Merge pull request #421 from nfdi4plants/CWL

CWL Model, Encoding & Decoding

ARCtrl.sln

@@ -88,6 +88,8 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Yaml.Tests", "tests\
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Contract.Tests", "tests\Contract\ARCtrl.Contract.Tests.fsproj", "{D10D12C7-B877-423B-867D-161D99E673C9}"
 EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.CWL.Tests", "tests\CWL\ARCtrl.CWL.Tests.fsproj", "{0F2188D3-144C-41BF-89F6-AA85883AE0D3}"
+EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ROCrate", "src\ROCrate\ARCtrl.ROCrate.fsproj", "{658BF141-B4B5-4B90-891D-AC36A3FD7574}"
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ROCrate.Tests", "tests\ROCrate\ARCtrl.ROCrate.Tests.fsproj", "{212A1C64-02FC-465A-B0FA-F69735F37ACC}"
@@ -180,6 +182,10 @@ Global
 		{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
+		{0F2188D3-144C-41BF-89F6-AA85883AE0D3}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{0F2188D3-144C-41BF-89F6-AA85883AE0D3}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{0F2188D3-144C-41BF-89F6-AA85883AE0D3}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{0F2188D3-144C-41BF-89F6-AA85883AE0D3}.Release|Any CPU.Build.0 = Release|Any CPU
 		{658BF141-B4B5-4B90-891D-AC36A3FD7574}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
 		{658BF141-B4B5-4B90-891D-AC36A3FD7574}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{658BF141-B4B5-4B90-891D-AC36A3FD7574}.Release|Any CPU.ActiveCfg = Release|Any CPU
@@ -218,6 +224,7 @@ Global
 		{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}
+		{0F2188D3-144C-41BF-89F6-AA85883AE0D3} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 		{658BF141-B4B5-4B90-891D-AC36A3FD7574} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
 		{212A1C64-02FC-465A-B0FA-F69735F37ACC} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 		{243ACD5F-10AD-4BE6-9932-829667BE2053} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}

Directory.Packages.props

@@ -11,7 +11,7 @@
     <PackageVersion Include="Thoth.Json.Python"     Version="0.4.0" />
     <PackageVersion Include="Thoth.Json.Newtonsoft" Version="0.2.0" />
     <PackageVersion Include="FsSpreadsheet"         Version="6.3.0-alpha.4" />
-    <PackageVersion Include="YAMLicious"            Version="0.0.1" />
+    <PackageVersion Include="YAMLicious"            Version="0.0.3" />
     <PackageVersion Include="DynamicObj"            Version="4.0.3" />
     <PackageVersion Include="Fable.SimpleHttp"      Version="3.5.0" />
     <PackageVersion Include="Fable.Fetch"           Version="2.6.0" />

src/ARCtrl/ARC.fs

@@ -55,7 +55,7 @@ module ARCAux =
             |> FileSystem.create
         fs.Union(tree)
 
-    let updateFSByCWL (cwl : CWL.CWL option) (fs : FileSystem) =       
+    let updateFSByCWL (cwl : unit option) (fs : FileSystem) =       
         let workflows = FileSystemTree.createWorkflowsFolder [||]
         let runs = FileSystemTree.createRunsFolder [||]       
         let tree = 
@@ -65,7 +65,7 @@ module ARCAux =
 
 
 [<AttachMembers>]
-type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
+type ARC(?isa : ArcInvestigation, ?cwl : unit, ?fs : FileSystem.FileSystem) =
 
     let mutable _isa = isa
     let mutable _cwl = cwl

src/CWL/ARCtrl.CWL.fsproj

@@ -8,6 +8,18 @@
   <Import Project="../Package.Metadata.props" />
 
   <ItemGroup> 
-    <Compile Include="Library.fs" />
+    <Compile Include="CWLTypes.fs" /> 
+    <Compile Include="Requirements.fs" /> 
+    <Compile Include="Outputs.fs" /> 
+    <Compile Include="Inputs.fs" /> 
+    <Compile Include="WorkflowSteps.fs" /> 
+    <Compile Include="ToolDescription.fs" /> 
+    <Compile Include="WorkflowDescription.fs" /> 
+    <Compile Include="Decode.fs" />
+    <Compile Include="Encode.fs" />
+  </ItemGroup>
+  <ItemGroup>
+    <PackageReference Include="YAMLicious" />
+    <PackageReference Include="DynamicObj" />
   </ItemGroup>
 </Project>

src/CWL/CWLTypes.fs

@@ -0,0 +1,56 @@
+namespace ARCtrl.CWL
+
+open DynamicObj
+
+type FileInstance () =
+    inherit DynamicObj ()
+
+type DirectoryInstance () =
+    inherit DynamicObj ()
+
+type DirentInstance = {
+    // can be string or expression, but expression is string as well
+    Entry: string
+    Entryname: string option
+    Writable: bool option
+}
+
+/// Primitive types with the concept of a file and directory as a builtin type.
+type CWLType =
+    /// Represents a file (or group of files when secondaryFiles is provided)
+    | File of FileInstance
+    /// Represents a directory to present to a command line tool.
+    /// Directories are represented as objects with class of Directory. Directory objects have a number of properties that provide metadata about the directory.
+    | Directory of DirectoryInstance
+    /// Define a file or subdirectory that must be placed in the designated output directory prior to executing the command line tool.
+    /// May be the result of executing an expression, such as building a configuration file from a template.
+    | Dirent of DirentInstance
+    | String
+    | Int
+    | Long
+    | Float
+    | Double
+    | Boolean
+    | Stdout
+    | Null
+    | Array of CWLType
+
+type InputRecordSchema () =
+    inherit DynamicObj ()
+
+type InputEnumSchema () =
+    inherit DynamicObj ()
+
+type InputArraySchema () =
+    inherit DynamicObj ()
+
+type SchemaDefRequirementType (types, definitions) as this =
+    inherit DynamicObj ()
+    do
+        DynObj.setProperty (nameof types) definitions this
+
+type SoftwarePackage = {
+    Package: string
+    Version: ResizeArray<string> option
+    Specs: ResizeArray<string> option
+}