finish thoth conversion

nfdi4plants · Feb 29, 2024 · c482c86 · c482c86
1 parent d0a99a3
commit c482c86
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Showing 9 changed files with 163 additions and 197 deletions.
diff --git a/src/ARCtrl/Templates/Template.Json.fs b/src/ARCtrl/Templates/Template.Json.fs
@@ -3,12 +3,10 @@
 open ARCtrl.Template
 open ARCtrl.ISA
 open System
-#if FABLE_COMPILER
-open Thoth.Json
-#else
-open Thoth.Json.Net
 open ARCtrl
-#endif
+
+open Thoth.Json.Core
+open ARCtrl.ISA.Json
 
 //https://thoth-org.github.io/Thoth.Json/documentation/auto/extra-coders.html#ready-to-use-extra-coders
 
@@ -25,7 +23,7 @@ module Organisation =
 
 module Template =
 
-    open ARCtrl.ISA.Json
+
 
     let encode (template: Template) =
         let personEncoder = ARCtrl.ISA.Json.Person.encoder (ConverterOptions())
@@ -68,12 +66,11 @@ module Template =
         )
 
     let fromJsonString (jsonString: string) =
-        match Decode.fromString decode jsonString with
-        | Ok template   -> template
-        | Error exn     -> failwithf "Error. Given json string cannot be parsed to Template: %A" exn
+        try GDecode.fromJsonString decode jsonString with
+        | exn     -> failwithf "Error. Given json string cannot be parsed to Template: %A" exn
 
     let toJsonString (spaces: int) (template:Template) =
-        Encode.toString spaces (encode template)
+        GEncode.toJsonString spaces (encode template)
 
 module Templates =
 
@@ -84,16 +81,15 @@ module Templates =
         |> Encode.object
 
     let decode =
-        let d = Decode.dict Template.decode
-        Decode.fromString d
+        Decode.dict Template.decode
+
 
     let fromJsonString (jsonString: string) =
-        match decode jsonString with
-        | Ok templateMap    -> templateMap.Values |> Array.ofSeq
-        | Error exn         -> failwithf "Error. Given json string cannot be parsed to Templates map: %A" exn
+        try GDecode.fromJsonString decode jsonString with
+        | exn         -> failwithf "Error. Given json string cannot be parsed to Templates map: %A" exn
 
     let toJsonString (spaces: int) (templateList: (string*Template) []) =
-        Encode.toString spaces (encode templateList)
+        GEncode.toJsonString spaces (encode templateList)
 
 
 [<AutoOpen>]

diff --git a/src/ISA/ISA.Json/ArcTypes/ArcAssay.fs b/src/ISA/ISA.Json/ArcTypes/ArcAssay.fs
@@ -119,9 +119,8 @@ module ArcAssay =
         GEncode.toJsonString spaces (encoder a)
 
     let fromArcJsonString (jsonString: string) =
-        match Decode.fromString decoder jsonString with
-        | Ok a -> a
-        | Error e -> failwithf "Error. Unable to parse json string to ArcAssay: %s" e
+        try GDecode.fromJsonString decoder jsonString with
+        | e -> failwithf "Error. Unable to parse json string to ArcAssay: %s" e.Message
 
 [<AutoOpen>]
 module ArcAssayExtensions =
@@ -130,9 +129,8 @@ module ArcAssayExtensions =
 
     type ArcAssay with
         static member fromArcJsonString (jsonString: string) : ArcAssay = 
-            match Decode.fromString ArcAssay.decoder jsonString with
-            | Ok a -> a
-            | Error e -> failwithf "Error. Unable to parse json string to ArcAssay: %s" e
+            try GDecode.fromJsonString ArcAssay.decoder jsonString with
+            | e -> failwithf "Error. Unable to parse json string to ArcAssay: %s" e.Message
 
         member this.ToArcJsonString(?spaces) : string =
             let spaces = defaultArg spaces 0
@@ -148,9 +146,8 @@ module ArcAssayExtensions =
                     let cellTable = get.Required.Field "cellTable" (CellTable.decoder stringTable oaTable)
                     get.Required.Field "assay" (ArcAssay.compressedDecoder stringTable oaTable cellTable)
                 )
-            match Decode.fromString decoder jsonString with
-            | Ok r -> r
-            | Error e -> failwithf "Error. Unable to parse json string to ArcAssay: %s" e
+            try GDecode.fromJsonString decoder jsonString with
+            | e -> failwithf "Error. Unable to parse json string to ArcAssay: %s" e.Message
 
         member this.ToCompressedJsonString(?spaces) : string =
             let spaces = defaultArg spaces 0

diff --git a/src/ISA/ISA.Json/ArcTypes/ArcInvestigation.fs b/src/ISA/ISA.Json/ArcTypes/ArcInvestigation.fs
@@ -75,18 +75,16 @@ module ArcInvestigation =
         GEncode.toJsonString spaces (encoder a)
 
     let fromArcJsonString (jsonString: string) =
-        match Decode.fromString decoder jsonString with
-        | Ok a -> a
-        | Error e -> failwithf "Error. Unable to parse json string to ArcInvestigation: %s" e
+        try GDecode.fromJsonString decoder jsonString with
+        | e -> failwithf "Error. Unable to parse json string to ArcInvestigation: %s" e.Message
 
 [<AutoOpen>]
 module ArcInvestigationExtensions =
 
     type ArcInvestigation with
         static member fromArcJsonString (jsonString: string) : ArcInvestigation = 
-            match Decode.fromString ArcInvestigation.decoder jsonString with
-            | Ok r -> r
-            | Error e -> failwithf "Error. Unable to parse json string to ArcInvestigation: %s" e
+            try GDecode.fromJsonString ArcInvestigation.decoder jsonString with
+            | e -> failwithf "Error. Unable to parse json string to ArcInvestigation: %s" e.Message
 
         member this.ToArcJsonString(?spaces) : string =
             let spaces = defaultArg spaces 0

diff --git a/src/ISA/ISA.Json/ArcTypes/ArcStudy.fs b/src/ISA/ISA.Json/ArcTypes/ArcStudy.fs
@@ -118,9 +118,8 @@ module ArcStudy =
         GEncode.toJsonString spaces (encoder a)
 
     let fromArcJsonString (jsonString: string) =
-        match Decode.fromString decoder jsonString with
-        | Ok a -> a
-        | Error e -> failwithf "Error. Unable to parse json string to ArcStudy: %s" e
+        try GDecode.fromJsonString decoder jsonString with
+        | e -> failwithf "Error. Unable to parse json string to ArcStudy: %s" e.Message
 
 [<AutoOpen>]
 module ArcStudyExtensions =
@@ -129,9 +128,8 @@ module ArcStudyExtensions =
 
     type ArcStudy with
         static member fromArcJsonString (jsonString: string) : ArcStudy = 
-            match Decode.fromString ArcStudy.decoder jsonString with
-            | Ok r -> r
-            | Error e -> failwithf "Error. Unable to parse json string to ArcStudy: %s" e
+            try GDecode.fromJsonString ArcStudy.decoder jsonString with
+            | e -> failwithf "Error. Unable to parse json string to ArcStudy: %s" e.Message
 
         member this.ToArcJsonString(?spaces) : string =
             let spaces = defaultArg spaces 0
@@ -147,9 +145,8 @@ module ArcStudyExtensions =
                     let cellTable = get.Required.Field "cellTable" (CellTable.decoder stringTable oaTable)
                     get.Required.Field "study" (ArcStudy.compressedDecoder stringTable oaTable cellTable)
                 )
-            match Decode.fromString decoder jsonString with
-            | Ok r -> r
-            | Error e -> failwithf "Error. Unable to parse json string to ArcAssay: %s" e
+            try GDecode.fromJsonString decoder jsonString with
+            | e -> failwithf "Error. Unable to parse json string to ArcAssay: %s" e.Message
 
         member this.ToCompressedJsonString(?spaces) : string =
             let spaces = defaultArg spaces 0

diff --git a/src/ISA/ISA.Json/ArcTypes/ArcTable.fs b/src/ISA/ISA.Json/ArcTypes/ArcTable.fs
@@ -48,22 +48,60 @@ module ArcTable =
                 yield Encode.object ["f",Encode.int from; "t", Encode.int(rowCount-1); "v",CellTable.encodeCell cellTable current]
             |]
             |> Encode.array
+
+    let compressedColumnDecoder (cellTable : CellTableArray) (table: ArcTable) (columnIndex : int)  =
+        {new Decoder<unit> with
+            member this.Decode (helper,column) =
+                match (Decode.array (CellTable.decodeCell cellTable)).Decode(helper,column) with
+                | Ok a ->             
+                    a |> Array.iteri (fun r cell -> table.Values.Add((columnIndex,r),cell))
+                    Ok(())
+                | Error err -> 
+                    let rangeDecoder = 
+                        Decode.object (fun get -> 
+                            let from = get.Required.Field "f" Decode.int
+                            let to_ = get.Required.Field "t" Decode.int
+                            let value = get.Required.Field "v" (CellTable.decodeCell cellTable)
+                            for i = from to to_ do
+                                table.Values.Add((columnIndex,i),value)
+                        )
+                    match (Decode.array (rangeDecoder)).Decode(helper,column) with
+                    | Ok _ -> Ok ()
+                    | Error err -> Error err
+        } 
 
-    let compressedColumnDecoder (columnIndex : int) (cellTable : CellTableArray) (table: ArcTable) (column : JsonValue)  =
-        match (Decode.array (CellTable.decodeCell cellTable)).Decode "" column with
-        | Ok a ->             
-            a |> Array.iteri (fun r cell -> table.Values.Add((columnIndex,r),cell))
-        | Error err -> 
-            let rangeDecoder s jv = 
-                Decode.object (fun get -> 
-                    let from = get.Required.Field "f" Decode.int
-                    let to_ = get.Required.Field "t" Decode.int
-                    let value = get.Required.Field "v" (CellTable.decodeCell cellTable)
-                    for i = from to to_ do
-                        table.Values.Add((columnIndex,i),value)
-                ) s jv 
-            Decode.array (rangeDecoder) "" column |> ignore
-
+
+    let arrayi (decoderi: int -> Decoder<'value>) : Decoder<'value array> =
+        { new Decoder<'value array> with
+            member _.Decode(helpers, value) =
+                if helpers.isArray value then
+                    let mutable i = -1
+                    let tokens = helpers.asArray value
+                    let arr = Array.zeroCreate tokens.Length
+
+                    (Ok arr, tokens)
+                    ||> Array.fold (fun acc value ->
+                        i <- i + 1
+
+                        match acc with
+                        | Error _ -> acc
+                        | Ok acc ->
+                            match (decoderi i).Decode(helpers, value) with
+                            | Error er ->
+                                Error(
+                                    er
+                                    |> Decode.Helpers.prependPath (
+                                        ".[" + (i.ToString()) + "]"
+                                    )
+                                )
+                            | Ok value ->
+                                acc.[i] <- value
+                                Ok acc
+                    )
+                else
+                    ("", BadPrimitive("an array", value)) |> Error
+        }
+
 
     let compressedEncoder (stringTable : StringTableMap) (oaTable : OATableMap) (cellTable : CellTableMap) (table: ArcTable) =
         Encode.object [
@@ -88,9 +126,11 @@ module ArcTable =
                     decodedHeader,
                     Dictionary()
                 )
-            let columns = get.Optional.Field "c" (Decode.array Decode.value)
-            columns
-            |> Option.iter (Array.iteri (fun c col -> compressedColumnDecoder c cellTable table col))
+
+            // Columns
+            get.Optional.Field "c" (arrayi (compressedColumnDecoder cellTable table)) |> ignore
+
+
             table 
 
         )
@@ -100,9 +140,7 @@ module ArcTableExtensions =
 
     type ArcTable with
         static member fromJsonString (jsonString: string) : ArcTable = 
-            match Decode.fromString ArcTable.decoder jsonString with
-            | Ok r -> r
-            | Error e -> failwithf "Error. Unable to parse json string to ArcTable: %s" e
+            GDecode.fromJsonString ArcTable.decoder jsonString
 
         member this.ToJsonString(?spaces) : string =
             let spaces = defaultArg spaces 0
@@ -118,9 +156,7 @@ module ArcTableExtensions =
                     let cellTable = get.Required.Field "cellTable" (CellTable.decoder stringTable oaTable)
                     get.Required.Field "table" (ArcTable.compressedDecoder stringTable oaTable cellTable)
                 )
-            match Decode.fromString decoder jsonString with
-            | Ok r -> r
-            | Error e -> failwithf "Error. Unable to parse json string to ArcTable: %s" e
+            GDecode.fromJsonString decoder jsonString
 
         member this.ToCompressedJsonString(?spaces) : string =
             let spaces = defaultArg spaces 0

diff --git a/src/ISA/ISA/JsonTypes/Value.fs b/src/ISA/ISA/JsonTypes/Value.fs
@@ -1,6 +1,7 @@
 namespace ARCtrl.ISA
 
 open Fable.Core
+open System.Globalization
 
 [<AttachMembers>]
 type Value =
@@ -10,10 +11,11 @@ type Value =
     | Name of string
 
     static member fromString (value : string) =
-        match System.Int32.TryParse value with
+        match System.Int32.TryParse value  with
         | (true, i) -> Value.Int i
         | _ -> 
-            match System.Double.TryParse value with
+
+            match System.Double.TryParse(value,NumberStyles.Any,CultureInfo.InvariantCulture) with
             | (true, f) -> Value.Float f
             | _ -> Value.Name value