Merge pull request #409 from nfdi4plants/validation-packages

support `validation_packages_yml` (continued)

ARCtrl.sln

@@ -76,6 +76,12 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ValidationPackages",
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Yaml", "src\Yaml\ARCtrl.Yaml.fsproj", "{4CC3AAC2-030B-4B2E-A386-9C1F68E42238}"
 EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ValidationPackages.Tests", "tests\ValidationPackages\ARCtrl.ValidationPackages.Tests.fsproj", "{1CA11165-4B70-41D2-A846-50374E85385E}"
+EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Yaml.Tests", "tests\Yaml\ARCtrl.Yaml.Tests.fsproj", "{5810EF87-4F85-4B4C-98E3-833AE914C628}"
+EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Contract.Tests", "tests\Contract\ARCtrl.Contract.Tests.fsproj", "{D10D12C7-B877-423B-867D-161D99E673C9}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -150,6 +156,18 @@ Global
 		{4CC3AAC2-030B-4B2E-A386-9C1F68E42238}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{4CC3AAC2-030B-4B2E-A386-9C1F68E42238}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{4CC3AAC2-030B-4B2E-A386-9C1F68E42238}.Release|Any CPU.Build.0 = Release|Any CPU
+		{1CA11165-4B70-41D2-A846-50374E85385E}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{1CA11165-4B70-41D2-A846-50374E85385E}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{1CA11165-4B70-41D2-A846-50374E85385E}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{1CA11165-4B70-41D2-A846-50374E85385E}.Release|Any CPU.Build.0 = Release|Any CPU
+		{5810EF87-4F85-4B4C-98E3-833AE914C628}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{5810EF87-4F85-4B4C-98E3-833AE914C628}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{5810EF87-4F85-4B4C-98E3-833AE914C628}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{5810EF87-4F85-4B4C-98E3-833AE914C628}.Release|Any CPU.Build.0 = Release|Any CPU
+		{D10D12C7-B877-423B-867D-161D99E673C9}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{D10D12C7-B877-423B-867D-161D99E673C9}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{D10D12C7-B877-423B-867D-161D99E673C9}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{D10D12C7-B877-423B-867D-161D99E673C9}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
@@ -173,6 +191,9 @@ Global
 		{501F6D1E-6300-4CA4-8E61-3523BCF4D533} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 		{0C35D768-BF55-4BD9-B915-35125CED65A0} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
 		{4CC3AAC2-030B-4B2E-A386-9C1F68E42238} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
+		{1CA11165-4B70-41D2-A846-50374E85385E} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
+		{5810EF87-4F85-4B4C-98E3-833AE914C628} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
+		{D10D12C7-B877-423B-867D-161D99E673C9} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 		SolutionGuid = {1E354DE6-99BA-421E-9EF8-E808B855A85F}

build/ProjectInfo.fs

@@ -1,4 +1,4 @@
-module ProjectInfo
+module ProjectInfo
 
 open Fake.Core
 open Helpers
@@ -13,6 +13,9 @@ let testProjects =
         "tests/Spreadsheet"
         "tests/FileSystem"
         "tests/ARCtrl"
+        "tests/Yaml"
+        "tests/ValidationPackages"
+        "tests/Contract"
     ]
 
 /// Native JS test paths

src/ARCtrl/ARC.fs

@@ -1,5 +1,6 @@
 namespace ARCtrl
 
+open ARCtrl.ValidationPackages
 open ARCtrl.FileSystem
 open ARCtrl.Contract
 open ARCtrl
@@ -60,7 +61,8 @@ module ARCAux =
         let tree = 
             FileSystemTree.createRootFolder [|workflows;runs|]
             |> FileSystem.create
-        fs.Union(tree)    
+        fs.Union(tree)
+
 
 [<AttachMembers>]
 type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
@@ -570,6 +572,46 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
             ARCtrl.Json.ARC.ROCrate.encoder (Option.get obj.ISA)
             |> ARCtrl.Json.Encode.toJsonString (ARCtrl.Json.Encode.defaultSpaces spaces)
 
+    /// <summary>
+    /// Returns the write contract for the input ValidationPackagesConfig object.
+    ///
+    /// This will mutate the ARC file system to include the `.arc/validation_packages.yml` file if it is not already included.
+    /// </summary>
+    /// <param name="vpc">the config to write</param>
+    member this.GetValidationPackagesConfigWriteContract(vpc: ValidationPackagesConfig) =
+        let paths = this.FileSystem.Tree.ToFilePaths()
+        if not (Array.contains ValidationPackagesConfigHelper.ConfigFilePath paths) then
+            Array.append [|ValidationPackagesConfigHelper.ConfigFilePath|] paths
+            |> this.SetFilePaths
+        ValidationPackagesConfig.toCreateContract vpc
+
+    /// <summary>
+    /// Returns the delete contract for `.arc/validation_packages.yml`
+    ///
+    /// If the ARC file system includes the `.arc/validation_packages.yml` file, it is removed.
+    /// </summary>
+    /// <param name="vpc"></param>
+    member this.GetValidationPackagesConfigDeleteContract(vpc) =
+        let paths = this.FileSystem.Tree.ToFilePaths()
+        if (Array.contains ValidationPackagesConfigHelper.ConfigFilePath paths) then
+            paths
+            |> Array.filter (fun p -> not (p = ValidationPackagesConfigHelper.ConfigFilePath))
+            |> this.SetFilePaths
+        ValidationPackagesConfig.toDeleteContract vpc
+
+    /// <summary>
+    /// Returns the read contract for `.arc/validation_packages.yml`
+    /// </summary>
+    member this.GetValidationPackagesConfigReadContract() =
+        ValidationPackagesConfigHelper.ReadContract
+
+    /// <summary>
+    /// Returns the ValidationPackagesConfig object from the given read contract if possible, otherwise returns None/null.
+    /// </summary>
+    /// <param name="contract">the input contract that contains the config in it's DTO</param>
+    member this.GetValidationPackagesConfigFromReadContract(contract) =
+        ValidationPackagesConfig.tryFromReadContract contract
+
 //-Pseudo code-//
 //// Option 1
 //let fs, readcontracts = ARC.FSFromFilePaths filepaths

src/Contract/ValidationPackagesConfig.fs

@@ -1,47 +1,45 @@
 namespace ARCtrl.Contract
 
 open ARCtrl.FileSystem
-open ARCtrl.ArcPathHelper
 open ARCtrl
 open ARCtrl.Yaml
 open ARCtrl.Helper
 open ARCtrl.ValidationPackages
 
+module ValidationPackagesConfigHelper = 
+
+    let ConfigFilePath = [|ArcPathHelper.ARCConfigFolderName; ArcPathHelper.ValidationPackagesYamlFileName|] |> ArcPathHelper.combineMany
+
+    let ReadContract : Contract = {Operation = READ; DTOType = Some DTOType.YAML; Path = ConfigFilePath; DTO = None}
+
+
 [<AutoOpen>]
 module ValidationPackagesConfigExtensions = 
 
     let (|ValidationPackagesYamlPath|_|) (input) =
         match input with
-        | [|ARCConfigFolderName; ValidationPackagesYamlFileName|] -> 
-            let path = ARCtrl.ArcPathHelper.combineMany input
+        | [|ArcPathHelper.ARCConfigFolderName; ArcPathHelper.ValidationPackagesYamlFileName|] -> 
+            let path = ArcPathHelper.combineMany input
             Some path
         | _ -> None
 
-    let internal config_file_path = [|ARCConfigFolderName; ValidationPackagesYamlFileName|] |> ARCtrl.ArcPathHelper.combineMany
-
     type ValidationPackagesConfig with
 
         member this.ToCreateContract () =
-            Contract.createCreate(config_file_path, DTOType.YAML, DTO.Text (this |> ValidationPackagesConfig.toYamlString()))
-
-        member this.ToUpdateContract () =
-            Contract.createUpdate(config_file_path, DTOType.YAML, DTO.Text (this |> ValidationPackagesConfig.toYamlString()))
+            Contract.createCreate(ValidationPackagesConfigHelper.ConfigFilePath, DTOType.YAML, DTO.Text (this |> ValidationPackagesConfig.toYamlString()))
 
         member this.ToDeleteContract () =
-            Contract.createDelete(config_file_path)
+            Contract.createDelete(ValidationPackagesConfigHelper.ConfigFilePath)
 
         static member toDeleteContract (config: ValidationPackagesConfig) : Contract =
             config.ToDeleteContract()
 
         static member toCreateContract (config: ValidationPackagesConfig) : Contract =
             config.ToCreateContract()
 
-        static member toUpdateContract (config: ValidationPackagesConfig) : Contract =
-            config.ToUpdateContract()
-
         static member tryFromReadContract (c:Contract) =
             match c with
-            | {Operation = READ; DTOType = Some DTOType.YAML; DTO = Some (DTO.Text yaml)} ->
+            | {Operation = READ; DTOType = Some DTOType.YAML; Path = p; DTO = Some (DTO.Text yaml)} when p = ValidationPackagesConfigHelper.ConfigFilePath ->
                 yaml
                 |> ValidationPackagesConfig.fromYamlString
                 |> Some 

src/ValidationPackages/ValidationPackage.fs

@@ -1,4 +1,4 @@
-namespace ARCtrl.ValidationPackages
+namespace ARCtrl.ValidationPackages
 
 open ARCtrl.Helper
 open Fable.Core
@@ -22,6 +22,16 @@ type ValidationPackage(name, ?version) =
     member this.Copy() =
         ValidationPackage.make this.Name this.Version
 
+    /// Pretty printer 
+    override this.ToString() =
+        [
+            "{"
+            $" Name = {this.Name}"
+            if version.IsSome then $" Version = {this.Version.Value}"
+            "}"
+        ]
+        |> String.concat System.Environment.NewLine
+
     override this.Equals(obj) =
         match obj with
         | :? ValidationPackage as other_vp -> other_vp.Name = this.Name && other_vp.Version = this.Version

src/ValidationPackages/ValidationPackagesConfig.fs

@@ -1,13 +1,13 @@
-namespace ARCtrl.ValidationPackages
+namespace ARCtrl.ValidationPackages
 
 open ARCtrl.Helper
 open Fable.Core
 
 [<AttachMembers>]
 type ValidationPackagesConfig(validation_packages, ?arc_specification) =
 
-    let mutable _validation_packages : ResizeArray<ValidationPackage> = validation_packages
     let mutable _arc_specification : string option = arc_specification
+    let mutable _validation_packages : ResizeArray<ValidationPackage> = validation_packages
 
     member this.ValidationPackages 
         with get() = _validation_packages
@@ -22,15 +22,39 @@ type ValidationPackagesConfig(validation_packages, ?arc_specification) =
     member this.Copy() =
         ValidationPackagesConfig.make this.ValidationPackages this.ARCSpecification
 
-    override this.Equals(obj) =
-        match obj with
-        | :? ValidationPackagesConfig as other_vpc -> other_vpc.ValidationPackages = this.ValidationPackages && other_vpc.ARCSpecification = this.ARCSpecification
+
+    /// Pretty printer 
+    override this.ToString() =
+        [
+            "{"
+            if this.ARCSpecification.IsSome then $" ARCSpecification = {this.ARCSpecification.Value}"
+            " ValidationPackages = ["
+            this.ValidationPackages
+            |> Seq.map (fun vp -> vp.ToString())
+            |> String.concat $";{System.Environment.NewLine}"
+            "]"
+            "}"
+        ]
+        |> String.concat System.Environment.NewLine
+
+    member this.StructurallyEquals (other: ValidationPackagesConfig) =
+        let sort = Array.ofSeq >> Array.sortBy (fun (vp: ValidationPackage) -> vp.Name, vp.Version)
+        let specs = this.ARCSpecification = other.ARCSpecification
+        let packages = Seq.compare (sort this.ValidationPackages) (sort other.ValidationPackages)
+        specs && packages
+
+    member this.ReferenceEquals (other: ValidationPackagesConfig) = System.Object.ReferenceEquals(this,other)
+
+    override this.Equals other =
+        match other with
+        | :? ValidationPackagesConfig as other_vp -> 
+            this.StructurallyEquals(other_vp)
         | _ -> false
 
     override this.GetHashCode() =        
         [|
-            this.ValidationPackages.GetHashCode() |> box
             HashCodes.boxHashOption this.ARCSpecification
+            this.ValidationPackages |> HashCodes.boxHashSeq 
         |]
         |> HashCodes.boxHashArray
         |> fun x -> x :?> int

src/Yaml/Decode.fs

@@ -1,33 +1,7 @@
-namespace Arctrl.Yaml
+namespace ARCtrl.Yaml
 
 module Decode =
 
-    // yamlicious equivalents for this?
-
-    //let helpers = 
-    //    #if FABLE_COMPILER_PYTHON
-    //    Thoth.Json.Python.Decode.helpers
-    //    #endif
-    //    #if FABLE_COMPILER_JAVASCRIPT
-    //    Thoth.Json.JavaScript.Decode.helpers
-    //    #endif
-    //    #if !FABLE_COMPILER
-    //    Thoth.Json.Newtonsoft.Decode.helpers
-    //    #endif
-
-    //let inline fromJsonString (decoder : Decoder<'a>) (s : string) : 'a = 
-    //    #if FABLE_COMPILER_PYTHON
-    //    match Thoth.Json.Python.Decode.fromString decoder s with
-    //    #endif
-    //    #if FABLE_COMPILER_JAVASCRIPT
-    //    match Thoth.Json.JavaScript.Decode.fromString decoder s with
-    //    #endif
-    //    #if !FABLE_COMPILER
-    //    match Thoth.Json.Newtonsoft.Decode.fromString decoder s with
-    //    #endif
-    //    | Ok a -> a
-    //    | Error e -> failwith (sprintf "Error decoding string: %O" e)
-
     open YAMLicious
     open YAMLicious.YAMLiciousTypes
     open YAMLicious.Reader

src/Yaml/Encode.fs

@@ -1,4 +1,4 @@
-namespace Arctrl.Yaml
+namespace ARCtrl.Yaml
 
 module Encode =
 

src/Yaml/ValidationPackage.fs

@@ -1,31 +1,34 @@
-namespace ARCtrl.Yaml
+namespace ARCtrl.Yaml
 
 open ARCtrl.ValidationPackages
 open YAMLicious
 open YAMLicious.YAMLiciousTypes
 
 module ValidationPackage = 
 
+    let [<Literal>] NAME_KEY = "name"
+    let [<Literal>] VERSION_KEY = "version"
+
     let encoder (validationpackage : ValidationPackage) = 
         [
-            "name", Encode.string validationpackage.Name
-            Encode.tryInclude "version" Encode.string (validationpackage.Version)
+            NAME_KEY, Encode.string validationpackage.Name
+            Encode.tryInclude VERSION_KEY Encode.string (validationpackage.Version)
         ]
         |> Encode.choose
         |> Encode.object
 
     let decoder : (YAMLElement -> ValidationPackage) = 
         Decode.object (fun get ->
             ValidationPackage(
-                name = get.Required.Field "name" Decode.string,
-                ?version = get.Optional.Field "version" Decode.string
+                name = get.Required.Field NAME_KEY Decode.string,
+                ?version = get.Optional.Field VERSION_KEY Decode.string
             )
         )
 
 [<AutoOpen>]
 module ValidationPackageExtensions =
 
-    open Arctrl.Yaml
+    open ARCtrl.Yaml
     type ValidationPackage with
 
         static member fromYamlString (s:string)  = 

src/Yaml/ValidationPackagesConfig.fs

@@ -1,31 +1,34 @@
-namespace ARCtrl.Yaml
+namespace ARCtrl.Yaml
 
 open ARCtrl.ValidationPackages
 open YAMLicious
 open YAMLicious.YAMLiciousTypes
 
 module ValidationPackagesConfig = 
 
+    let [<Literal>] ARC_SPECIFICATION_KEY = "arc_specification"
+    let [<Literal>] VALIDATION_PACKAGES_KEY = "validation_packages"
+
     let encoder (validationpackage : ValidationPackagesConfig) = 
         [
-            "validation_packages", Encode.resizearray ValidationPackage.encoder validationpackage.ValidationPackages
-            Encode.tryInclude "arc_specification" Encode.string  (validationpackage.ARCSpecification)
+            Encode.tryInclude ARC_SPECIFICATION_KEY Encode.string  (validationpackage.ARCSpecification)
+            VALIDATION_PACKAGES_KEY, Encode.resizearray ValidationPackage.encoder validationpackage.ValidationPackages
         ]
         |> Encode.choose
         |> Encode.object
 
     let decoder : (YAMLElement -> ValidationPackagesConfig) = 
         Decode.object (fun get ->
             ValidationPackagesConfig(
-                validation_packages = get.Required.Field "validation_packages" (Decode.resizearray ValidationPackage.decoder),
-                ?arc_specification = get.Optional.Field "arc_specification" Decode.string
+                validation_packages = get.Required.Field VALIDATION_PACKAGES_KEY (Decode.resizearray ValidationPackage.decoder),
+                ?arc_specification = get.Optional.Field ARC_SPECIFICATION_KEY Decode.string
             )
         )
 
 [<AutoOpen>]
 module ValidationPackageConfigExtensions =
 
-    open Arctrl.Yaml
+    open ARCtrl.Yaml
     type ValidationPackagesConfig with
 
         static member fromYamlString (s:string)  = 

tests/ARCtrl/ARCtrl.Tests.fsproj

@@ -11,6 +11,7 @@
     <Compile Include="WebRequest.Tests.fs" />
     <Compile Include="ARCtrl.Contracts.Tests.fs" />
     <Compile Include="ARCtrl.Tests.fs" />
+    <Compile Include="ValidationPackagesConfig.Tests.fs" />
     <Compile Include="Main.fs" />
   </ItemGroup>
   <ItemGroup>