several fixes for xlsx io

src/ISADotNet.XLSX/AssayFile/MetaData.fs

@@ -49,12 +49,19 @@ module MetaData =
             failwith "emptyInvestigationFile"
 
 
-    let rowOfSparseRow (vs : SparseRow) =
-        vs
-        |> Seq.fold (fun r (i,v) -> Row.insertValueAt None (uint32 (i+1)) v r) (Row.empty())
-
     /// Diesen Block durch JS ersetzen ----> 
 
+    /// Creates a new row from the given values.
+    let ofSparseValues rowIndex (vals : 'T option seq) =
+        let spans = Row.Spans.fromBoundaries 1u (Seq.length vals |> uint)
+        vals
+        |> Seq.mapi (fun i value -> 
+            value
+            |> Option.map (Cell.fromValue None (i + 1 |> uint) rowIndex)
+        )
+        |> Seq.choose id
+        |> Row.create rowIndex spans 
+
     /// Append an assay metadata sheet with the given sheetname to an existing assay file excel spreadsheet
     let init sheetName (doc: DocumentFormat.OpenXml.Packaging.SpreadsheetDocument) = 
 
@@ -65,8 +72,10 @@ module MetaData =
 
         toRows Assay.empty [personWithComment]
         |> Seq.mapi (fun i row -> 
-            rowOfSparseRow row
-            |> Row.updateRowIndex (i+1 |> uint))
+            row
+            |> SparseRow.getAllValues
+            |> ofSparseValues (i+1 |> uint)
+        )
         |> Seq.fold (fun s r -> 
             SheetData.appendRow r s
         ) sheet

src/ISADotNet.XLSX/InvestigationFile/Assays.fs

@@ -64,10 +64,11 @@ module Assays =
         )
 
     let toSparseTable (assays: Assay list) =
-        let matrix = SparseTable.Create (keys = labels,length=assays.Length)
+        let matrix = SparseTable.Create (keys = labels,length=assays.Length + 1)
         let mutable commentKeys = []
         assays
         |> List.iteri (fun i a ->
+            let i = i + 1
             let measurementType,measurementSource,measurementAccession = Option.defaultValue OntologyAnnotation.empty a.MeasurementType |> OntologyAnnotation.toString 
             let technologyType,technologySource,technologyAccession = Option.defaultValue OntologyAnnotation.empty  a.TechnologyType |> OntologyAnnotation.toString
             do matrix.Matrix.Add ((measurementTypeLabel,i),                       measurementType)

src/ISADotNet.XLSX/InvestigationFile/Contacts.fs

@@ -62,10 +62,11 @@ module Contacts =
         )
 
     let toSparseTable (persons:Person list) =
-        let matrix = SparseTable.Create (keys = labels,length=persons.Length)
+        let matrix = SparseTable.Create (keys = labels,length=persons.Length + 1)
         let mutable commentKeys = []
         persons
         |> List.iteri (fun i p ->
+            let i = i + 1
             let role,rolesTermSourceREF,rolesTermAccessionNumber = Option.defaultValue [] p.Roles |> OntologyAnnotation.toAggregatedStrings ';'
             do matrix.Matrix.Add ((lastNameLabel,i),                    (Option.defaultValue ""  p.LastName     ))
             do matrix.Matrix.Add ((firstNameLabel,i),                   (Option.defaultValue ""  p.FirstName    ))

src/ISADotNet.XLSX/InvestigationFile/DesignDescriptors.fs

@@ -41,10 +41,11 @@ module DesignDescriptors =
         )
 
     let toSparseTable (designs: OntologyAnnotation list) =
-        let matrix = SparseTable.Create (keys = labels,length=designs.Length)
+        let matrix = SparseTable.Create (keys = labels,length=designs.Length + 1)
         let mutable commentKeys = []
         designs
         |> List.iteri (fun i d ->
+            let i = i + 1
             let name,source,accession = OntologyAnnotation.toString d
             do matrix.Matrix.Add ((designTypeLabel,i),                      name)
             do matrix.Matrix.Add ((designTypeTermAccessionNumberLabel,i),   accession)

src/ISADotNet.XLSX/InvestigationFile/Factors.fs

@@ -44,10 +44,11 @@ module Factors =
         )
 
     let toSparseTable (factors: Factor list) =
-        let matrix = SparseTable.Create (keys = labels,length=factors.Length)
+        let matrix = SparseTable.Create (keys = labels,length=factors.Length + 1)
         let mutable commentKeys = []
         factors
         |> List.iteri (fun i f ->
+            let i = i + 1
             let factorType,source,accession = f.FactorType |> Option.defaultValue OntologyAnnotation.empty |> OntologyAnnotation.toString 
             do matrix.Matrix.Add ((nameLabel,i),                    (Option.defaultValue "" f.Name))
             do matrix.Matrix.Add ((factorTypeLabel,i),              factorType)

src/ISADotNet.XLSX/InvestigationFile/Investigation.fs

@@ -66,8 +66,8 @@ module Investigation =
 
 
         static member ToSparseTable (investigation: Investigation) =
-            let i = 0
-            let matrix = SparseTable.Create (keys = InvestigationInfo.Labels,length=1)
+            let i = 1
+            let matrix = SparseTable.Create (keys = InvestigationInfo.Labels,length=2)
             let mutable commentKeys = []
 
             do matrix.Matrix.Add ((identifierLabel,i),          (Option.defaultValue "" investigation.Identifier))
@@ -191,9 +191,16 @@ module Investigation =
 
     /// Diesen Block durch JS ersetzen ----> 
 
-    let rowOfSparseRow (vs : SparseRow) =
-        vs
-        |> Seq.fold (fun r (i,v) -> Row.insertValueAt None (uint32 (i+1)) v r) (Row.empty())
+    /// Creates a new row from the given values.
+    let ofSparseValues rowIndex (vals : 'T option seq) =
+        let spans = Row.Spans.fromBoundaries 1u (Seq.length vals |> uint)
+        vals
+        |> Seq.mapi (fun i value -> 
+            value
+            |> Option.map (Cell.fromValue None (i + 1 |> uint) rowIndex)
+        )
+        |> Seq.choose id
+        |> Row.create rowIndex spans 
 
     let fromSpreadsheet (doc:DocumentFormat.OpenXml.Packaging.SpreadsheetDocument) =           
         doc
@@ -224,8 +231,10 @@ module Investigation =
         investigation
         |> toRows
         |> Seq.mapi (fun i row -> 
-            rowOfSparseRow row
-            |> Row.updateRowIndex (i+1 |> uint))
+            row
+            |> SparseRow.getAllValues
+            |> ofSparseValues (i+1 |> uint)
+            )
         |> Seq.fold (fun s r -> 
             SheetData.appendRow r s
         ) sheet

src/ISADotNet.XLSX/InvestigationFile/OntologySourceReference.fs

@@ -44,10 +44,11 @@ module OntologySourceReference =
         )
 
     let toSparseTable (ontologySources: OntologySourceReference list) =
-        let matrix = SparseTable.Create (keys = labels,length=ontologySources.Length)
+        let matrix = SparseTable.Create (keys = labels,length=ontologySources.Length + 1)
         let mutable commentKeys = []
         ontologySources
         |> List.iteri (fun i o ->
+            let i = i + 1
             do matrix.Matrix.Add ((nameLabel,i),        (Option.defaultValue "" o.Name))
             do matrix.Matrix.Add ((fileLabel,i),        (Option.defaultValue "" o.File))
             do matrix.Matrix.Add ((versionLabel,i),     (Option.defaultValue "" o.Version))

src/ISADotNet.XLSX/InvestigationFile/Protocols.fs

@@ -77,10 +77,11 @@ module Protocols =
         )
 
     let toSparseTable (protocols: Protocol list) =
-        let matrix = SparseTable.Create (keys = labels,length=protocols.Length)
+        let matrix = SparseTable.Create (keys = labels,length=protocols.Length + 1)
         let mutable commentKeys = []
         protocols
         |> List.iteri (fun i p ->
+            let i = i + 1
             let protocolType,protocolSource,protocolAccession = p.ProtocolType |> Option.defaultValue OntologyAnnotation.empty |> OntologyAnnotation.toString 
             let parameterType,parameterSource,parameterAccession = p.Parameters |> Option.defaultValue [] |> ProtocolParameter.toAggregatedStrings ';' 
             let componentName,componentType,componentSource,componentAccession = p.Components |> Option.defaultValue [] |> Component.toAggregatedStrings ';' 

src/ISADotNet.XLSX/InvestigationFile/Publication.fs

@@ -52,10 +52,11 @@ module Publications =
         )
 
     let toSparseTable (publications: Publication list) =
-        let matrix = SparseTable.Create (keys = labels,length=publications.Length)
+        let matrix = SparseTable.Create (keys = labels,length=publications.Length + 1)
         let mutable commentKeys = []
         publications
         |> List.iteri (fun i p ->
+            let i = i + 1
             let status,source,accession = Option.defaultValue OntologyAnnotation.empty p.Status |> OntologyAnnotation.toString 
             do matrix.Matrix.Add ((pubMedIDLabel,i),                    (Option.defaultValue "" p.PubMedID))
             do matrix.Matrix.Add ((doiLabel,i),                         (Option.defaultValue "" p.DOI))

src/ISADotNet.XLSX/InvestigationFile/SparseTable.fs

@@ -33,6 +33,7 @@ type SparseTable =
         Matrix : Dictionary<string*int,string>
         Keys : string list
         CommentKeys : string list
+        ///Column Count
         Length : int
     }
 
@@ -51,14 +52,11 @@ type SparseTable =
         }
 
     static member AddRow key (values:seq<int*string>) (matrix : SparseTable) =
-        let values = 
-            values 
-            |> Seq.map (fun (i,v) -> 
-                let i = i-1
-                matrix.Matrix.Add((key,i),v)
-                i,v
-            )
-            |> Seq.toArray
+
+        values 
+        |> Seq.iter (fun (i,v) -> 
+            matrix.Matrix.Add((key,i),v)
+        )
 
         let length = 
             if Seq.isEmpty values then 0
@@ -70,14 +68,12 @@ type SparseTable =
         }
 
     static member AddComment key (values:seq<int*string>) (matrix : SparseTable) =
-        let values = 
-            values 
-            |> Seq.map (fun (i,v) -> 
-                let i = i-1
-                matrix.Matrix.Add((key,i),v)
-                i,v
-            )
-            |> Seq.toArray
+
+        values 
+        |> Seq.iter (fun (i,v) -> 
+            matrix.Matrix.Add((key,i),v)
+        )
+
         let length = 
             if Seq.isEmpty values then 0
             else Seq.maxBy fst values |> fst |> (+) 1
@@ -115,8 +111,8 @@ type SparseTable =
         let prefix = match prefix with | Some p -> p + " " | None -> ""
         seq {
             for key in matrix.Keys do
-                (SparseRow.fromValues (prefix + key :: List.init matrix.Length (fun i -> matrix.TryGetValueDefault("",(key,i)))))
+                (SparseRow.fromValues (prefix + key :: List.init (matrix.Length - 1) (fun i -> matrix.TryGetValueDefault("",(key,i + 1)))))
             for key in matrix.CommentKeys do
-                (SparseRow.fromValues (Comment.wrapCommentKey key :: List.init matrix.Length (fun i -> matrix.TryGetValueDefault("",(key,i)))))
+                (SparseRow.fromValues (Comment.wrapCommentKey key :: List.init (matrix.Length - 1) (fun i -> matrix.TryGetValueDefault("",(key,i + 1)))))
         }
 

src/ISADotNet.XLSX/InvestigationFile/Study.fs

@@ -75,8 +75,8 @@ module Study =
 
 
         static member ToSparseTable (study: Study) =
-            let i = 0
-            let matrix = SparseTable.Create (keys = StudyInfo.Labels,length = 1)
+            let i = 1
+            let matrix = SparseTable.Create (keys = StudyInfo.Labels,length = 2)
             let mutable commentKeys = []
 
             do matrix.Matrix.Add ((identifierLabel,i),          (Option.defaultValue "" study.Identifier))

tests/ISADotNet.Tests/ISADotNet.XLSX/InvestigationFileTests.fs

@@ -340,21 +340,21 @@ let testStringConversions =
     |> testSequenced
 
 [<Tests>]
-let testSparseMatrix =
+let testSparseTable =
 
-    testList "SparseMatrixTests" [
+    testList "SparseTableTests" [
 
         testCase "Create" (fun () -> 
 
             let keys = ["A";"B"]
             let length = 2
 
-            let sparseMatrix = SparseMatrix.Create(keys = keys,length = length)
+            let sparseTable = SparseTable.Create(keys = keys,length = length)
 
-            Expect.equal sparseMatrix.Matrix.Count 0 "Dictionary was not empty"
-            Expect.equal sparseMatrix.Keys keys "Keys were not taken properly"
-            Expect.equal sparseMatrix.CommentKeys [] "Comment keys should be empty"
-            Expect.equal sparseMatrix.Length length "Length did not match"
+            Expect.equal sparseTable.Matrix.Count 0 "Dictionary was not empty"
+            Expect.equal sparseTable.Keys keys "Keys were not taken properly"
+            Expect.equal sparseTable.CommentKeys [] "Comment keys should be empty"
+            Expect.equal sparseTable.Length length "Length did not match"
 
         )
 
@@ -363,23 +363,23 @@ let testSparseMatrix =
             let firstKey,firstRow = "Greetings",[1,"Hello";2,"Bye"]
             let secondKey,secondRow = "AndAgain",[4,"Hello Again"]
 
-            let sparseMatrixFirstRow = 
-                SparseMatrix.Create()
-                |> SparseMatrix.AddRow firstKey firstRow
+            let sparseTableFirstRow = 
+                SparseTable.Create()
+                |> SparseTable.AddRow firstKey firstRow
 
-            Expect.equal sparseMatrixFirstRow.Matrix.Count  2           "FirstRowAdded: Dictionary was not empty"
-            Expect.equal sparseMatrixFirstRow.Keys          [firstKey]  "FirstRowAdded: Keys were not updated properly"
-            Expect.equal sparseMatrixFirstRow.CommentKeys   []          "FirstRowAdded: Comment keys should be empty"
-            Expect.equal sparseMatrixFirstRow.Length        2           "FirstRowAdded: Length did not update according to item count"
+            Expect.equal sparseTableFirstRow.Matrix.Count  2           "FirstRowAdded: Dictionary was not empty"
+            Expect.equal sparseTableFirstRow.Keys          [firstKey]  "FirstRowAdded: Keys were not updated properly"
+            Expect.equal sparseTableFirstRow.CommentKeys   []          "FirstRowAdded: Comment keys should be empty"
+            Expect.equal sparseTableFirstRow.Length        3           "FirstRowAdded: Length did not update according to item count"
 
-            let sparseMatrixSecondRow = 
-                sparseMatrixFirstRow
-                |> SparseMatrix.AddRow secondKey secondRow
+            let sparseTableSecondRow = 
+                sparseTableFirstRow
+                |> SparseTable.AddRow secondKey secondRow
 
-            Expect.equal sparseMatrixSecondRow.Matrix.Count  3                       "SecondRowAdded: Dictionary was not empty"
-            Expect.equal sparseMatrixSecondRow.Keys          [firstKey;secondKey]    "SecondRowAdded: Keys were not updated properly"
-            Expect.equal sparseMatrixSecondRow.CommentKeys   []                      "SecondRowAdded: Comment keys should be empty"
-            Expect.equal sparseMatrixSecondRow.Length        4                       "SecondRowAdded: Length did not update according to item count"            
+            Expect.equal sparseTableSecondRow.Matrix.Count  3                       "SecondRowAdded: Dictionary was not empty"
+            Expect.equal sparseTableSecondRow.Keys          [firstKey;secondKey]    "SecondRowAdded: Keys were not updated properly"
+            Expect.equal sparseTableSecondRow.CommentKeys   []                      "SecondRowAdded: Comment keys should be empty"
+            Expect.equal sparseTableSecondRow.Length        5                       "SecondRowAdded: Length did not update according to item count"            
 
         )
 
@@ -390,25 +390,25 @@ let testSparseMatrix =
             let firstComment,firstCommentRow = "CommentSameLength",[1,"Lel";2,"Lal";3,"Lul"]
             let secondComment,secondCommentRow = "CommentLonger",[2,"Lal";5,"Sho"]
 
-            let sparseMatrixFirstComment = 
-                SparseMatrix.Create()
-                |> SparseMatrix.AddRow firstKey firstRow
-                |> SparseMatrix.AddRow secondKey secondRow
-                |> SparseMatrix.AddComment firstComment firstCommentRow
-
-            Expect.equal sparseMatrixFirstComment.Matrix.Count  6                       "FirstCommentAdded: Dictionary was not empty"
-            Expect.equal sparseMatrixFirstComment.Keys          [firstKey;secondKey]    "FirstCommentAdded: Keys were not updated properly"
-            Expect.equal sparseMatrixFirstComment.CommentKeys   [firstComment]          "FirstCommentAdded: Comment keys should be empty"
-            Expect.equal sparseMatrixFirstComment.Length        4                       "FirstCommentAdded: Length did not update according to item count"
-
-            let sparseMatrixSecondComment = 
-                sparseMatrixFirstComment
-                |> SparseMatrix.AddComment secondComment secondCommentRow
-
-            Expect.equal sparseMatrixSecondComment.Matrix.Count  8                              "SecondCommentAdded: Dictionary was not empty"
-            Expect.equal sparseMatrixSecondComment.Keys          [firstKey;secondKey]           "SecondCommentAdded: Keys were not update properly"
-            Expect.equal sparseMatrixSecondComment.CommentKeys   [firstComment;secondComment]   "SecondCommentAdded: Comment keys should be empty"
-            Expect.equal sparseMatrixSecondComment.Length        5                              "SecondCommentAdded: Length did not update according to item count"                    
+            let sparseTableFirstComment = 
+                SparseTable.Create()
+                |> SparseTable.AddRow firstKey firstRow
+                |> SparseTable.AddRow secondKey secondRow
+                |> SparseTable.AddComment firstComment firstCommentRow
+
+            Expect.equal sparseTableFirstComment.Matrix.Count  6                       "FirstCommentAdded: Dictionary was not empty"
+            Expect.equal sparseTableFirstComment.Keys          [firstKey;secondKey]    "FirstCommentAdded: Keys were not updated properly"
+            Expect.equal sparseTableFirstComment.CommentKeys   [firstComment]          "FirstCommentAdded: Comment keys should be empty"
+            Expect.equal sparseTableFirstComment.Length        5                       "FirstCommentAdded: Length did not update according to item count"
+
+            let sparseTableSecondComment = 
+                sparseTableFirstComment
+                |> SparseTable.AddComment secondComment secondCommentRow
+
+            Expect.equal sparseTableSecondComment.Matrix.Count  8                              "SecondCommentAdded: Dictionary was not empty"
+            Expect.equal sparseTableSecondComment.Keys          [firstKey;secondKey]           "SecondCommentAdded: Keys were not update properly"
+            Expect.equal sparseTableSecondComment.CommentKeys   [firstComment;secondComment]   "SecondCommentAdded: Comment keys should be empty"
+            Expect.equal sparseTableSecondComment.Length        6                              "SecondCommentAdded: Length did not update according to item count"                    
         )
         |> testSequenced
 
@@ -419,12 +419,12 @@ let testSparseMatrix =
             let firstComment,firstCommentRow = "CommentSameLength",[1,"Lel";2,"Lal";3,"Lul"]
             let secondComment,secondCommentRow = "CommentLonger",[2,"Lal";5,"Sho"]
 
-            let sparseMatrix = 
-                SparseMatrix.Create()
-                |> SparseMatrix.AddRow firstKey firstRow
-                |> SparseMatrix.AddRow secondKey secondRow
-                |> SparseMatrix.AddComment firstComment firstCommentRow
-                |> SparseMatrix.AddComment secondComment secondCommentRow
+            let sparseTable = 
+                SparseTable.Create()
+                |> SparseTable.AddRow firstKey firstRow
+                |> SparseTable.AddRow secondKey secondRow
+                |> SparseTable.AddComment firstComment firstCommentRow
+                |> SparseTable.AddComment secondComment secondCommentRow
 
 
             let testRows = 
@@ -435,11 +435,11 @@ let testSparseMatrix =
                     Comment.wrapCommentKey secondComment :: List.init 5 (fun i -> match Seq.tryFind (fst >> (=) (i+1)) secondCommentRow with | Some (_,v) -> v | None -> "")               
                 ]
 
-            sparseMatrix
-            |> SparseMatrix.ToRows
+            sparseTable
+            |> SparseTable.ToRows
             |> Seq.iteri (fun i r ->               
                 let testSeq = Seq.item i testRows
-                Expect.sequenceEqual (Row.getRowValues None r) testSeq ""
+                Expect.sequenceEqual (SparseRow.getValues r) testSeq ""
 
             )