Merge pull request #444 from nfdi4plants/rework-jsonIO-dependency

JsonIO rework
nfdi4plants · Sep 27, 2024 · 9af0c63 · 9af0c63
2 parents 32875d5 + 29d1bb2
commit 9af0c63
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Showing 28 changed files with 140 additions and 136 deletions.
diff --git a/src/ARCtrl/WebRequest/WebRequest.Node.fs b/src/ARCtrl/WebRequest/WebRequest.Node.fs
@@ -1,9 +1,9 @@
-module ARCtrl.WebRequestHelpers.NodeJs
+module ARCtrl.WebRequestHelpers.NodeJs
 
+#if FABLE_COMPILER_JAVASCRIPT
 open Fable.Core
 open Fable.SimpleHttp
 
-#if FABLE_COMPILER_JAVASCRIPT
 open Fable.Core.JsInterop
 
 open Fable.SimpleHttp 

diff --git a/src/Json/ARC.fs b/src/Json/ARC.fs
@@ -1,4 +1,4 @@
-namespace ARCtrl.Json
+namespace ARCtrl.Json
 
 open Thoth.Json.Core
 
@@ -17,8 +17,8 @@ module ARC =
                 Encode.tryInclude "@type" Encode.string (Some "CreativeWork")
                 Encode.tryInclude "@id" Encode.string (Some "ro-crate-metadata.json")
                 Encode.tryInclude "about" Investigation.ROCrate.encoder (Some isa)
-                "conformsTo", ROCrateContext.ROCrate.conformsTo_jsonvalue
-                "@context", ROCrateContext.ROCrate.context_jsonvalue
+                "conformsTo", ROCrateContext.ROCrate.conformsTo_jsonvalue |> Some
+                "@context", ROCrateContext.ROCrate.context_jsonvalue |> Some
                 ]
             |> Encode.choose
             |> Encode.object

diff --git a/src/Json/ARCtrl.Json.fsproj b/src/Json/ARCtrl.Json.fsproj
@@ -82,10 +82,10 @@
   </ItemGroup>
   <ItemGroup>
     <PackageReference Include="NJsonSchema" Version="10.8.0" />
-    <PackageReference Include="Thoth.Json.Core" Version="0.2.1" />
-    <PackageReference Include="Thoth.Json.Newtonsoft" Version="0.1.0" />
-    <PackageReference Condition="'$(FABLE_COMPILER_PYTHON)' == 'true'" Include="Thoth.Json.Python" Version="0.2.0" />
-    <PackageReference Condition="'$(FABLE_COMPILER_JAVASCRIPT)' == 'true'" Include="Thoth.Json.JavaScript" Version="0.1.0" />
+    <PackageReference Include="Thoth.Json.Core" Version="0.4.0" />
+    <PackageReference Include="Thoth.Json.Newtonsoft" Version="0.2.0" />
+    <PackageReference Include="FsSpreadsheet.Js" Version="6.3.0-alpha.3" />
+    <PackageReference Include="FsSpreadsheet.Py" Version="6.3.0-alpha.3" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\Core\ARCtrl.Core.fsproj" />

diff --git a/src/Json/Assay.fs b/src/Json/Assay.fs
@@ -11,7 +11,7 @@ module Assay =
 
     let encoder (assay:ArcAssay) = 
         [ 
-            "Identifier", Encode.string assay.Identifier
+            "Identifier", Encode.string assay.Identifier |> Some
             Encode.tryInclude "MeasurementType" OntologyAnnotation.encoder assay.MeasurementType
             Encode.tryInclude "TechnologyType" OntologyAnnotation.encoder assay.TechnologyType
             Encode.tryInclude "TechnologyPlatform" OntologyAnnotation.encoder assay.TechnologyPlatform
@@ -43,7 +43,7 @@ module Assay =
 
     let encoderCompressed (stringTable : StringTableMap) (oaTable : OATableMap) (cellTable : CellTableMap) (assay:ArcAssay) =
         [ 
-            "Identifier", Encode.string assay.Identifier
+            "Identifier", Encode.string assay.Identifier |> Some
             Encode.tryInclude "MeasurementType" OntologyAnnotation.encoder assay.MeasurementType
             Encode.tryInclude "TechnologyType" OntologyAnnotation.encoder assay.TechnologyType
             Encode.tryInclude "TechnologyPlatform" OntologyAnnotation.encoder assay.TechnologyPlatform
@@ -84,19 +84,19 @@ module Assay =
             let dataFiles = ProcessSequence.getData processes
 
             [
-                "@id", Encode.string (a |> genID)
-                "@type", (Encode.list [ Encode.string "Assay"])
-                "additionalType", Encode.string "Assay"
-                "identifier", Encode.string a.Identifier
-                "filename", Encode.string fileName
+                "@id", Encode.string (a |> genID) |> Some
+                "@type", (Encode.list [ Encode.string "Assay"]) |> Some
+                "additionalType", Encode.string "Assay" |> Some
+                "identifier", Encode.string a.Identifier |> Some
+                "filename", Encode.string fileName |> Some
                 Encode.tryInclude "measurementType" OntologyAnnotation.ROCrate.encoderPropertyValue a.MeasurementType
                 Encode.tryInclude "technologyType" OntologyAnnotation.ROCrate.encoderDefinedTerm a.TechnologyType
                 Encode.tryInclude "technologyPlatform" OntologyAnnotation.ROCrate.encoderDefinedTerm a.TechnologyPlatform
                 Encode.tryIncludeSeq "performers" Person.ROCrate.encoder a.Performers
                 Encode.tryIncludeList "dataFiles" Data.ROCrate.encoder dataFiles
                 Encode.tryIncludeList "processSequence" (Process.ROCrate.encoder studyName (Some a.Identifier)) processes
                 Encode.tryIncludeSeq "comments" Comment.ROCrate.encoder a.Comments
-                "@context", ROCrateContext.Assay.context_jsonvalue
+                "@context", ROCrateContext.Assay.context_jsonvalue |> Some
             ]
             |> Encode.choose
             |> Encode.object
@@ -139,7 +139,7 @@ module Assay =
                     |> Encode.tryIncludeList "dataFiles" (Data.ISAJson.encoder idMap) 
                 let units = ProcessSequence.getUnits processes
                 [
-                    "filename", Encode.string fileName
+                    "filename", Encode.string fileName |> Some
                     Encode.tryInclude "@id" Encode.string (ROCrate.genID a |> Some)
                     Encode.tryInclude "measurementType" (OntologyAnnotation.ISAJson.encoder idMap) a.MeasurementType
                     Encode.tryInclude "technologyType" (OntologyAnnotation.ISAJson.encoder idMap) a.TechnologyType
@@ -199,7 +199,7 @@ module AssayExtensions =
 
         static member fromCompressedJsonString (s: string) =
             try Decode.fromJsonString (Compression.decode Assay.decoderCompressed) s with
-            | e -> failwithf "Error. Unable to parse json string to ArcStudy: %s" e.Message
+            | e -> failwithf "Error. Unable to parse json string to ArcAssay: %s" e.Message
 
         static member toCompressedJsonString(?spaces) =
             fun (obj:ArcAssay) ->

diff --git a/src/Json/Comment.fs b/src/Json/Comment.fs
@@ -32,11 +32,11 @@ module Comment =
 
         let encoder (comment : Comment) = 
             [
-                "@id", Encode.string (comment |> genID)
-                "@type", Encode.string "Comment"
+                "@id", Encode.string (comment |> genID) |> Some
+                "@type", Encode.string "Comment" |> Some
                 Encode.tryInclude "name" Encode.string (comment.Name)
                 Encode.tryInclude "value" Encode.string (comment.Value)
-                "@context", ROCrateContext.Comment.context_jsonvalue
+                "@context", ROCrateContext.Comment.context_jsonvalue |> Some
             ]
             |> Encode.choose
             |> Encode.object

diff --git a/src/Json/Data.fs b/src/Json/Data.fs
@@ -76,14 +76,14 @@ module Data =
 
         let encoder (oa : Data) = 
             [
-                "@id", Encode.string (oa |> genID)           
-                "@type", (Encode.list [Encode.string "Data"])
+                "@id", Encode.string (oa |> genID) |> Some           
+                "@type", (Encode.list [Encode.string "Data"]) |> Some
                 Encode.tryInclude "name" Encode.string (oa.Name)
                 Encode.tryInclude "type" DataFile.ROCrate.encoder oa.DataType
                 Encode.tryInclude "encodingFormat" Encode.string oa.Format
                 Encode.tryInclude "usageInfo" Encode.string oa.SelectorFormat
                 Encode.tryIncludeSeq "comments" Comment.ROCrate.encoder oa.Comments
-                "@context", ROCrateContext.Data.context_jsonvalue
+                "@context", ROCrateContext.Data.context_jsonvalue |> Some
             ]
             |> Encode.choose
             |> Encode.object

diff --git a/src/Json/DataMap/DataContext.fs b/src/Json/DataMap/DataContext.fs
@@ -11,7 +11,7 @@ module DataContext =
 
     let encoder (dc:DataContext) = 
         [ 
-            "data", Data.encoder dc
+            "data", Data.encoder dc |> Some
             Encode.tryInclude "explication" OntologyAnnotation.encoder dc.Explication 
             Encode.tryInclude "unit" OntologyAnnotation.encoder dc.Unit
             Encode.tryInclude "objectType" OntologyAnnotation.encoder dc.ObjectType

diff --git a/src/Json/Encode.fs b/src/Json/Encode.fs
@@ -14,7 +14,7 @@ open Fable.Core.JsInterop
 [<RequireQualifiedAccess>]
 module Encode = 
 
-    let inline toJsonString spaces (value : Json) = 
+    let inline toJsonString spaces (value : IEncodable) = 
         #if FABLE_COMPILER_PYTHON
         Thoth.Json.Python.Encode.toString spaces value
         #endif
@@ -25,44 +25,43 @@ module Encode =
         Thoth.Json.Newtonsoft.Encode.toString spaces value
         #endif
 
-    let inline choose (kvs : (string * Json) list) = 
+    let inline choose (kvs : (string * IEncodable option) list) = 
         kvs
-        |> List.choose (fun (k,v) -> 
-            if v = Encode.nil then None
-            else Some (k,v)
+        |> List.choose (fun (k,v) ->
+            v
+            |> Option.map (fun v -> k,v)
         )       
 
     /// Try to encode the given object using the given encoder, or return Encode.nil if the object is null
-    let tryInclude (name : string) (encoder : 'Value -> Json) (value : 'Value option) = 
+    let tryInclude (name : string) (encoder : 'Value -> IEncodable) (value : 'Value option) = 
         name,
-        match value with
-        | Some(o) -> encoder o
-        | _ -> Encode.nil
+        value
+        |> Option.map encoder
 
     /// Try to encode the given object using the given encoder, or return Encode.nil if the object is null
-    let tryIncludeSeq name (encoder : 'Value -> Json) (value : #seq<'Value>) = 
+    let tryIncludeSeq name (encoder : 'Value -> IEncodable) (value : #seq<'Value>) = 
         name,
-        if Seq.isEmpty value then Encode.nil
-        else value |> Seq.map encoder |> Encode.seq
+        if Seq.isEmpty value then None 
+        else value |> Seq.map encoder |> Encode.seq |> Some
 
-    let tryIncludeArray name (encoder : 'Value -> Json) (value : 'Value array) = 
+    let tryIncludeArray name (encoder : 'Value -> IEncodable) (value : 'Value array) = 
         name,
-        if Array.isEmpty value then Encode.nil
-        else value |> Array.map encoder |> Encode.array
+        if Array.isEmpty value then None
+        else value |> Array.map encoder |> Encode.array |> Some
 
-    let tryIncludeList name (encoder : 'Value -> Json) (value : 'Value list) = 
+    let tryIncludeList name (encoder : 'Value -> IEncodable) (value : 'Value list) = 
         name,
-        if List.isEmpty value then Encode.nil
-        else value |> List.map encoder |> Encode.list
+        if List.isEmpty value then None
+        else value |> List.map encoder |> Encode.list |> Some
 
-    let tryIncludeListOpt name (encoder : 'Value -> Json) (value : 'Value list option) = 
+    let tryIncludeListOpt name (encoder : 'Value -> IEncodable) (value : 'Value list option) = 
         name,
         match value with
         | Some(o) -> 
-            if List.isEmpty o then Encode.nil
-            else o |> List.map encoder |> Encode.list
+            if List.isEmpty o then None
+            else o |> List.map encoder |> Encode.list |> Some
         | _ -> 
-            Encode.nil
+            None
 
     let DefaultSpaces = 0
 

diff --git a/src/Json/IDTable.fs b/src/Json/IDTable.fs
@@ -1,4 +1,4 @@
-namespace ARCtrl.Json
+namespace ARCtrl.Json
 
 open System.Collections.Generic
 open Thoth.Json.Core
@@ -8,15 +8,15 @@ open ARCtrl.Helper
 
 module IDTable =
 
-    type IDTableWrite = Dictionary<URI,Json>
+    type IDTableWrite = Dictionary<URI,IEncodable>
 
     type IDTableRead = Dictionary<URI,obj>
 
     let encodeID id =
         ["@id",Encode.string id]
         |> Encode.object
 
-    let encode (genID: 'Value -> URI) (encoder : 'Value -> Json) (value : 'Value) (table:IDTableWrite) =
+    let encode (genID: 'Value -> URI) (encoder : 'Value -> IEncodable) (value : 'Value) (table:IDTableWrite) =
         let id = genID value
         if table.ContainsKey id then 
            encodeID id

diff --git a/src/Json/Investigation.fs b/src/Json/Investigation.fs
@@ -9,7 +9,7 @@ module Investigation =
 
     let encoder (inv : ArcInvestigation) = 
         [ 
-            "Identifier", Encode.string inv.Identifier
+            "Identifier", Encode.string inv.Identifier |> Some
             Encode.tryInclude "Title" Encode.string inv.Title
             Encode.tryInclude "Description" Encode.string inv.Description
             Encode.tryInclude "SubmissionDate" Encode.string inv.SubmissionDate
@@ -50,7 +50,7 @@ module Investigation =
 
     let encoderCompressed (stringTable : StringTableMap) (oaTable : OATableMap) (cellTable : CellTableMap) (inv : ArcInvestigation) = 
         [ 
-            "Identifier", Encode.string inv.Identifier
+            "Identifier", Encode.string inv.Identifier |> Some
             Encode.tryInclude "Title" Encode.string inv.Title
             Encode.tryInclude "Description" Encode.string inv.Description
             Encode.tryInclude "SubmissionDate" Encode.string inv.SubmissionDate
@@ -100,11 +100,11 @@ module Investigation =
 
         let encoder (oa : ArcInvestigation) = 
             [
-                "@id", Encode.string (oa |> genID)
-                "@type", Encode.string "Investigation"
-                "additionalType", Encode.string "Investigation"
-                "identifier", Encode.string oa.Identifier
-                "filename", Encode.string ArcInvestigation.FileName
+                "@id", Encode.string (oa |> genID) |> Some
+                "@type", Encode.string "Investigation" |> Some
+                "additionalType", Encode.string "Investigation" |> Some
+                "identifier", Encode.string oa.Identifier |> Some
+                "filename", Encode.string ArcInvestigation.FileName |> Some
                 Encode.tryInclude "title" Encode.string oa.Title
                 Encode.tryInclude "description" Encode.string oa.Description
                 Encode.tryInclude "submissionDate" Encode.string oa.SubmissionDate
@@ -114,7 +114,7 @@ module Investigation =
                 Encode.tryIncludeSeq "people" Person.ROCrate.encoder oa.Contacts
                 Encode.tryIncludeSeq "studies" (Study.ROCrate.encoder None) oa.Studies
                 Encode.tryIncludeSeq "comments" Comment.ROCrate.encoder oa.Comments
-                "@context", ROCrateContext.Investigation.context_jsonvalue
+                "@context", ROCrateContext.Investigation.context_jsonvalue |> Some
             ]
             |> Encode.choose
             |> Encode.object
@@ -155,8 +155,8 @@ module Investigation =
                 Encode.tryInclude "@type" Encode.string (Some "CreativeWork")
                 Encode.tryInclude "@id" Encode.string (Some "ro-crate-metadata.json")
                 Encode.tryInclude "about" encoder (Some oa)
-                "conformsTo", ROCrateContext.ROCrate.conformsTo_jsonvalue
-                "@context", ROCrateContext.ROCrate.context_jsonvalue
+                "conformsTo", ROCrateContext.ROCrate.conformsTo_jsonvalue |> Some
+                "@context", ROCrateContext.ROCrate.context_jsonvalue |> Some
                 ]
             |> Encode.choose
             |> Encode.object
@@ -167,9 +167,9 @@ module Investigation =
 
         let encoder idMap (inv: ArcInvestigation) = 
             [
-                "@id", Encode.string (inv |> ROCrate.genID)
-                "filename", Encode.string ArcInvestigation.FileName
-                "identifier", Encode.string (inv.Identifier)
+                "@id", Encode.string (inv |> ROCrate.genID) |> Some
+                "filename", Encode.string ArcInvestigation.FileName |> Some
+                "identifier", Encode.string (inv.Identifier) |> Some
                 Encode.tryInclude "title" Encode.string (inv.Title)
                 Encode.tryInclude "description" Encode.string (inv.Description)
                 Encode.tryInclude "submissionDate" Encode.string (inv.SubmissionDate)

diff --git a/src/Json/OntologyAnnotation.fs b/src/Json/OntologyAnnotation.fs
@@ -79,13 +79,13 @@ module OntologyAnnotation =
 
         let encoderDefinedTerm (oa : OntologyAnnotation) = 
             [
-                "@id", Encode.string (oa |> genID)
-                "@type", Encode.string "OntologyAnnotation"
+                "@id", Encode.string (oa |> genID) |> Some
+                "@type", Encode.string "OntologyAnnotation" |> Some
                 Encode.tryInclude "annotationValue" Encode.string (oa.Name)
                 Encode.tryInclude "termSource" Encode.string (oa.TermSourceREF)
                 Encode.tryInclude "termAccession" Encode.string (oa.TermAccessionNumber)
                 Encode.tryIncludeSeq "comments" Comment.ROCrate.encoderDisambiguatingDescription (oa.Comments)
-                "@context", ROCrateContext.OntologyAnnotation.context_jsonvalue
+                "@context", ROCrateContext.OntologyAnnotation.context_jsonvalue |> Some
             ]
             |> Encode.choose
             |> Encode.object
@@ -102,13 +102,13 @@ module OntologyAnnotation =
 
         let encoderPropertyValue (oa : OntologyAnnotation) = 
             [
-                "@id", Encode.string (oa |> genID)
-                "@type", Encode.string "PropertyValue"
+                "@id", Encode.string (oa |> genID) |> Some
+                "@type", Encode.string "PropertyValue" |> Some
 
                 Encode.tryInclude "category" Encode.string oa.Name
                 Encode.tryInclude "categoryCode" Encode.string oa.TermAccessionNumber
                 Encode.tryIncludeSeq "comments" Comment.ROCrate.encoderDisambiguatingDescription (oa.Comments)
-                "@context", ROCrateContext.PropertyValue.context_jsonvalue
+                "@context", ROCrateContext.PropertyValue.context_jsonvalue |> Some
             ]
             |> Encode.choose
             |> Encode.object

diff --git a/src/Json/OntologySourceReference.fs b/src/Json/OntologySourceReference.fs
@@ -1,4 +1,4 @@
-namespace ARCtrl.Json
+namespace ARCtrl.Json
 
 open Thoth.Json.Core
 open ARCtrl
@@ -42,14 +42,14 @@ module OntologySourceReference =
 
         let encoder (osr : OntologySourceReference) = 
             [
-                "@id", Encode.string (osr |> genID)
-                "@type", Encode.string "OntologySourceReference"
+                "@id", Encode.string (osr |> genID) |> Some
+                "@type", Encode.string "OntologySourceReference" |> Some
                 Encode.tryInclude "description" Encode.string (osr.Description)
                 Encode.tryInclude "file" Encode.string (osr.File)
                 Encode.tryInclude "name" Encode.string (osr.Name)
                 Encode.tryInclude "version" Encode.string (osr.Version)
                 Encode.tryIncludeSeq "comments" Comment.encoder (osr.Comments)
-                "@context", ROCrateContext.OntologySourceReference.context_jsonvalue
+                "@context", ROCrateContext.OntologySourceReference.context_jsonvalue |> Some
             ]
             |> Encode.choose
             |> Encode.object