add ARC RO-Crate serialization

nfdi4plants · Mar 25, 2024 · e3437b2 · e3437b2
1 parent 4cd6d63
commit e3437b2
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Showing 6 changed files with 58 additions and 17 deletions.
diff --git a/src/ARCtrl/ARC.fs b/src/ARCtrl/ARC.fs
@@ -464,6 +464,16 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
         ARCtrl.Contract.Git.gitignoreFileName, ARCtrl.Contract.Git.gitignoreContract
     |]
 
+    static member fromROCrateJsonString (s:string) = 
+        let isa = ARCtrl.Json.Decode.fromJsonString ARCtrl.Json.ARC.ROCrate.decoder s
+        ARC(?isa = isa)
+
+        /// exports in json-ld format
+    static member toROCrateJsonString(?spaces) =
+        fun (obj:ARC) ->
+            ARCtrl.Json.ARC.ROCrate.encoder (Option.get obj.ISA)
+            |> ARCtrl.Json.Encode.toJsonString (ARCtrl.Json.Encode.defaultSpaces spaces)
+
 //-Pseudo code-//
 //// Option 1
 //let fs, readcontracts = ARC.FSFromFilePaths filepaths

diff --git a/src/Core/ARCtrl.Core.fsproj b/src/Core/ARCtrl.Core.fsproj
@@ -58,8 +58,8 @@
     <Compile Include="Conversion.fs" />
     <Compile Include="IdentifierSetters.fs" />
   </ItemGroup>
-  <ItemGroup />
   <ItemGroup>
+    <ProjectReference Include="..\CWL\ARCtrl.CWL.fsproj" />
     <ProjectReference Include="..\FileSystem\ARCtrl.FileSystem.fsproj" />
   </ItemGroup>
   <PropertyGroup>

diff --git a/src/Json/ARC.fs b/src/Json/ARC.fs
@@ -0,0 +1,30 @@
+namespace ARCtrl.Json
+
+open Thoth.Json.Core
+
+open ARCtrl
+open ARCtrl.Helper
+
+module ARC =
+
+    /// Functions for serializing and deserializing ARC objects to RO-Crate Root Data Entity
+    ///
+    /// See https://www.researchobject.org/ro-crate/1.1/root-data-entity.html for more information
+    module ROCrate = 
+
+        let encoder (isa : ArcInvestigation) = 
+            [
+                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
+                ]
+            |> Encode.choose
+            |> Encode.object
+
+        let decoder : Decoder<ArcInvestigation option> = 
+            Decode.object (fun get ->
+                let isa = get.Optional.Field "about" Investigation.ROCrate.decoder
+                isa
+            )
diff --git a/src/Json/ARCtrl.Json.fsproj b/src/Json/ARCtrl.Json.fsproj
@@ -71,6 +71,7 @@
     <Compile Include="Assay.fs" />
     <Compile Include="Study.fs" />
     <Compile Include="Investigation.fs" />
+    <Compile Include="ARC.fs" />
   </ItemGroup>
   <ItemGroup>
     <PackageReference Include="NJsonSchema" Version="10.8.0" />

diff --git a/src/Json/Investigation.fs b/src/Json/Investigation.fs
@@ -229,14 +229,14 @@ module InvestigationExtensions =
                 let spaces = defaultArg spaces 0
                 Encode.toJsonString spaces (Compression.encode Investigation.encoderCompressed obj)
 
-        //static member fromROCrateJsonString (s:string) = 
-        //    Decode.fromJsonString Investigation.ROCrate.decoder s
-
-        ///// exports in json-ld format
-        //static member toROCrateJsonString(?spaces) =
-        //    fun (obj:ArcInvestigation) ->
-        //        Investigation.ROCrate.encoder obj
-        //        |> Encode.toJsonString (Encode.defaultSpaces spaces)
+        static member fromROCrateJsonString (s:string) = 
+            Decode.fromJsonString Investigation.ROCrate.decoder s
+
+        /// exports in json-ld format
+        static member toROCrateJsonString(?spaces) =
+            fun (obj:ArcInvestigation) ->
+                Investigation.ROCrate.encoder obj
+                |> Encode.toJsonString (Encode.defaultSpaces spaces)
 
         static member toISAJsonString(?spaces) =
             fun (obj:ArcInvestigation) ->

diff --git a/src/Json/Study.fs b/src/Json/Study.fs
@@ -228,14 +228,14 @@ module StudyExtensions =
                 let spaces = defaultArg spaces 0
                 Encode.toJsonString spaces (Compression.encode Study.encoderCompressed obj)
 
-        //static member fromROCrateJsonString (s:string) = 
-        //    Decode.fromJsonString Study.ROCrate.decoder s
-
-        ///// exports in json-ld format
-        //static member toROCrateJsonString(?spaces) =
-        //    fun (obj:ArcStudy) ->
-        //        Study.ROCrate.encoder obj
-        //        |> Encode.toJsonString (Encode.defaultSpaces spaces)
+        static member fromROCrateJsonString (s:string) = 
+            Decode.fromJsonString Study.ROCrate.decoder s
+
+        /// exports in json-ld format
+        static member toROCrateJsonString(?spaces) =
+            fun (obj:ArcStudy) ->
+                Study.ROCrate.encoder obj
+                |> Encode.toJsonString (Encode.defaultSpaces spaces)
 
         static member toISAJsonString(?spaces) =
             fun (obj:ArcStudy) ->