rename ROCrateObject to LDObject

RELEASE_NOTES.md

@@ -5,10 +5,10 @@
     * [[#ef15f35](https://github.com/nfdi4plants/ARCtrl/commit/ef15f35779606a1bfcaecdadfc7532886466ec46)] implement first POC of ISA ROCrate profile
     * [[#168ead8](https://github.com/nfdi4plants/ARCtrl/commit/168ead84ca93dc0fae911e760673ef6e33180447)] add test project
     * [[#2cea57c](https://github.com/nfdi4plants/ARCtrl/commit/2cea57cc1415310e36f5931ef376ea183b85fb71)] update solution
-    * [[#ccd1805](https://github.com/nfdi4plants/ARCtrl/commit/ccd18053a83c80f4ca4b7a2ac7008a4a0cf3d348)] Unify Inheritance to ROCrateObject
+    * [[#ccd1805](https://github.com/nfdi4plants/ARCtrl/commit/ccd18053a83c80f4ca4b7a2ac7008a4a0cf3d348)] Unify Inheritance to LDObject
     * [[#95cab6f](https://github.com/nfdi4plants/ARCtrl/commit/95cab6f0f85f71a7adea887a25bd47c714e5af35)] wip ro-crate tests
     * [[#9ef48d7](https://github.com/nfdi4plants/ARCtrl/commit/9ef48d75f5439d3a71ca943941b70c5af3ff9261)] only use primary constructor
-    * [[#9deffb7](https://github.com/nfdi4plants/ARCtrl/commit/9deffb7ea81f76c067de5618f2b3388303402191)] Add basic tests for I/S/A ROCrateObjects
+    * [[#9deffb7](https://github.com/nfdi4plants/ARCtrl/commit/9deffb7ea81f76c067de5618f2b3388303402191)] Add basic tests for I/S/A LDObjects
     * [[#4b4a2fc](https://github.com/nfdi4plants/ARCtrl/commit/4b4a2fcc3bd32b31ec5aa3b4f1127883f7af83fc)] temp workaround in tests for https://github.com/CSBiology/DynamicObj/issues/25
     * [[#f67e78b](https://github.com/nfdi4plants/ARCtrl/commit/f67e78b068350a8e1aecf80fa8b9dd4646fb9ddd)] Use unblocking version of DynamicObj, introduce runTestProject target
     * [[#4e91e9d](https://github.com/nfdi4plants/ARCtrl/commit/4e91e9dcc5b34747a2e4a16f33aee1a227eb08ef)] finish basic property tests for isa profile types
@@ -22,11 +22,11 @@
     * [[#93030e9](https://github.com/nfdi4plants/ARCtrl/commit/93030e915329c23b4b4f8cddc5b622312de6cedb)] Make use of Fable.Package.SDK
     * [[#99b2659](https://github.com/nfdi4plants/ARCtrl/commit/99b2659d1dd5c3815693f4df85691f9bead3e26d)] rename json IO implementations folder to reduce ambiguity in py and javascript packages
 * Deletions:
-    * [[#c71b8a3](https://github.com/nfdi4plants/ARCtrl/commit/c71b8a301fbdf95531a9ba0d33f8e6d0d238adc9)] correct interface implementation on ROCrateObject, remove interface implementation from Dataset
+    * [[#c71b8a3](https://github.com/nfdi4plants/ARCtrl/commit/c71b8a301fbdf95531a9ba0d33f8e6d0d238adc9)] correct interface implementation on LDObject, remove interface implementation from Dataset
     * [[#c429686](https://github.com/nfdi4plants/ARCtrl/commit/c4296864a7443a990257f7eb47fed92458fa0a7b)] remove javascript and pyton packages from main solution
     * [[#3586dee](https://github.com/nfdi4plants/ARCtrl/commit/3586dee6a736d3ad2ed9e79778e3ea136c638eac)] remove restorelockedmode flag
 * Bugfixes:
-    * [[#9d526b8](https://github.com/nfdi4plants/ARCtrl/commit/9d526b82df1d7ac04283cbe23c9832f1d5818771)] add LabProcess tests, fix schematype of ROCrateObject base constructor
+    * [[#9d526b8](https://github.com/nfdi4plants/ARCtrl/commit/9d526b82df1d7ac04283cbe23c9832f1d5818771)] add LabProcess tests, fix schematype of LDObject base constructor
     * [[#192812d](https://github.com/nfdi4plants/ARCtrl/commit/192812d43569270845883ca116de9931dea6ba62)] fix error messages of ROCrate testing utils
     * [[#43d65db](https://github.com/nfdi4plants/ARCtrl/commit/43d65db3fb121a4832e771541880c1fe79cfe89c)] various test fixes for Fable logic transition
     * [[#8552f9e](https://github.com/nfdi4plants/ARCtrl/commit/8552f9ea7b2183c4cb382049c71793918d4128b3)] fix fable ready packaging and/by update package tags

src/ARCtrl/ARCtrl.Common.props

@@ -40,7 +40,7 @@
     <Compile Include="JsonIO\Assay.fs" />
     <Compile Include="JsonIO\Study.fs" />
     <Compile Include="JsonIO\Investigation.fs" />
-    <Compile Include="JsonIO\ROCrateObject.fs" />
+    <Compile Include="JsonIO\LDObject.fs" />
     <Compile Include="JsonIO\ARC.fs" />
     <None Include="README.md" />
   </ItemGroup>-->

src/ARCtrl/ARCtrl.Javascript.fsproj

@@ -46,7 +46,7 @@
     <Compile Include="JsonIO\Assay.fs" />
     <Compile Include="JsonIO\Study.fs" />
     <Compile Include="JsonIO\Investigation.fs" />
-    <Compile Include="JsonIO\ROCrateObject.fs" />
+    <Compile Include="JsonIO\LDObject.fs" />
     <Compile Include="JsonIO\ARC.fs" />
     <None Include="README.md" />
   </ItemGroup>

src/ARCtrl/ARCtrl.Python.fsproj

@@ -46,7 +46,7 @@
     <Compile Include="JsonIO\Assay.fs" />
     <Compile Include="JsonIO\Study.fs" />
     <Compile Include="JsonIO\Investigation.fs" />
-    <Compile Include="JsonIO\ROCrateObject.fs" />
+    <Compile Include="JsonIO\LDObject.fs" />
     <Compile Include="JsonIO\ARC.fs" />
     <None Include="README.md" />
   </ItemGroup>

src/ARCtrl/ARCtrl.fsproj

@@ -45,7 +45,7 @@
     <Compile Include="JsonIO\Assay.fs" />
     <Compile Include="JsonIO\Study.fs" />
     <Compile Include="JsonIO\Investigation.fs" />
-    <Compile Include="JsonIO\ROCrateObject.fs" />
+    <Compile Include="JsonIO\LDObject.fs" />
     <Compile Include="JsonIO\ARC.fs" />
     <None Include="README.md" />
   </ItemGroup>

src/ARCtrl/JsonIO/ROCrateObject.fs → src/ARCtrl/JsonIO/LDObject.fs

@@ -8,18 +8,18 @@ open Thoth.Json.Core
 open DynamicObj
 
 [<AutoOpen>]
-module ROCrateObjectExtensions =
+module LDObjectExtensions =
 
-    type ROCrateObject with
+    type LDObject with
 
         static member fromROCrateJsonString (s:string) = 
-            Decode.fromJsonString ROCrateObject.decoder s
+            Decode.fromJsonString LDObject.decoder s
 
         /// exports in json-ld format
         static member toROCrateJsonString(?spaces) =
-            fun (obj:ROCrateObject) ->
-                ROCrateObject.encoder obj
+            fun (obj:LDObject) ->
+                LDObject.encoder obj
                 |> Encode.toJsonString (Encode.defaultSpaces spaces)
 
         member this.ToROCrateJsonString(?spaces) = 
-            ROCrateObject.toROCrateJsonString(?spaces=spaces) this
+            LDObject.toROCrateJsonString(?spaces=spaces) this

src/Json/ARCtrl.Json.fsproj

@@ -75,7 +75,7 @@
     <Compile Include="Assay.fs" />
     <Compile Include="Study.fs" />
     <Compile Include="Investigation.fs" />
-    <Compile Include="ROCrateObject.fs" />
+    <Compile Include="LDObject.fs" />
     <Compile Include="ARC.fs" />
   </ItemGroup>
   <ItemGroup>

src/Json/ROCrateObject.fs → src/Json/LDObject.fs

@@ -6,7 +6,7 @@ open ARCtrl.ROCrate
 open Thoth.Json.Core
 open DynamicObj
 
-module rec ROCrateObject =
+module rec LDObject =
 
     #if !FABLE_COMPILER
     let (|SomeObj|_|) =
@@ -36,15 +36,15 @@ module rec ROCrateObject =
         | :? bool as b -> Encode.bool b
         | :? float as f -> Encode.float f
         | :? DateTime as d -> Encode.dateTime d
-        | :? ROCrateObject as o -> encoder o
+        | :? LDObject as o -> encoder o
         #if !FABLE_COMPILER
         | SomeObj o -> genericEncoder o
         #endif
         | null -> Encode.nil
         | :? System.Collections.IEnumerable as l -> [ for x in l -> genericEncoder x] |> Encode.list
         | _ -> failwith "Unknown type"
 
-    let rec encoder(obj: ROCrateObject) =
+    let rec encoder(obj: LDObject) =
         obj.GetProperties true
         |> Seq.choose (fun kv ->
             let l = kv.Key.ToLower()
@@ -67,8 +67,8 @@ module rec ROCrateObject =
     /// If expectObject is set to true, decoder fails if top-level value is not an ROCrate object
     let rec getDecoder (expectObject : bool) : Decoder<obj> = 
         let rec decode(expectObject) = 
-            let decodeObject : Decoder<ROCrateObject> =
-                { new Decoder<ROCrateObject> with
+            let decodeObject : Decoder<LDObject> =
+                { new Decoder<LDObject> with
                     member _.Decode(helpers, value) =     
                         if helpers.isObject value then
                             let getters = Decode.Getters(helpers, value)
@@ -77,7 +77,7 @@ module rec ROCrateObject =
                                 fun (get : Decode.IGetters) ->
                                     let t = get.Required.Field "@type" Decode.string
                                     let id = get.Required.Field "@id" Decode.string
-                                    let o = ROCrateObject(id,t)
+                                    let o = LDObject(id,t)
                                     for property in properties do
                                         if property <> "@id" && property <> "@type" then
                                             o.SetProperty(property,get.Required.Field property (decode(false)))
@@ -136,6 +136,6 @@ module rec ROCrateObject =
                 ]
         decode(expectObject)
 
-    let decoder : Decoder<ROCrateObject> = Decode.map unbox (getDecoder(true))
+    let decoder : Decoder<LDObject> = Decode.map unbox (getDecoder(true))
 
     let genericDecoder : Decoder<obj> = getDecoder(false)

src/ROCrate/ARCtrl.ROCrate.fsproj

@@ -8,7 +8,7 @@
 
   <ItemGroup>
     <Compile Include="DynObjExtensions.fs" />
-    <Compile Include="ROCrateObject.fs" />
+    <Compile Include="LDObject.fs" />
     <Compile Include="ISAProfile\Dataset.fs" />
     <Compile Include="ISAProfile\Investigation.fs" />
     <Compile Include="ISAProfile\Study.fs" />
@@ -20,6 +20,7 @@
     <Compile Include="ISAProfile\PropertyValue.fs" />
     <Compile Include="ISAProfile\Person.fs" />
     <Compile Include="ISAProfile\ScholarlyArticle.fs" />
+    <Compile Include="ArcROCrateMetadata.fs" />
     <None Include="playground.fsx" />
   </ItemGroup>
   <ItemGroup>

src/ROCrate/ArcROCrateMetadata.fs

@@ -0,0 +1,24 @@
+namespace ARCtrl.ROCrate
+
+open DynamicObj
+
+type ArcROCrateMetadata(?about : LDObject) as this =
+
+    inherit LDObject(id = "ro-crate-metadata",schemaType = "CreativeWork")
+
+    do DynObj.setOptionalProperty (nameof about) about this
+
+    do
+        let conformsTo = DynamicObj()
+        conformsTo.SetProperty("@id", "https://w3id.org/ro/crate/1.1")
+        this.SetProperty("conformsTo", conformsTo)
+
+    do
+        let context = LDContext()
+        context.SetProperty("sdo", "http://schema.org/")
+        context.SetProperty("arc", "http://purl.org/nfdi4plants/ontology/")
+        context.SetProperty("CreativeWork", "sdo:CreativeWork")
+        context.SetProperty("about", "sdo:about")
+        context.SetProperty("conformsTo", "sdo:conformsTo")
+        this.SetProperty("@context", context)
+

src/ROCrate/ISAProfile/Data.fs

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

src/ROCrate/ISAProfile/Dataset.fs

@@ -6,4 +6,4 @@ open Fable.Core
 ///
 [<AttachMembers>]
 type Dataset (id: string, ?additionalType: string) =
-    inherit ROCrateObject(id = id, schemaType = "schema.org/Dataset", ?additionalType = additionalType)
+    inherit LDObject(id = id, schemaType = "schema.org/Dataset", ?additionalType = additionalType)

src/ROCrate/ISAProfile/LabProcess.fs

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

src/ROCrate/ISAProfile/LabProtocol.fs

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

src/ROCrate/ISAProfile/Person.fs

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

src/ROCrate/ISAProfile/PropertyValue.fs

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

src/ROCrate/ISAProfile/Sample.fs

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

src/ROCrate/ISAProfile/ScholarlyArticle.fs

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

src/ROCrate/ROCrateObject.fs → src/ROCrate/LDObject.fs

@@ -8,15 +8,15 @@ open System
 type LDContext() = inherit DynamicObj()
 
 /// Base interface implemented by all explicitly known objects in our ROCrate profiles.
-type IROCrateObject =
+type ILDObject =
     abstract member SchemaType : string with get, set
     abstract member Id: string
     abstract member AdditionalType: string option with get, set
 
 /// Base class for all explicitly known objects in our ROCrate profiles to inherit from.
-/// Basically a DynamicObj that implements the IROPCrateObject interface.
+/// Basically a DynamicObj that implements the ILDObject interface.
 [<AttachMembers>]
-type ROCrateObject(id:string, schemaType: string, ?additionalType) =
+type LDObject(id:string, schemaType: string, ?additionalType) =
     inherit DynamicObj()
 
     let mutable schemaType = schemaType
@@ -33,7 +33,7 @@ type ROCrateObject(id:string, schemaType: string, ?additionalType) =
         with get() = additionalType
         and set(value) = additionalType <- value
 
-    interface IROCrateObject with
+    interface ILDObject with
 
         member this.SchemaType
             with get() = schemaType
@@ -48,12 +48,12 @@ type ROCrateObject(id:string, schemaType: string, ?additionalType) =
     member this.SetContext (context: LDContext) =
         this.SetProperty("@context", context)
 
-    static member setContext (context: LDContext) = fun (roc: #ROCrateObject) -> roc.SetContext(context)
+    static member setContext (context: LDContext) = fun (roc: #LDObject) -> roc.SetContext(context)
 
     member this.TryGetContext() = DynObj.tryGetTypedPropertyValue<DynamicObj>("@context") this
 
-    static member tryGetContext () = fun (roc: #ROCrateObject) -> roc.TryGetContext()
+    static member tryGetContext () = fun (roc: #LDObject) -> roc.TryGetContext()
 
     member this.RemoveContext() = this.RemoveProperty("@context")
 
-    static member removeContext () = fun (roc: #ROCrateObject) -> roc.RemoveContext() 
+    static member removeContext () = fun (roc: #LDObject) -> roc.RemoveContext() 

src/ROCrate/playground.fsx

@@ -2,12 +2,12 @@
 
 open DynamicObj
 
-type IROCrateObject =
+type ILDObject =
     abstract member SchemaType : string
     abstract member Id: string
     abstract member AdditionalType: string option
 
-type ROCrateObject(id:string, schemaType: string, ?additionalType) =
+type LDObject(id:string, schemaType: string, ?additionalType) =
     inherit DynamicObj()
 
     let mutable _schemaType = "schema.org/Dataset"
@@ -24,16 +24,16 @@ type ROCrateObject(id:string, schemaType: string, ?additionalType) =
         with get() = _additionalType
         and set(value) = _additionalType <- value
 
-    interface IROCrateObject with
+    interface ILDObject with
         member this.SchemaType = schemaType
         member this.Id = id
         member this.AdditionalType = additionalType
 
 type Dataset (id: string, ?additionalType: string) =
-    inherit ROCrateObject(id = id, schemaType = "schema.org/Dataset", ?additionalType = additionalType)
+    inherit LDObject(id = id, schemaType = "schema.org/Dataset", ?additionalType = additionalType)
 
      //interface implementations
-    interface IROCrateObject with 
+    interface ILDObject with 
         member this.Id with get () = this.Id
         member this.SchemaType with get (): string = this.SchemaType
         member this.AdditionalType with get (): string option = this.AdditionalType

tests/Json/ARCtrl.Json.Tests.fsproj

@@ -33,7 +33,7 @@
     <Compile Include="Process\Protocol.Tests.fs" />
     <Compile Include="Process\Process.Tests.fs" />
     <Compile Include="Template.Tests.fs" />
-    <Compile Include="ROCrateObject.Tests.fs" />
+    <Compile Include="LDObject.Tests.fs" />
     <Compile Include="JsonSchema.Tests.fs" />
     <Compile Include="Main.fs" />
   </ItemGroup>