
 
         template.Table
-        |> ArcTable.toFsWorksheet 
+        |> ArcTable.toFsWorksheet None
         |> doc.AddWorksheet
 
         doc

tests/Spreadsheet/ArcTableTests.fs

@@ -13,13 +13,13 @@ let private dataColumnsTable =
         testCase "Only Freetext" <| fun _ ->
             let table = ArcTable.init("MyTable")
             table.AddColumn(CompositeHeader.Input(IOType.Data), [|for i in 1 .. 5 do mkInputStr i |> CompositeCell.FreeText|])
-            let fsws = ArcTable.toFsWorksheet table
+            let fsws = ArcTable.toFsWorksheet None table
             let actualColValues = (fsws.Column(1).Cells |> Seq.map (fun c -> c.ValueAsString())) 
             Expect.sequenceEqual actualColValues ["Input [Data]"; "Input_1"; "Input_2"; "Input_3"; "Input_4"; "Input_5"] ""
         testCase "Only Data" <| fun _ ->
             let table = ArcTable.init("MyTable")
             table.AddColumn(CompositeHeader.Input(IOType.Data), [|for i in 1 .. 5 do CompositeCell.createData (Data(name = mkDataNameStr i, format = "text/csv", selectorFormat = "MySelector"))|])
-            let fsws = ArcTable.toFsWorksheet table
+            let fsws = ArcTable.toFsWorksheet None table
             fsws.RescanRows()
             let rows = fsws.Rows |> Seq.map (fun x -> x.Cells |> Seq.map (fun c -> c.ValueAsString()) |> Array.ofSeq) |> Array.ofSeq
             Expect.equal rows.[0].Length 3 "col count"
@@ -37,7 +37,7 @@ let private dataColumnsTable =
                         mkInputStr i |> CompositeCell.FreeText
                 |]
             )
-            let fsws = ArcTable.toFsWorksheet table
+            let fsws = ArcTable.toFsWorksheet None table
             fsws.RescanRows()
             let rows = fsws.Rows |> Seq.map (fun x -> x.Cells |> Seq.map (fun c -> c.ValueAsString()) |> Array.ofSeq) |> Array.ofSeq
             Expect.equal rows.[0].Length 3 "col count"
@@ -170,7 +170,7 @@ let private simpleTable =
 
             let table = ArcTable.tryFromFsWorksheet ws        
             Expect.isSome table "Table was not created"
-            let out = ArcTable.toFsWorksheet table.Value
+            let out = ArcTable.toFsWorksheet None table.Value
             Expect.workSheetEqual out ws "Worksheet was not correctly written"
 
         )
@@ -262,7 +262,7 @@ let private mixedTable =
 
             let table = ArcTable.tryFromFsWorksheet ws        
             Expect.isSome table "Table was not created"
-            let out = ArcTable.toFsWorksheet table.Value
+            let out = ArcTable.toFsWorksheet None table.Value
             Expect.workSheetEqual out ws "Worksheet was not correctly written"
 
         )
@@ -317,7 +317,7 @@ let private ioTable =
 
             let table = ArcTable.tryFromFsWorksheet ws        
             Expect.isSome table "Table was not created"
-            let out = ArcTable.toFsWorksheet table.Value
+            let out = ArcTable.toFsWorksheet None table.Value
             Expect.workSheetEqual out ws "Worksheet was not correctly written"
 
         )
@@ -366,7 +366,7 @@ let private fullDataTable =
 
             let table = ArcTable.tryFromFsWorksheet ws        
             Expect.isSome table "Table was not created"
-            let out = ArcTable.toFsWorksheet table.Value
+            let out = ArcTable.toFsWorksheet None table.Value
             Expect.workSheetEqual out ws "Worksheet was not correctly written"
 
         )
@@ -414,7 +414,7 @@ let private commentTable =
 
             let table = ArcTable.tryFromFsWorksheet ws        
             Expect.isSome table "Table was not created"
-            let out = ArcTable.toFsWorksheet table.Value
+            let out = ArcTable.toFsWorksheet None table.Value
             Expect.workSheetEqual out ws "Worksheet was not correctly written"
 
         )
@@ -483,7 +483,7 @@ let private writeOrder =
                     ]
 
             let mixedTable = ArcTable.tryFromFsWorksheet mixedWs |> Option.get
-            let mixedOut = ArcTable.toFsWorksheet mixedTable
+            let mixedOut = ArcTable.toFsWorksheet None mixedTable
 
             let orderedWs =  
                 initWorksheet wsName
@@ -506,12 +506,12 @@ let private emptyTable =
         let name = "EmptyTable"
         let t = ArcTable.init(name)
         testCase "Write" (fun () -> 
-            let sheet = ArcTable.toFsWorksheet t
+            let sheet = ArcTable.toFsWorksheet None t
             Expect.equal name sheet.Name "Worksheet name did not match"
             Expect.equal 0 sheet.Rows.Count "Row count should be 0"
         )
         testCase "Read" (fun () ->
-            let sheet = ArcTable.toFsWorksheet t
+            let sheet = ArcTable.toFsWorksheet None t
             Expect.isNone (ArcTable.tryFromFsWorksheet sheet) "Table was not created"
         )
     ]

tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.Study.fs

@@ -1,4 +1,4 @@
-module TestObjects.Spreadsheet.Study
+module TestObjects.Spreadsheet.Study
 
 open FsSpreadsheet
 
@@ -539,7 +539,7 @@ module LargeFile =
             | Some t -> t
             | None -> createTable()
 
-        let fsws_large = Spreadsheet.ArcTable.toFsWorksheet table
+        let fsws_large = Spreadsheet.ArcTable.toFsWorksheet None table
         Workbook.AddWorksheet(fsws_large)
         Workbook.AddWorksheet studyMetadataEmpty