rework ARCtrl.Spreadsheet according to datamodel changes

src/Spreadsheet/AnnotationTable/ArcTable.fs

@@ -1,6 +1,7 @@
-module ARCtrl.ISA.Spreadsheet.ArcTable
+module ARCtrl.Spreadsheet.ArcTable
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open FsSpreadsheet
 
 // I think we really should not add FSharpAux for exactly one function.
@@ -93,7 +94,7 @@ let tryFromFsWorksheet (sheet : FsWorksheet) =
                 |> Seq.map CompositeColumn.fixDeprecatedIOHeader
                 |> composeColumns
             ArcTable.init sheet.Name
-            |> ArcTable.addColumns(compositeColumns,SkipFillMissing = true)
+            |> ArcTable.addColumns(compositeColumns,skipFillMissing = true)
             |> Some
         | None ->
             None

src/Spreadsheet/AnnotationTable/CompositeCell.fs

@@ -1,6 +1,7 @@
-module ARCtrl.ISA.Spreadsheet.CompositeCell
+module ARCtrl.Spreadsheet.CompositeCell
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open FsSpreadsheet
 
 let fromFsCells (cells : list<FsCell>) : CompositeCell =
@@ -18,7 +19,7 @@ let toFsCells isTerm hasUnit (cell : CompositeCell) : list<FsCell> =
     | CompositeCell.FreeText v when isTerm -> [FsCell(v); FsCell(""); FsCell("")]
     | CompositeCell.FreeText v -> [FsCell(v)]
 
-    | CompositeCell.Term v when hasUnit -> [FsCell(v.NameText); FsCell(""); FsCell(v.TermSourceREFString); FsCell(v.TermAccessionOntobeeUrl)]
-    | CompositeCell.Term v -> [FsCell(v.NameText); FsCell(v.TermSourceREFString); FsCell(v.TermAccessionOntobeeUrl)]
+    | CompositeCell.Term v when hasUnit -> [FsCell(v.NameText); FsCell(""); FsCell(Option.defaultValue "" v.TermSourceREF); FsCell(v.TermAccessionOntobeeUrl)]
+    | CompositeCell.Term v -> [FsCell(v.NameText); FsCell(Option.defaultValue "" v.TermSourceREF); FsCell(v.TermAccessionOntobeeUrl)]
 
-    | CompositeCell.Unitized (v,unit) -> [FsCell(v); FsCell(unit.NameText); FsCell(unit.TermSourceREFString); FsCell(unit.TermAccessionOntobeeUrl)]
+    | CompositeCell.Unitized (v,unit) -> [FsCell(v); FsCell(unit.NameText); FsCell(Option.defaultValue "" unit.TermSourceREF); FsCell(unit.TermAccessionOntobeeUrl)]

src/Spreadsheet/AnnotationTable/CompositeColumn.fs

@@ -1,6 +1,7 @@
-module ARCtrl.ISA.Spreadsheet.CompositeColumn
+module ARCtrl.Spreadsheet.CompositeColumn
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open FsSpreadsheet
 
 /// Checks if the column header is a deprecated IO Header. If so, fixes it.

src/Spreadsheet/AnnotationTable/CompositeHeader.fs

@@ -1,11 +1,12 @@
-module ARCtrl.ISA.Spreadsheet.CompositeHeader
+module ARCtrl.Spreadsheet.CompositeHeader
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open FsSpreadsheet
 
 module ActivePattern = 
 
-    open ARCtrl.ISA.Regex.ActivePatterns
+    open Regex.ActivePatterns
 
     let mergeIDInfo idSpace1 localID1 idSpace2 localID2 =
         if idSpace1 <> idSpace2 then failwithf "TermSourceRef %s and %s do not match" idSpace1 idSpace2
@@ -18,15 +19,15 @@ module ActivePattern =
         let cellValues = cells |> List.map (fun c -> c.ValueAsString())
         match cellValues with
         | [AC name] -> 
-            let ont = OntologyAnnotation.fromString(name)
+            let ont = OntologyAnnotation.create(name)
             f ont
             |> Some
         | [AC name; TSRColumnHeader term1; TANColumnHeader term2] 
         //| [AC name; TermAccessionNumber term1; TermSourceREF term2] 
         //| [AC name; Unit; TermAccessionNumber term1; TermSourceREF term2] 
         | [AC name; UnitColumnHeader _; TSRColumnHeader term1; TANColumnHeader term2] ->
             let term = mergeIDInfo term1.IDSpace term1.LocalID term2.IDSpace term2.LocalID
-            let ont = OntologyAnnotation.fromString(name, term.TermSourceRef, term.TermAccessionNumber)
+            let ont = OntologyAnnotation.create(name, term.TermSourceRef, term.TermAccessionNumber)
             f ont
             |> Some
         | _ -> None

src/Spreadsheet/ArcAssay.fs

@@ -1,6 +1,7 @@
-module ARCtrl.ISA.Spreadsheet.ArcAssay
+module ARCtrl.Spreadsheet.ArcAssay
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open FsSpreadsheet
 
 let [<Literal>] obsoleteAssaysLabel = "ASSAY METADATA"
@@ -20,7 +21,7 @@ let toMetadataSheet (assay : ArcAssay) : FsWorksheet =
             yield! Assays.toRows (Some assaysPrefix) [assay]
 
             yield SparseRow.fromValues [contactsLabel]
-            yield! Contacts.toRows (Some contactsPrefix) (List.ofArray assay.Performers)
+            yield! Contacts.toRows (Some contactsPrefix) (List.ofSeq assay.Performers)
         }
     let sheet = FsWorksheet(metaDataSheetName)
     assay
@@ -54,7 +55,7 @@ let fromMetadataSheet (sheet : FsWorksheet) : ArcAssay =
                         assays
                         |> Seq.tryHead 
                         |> Option.defaultValue (ArcAssay.create(Identifier.createMissingIdentifier()))
-                        |> ArcAssay.setPerformers (Array.ofList contacts)
+                        |> ArcAssay.setPerformers (ResizeArray contacts)
 
             if en.MoveNext () then
                 let currentLine = en.Current |> SparseRow.tryGetValueAt 0

src/Spreadsheet/ArcInvestigation.fs

@@ -1,6 +1,7 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open FsSpreadsheet
 open Comment
 open Remark
@@ -78,13 +79,12 @@ module ArcInvestigation =
             do matrix.Matrix.Add ((submissionDateLabel,i),      (Option.defaultValue "" investigation.SubmissionDate))
             do matrix.Matrix.Add ((publicReleaseDateLabel,i),   (Option.defaultValue "" investigation.PublicReleaseDate))
 
-            if Array.isEmpty investigation.Comments |> not then
-                investigation.Comments
-                |> Array.iter (fun comment -> 
-                    let n,v = comment |> Comment.toString
-                    commentKeys <- n :: commentKeys
-                    matrix.Matrix.Add((n,i),v)
-                )   
+            investigation.Comments
+            |> ResizeArray.iter (fun comment -> 
+                let n,v = comment |> Comment.toString
+                commentKeys <- n :: commentKeys
+                matrix.Matrix.Add((n,i),v)
+            )   
 
             {matrix with CommentKeys = commentKeys |> List.distinct |> List.rev}
 
@@ -106,14 +106,14 @@ module ArcInvestigation =
             (Option.fromValueWithDefault "" investigationInfo.Description) 
             (Option.fromValueWithDefault "" investigationInfo.SubmissionDate) 
             (Option.fromValueWithDefault "" investigationInfo.PublicReleaseDate)
-            (Array.ofList ontologySourceReference) 
-            (Array.ofList publications)  
-            (Array.ofList contacts)  
-            (ResizeArray(assays))
-            (ResizeArray(studies))  
-            (ResizeArray(studyIdentifiers))
-            (Array.ofList investigationInfo.Comments)  
-            (Array.ofList remarks)
+            (ResizeArray ontologySourceReference) 
+            (ResizeArray publications)  
+            (ResizeArray contacts)  
+            (ResizeArray assays)
+            (ResizeArray studies)
+            (ResizeArray studyIdentifiers)
+            (ResizeArray investigationInfo.Comments)  
+            (ResizeArray remarks)
 
 
     let fromRows (rows:seq<SparseRow>) =
@@ -183,24 +183,24 @@ module ArcInvestigation =
             with | _ -> rows |> Seq.toList
         seq {
             yield  SparseRow.fromValues [ontologySourceReferenceLabel]
-            yield! OntologySourceReference.toRows (List.ofArray investigation.OntologySourceReferences)
+            yield! OntologySourceReference.toRows (List.ofSeq investigation.OntologySourceReferences)
 
             yield  SparseRow.fromValues [investigationLabel]
             yield! InvestigationInfo.toRows investigation
 
             yield  SparseRow.fromValues [publicationsLabel]
-            yield! Publications.toRows (Some publicationsLabelPrefix) (List.ofArray investigation.Publications)
+            yield! Publications.toRows (Some publicationsLabelPrefix) (List.ofSeq investigation.Publications)
 
             yield  SparseRow.fromValues [contactsLabel]
-            yield! Contacts.toRows (Some contactsLabelPrefix) (List.ofArray investigation.Contacts)
+            yield! Contacts.toRows (Some contactsLabelPrefix) (List.ofSeq investigation.Contacts)
 
             if not isLight then
                 for studyIdentifier in investigation.RegisteredStudyIdentifiers do
                     let study = investigation.TryGetStudy(studyIdentifier) |> Option.defaultValue (ArcStudy(studyIdentifier))
                     yield  SparseRow.fromValues [studyLabel]
                     yield! Studies.toRows study None
         }
-        |> insertRemarks (List.ofArray investigation.Remarks)
+        |> insertRemarks (List.ofSeq investigation.Remarks)
         |> seq
 
     let fromFsWorkbook (doc:FsWorkbook) =  

src/Spreadsheet/ArcStudy.fs

@@ -1,9 +1,9 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
 open FsSpreadsheet
 
-open Aux
+open ARCtrl.Helper
 
 module ArcStudy = 
 

src/Spreadsheet/CollectionAux.fs

@@ -1,4 +1,4 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
 
 module Seq = 

src/Spreadsheet/Metadata/Assays.fs

@@ -1,9 +1,12 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
 open Comment
 open Remark
 open System.Collections.Generic
+open ARCtrl.Helper
+open ARCtrl.Process.Conversion
+
 
 module Assays = 
 
@@ -24,15 +27,15 @@ module Assays =
 
 
     let fromString measurementType measurementTypeTermSourceREF measurementTypeTermAccessionNumber technologyType technologyTypeTermSourceREF technologyTypeTermAccessionNumber technologyPlatform fileName comments : ArcAssay = 
-        let measurementType = OntologyAnnotation.fromString(?termName = measurementType,?tan = measurementTypeTermAccessionNumber,?tsr = measurementTypeTermSourceREF)
-        let technologyType = OntologyAnnotation.fromString(?termName = technologyType,?tan = technologyTypeTermAccessionNumber,?tsr = technologyTypeTermSourceREF)
+        let measurementType = OntologyAnnotation.create(?name = measurementType,?tan = measurementTypeTermAccessionNumber,?tsr = measurementTypeTermSourceREF)
+        let technologyType = OntologyAnnotation.create(?name = technologyType,?tan = technologyTypeTermAccessionNumber,?tsr = technologyTypeTermSourceREF)
         ArcAssay.make 
             (fileName)
-            (Option.fromValueWithDefault OntologyAnnotation.empty measurementType)
-            (Option.fromValueWithDefault OntologyAnnotation.empty technologyType) 
-            (technologyPlatform |> Option.map ArcAssay.decomposeTechnologyPlatform)
+            (Option.fromValueWithDefault (OntologyAnnotation()) measurementType)
+            (Option.fromValueWithDefault (OntologyAnnotation()) technologyType) 
+            (technologyPlatform |> Option.map JsonTypes.decomposeTechnologyPlatform)
             (ResizeArray())             
-            [||] 
+            (ResizeArray())      
             (comments)
 
     let fromSparseTable (matrix : SparseTable) : ArcAssay list=
@@ -47,7 +50,7 @@ module Assays =
                     matrix.CommentKeys 
                     |> List.map (fun k -> 
                         Comment.fromString k (matrix.TryGetValueDefault("",(k,i))))
-                    |> Array.ofList
+                    |> ResizeArray
 
                 fromString
                     (matrix.TryGetValue(measurementTypeLabel,i))            
@@ -69,24 +72,23 @@ module Assays =
             let processedFileName =
                 if a.Identifier.StartsWith(Identifier.MISSING_IDENTIFIER) then Identifier.removeMissingIdentifier(a.Identifier) else Identifier.Assay.fileNameFromIdentifier(a.Identifier)
             let i = i + 1
-            let mt = Option.defaultValue OntologyAnnotation.empty a.MeasurementType |> fun mt -> OntologyAnnotation.toString(mt,true)
-            let tt = Option.defaultValue OntologyAnnotation.empty a.TechnologyType |> fun tt -> OntologyAnnotation.toString(tt,true)
+            let mt = Option.defaultValue (OntologyAnnotation()) a.MeasurementType |> fun mt -> OntologyAnnotation.toString(mt,true)
+            let tt = Option.defaultValue (OntologyAnnotation()) a.TechnologyType |> fun tt -> OntologyAnnotation.toString(tt,true)
             do matrix.Matrix.Add ((measurementTypeLabel,i),                       mt.TermName)
             do matrix.Matrix.Add ((measurementTypeTermAccessionNumberLabel,i),    mt.TermAccessionNumber)
             do matrix.Matrix.Add ((measurementTypeTermSourceREFLabel,i),          mt.TermSourceREF)
             do matrix.Matrix.Add ((technologyTypeLabel,i),                        tt.TermName)
             do matrix.Matrix.Add ((technologyTypeTermAccessionNumberLabel,i),     tt.TermAccessionNumber)
             do matrix.Matrix.Add ((technologyTypeTermSourceREFLabel,i),           tt.TermSourceREF)
-            do matrix.Matrix.Add ((technologyPlatformLabel,i),                    (Option.defaultValue "" (a.TechnologyPlatform |> Option.map ArcAssay.composeTechnologyPlatform)))
+            do matrix.Matrix.Add ((technologyPlatformLabel,i),                    (Option.defaultValue "" (a.TechnologyPlatform |> Option.map JsonTypes.composeTechnologyPlatform)))
             do matrix.Matrix.Add ((fileNameLabel,i),                              processedFileName)
 
-            if Array.isEmpty a.Comments |> not then
-                a.Comments
-                |> Array.iter (fun comment -> 
-                    let n,v = comment |> Comment.toString
-                    commentKeys <- n :: commentKeys
-                    matrix.Matrix.Add((n,i),v)
-                )   
+            a.Comments
+            |> ResizeArray.iter (fun comment -> 
+                let n,v = comment |> Comment.toString
+                commentKeys <- n :: commentKeys
+                matrix.Matrix.Add((n,i),v)
+            )   
         )
         {matrix with CommentKeys = commentKeys |> List.distinct |> List.rev}
 

src/Spreadsheet/Metadata/Comment.fs

@@ -1,8 +1,8 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
 open System.Text.RegularExpressions
-open ARCtrl.ISA.Regex.ActivePatterns
+open ARCtrl.Helper.Regex.ActivePatterns
 
 module Comment = 
 
@@ -29,7 +29,6 @@ module Comment =
 
     let fromString k v =
         Comment.make 
-            None 
             (Option.fromValueWithDefault "" k) 
             (Option.fromValueWithDefault "" v)
 

src/Spreadsheet/Metadata/Contacts.fs

@@ -1,6 +1,8 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
+open ARCtrl.Process.Conversion
 open Comment
 open Remark
 open System.Collections.Generic
@@ -24,7 +26,6 @@ module Contacts =
     let fromString lastName firstName midInitials email phone fax address affiliation role rolesTermAccessionNumber rolesTermSourceREF comments =
         let roles = OntologyAnnotation.fromAggregatedStrings ';' role rolesTermSourceREF rolesTermAccessionNumber
         Person.make 
-            None 
             None
             (lastName   ) 
             (firstName  )
@@ -34,8 +35,8 @@ module Contacts =
             (fax        )
             (address    )
             (affiliation) 
-            (Option.fromValueWithDefault [||] roles    )
-            (Option.fromValueWithDefault [||] comments )
+            (roles    )
+            (comments )
         |> Person.setOrcidFromComments
 
     let fromSparseTable (matrix : SparseTable) =
@@ -49,7 +50,7 @@ module Contacts =
                     matrix.CommentKeys 
                     |> List.map (fun k -> 
                         Comment.fromString k (matrix.TryGetValueDefault("",(k,i))))
-                    |> Array.ofList
+                    |> ResizeArray
                 fromString
                     (matrix.TryGetValue(lastNameLabel,i))
                     (matrix.TryGetValue(firstNameLabel,i))
@@ -72,7 +73,7 @@ module Contacts =
         |> List.map Person.setCommentFromORCID
         |> List.iteri (fun i p ->
             let i = i + 1
-            let rAgg = Option.defaultValue [||] p.Roles |> OntologyAnnotation.toAggregatedStrings ';'
+            let rAgg = p.Roles |> Array.ofSeq |> OntologyAnnotation.toAggregatedStrings ';'
             do matrix.Matrix.Add ((lastNameLabel,i),                    (Option.defaultValue ""  p.LastName     ))
             do matrix.Matrix.Add ((firstNameLabel,i),                   (Option.defaultValue ""  p.FirstName    ))
             do matrix.Matrix.Add ((midInitialsLabel,i),                 (Option.defaultValue ""  p.MidInitials  ))
@@ -85,15 +86,12 @@ module Contacts =
             do matrix.Matrix.Add ((rolesTermAccessionNumberLabel,i),    rAgg.TermAccessionNumberAgg)
             do matrix.Matrix.Add ((rolesTermSourceREFLabel,i),          rAgg.TermSourceREFAgg)
 
-            match p.Comments with 
-            | None -> ()
-            | Some c ->
-                c
-                |> Array.iter (fun comment -> 
-                    let n,v = comment |> Comment.toString
-                    commentKeys <- n :: commentKeys
-                    matrix.Matrix.Add((n,i),v)
-                )
+            p.Comments
+            |> ResizeArray.iter (fun comment -> 
+                let n,v = comment |> Comment.toString
+                commentKeys <- n :: commentKeys
+                matrix.Matrix.Add((n,i),v)
+            )
         )
         {matrix with CommentKeys = commentKeys |> List.distinct |> List.rev}