rework ARCtrl.Core types to improve transpiled javascript

Author: HLWeil

src/Core/ARCtrl.Core.fsproj

@@ -13,6 +13,7 @@
     <Compile Include="Helper\HashCodes.fs" />
     <Compile Include="Helper\Update.fs" />
     <Compile Include="Helper\Printer.fs" />
+    <Compile Include="Helper\SemVer.fs" />
     <Compile Include="URI.fs" />
     <Compile Include="Comment.fs" />
     <Compile Include="CommentList.fs" />
@@ -52,6 +53,7 @@
     <Compile Include="Table\ArcTable.fs" />
     <Compile Include="Table\ArcTables.fs" />
     <Compile Include="ArcTypes.fs" />
+    <Compile Include="Template.fs" />
     <Compile Include="Conversion.fs" />
     <Compile Include="IdentifierSetters.fs" />
   </ItemGroup>

src/Core/ArcTypes.fs

@@ -4,53 +4,50 @@
 open ARCtrl.Helper 
 
 /// If a comment with the given key exists in the [], return its value, else return None
-let tryItem (key: string) (comments : Comment []) =
+let tryItem (key: string) (comments : ResizeArray<Comment>) =
     comments
-    |> Array.tryPick (fun c -> 
+    |> Seq.tryPick (fun c -> 
         match c.Name with
         | Some n when n = key -> c.Value
         | _ -> None        
     )
 
 /// Returns true, if the key exists in the []
-let containsKey (key: string) (comments : Comment []) =
+let containsKey (key: string) (comments : ResizeArray<Comment>) =
     comments
-    |> Array.exists (fun c -> 
+    |> Seq.exists (fun c -> 
         match c.Name with
         | Some n when n = key -> true
         | _ -> false        
     )
 
 /// If a comment with the given key exists in the [], return its value
-let item (key: string) (comments : Comment []) =
+let item (key: string) (comments : ResizeArray<Comment>) =
     (tryItem key comments).Value
 
 /// Create a map of comment keys to comment values
-let toMap (comments : Comment []) =
+let toMap (comments : ResizeArray<Comment>) =
     comments
-    |> Array.choose (fun c -> 
+    |> ResizeArray.choose (fun c -> 
         match c.Name with
         | Some n -> Some (n,c.Value)
         | _ -> None
     )
-    |> Map.ofArray
+    |> Map.ofSeq
 
-/// Adds the given comment to the comment []  
-let add (comment : Comment) (comments : Comment []) =
-    Array.append comments [|comment|]
 
 /// Add the given comment to the comment [] if it doesnt exist, else replace it 
-let set (comment : Comment) (comments : Comment []) =
+let set (comment : Comment) (comments : ResizeArray<Comment>) =
     if containsKey comment.Name.Value comments then
         comments
-        |> Array.map (fun c -> if c.Name = comment.Name then comment else c)
+        |> ResizeArray.map (fun c -> if c.Name = comment.Name then comment else c)
     else
-        Array.append comments [|comment|]
+        ResizeArray.appendSingleton comment comments 
 
 /// Returns a new comment [] where comments with the given key are filtered out
-let dropByKey (key: string) (comments : Comment []) =
+let dropByKey (key: string) (comments : ResizeArray<Comment>) =
     comments
-    |> Array.filter (fun c -> 
+    |> ResizeArray.filter (fun c -> 
         match c.Name with
         | Some n when n = key -> false
         | _ -> true        

src/Core/CommentList.fs

@@ -10,6 +10,7 @@ module Person =
     let orcidKey = "ORCID"
 
     let setOrcidFromComments (person : Person) =
+        let person = person.Copy()
         let isOrcidComment (c : Comment) = 
             c.Name.IsSome && (c.Name.Value.ToUpper().EndsWith(orcidKey))
         let orcid,comments = 
@@ -23,13 +24,16 @@ module Person =
             orcid, comments
         person.ORCID <- orcid
         person.Comments <- comments
+        person
 
     let setCommentFromORCID (person : Person) =
+        let person = person.Copy()
         match person.ORCID with
         | Some orcid -> 
-            let comment = Comment.create (Name = orcidKey, Value = orcid)
+            let comment = Comment.create (name = orcidKey, value = orcid)
             person.Comments.Add comment
         | None -> ()
+        person
 
 /// Functions for transforming base level ARC Table and ISA Json Objects
 module JsonTypes = 
@@ -170,8 +174,8 @@ module JsonTypes =
         match name with 
         | Regex.ActivePatterns.Regex pattern r -> 
             let oa = (r.Groups.Item "ontology").Value   |> OntologyAnnotation.fromTermAnnotation 
-            let v =  (r.Groups.Item "value").Value      |> Value.fromString
-            {oa with Name = (Some v.Text)}
+            let v =  (r.Groups.Item "value").Value
+            OntologyAnnotation.create(name = v, ?tan = oa.TermAccessionNumber, ?tsr = oa.TermSourceREF)
         | _ ->
             OntologyAnnotation.create(name = name)
 
@@ -185,7 +189,9 @@ module ProcessParsing =
     let tryComponentGetter (generalI : int) (valueI : int) (valueHeader : CompositeHeader) =
         match valueHeader with
         | CompositeHeader.Component oa ->
-            let cat = CompositeHeader.Component (oa.SetColumnIndex valueI)
+            let newOA = oa.Copy()
+            newOA.SetColumnIndex valueI
+            let cat = CompositeHeader.Component newOA
             fun (matrix : System.Collections.Generic.Dictionary<(int * int),CompositeCell>) i ->
                 JsonTypes.composeComponent cat matrix.[generalI,i]
             |> Some
@@ -195,7 +201,9 @@ module ProcessParsing =
     let tryParameterGetter (generalI : int) (valueI : int) (valueHeader : CompositeHeader) =
         match valueHeader with
         | CompositeHeader.Parameter oa ->
-            let cat = CompositeHeader.Parameter (oa.SetColumnIndex valueI)
+            let cat = 
+                OntologyAnnotation.setColumnIndex valueI oa 
+                |> CompositeHeader.Parameter
             fun (matrix : System.Collections.Generic.Dictionary<(int * int),CompositeCell>) i ->
                 JsonTypes.composeParameterValue cat matrix.[generalI,i]
             |> Some
@@ -204,7 +212,9 @@ module ProcessParsing =
     let tryFactorGetter (generalI : int) (valueI : int) (valueHeader : CompositeHeader) =
         match valueHeader with
         | CompositeHeader.Factor oa ->
-            let cat = CompositeHeader.Factor (oa.SetColumnIndex valueI)
+            let cat = 
+                OntologyAnnotation.setColumnIndex valueI oa
+                |> CompositeHeader.Factor
             fun (matrix : System.Collections.Generic.Dictionary<(int * int),CompositeCell>) i ->
                 JsonTypes.composeFactorValue cat matrix.[generalI,i]
             |> Some
@@ -213,7 +223,9 @@ module ProcessParsing =
     let tryCharacteristicGetter (generalI : int) (valueI : int) (valueHeader : CompositeHeader) =
         match valueHeader with
         | CompositeHeader.Characteristic oa ->
-            let cat = CompositeHeader.Characteristic (oa.SetColumnIndex valueI)
+            let cat = 
+                OntologyAnnotation.setColumnIndex valueI oa
+                |> CompositeHeader.Characteristic              
             fun (matrix : System.Collections.Generic.Dictionary<(int * int),CompositeCell>) i ->
                 JsonTypes.composeCharacteristicValue cat matrix.[generalI,i]
             |> Some
@@ -628,7 +640,7 @@ type ArcTable with
             |> Seq.fold (fun (p : Protocol) h -> 
                 match h with
                 | CompositeHeader.ProtocolType -> 
-                    Protocol.setProtocolType p OntologyAnnotation.empty
+                    Protocol.setProtocolType p (OntologyAnnotation())
                 | CompositeHeader.ProtocolVersion -> Protocol.setVersion p ""
                 | CompositeHeader.ProtocolUri -> Protocol.setUri p ""
                 | CompositeHeader.ProtocolDescription -> Protocol.setDescription p ""

src/Core/Conversion.fs

@@ -141,4 +141,21 @@ module ResizeArray =
         b
 
     let isEmpty (a : ResizeArray<_>) =
-        a.Count = 0
+        a.Count = 0
+
+    /// Immutable append
+    let append (a : ResizeArray<_>) (b : ResizeArray<_>) =
+        let c = ResizeArray<_>()
+        for i in a do
+            c.Add(i)
+        for i in b do
+            c.Add(i)
+        c
+
+    /// append a single element
+    let appendSingleton (b : 'T) (a : ResizeArray<_>) =
+        let c = ResizeArray<_>()
+        for i in a do
+            c.Add(i)
+        c.Add(b)
+        c

src/Core/Helper/Collections.fs

@@ -0,0 +1,64 @@
+module ARCtrl.Helper.SemVer
+
+open Regex.ActivePatterns
+
+module SemVerAux =
+
+    let Pattern =
+            @"^(?<major>\d+)" +
+            @"(\.(?<minor>\d+))?" +
+            @"(\.(?<patch>\d+))?" +
+            @"(-(?<pre>[0-9A-Za-z-\.]+))?" +
+            @"(\+(?<build>[0-9A-Za-z-\.]+))?$"
+
+
+type SemVer = {
+    Major: int
+    Minor: int
+    Patch: int
+    PreRelease: string option
+    Metadata: string option
+} with
+    static member make major minor patch pre meta = {
+        Major = major
+        Minor = minor
+        Patch = patch
+        PreRelease = pre
+        Metadata = meta
+    }
+
+    static member create(major: int, minor: int, patch: int, ?pre: string, ?meta: string) =
+        {
+            Major = major
+            Minor = minor
+            Patch = patch
+            PreRelease = pre
+            Metadata = meta
+        }
+
+    static member tryOfString (str: string) =
+        match str with
+        | Regex (SemVerAux.Pattern) m ->
+            let g = m.Groups
+            let major = int g.["major"].Value
+            let minor = int g.["minor"].Value
+            let patch = int g.["patch"].Value
+            let pre = 
+                match g.["pre"].Success with
+                | true -> Some g.["pre"].Value
+                | false -> None
+            let meta =
+                match g.["build"].Success with
+                | true -> Some g.["build"].Value
+                | false -> None
+            Some <| SemVer.create(major, minor, patch, ?pre=pre, ?meta=meta)
+        | _ -> None
+
+    member this.AsString() : string =
+        let sb = System.Text.StringBuilder()
+        sb.Append(sprintf "%i.%i.%i" this.Major this.Minor this.Patch) |> ignore
+        if this.PreRelease.IsSome then
+            sb.Append(sprintf "-%s" this.PreRelease.Value) |> ignore
+        if this.Metadata.IsSome then
+            sb.Append(sprintf "+%s" this.Metadata.Value) |> ignore
+        sb.ToString()

src/Core/Helper/SemVer.fs

@@ -41,8 +41,6 @@ type OntologyAnnotation(?name,?tsr,?tan, ?comments) =
     static member create(?name,?tsr,?tan,?comments) : OntologyAnnotation =
         OntologyAnnotation.make name tsr tan (defaultArg comments <| ResizeArray())
 
-    static member empty = OntologyAnnotation.create()
-
     member this.TANInfo = 
         match this.TermAccessionNumber with
         | Some v -> 
@@ -92,22 +90,22 @@ type OntologyAnnotation(?name,?tsr,?tan, ?comments) =
     ///
     /// `asOntobeePurlUrl`: option to return term accession in Ontobee purl-url format (`http://purl.obolibrary.org/obo/MS_1000121`)
     /// </summary>
-    // TODO: Not sure if still needed ~Kevin F. 2024.03.20
-    //static member toString (oa : OntologyAnnotation, ?asOntobeePurlUrlIfShort: bool) =
-    //    let asOntobeePurlUrlIfShort = Option.defaultValue false asOntobeePurlUrlIfShort
-    //    {|
-    //        TermName = oa.Name |> Option.defaultValue ""
-    //        TermSourceREF = oa.TermSourceREF |> Option.defaultValue ""
-    //        TermAccessionNumber = 
-    //            if asOntobeePurlUrlIfShort then
-    //                let url = oa.TermAccessionAndOntobeeUrlIfShort
-    //                if url = "" then 
-    //                    oa.TermAccessionNumber |> Option.defaultValue ""
-    //                else
-    //                    url
-    //            else
-    //                oa.TermAccessionNumber |> Option.defaultValue ""
-    //    |}
+    ///// TODO: Not sure if still needed ~Kevin F. 2024.03.20
+    static member toString (oa : OntologyAnnotation, ?asOntobeePurlUrlIfShort: bool) =
+        let asOntobeePurlUrlIfShort = Option.defaultValue false asOntobeePurlUrlIfShort
+        {|
+            TermName = oa.Name |> Option.defaultValue ""
+            TermSourceREF = oa.TermSourceREF |> Option.defaultValue ""
+            TermAccessionNumber = 
+                if asOntobeePurlUrlIfShort then
+                    let url = oa.TermAccessionAndOntobeeUrlIfShort
+                    if url = "" then 
+                        oa.TermAccessionNumber |> Option.defaultValue ""
+                    else
+                        url
+                else
+                    oa.TermAccessionNumber |> Option.defaultValue ""
+        |}
 
     interface IISAPrintable with
         member this.Print() =