Improve LDObject, add ISA model API

Directory.Packages.props

@@ -15,7 +15,7 @@
     <PackageVersion Include="FsSpreadsheet.Js"      Version="6.3.1" />
     <PackageVersion Include="FsSpreadsheet.Py"      Version="6.3.1" />
     <PackageVersion Include="YAMLicious"            Version="0.0.3" />
-    <PackageVersion Include="DynamicObj"            Version="4.0.3" />
+    <PackageVersion Include="DynamicObj"            Version="7.0.0" />
     <PackageVersion Include="Fable.SimpleHttp"      Version="3.5.0" />
     <PackageVersion Include="Fable.Fetch"           Version="2.6.0" />
     <PackageVersion Include="Fable.Node"            Version="1.2.0" />

build/ProjectInfo.fs

@@ -5,19 +5,22 @@ open Helpers
 
 let project = "ARCtrl"
 
+let allTestsProject = "tests/All"
+
 /// Dotnet and JS test paths
 let testProjects = 
     [
         "tests/All"
-        //"tests/Core"
-        //"tests/Json"
-        //"tests/Spreadsheet"
-        //"tests/FileSystem"
-        //"tests/ARCtrl"
-        //"tests/Yaml"
-        //"tests/ValidationPackages"
-        //"tests/Contract"
-        //"tests/ROCrate"
+        "tests/ARCtrl"
+        "tests/Contract"
+        "tests/Core"
+        "tests/CWL"
+        "tests/FileSystem"
+        "tests/Json"
+        "tests/ROCrate"
+        "tests/Spreadsheet"
+        "tests/ValidationPackages"
+        "tests/Yaml"
     ]
 
 /// Native JS test paths

build/TestTasks.fs

@@ -36,16 +36,14 @@ module RunTests =
     let runTestsJs = BuildTask.createFn "runTestsJS" [clean] (fun tp ->
         if tp.Context.Arguments |> List.exists (fun a -> a.ToLower() = skipTestsFlag.ToLower()) |> not then
             Trace.traceImportant "Start Js tests"
-            for path in ProjectInfo.testProjects do
-                // Setup test results directory after clean
-                System.IO.Directory.CreateDirectory("./tests/TestingUtils/TestResults/js") |> ignore
-                // transpile js files from fsharp code
-                run dotnet $"fable {path} -o {path}/js --nocache" ""
-
-                System.IO.File.Copy(jsHelperFilePath, $"{path}/js/{jsHelperFileName}") |> ignore
-                // run mocha in target path to execute tests
-                // "--timeout 20000" is used, because json schema validation takes a bit of time.
-                run node $"{path}/js/Main.js" ""
+            // Setup test results directory after clean
+            System.IO.Directory.CreateDirectory("./tests/TestingUtils/TestResults/js") |> ignore
+            // transpile js files from fsharp code
+            run dotnet $"fable {allTestsProject} -o {allTestsProject}/js --nocache" ""
+            System.IO.File.Copy(jsHelperFilePath, $"{allTestsProject}/js/{jsHelperFileName}") |> ignore
+            // run mocha in target path to execute tests
+            // "--timeout 20000" is used, because json schema validation takes a bit of time.
+            run node $"{allTestsProject}/js/Main.js" ""
         else
             Trace.traceImportant "Skipping Js tests"
     )
@@ -65,13 +63,12 @@ module RunTests =
     let runTestsPy = BuildTask.createFn "runTestsPy" [clean] (fun tp ->
         if tp.Context.Arguments |> List.exists (fun a -> a.ToLower() = skipTestsFlag.ToLower()) |> not then
             Trace.traceImportant "Start Python tests"
-            for path in ProjectInfo.testProjects do
-                // Setup test results directory after clean
-                System.IO.Directory.CreateDirectory("./tests/TestingUtils/TestResults/py") |> ignore
-                //transpile py files from fsharp code
-                run dotnet $"fable {path} -o {path}/py --lang python --nocache" ""
-                // run pyxpecto in target path to execute tests in python
-                run python $"{path}/py/main.py" ""
+            // Setup test results directory after clean
+            System.IO.Directory.CreateDirectory("./tests/TestingUtils/TestResults/py") |> ignore
+            //transpile py files from fsharp code
+            run dotnet $"fable {allTestsProject} -o {allTestsProject}/py --lang python --nocache" ""
+            // run pyxpecto in target path to execute tests in python
+            run python $"{allTestsProject}/py/main.py" ""
         else
             Trace.traceImportant "Skipping Python tests"
 
@@ -81,8 +78,7 @@ module RunTests =
         if tp.Context.Arguments |> List.exists (fun a -> a.ToLower() = skipTestsFlag.ToLower()) |> not then
             Trace.traceImportant "Start .NET tests"
             let dotnetRun = run dotnet "run"
-            testProjects
-            |> Seq.iter dotnetRun
+            dotnetRun allTestsProject
         else
             Trace.traceImportant "Skipping .NET tests"
     )
@@ -105,6 +101,7 @@ module RunTests =
                 run python $"{p}/py/main.py" ""
                 // transpile js files from fsharp code
                 run dotnet $"fable {p} -o {p}/js" ""
+                System.IO.Directory.CreateDirectory("./tests/TestingUtils/TestResults/js") |> ignore
                 System.IO.File.Copy(jsHelperFilePath, $"{p}/js/{jsHelperFileName}") |> ignore
                 // run mocha in target path to execute tests
                 // "--timeout 20000" is used, because json schema validation takes a bit of time.

src/Json/Decode.fs

@@ -93,9 +93,7 @@ module Decode =
                     decoder.Decode(helpers,value)
         }
 
-
-
-    let resizeArray (decoder: Decoder<'value>) : Decoder<ResizeArray<'value>> =
+    let resizeArrayOrSingleton (decoder: Decoder<'value>) : Decoder<ResizeArray<'value>> =
         { new Decoder<ResizeArray<'value>> with
             member _.Decode(helpers, value) =
                 if helpers.isArray value then
@@ -123,7 +121,7 @@ module Decode =
                                 Ok acc
                     )
                 else
-                    ("", BadPrimitive("an array", value)) |> Error
+                    decoder.Decode(helpers, value) |> Result.map (fun x -> ResizeArray[x])
         }
 
     let datetime: Decoder<System.DateTime> =

src/Json/Encode.fs

@@ -63,4 +63,12 @@ module Encode =
     let addPropertyToObject (name : string) (value : Json) (obj : Json) = 
         match obj with
         | Json.Object kvs -> Json.Object (Seq.append kvs [name, value] )
-        | _ -> failwith "Expected object"
+        | _ -> failwith "Expected object"
+
+    let resizeArrayOrSingleton (encoder : 'T -> IEncodable) (values: ResizeArray<'T>) =
+        if values.Count = 1 then
+            values.[0] |> encoder
+        else
+            values
+            |> Seq.map encoder
+            |> Encode.seq

src/Json/LDObject.fs

@@ -6,8 +6,39 @@ open ARCtrl.ROCrate
 open Thoth.Json.Core
 open DynamicObj
 
-module rec LDObject =
+module LDContext =
+
+    let decoder : Decoder<LDContext> =
+        { new Decoder<LDContext> with
+            member _.Decode(helpers, value) =     
+                if helpers.isObject value then
+                    let getters = Decode.Getters(helpers, value)
+                    let properties = helpers.getProperties value
+                    let builder =
+                        fun (get : Decode.IGetters) ->
+                            let o = LDContext()
+                            for property in properties do
+                                if property <> "@id" && property <> "@type" then
+                                    o.SetProperty(property,get.Required.Field property Decode.string)
+                            o
+                    let result = builder getters               
+                    match getters.Errors with
+                    | [] -> Ok result
+                    | fst :: _ as errors ->
+                        if errors.Length > 1 then
+                            ("", BadOneOf errors) |> Error
+                        else
+                            Error fst                
+                else 
+                    ("", BadPrimitive("an object", value)) |> Error
+        }
 
+    let encoder (ctx: LDContext) =
+        ctx.GetProperties true
+        |> Seq.map (fun kv -> kv.Key, kv.Value |> string |> Encode.string )
+        |> Encode.object
+
+module rec LDObject =
     #if !FABLE_COMPILER
     let (|SomeObj|_|) =
         // create generalized option type
@@ -45,20 +76,36 @@ module rec LDObject =
         | _ -> failwith "Unknown type"
 
     let rec encoder(obj: LDObject) =
-        obj.GetProperties true
-        |> Seq.choose (fun kv ->
-            let l = kv.Key.ToLower()
-            if l <> "id" && l <> "schematype" && l <> "additionaltype" then
-                Some(kv.Key, genericEncoder kv.Value)
-            else
-                None
+        //obj.GetProperties true
+        //|> Seq.choose (fun kv ->
+        //    let l = kv.Key.ToLower()
+        //    if l <> "id" && l <> "schematype" && l <> "additionaltype" && l <> "@context" then
+        //        Some(kv.Key, genericEncoder kv.Value)
+        //    else
+        //        None
 
-        )
-        |> Seq.append [
-            "@id", Encode.string obj.Id
-            "@type", Encode.string obj.SchemaType
-            if obj.AdditionalType.IsSome then
-                "additionalType", Encode.string obj.AdditionalType.Value
+        //)
+        //|> Seq.append [
+        //    "@id", Encode.string obj.Id
+        //    "@type", LDType.encoder obj.SchemaType
+        //    if obj.AdditionalType.IsSome then
+        //        "additionalType", Encode.string obj.AdditionalType.Value
+        //    match obj.TryGetContext() with
+        //    | Some ctx -> "@context", LDContext.encoder ctx
+        //    | _ -> ()
+        //]
+        [
+            yield "@id", Encode.string obj.Id
+            yield "@type", Encode.resizeArrayOrSingleton Encode.string obj.SchemaType
+            if obj.AdditionalType.Count <> 0 then
+                yield "additionalType", Encode.resizeArrayOrSingleton Encode.string obj.AdditionalType
+            match obj.TryGetContext() with
+            | Some ctx -> yield "@context", LDContext.encoder ctx
+            | _ -> ()
+            for kv in (obj.GetProperties true) do
+                let l = kv.Key.ToLower()
+                if l <> "id" && l <> "schematype" && l <> "additionaltype" && l <> "@context" then 
+                    yield kv.Key, genericEncoder kv.Value
         ]
         |> Encode.object
 
@@ -75,12 +122,15 @@ module rec LDObject =
                             let properties = helpers.getProperties value
                             let builder =
                                 fun (get : Decode.IGetters) ->
-                                    let t = get.Required.Field "@type" Decode.string
+                                    let t = get.Required.Field "@type" (Decode.resizeArrayOrSingleton Decode.string)
                                     let id = get.Required.Field "@id" Decode.string
-                                    let o = LDObject(id,t)
+                                    let context = get.Optional.Field "@context" LDContext.decoder
+                                    let at = get.Optional.Field "additionalType" (Decode.resizeArrayOrSingleton Decode.string)
+                                    let o = LDObject(id, t, ?additionalType = at)
                                     for property in properties do
-                                        if property <> "@id" && property <> "@type" then
+                                        if property <> "@id" && property <> "@type" && property <> "@context" then
                                             o.SetProperty(property,get.Required.Field property (decode(false)))
+                                    if context.IsSome then o.SetContext context.Value
                                     o
                             let result = builder getters               
                             match getters.Errors with

src/ROCrate/ArcROCrateMetadata.fs

@@ -4,7 +4,7 @@ open DynamicObj
 
 type ArcROCrateMetadata(?about : LDObject) as this =
 
-    inherit LDObject(id = "ro-crate-metadata",schemaType = "CreativeWork")
+    inherit LDObject(id = "ro-crate-metadata",schemaType = ResizeArray([|"CreativeWork"|]))
 
     do DynObj.setOptionalProperty (nameof about) about this
 

src/ROCrate/DynObjExtensions.fs

@@ -6,10 +6,16 @@
 
     let inline hasProperty (propertyName: string) (obj: #DynamicObj) = DynObj.tryGetPropertyValue propertyName obj |> Option.isSome
 
     let inline getMandatoryDynamicPropertyOrThrow<'TPropertyValue> (className:string) (propertyName: string) (obj: #DynamicObj) =
         if hasProperty propertyName obj then
             match DynObj.tryGetTypedPropertyValue<'TPropertyValue> propertyName obj with
             | Some value -> value
             | None -> raise (System.InvalidCastException($"Property '{propertyName}' is set on this '{className}' object but cannot be cast to '{(typeof<'TPropertyValue>).Name}'"))
         else
-            raise (System.MissingMemberException($"No property '{propertyName}' set on this '{className}' object although it is mandatory. Was it created correctly?"))
+            raise (System.MissingMemberException($"No property '{propertyName}' set on this '{className}' object although it is mandatory. Was it created correctly?"))
+
+    let inline tryGetTypedPropertyValueAsResizeArray<'T> (name : string) (obj : DynamicObj) =
+        match obj.TryGetPropertyValue(name) with
+        | Some (:? ResizeArray<'T> as ra) -> Some ra
+        | Some (:? 'T as singleton) -> Some (ResizeArray [singleton])
+        | _ -> None

src/ROCrate/ISAProfile/Assay.fs

@@ -17,7 +17,7 @@ type Assay(
     ?url,
     ?variableMeasured
 ) as this =
-    inherit Dataset(id, "Assay")
+    inherit Dataset(id = id, additionalType = ResizeArray[|"Assay"|])
     do
         DynObj.setProperty (nameof identifier) identifier this
 

src/ROCrate/ISAProfile/Data.fs

@@ -13,7 +13,11 @@ type Data(
     ?encodingFormat,
     ?disambiguatingDescription
 ) as this =
-    inherit LDObject(id = id, schemaType = "schema.org/MediaObject", ?additionalType = additionalType)
+    inherit LDObject(
+        id = id,
+        schemaType = ResizeArray[|"schema.org/MediaObject"|],
+        additionalType = defaultArg additionalType (ResizeArray[||])
+    )
     do
         DynObj.setProperty (nameof name) name this
 

src/ROCrate/ISAProfile/Dataset.fs

@@ -2,8 +2,12 @@ namespace ARCtrl.ROCrate
 
 open DynamicObj
 open Fable.Core
- 
+
 ///
 [<AttachMembers>]
-type Dataset (id: string, ?additionalType: string) =
-    inherit LDObject(id = id, schemaType = "schema.org/Dataset", ?additionalType = additionalType)
+type Dataset (id: string, ?additionalType: ResizeArray<string>) =
+    inherit LDObject(
+        id = id,
+        schemaType = ResizeArray[|"schema.org/Dataset"|],
+        additionalType = defaultArg additionalType (ResizeArray[||])
+    )

src/ROCrate/ISAProfile/Investigation.fs

@@ -20,7 +20,7 @@ type Investigation(
     ?url,
     ?description
 ) as this =
-    inherit Dataset(id, "Investigation")
+    inherit Dataset(id = id, additionalType = ResizeArray[|"Investigation"|])
     do 
         DynObj.setProperty (nameof identifier) identifier this
 

src/ROCrate/ISAProfile/LabProcess.fs

@@ -17,7 +17,11 @@ type LabProcess(
     ?endTime,
     ?disambiguatingDescription
 ) as this =
-    inherit LDObject(id = id, schemaType = "bioschemas.org/LabProcess", ?additionalType = additionalType)
+    inherit LDObject(
+        id = id,
+        schemaType = ResizeArray[|"bioschemas.org/LabProcess"|],
+        additionalType = defaultArg additionalType (ResizeArray[||])
+    )
     do
         DynObj.setProperty (nameof name) name     this
         DynObj.setProperty (nameof agent) agent   this

src/ROCrate/ISAProfile/LabProtocol.fs

@@ -18,7 +18,11 @@ type LabProtocol(
     ?reagent,
     ?computationalTool
 ) as this =
-    inherit LDObject(id = id, schemaType = "bioschemas.org/LabProtocol", ?additionalType = additionalType)
+    inherit LDObject(
+        id = id,
+        schemaType = ResizeArray[|"bioschemas.org/LabProtocol"|],
+        additionalType = defaultArg additionalType (ResizeArray[||])
+    )
     do
         DynObj.setOptionalProperty (nameof name) name                            this
         DynObj.setOptionalProperty (nameof intendedUse) intendedUse              this

src/ROCrate/ISAProfile/Person.fs

@@ -20,7 +20,11 @@ type Person(
     ?faxNumber,
     ?disambiguatingDescription
 ) as this=
-    inherit LDObject(id = id, schemaType = "schema.org/Person", ?additionalType = additionalType)
+    inherit LDObject(
+        id = id,
+        schemaType = ResizeArray[|"schema.org/Person"|],
+        additionalType = defaultArg additionalType (ResizeArray[||])
+    )
     do
 
         DynObj.setProperty (nameof givenName) givenName this

src/ROCrate/ISAProfile/PropertyValue.fs

@@ -15,7 +15,11 @@ type PropertyValue(
     ?valueReference,
     ?additionalType
 ) as this =
-    inherit LDObject(id = id, schemaType = "schema.org/PropertyValue", ?additionalType = additionalType)
+    inherit LDObject(
+        id = id,
+        schemaType = ResizeArray[|"schema.org/PropertyValue"|],
+        additionalType = defaultArg additionalType (ResizeArray[||])
+    )
     do
 
         DynObj.setProperty (nameof name) name this

src/ROCrate/ISAProfile/Sample.fs

@@ -12,7 +12,11 @@ type Sample(
     ?additionalProperty,
     ?derivesFrom
 ) as this =
-    inherit LDObject(id = id, schemaType = "bioschemas.org/Sample", ?additionalType = additionalType)
+    inherit LDObject(
+        id = id,
+        schemaType = ResizeArray[|"bioschemas.org/Sample"|], 
+        additionalType = defaultArg additionalType (ResizeArray[||])
+    )
     do
         DynObj.setProperty (nameof name) name this
 

src/ROCrate/ISAProfile/ScholarlyArticle.fs

@@ -16,7 +16,11 @@ type ScholarlyArticle(
     ?disambiguatingDescription
 
 ) as this =
-    inherit LDObject(id = id, schemaType = "schema.org/ScholarlyArticle", ?additionalType = additionalType)
+    inherit LDObject(
+        id = id,
+        schemaType = ResizeArray[|"schema.org/ScholarlyArticle"|],
+        additionalType = defaultArg additionalType (ResizeArray[||])
+    )
     do
 
         DynObj.setProperty (nameof headline) headline     this