change member syntax to true js members #241

src/ISA/ISA/ArcTypes/ArcTable.fs

@@ -17,12 +17,18 @@ type TableJoinOptions =
 [<AttachMembers>]
 type ArcTable(name: string, headers: ResizeArray<CompositeHeader>, values: System.Collections.Generic.Dictionary<int*int,CompositeCell>) = 
 
-    let mutable _name = name
-    member val Headers = headers with get, set
-    member val Values = values with get, set
+    let mutable name = name
+    let mutable headers = headers
+    let mutable values = values
+    member this.Headers
+        with get() = headers
+        and set(newHeaders) = headers <- newHeaders
+    member this.Values
+        with get() = values
+        and set(newValues) = values <- newValues
     member this.Name  
-        with get() = _name
-        and internal set (newName) = _name <- newName
+        with get() = name
+        and internal set (newName) = name <- newName
 
     static member create(name, headers, values) =
         ArcTable(name, headers, values)

src/ISA/ISA/ArcTypes/ArcTables.fs

@@ -145,14 +145,17 @@ open Fable.Core
 [<AttachMembers>]
 type ArcTables(initTables:ResizeArray<ArcTable>) = 
 
+    let mutable tables = initTables
+    member this.Tables 
+        with get() = tables
+        and set(newTables) = tables <- newTables
+
     interface IEnumerable<ArcTable> with
         member this.GetEnumerator() : IEnumerator<ArcTable> =
             this.Tables.GetEnumerator()
         member this.GetEnumerator(): System.Collections.IEnumerator = 
             this.Tables.GetEnumerator()
 
-    member val Tables = initTables with get, set
-
     member this.Item 
         with get(index) = 
             this.Tables.[index] 

src/ISA/ISA/ArcTypes/ArcTypes.fs

@@ -64,7 +64,8 @@ module ArcTypesAux =
     let inline removeMissingRegisteredAssays (inv: ArcInvestigation) : unit =
         let existingAssays = inv.AssayIdentifiers
         for study in inv.Studies do
-            let registeredAssays = ResizeArray(study.RegisteredAssayIdentifiers)
+            let rai : ResizeArray<string> = study.RegisteredAssayIdentifiers
+            let registeredAssays = ResizeArray(rai)
             for registeredAssay in registeredAssays do
                 if Seq.contains registeredAssay existingAssays |> not then
                     study.DeregisterAssay registeredAssay |> ignore
@@ -94,24 +95,21 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno
     let comments = defaultArg comments [||]
     let mutable identifier : string = identifier
     let mutable investigation : ArcInvestigation option = None
+    let mutable measurementType : OntologyAnnotation option = measurementType
+    let mutable technologyType : OntologyAnnotation option = technologyType
+    let mutable technologyPlatform : OntologyAnnotation option = technologyPlatform
+    let mutable performers : Person [] = performers
+    let mutable comments : Comment [] = comments
 
     /// Must be unique in one study
-    member this.Identifier 
-        with get() = identifier
-        and internal set(i) = identifier <- i
-
+    member this.Identifier with get() = identifier and internal set(i) = identifier <- i
     // read-online
-    member this.Investigation 
-        with get() = investigation
-        and internal set(i) = investigation <- i
-
-    static member FileName = ARCtrl.Path.AssayFileName
-
-    member val MeasurementType : OntologyAnnotation option = measurementType with get, set
-    member val TechnologyType : OntologyAnnotation option = technologyType with get, set
-    member val TechnologyPlatform : OntologyAnnotation option = technologyPlatform with get, set
-    member val Performers : Person [] = performers with get, set
-    member val Comments : Comment [] = comments with get, set
+    member this.Investigation with get() = investigation and internal set(i) = investigation <- i
+    member this.MeasurementType with get() = measurementType and set(n) = measurementType <- n
+    member this.TechnologyType with get() = technologyType and set(n) = technologyType <- n
+    member this.TechnologyPlatform with get() = technologyPlatform and set(n) = technologyPlatform <- n
+    member this.Performers with get() = performers and set(n) = performers <- n
+    member this.Comments with get() = comments and set(n) = comments <- n
 
     static member init (identifier : string) = ArcAssay(identifier)
     static member create (identifier: string, ?measurementType : OntologyAnnotation, ?technologyType : OntologyAnnotation, ?technologyPlatform : OntologyAnnotation, ?tables: ResizeArray<ArcTable>, ?performers : Person [], ?comments : Comment []) = 
@@ -127,6 +125,7 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno
         (comments : Comment []) = 
         ArcAssay(identifier = identifier, ?measurementType = measurementType, ?technologyType = technologyType, ?technologyPlatform = technologyPlatform, tables =tables, performers = performers, comments = comments)
 
+    static member FileName = ARCtrl.Path.AssayFileName
     member this.StudiesRegisteredIn
         with get () = 
             match this.Investigation with
@@ -570,25 +569,30 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi
 
     let mutable identifier = identifier
     let mutable investigation : ArcInvestigation option = None
+    let mutable title : string option = title
+    let mutable description : string option = description 
+    let mutable submissionDate : string option = submissionDate
+    let mutable publicReleaseDate : string option = publicReleaseDate
+    let mutable publications : Publication [] = publications
+    let mutable contacts : Person [] = contacts
+    let mutable studyDesignDescriptors : OntologyAnnotation [] = studyDesignDescriptors
+    let mutable registeredAssayIdentifiers : ResizeArray<string> = registeredAssayIdentifiers
+    let mutable factors : Factor [] = factors
+    let mutable comments : Comment [] = comments
     /// Must be unique in one investigation
-    member this.Identifier 
-        with get() = identifier
-        and internal set(i) = identifier <- i
+    member this.Identifier with get() = identifier and internal set(i) = identifier <- i
     // read-online
-    member this.Investigation 
-        with get() = investigation
-        and internal set(i) = investigation <- i
-
-    member val Title : string option = title with get, set
-    member val Description : string option = description with get, set
-    member val SubmissionDate : string option = submissionDate with get, set
-    member val PublicReleaseDate : string option = publicReleaseDate with get, set
-    member val Publications : Publication [] = publications with get, set
-    member val Contacts : Person [] = contacts with get, set
-    member val StudyDesignDescriptors : OntologyAnnotation [] = studyDesignDescriptors with get, set
-    member val RegisteredAssayIdentifiers : ResizeArray<string> = registeredAssayIdentifiers with get, set
-    member val Factors : Factor [] = factors with get, set
-    member val Comments : Comment []= comments with get, set
+    member this.Investigation with get() = investigation and internal set(i) = investigation <- i
+    member this.Title with get() = title and set(n) = title <- n
+    member this.Description with get() = description and set(n) = description <- n
+    member this.SubmissionDate with get() = submissionDate and set(n) = submissionDate <- n
+    member this.PublicReleaseDate with get() = publicReleaseDate and set(n) = publicReleaseDate <- n
+    member this.Publications with get() = publications and set(n) = publications <- n
+    member this.Contacts with get() = contacts and set(n) = contacts <- n
+    member this.StudyDesignDescriptors with get() = studyDesignDescriptors and set(n) = studyDesignDescriptors <- n
+    member this.RegisteredAssayIdentifiers with get() = registeredAssayIdentifiers and set(n) = registeredAssayIdentifiers <- n
+    member this.Factors with get() = factors and set(n) = factors <- n
+    member this.Comments with get() = comments and set(n) = comments <- n
 
     static member init(identifier : string) = ArcStudy identifier
 
@@ -1167,23 +1171,32 @@ type ArcInvestigation(identifier : string, ?title : string, ?description : strin
     let remarks = defaultArg remarks [||]
 
     let mutable identifier = identifier
+    let mutable title : string option = title
+    let mutable description : string option = description
+    let mutable submissionDate : string option = submissionDate
+    let mutable publicReleaseDate : string option = publicReleaseDate
+    let mutable ontologySourceReferences : OntologySourceReference [] = ontologySourceReferences
+    let mutable publications : Publication [] = publications
+    let mutable contacts : Person [] = contacts
+    let mutable assays : ResizeArray<ArcAssay> = assays
+    let mutable studies : ResizeArray<ArcStudy> = studies
+    let mutable registeredStudyIdentifiers : ResizeArray<string> = registeredStudyIdentifiers
+    let mutable comments : Comment [] = comments
+    let mutable remarks : Remark [] = remarks
     /// Must be unique in one investigation
-    member this.Identifier 
-        with get() = identifier
-        and internal set(i) = identifier <- i
-
-    member val Title : string option = title with get, set
-    member val Description : string option = description with get, set
-    member val SubmissionDate : string option = submissionDate with get, set
-    member val PublicReleaseDate : string option = publicReleaseDate with get, set
-    member val OntologySourceReferences : OntologySourceReference [] = ontologySourceReferences with get, set
-    member val Publications : Publication [] = publications with get, set
-    member val Contacts : Person [] = contacts with get, set
-    member val Assays : ResizeArray<ArcAssay> = assays with get, set
-    member val Studies : ResizeArray<ArcStudy> = studies with get, set
-    member val RegisteredStudyIdentifiers : ResizeArray<string> = registeredStudyIdentifiers with get, set
-    member val Comments : Comment [] = comments with get, set
-    member val Remarks : Remark [] = remarks with get, set
+    member this.Identifier with get() = identifier and internal set(i) = identifier <- i
+    member this.Title with get() = title and set(n) = title <- n
+    member this.Description with get() = description and set(n) = description <- n
+    member this.SubmissionDate with get() = submissionDate and set(n) = submissionDate <- n
+    member this.PublicReleaseDate with get() = publicReleaseDate and set(n) = publicReleaseDate <- n
+    member this.OntologySourceReferences with get() = ontologySourceReferences and set(n) = ontologySourceReferences <- n
+    member this.Publications with get() = publications and set(n) = publications <- n
+    member this.Contacts with get() = contacts and set(n) = contacts <- n
+    member this.Assays with get() : ResizeArray<ArcAssay> = assays and set(n) = assays <- n
+    member this.Studies with get() : ResizeArray<ArcStudy> = studies and set(n) = studies <- n
+    member this.RegisteredStudyIdentifiers with get() = registeredStudyIdentifiers and set(n) = registeredStudyIdentifiers <- n
+    member this.Comments with get() = comments and set(n) = comments <- n
+    member this.Remarks with get() = remarks and set(n) = remarks <- n
 
     static member FileName = ARCtrl.Path.InvestigationFileName