merge json-ld changes into thoth.json update changes and refactor

package.json

@@ -22,7 +22,7 @@
     "pretestui": "dotnet fable src/ARCtrl -o tests/UI/ARCtrl ",
     "testui": "cd tests/UI & npx cypress run --component ",
     "testpy": "",
-    "postinstall": "cd src/ISA & npm install",
+    "postinstall": "cd src/ISA && npm install",
     "devui": "cd tests/UI & npx vite"
   },
   "author": "Heinrich Lukas Weil <[email protected]> (https://github.com/HLWeil)",
@@ -33,7 +33,8 @@
     "exceljs": "^4.3.0",
     "fable-library": "^1.1.1",
     "fsspreadsheet": "^4.0.0-alpha2",
-    "isomorphic-fetch": "^3.0.0"
+    "isomorphic-fetch": "^3.0.0",
+    "jsonschema": "^1.4.1"
   },
   "devDependencies": {
     "@vitejs/plugin-vue": "^4.4.1",

src/ISA/ISA.Json/ARCtrl.ISA.Json.fsproj

@@ -11,6 +11,29 @@
     <Compile Include="Validation/ValidationResult.fs" />
     <Compile Include="Validation/Fable.fs" />
     <Compile Include="Validation/JsonSchemaValidation.fs" />
+    <Compile Include="context/ro-crate/isa_assay_context.fs" />
+    <Compile Include="context/ro-crate/isa_comment_context.fs" />
+    <Compile Include="context/ro-crate/isa_component_context.fs" />
+    <Compile Include="context/ro-crate/isa_data_context.fs" />
+    <Compile Include="context/ro-crate/isa_factor_context.fs" />
+    <Compile Include="context/ro-crate/isa_factor_value_context.fs" />
+    <Compile Include="context/ro-crate/isa_investigation_context.fs" />
+    <Compile Include="context/ro-crate/isa_material_attribute_context.fs" />
+    <Compile Include="context/ro-crate/isa_material_attribute_value_context.fs" />
+    <Compile Include="context/ro-crate/isa_material_context.fs" />
+    <Compile Include="context/ro-crate/isa_ontology_annotation_context.fs" />
+    <Compile Include="context/ro-crate/isa_ontology_source_reference_context.fs" />
+    <Compile Include="context/ro-crate/isa_organization_context.fs" />
+    <Compile Include="context/ro-crate/isa_person_context.fs" />
+    <Compile Include="context/ro-crate/isa_process_context.fs" />
+    <Compile Include="context/ro-crate/isa_process_parameter_value_context.fs" />
+    <Compile Include="context/ro-crate/isa_protocol_context.fs" />
+    <Compile Include="context/ro-crate/isa_protocol_parameter_context.fs" />
+    <Compile Include="context/ro-crate/isa_publication_context.fs" />
+    <Compile Include="context/ro-crate/isa_sample_context.fs" />
+    <Compile Include="context/ro-crate/isa_source_context.fs" />
+    <Compile Include="context/ro-crate/isa_study_context.fs" />
+    <Compile Include="context/ro-crate/rocrate_context.fs" />
     <Compile Include="ConverterOptions.fs" />
     <Compile Include="Decode.fs" />
     <Compile Include="GEncode.fs" />

src/ISA/ISA.Json/ArcTypes/ArcAssay.fs

@@ -102,16 +102,20 @@ module ArcAssay =
 
 
     /// exports in json-ld format
-    let toStringLD (a:ArcAssay) = 
-        Assay.encoder (ConverterOptions(SetID=true,IncludeType=true)) (a.ToAssay())
+    let toJsonldString (a:ArcAssay) = 
+        Assay.encoder (ConverterOptions(SetID=true,IncludeType=true)) None (a.ToAssay())
+        |> GEncode.toJsonString 2
+
+    let toJsonldStringWithContext (a:ArcAssay) = 
+        Assay.encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) None (a.ToAssay())
         |> GEncode.toJsonString 2
 
     let fromJsonString (s:string) = 
         GDecode.fromJsonString (Assay.decoder (ConverterOptions())) s
         |> ArcAssay.fromAssay
 
     let toJsonString (a:ArcAssay) = 
-        Assay.encoder (ConverterOptions()) (a.ToAssay())
+        Assay.encoder (ConverterOptions()) None (a.ToAssay())
         |> GEncode.toJsonString 2
 
     let toArcJsonString (a:ArcAssay) : string =

src/ISA/ISA.Json/ArcTypes/ArcInvestigation.fs

@@ -58,10 +58,14 @@ module ArcInvestigation =
         )
 
     /// exports in json-ld format
-    let toStringLD (a:ArcInvestigation) = 
+    let toJsonldString (a:ArcInvestigation) = 
         Investigation.encoder (ConverterOptions(SetID=true,IncludeType=true)) (a.ToInvestigation())
         |> GEncode.toJsonString 2
 
+    let toJsonldStringWithContext (a:ArcInvestigation) = 
+        Investigation.encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) (a.ToInvestigation())
+        |> GEncode.toJsonString 2
+
     let fromJsonString (s:string) = 
         GDecode.fromJsonString (Investigation.decoder (ConverterOptions())) s
         |> ArcInvestigation.fromInvestigation

src/ISA/ISA.Json/ArcTypes/ArcStudy.fs

@@ -101,10 +101,14 @@ module ArcStudy =
 
 
     /// exports in json-ld format
-    let toStringLD (a:ArcStudy) (assays: ResizeArray<ArcAssay>) = 
+    let toJsonldString (a:ArcStudy) (assays: ResizeArray<ArcAssay>) = 
         Study.encoder (ConverterOptions(SetID=true,IncludeType=true)) (a.ToStudy(assays))
         |> GEncode.toJsonString 2
 
+    let toJsonldStringWithContext (a:ArcStudy) (assays: ResizeArray<ArcAssay>) = 
+        Study.encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) (a.ToStudy(assays))
+        |> GEncode.toJsonString 2
+
     let fromJsonString (s:string) = 
         GDecode.fromJsonString (Study.decoder (ConverterOptions())) s
         |> ArcStudy.fromStudy

src/ISA/ISA.Json/Assay.fs

@@ -31,29 +31,49 @@ module Assay =
         match a.ID with
         | Some id -> URI.toString id
         | None -> match a.FileName with
-                  | Some n -> n
+                  | Some n -> n.Replace(" ","_").Remove(0,1 + (max (n.LastIndexOf('/')) (n.LastIndexOf('\\'))))
                   | None -> "#EmptyAssay"
 
-    let encoder (options : ConverterOptions) (oa : Assay) = 
+    let encoder (options : ConverterOptions) (studyName:string Option) (oa : Assay) = 
+        let assayName =
+                try 
+                    match (oa).FileName with
+                    | Some fn -> Some (Identifier.Assay.identifierFromFileName fn)
+                    | None -> None
+                with 
+                    | Failure(msg) -> None
+        let a = ["Assay";"ArcAssay"]
         [
-            if options.SetID then "@id", Encode.string (oa |> genID)
-                else GEncode.tryInclude "@id" Encode.string (oa.ID)
-            if options.IncludeType then "@type", Encode.string "Assay"
+            if options.SetID then 
+                "@id", Encode.string (oa |> genID)
+            else 
+                GEncode.tryInclude "@id" Encode.string (oa.ID)
+            if options.IncludeType then 
+                "@type", (Encode.list [ GEncode.toJsonString "Assay";  GEncode.toJsonString "ArcAssay"])
             GEncode.tryInclude "filename" Encode.string (oa.FileName)
             GEncode.tryInclude "measurementType" (OntologyAnnotation.encoder options) (oa.MeasurementType)
             GEncode.tryInclude "technologyType" (OntologyAnnotation.encoder options) (oa.TechnologyType)
             GEncode.tryInclude "technologyPlatform" Encode.string (oa.TechnologyPlatform)
             GEncode.tryIncludeList "dataFiles" (Data.encoder options) (oa.DataFiles)
-            GEncode.tryInclude "materials" (AssayMaterials.encoder options) (oa.Materials)
+             if options.IsRoCrate then
+                match oa.Materials with
+                | Some m -> 
+                    GEncode.tryIncludeList "samples" (Sample.encoder options) m.Samples
+                    GEncode.tryIncludeList "materials" (Material.encoder options) m.OtherMaterials
+                | None -> ()
+            if not options.IsRoCrate then
+                GEncode.tryInclude "materials" (AssayMaterials.encoder options) oa.Materials
             GEncode.tryIncludeList "characteristicCategories" (MaterialAttribute.encoder options) (oa.CharacteristicCategories)
             GEncode.tryIncludeList "unitCategories" (OntologyAnnotation.encoder options) (oa.UnitCategories)
-            GEncode.tryIncludeList "processSequence" (Process.encoder options) (oa.ProcessSequence)
+            GEncode.tryIncludeList "processSequence" (Process.encoder assayName options) (oa.ProcessSequence)
             GEncode.tryIncludeList "comments" (Comment.encoder options) (oa.Comments)
+            if options.IncludeContext then
+                "@context", ROCrateContext.Assay.context_jsonvalue
         ]
         |> GEncode.choose
         |> Encode.object
 
-    let allowedFields = ["@id";"filename";"measurementType";"technologyType";"technologyPlatform";"dataFiles";"materials";"characteristicCategories";"unitCategories";"processSequence";"comments";"@type"]
+    let allowedFields = ["@id";"filename";"measurementType";"technologyType";"technologyPlatform";"dataFiles";"materials";"characteristicCategories";"unitCategories";"processSequence";"comments";"@type"; "@context"]
 
     let decoder (options : ConverterOptions) : Decoder<Assay> =
         GDecode.object allowedFields (fun get ->
@@ -76,17 +96,21 @@ module Assay =
         GDecode.fromJsonString (decoder (ConverterOptions())) s
 
     let toJsonString (p:Assay) = 
-        encoder (ConverterOptions()) p
+        encoder (ConverterOptions()) None p
         |> GEncode.toJsonString 2
 
     /// exports in json-ld format
-    let toStringLD (a:Assay) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true)) a
+    let toJsonldString (a:Assay) = 
+        encoder (ConverterOptions(SetID=true,IncludeType=true)) None a
+        |> GEncode.toJsonString 2
+
+    let toJsonldStringWithContext (a:Assay) = 
+        encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) None a
         |> GEncode.toJsonString 2
 
     //let fromFile (path : string) = 
     //    File.ReadAllText path 
     //    |> fromString
 
     //let toFile (path : string) (p:Assay) = 
-    //    File.WriteAllText(path,toString p)
+    //    File.WriteAllText(path,toString p)

src/ISA/ISA.Json/Comment.fs

@@ -21,11 +21,16 @@ module Comment =
 
     let encoder (options : ConverterOptions) (comment : Comment) = 
         [
-            if options.SetID then "@id", Encode.string (comment |> genID)
-                else GEncode.tryInclude "@id" Encode.string (comment.ID)
-            if options.IncludeType then "@type", Encode.string "Comment"
+            if options.SetID then "@id", 
+                Encode.string (comment |> genID)
+            else 
+                GEncode.tryInclude "@id" Encode.string (comment.ID)
+            if options.IncludeType then 
+                "@type", Encode.string "Comment"
             GEncode.tryInclude "name" Encode.string (comment.Name)
             GEncode.tryInclude "value" Encode.string (comment.Value)
+            if options.IncludeContext then
+                "@context", ROCrateContext.Comment.context_jsonvalue
         ]
         |> GEncode.choose
         |> Encode.object
@@ -47,13 +52,17 @@ module Comment =
         |> GEncode.toJsonString 2
 
     /// exports in json-ld format
-    let toStringLD (c:Comment) = 
+    let toJsonldString (c:Comment) = 
         encoder (ConverterOptions(SetID=true,IncludeType=true)) c
         |> GEncode.toJsonString 2
 
+    let toJsonldStringWithContext (a:Comment) = 
+        encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) a
+        |> GEncode.toJsonString 2
+
     //let fromFile (path : string) = 
     //    File.ReadAllText path 
     //    |> fromString
 
     //let toFile (path : string) (c:Comment) = 
-    //    File.WriteAllText(path,toString c)
+    //    File.WriteAllText(path,toString c)

src/ISA/ISA.Json/ConverterOptions.fs

@@ -4,10 +4,14 @@ type ConverterOptions() =
 
     let mutable setID = false
     let mutable includeType = false
+    let mutable includeContext = false
+    let mutable isRoCrate = false
 
-    member this.SetID 
-        with get() = setID
-        and set(setId) = setID <- setId
-    member this.IncludeType 
-        with get() = includeType
-        and set(iT) = includeType <- iT
+    member this.SetID with get() = setID
+                      and set(setId) = setID <- setId
+    member this.IncludeType with get() = includeType
+                            and set(iT) = includeType <- iT
+    member this.IncludeContext with get() = includeContext
+                               and set(iC) = includeContext <- iC
+    member this.IsRoCrate with get() = isRoCrate
+                          and set(iR) = isRoCrate <- iR