move all filesystem information into filesystem project

Author: HLWeil

src/ARCtrl/ARCtrl.fsproj

@@ -18,8 +18,6 @@
     <None Include="../../build/logo.png" Pack="true" PackagePath="\" />
   </ItemGroup>
   <ItemGroup>
-    <Compile Include="Path.fs" />
-    <Compile Include="FileSystemTree.fs" />
     <Compile Include="SemVer.fs" />
     <Compile Include="WebRequest\WebRequest.Node.fs" />
     <Compile Include="WebRequest\WebRequest.Py.fs" />

src/ARCtrl/FileSystemTree.fs

@@ -6,7 +6,6 @@
   </PropertyGroup>
   <ItemGroup>
     <None Include="../../build/logo.png" Pack="true" PackagePath="\" />
-    <Compile Include="Path.fs" />
     <Compile Include="Library.fs" />
   </ItemGroup>
   <ItemGroup>

src/ARCtrl/Path.fs

@@ -181,4 +181,57 @@ type FileSystemTree =
         | Folder(name,children) -> 
             Folder (name, children |> Array.map (fun c -> c.Copy()))
         | File(name) -> 
-            File name
+            File name
+
+
+
+
+    static member createGitKeepFile() = 
+        FileSystemTree.createFile ARCtrl.Path.GitKeepFileName
+
+    static member createReadmeFile() = 
+        FileSystemTree.createFile ARCtrl.Path.READMEFileName
+
+    static member createEmptyFolder (name : string) = 
+        FileSystemTree.createFolder(name, [|FileSystemTree.createGitKeepFile()|])
+
+    static member createAssayFolder(assayName : string) = 
+        let dataset = FileSystemTree.createEmptyFolder ARCtrl.Path.AssayDatasetFolderName
+        let protocols = FileSystemTree.createEmptyFolder ARCtrl.Path.AssayProtocolsFolderName
+        let readme = FileSystemTree.createReadmeFile()
+        let assayFile = FileSystemTree.createFile ARCtrl.Path.AssayFileName
+        FileSystemTree.createFolder(assayName, [|dataset; protocols; assayFile; readme|])
+
+    static member createStudyFolder(studyName : string) = 
+        let resources = FileSystemTree.createEmptyFolder ARCtrl.Path.StudiesResourcesFolderName
+        let protocols = FileSystemTree.createEmptyFolder ARCtrl.Path.StudiesProtocolsFolderName
+        let readme = FileSystemTree.createReadmeFile()
+        let studyFile = FileSystemTree.createFile ARCtrl.Path.StudyFileName
+        FileSystemTree.createFolder(studyName, [|resources; protocols; studyFile; readme|])
+
+    static member createInvestigationFile() = 
+        FileSystemTree.createFile ARCtrl.Path.InvestigationFileName
+
+    static member createAssaysFolder(assays : FileSystemTree array) =
+        FileSystemTree.createFolder(
+            ARCtrl.Path.AssaysFolderName, 
+            Array.append [|FileSystemTree.createGitKeepFile()|] assays
+        )
+
+    static member createStudiesFolder(studies : FileSystemTree array) =
+        FileSystemTree.createFolder(
+            ARCtrl.Path.StudiesFolderName,
+            Array.append [|FileSystemTree.createGitKeepFile()|] studies
+        )
+
+    static member createWorkflowsFolder(workflows : FileSystemTree array) =
+        FileSystemTree.createFolder(
+            ARCtrl.Path.WorkflowsFolderName, 
+            Array.append [|FileSystemTree.createGitKeepFile()|] workflows
+        )
+
+    static member createRunsFolder(runs : FileSystemTree array) = 
+        FileSystemTree.createFolder(
+            ARCtrl.Path.RunsFolderName, 
+            Array.append [|FileSystemTree.createGitKeepFile()|] runs
+        )

src/CWL/ARCtrl.CWL.fsproj

@@ -6,6 +6,29 @@ let [<Literal>] PathSeperator = '/'
 let [<Literal>] PathSeperatorWindows = '\\'
 let seperators = [|PathSeperator; PathSeperatorWindows|]
 
+
+
+// Files
+let [<Literal>] AssayFileName = "isa.assay.xlsx"
+let [<Literal>] StudyFileName = "isa.study.xlsx"
+let [<Literal>] InvestigationFileName = "isa.investigation.xlsx"
+let [<Literal>] GitKeepFileName = ".gitkeep" 
+let [<Literal>] READMEFileName = "README.md"
+
+// Folder
+let [<Literal>] AssaysFolderName = "assays"
+let [<Literal>] StudiesFolderName = "studies"
+let [<Literal>] WorkflowsFolderName = "workflows"
+let [<Literal>] RunsFolderName = "runs"
+let [<Literal>] AssayProtocolsFolderName = "protocols"
+let [<Literal>] AssayDatasetFolderName = "dataset"
+let [<Literal>] StudiesProtocolsFolderName = "protocols"
+let [<Literal>] StudiesResourcesFolderName = "resources"
+
+
+
+//let assaySubFolderNames = [|assayDatasetFolderName;assayProtocolsFolderName|]
+
 let split(path: string) = 
     path.Split(seperators, enum<StringSplitOptions>(3))
 
@@ -33,4 +56,11 @@ let getFileName (path: string) : string =
 /// </summary>
 /// <param name="fileName">The name of the file the path should point to.</param>
 /// <param name="path">The path to a file.</param>
-let isFile (fileName: string) (path: string) = (getFileName path) = fileName
+let isFile (fileName: string) (path: string) = (getFileName path) = fileName
+
+
+let getAssayFolderPath (assayIdentifier: string) =
+    combine AssaysFolderName assayIdentifier
+
+let getStudyFolderPath (studyIdentifier: string) =
+    combine StudiesFolderName studyIdentifier 

src/CWL/Path.fs

@@ -4,8 +4,7 @@
     <TargetFrameworks>netstandard2.0</TargetFrameworks>
     <GenerateDocumentationFile>true</GenerateDocumentationFile>
   </PropertyGroup>
-  <ItemGroup> 
-    <Compile Include="Path.fs" />
+  <ItemGroup>
     <Compile Include="Url.fs" />
     <Compile Include="Regex.fs" />
     <Compile Include="Identifier.fs" />
@@ -53,10 +52,6 @@
     <Compile Include="ArcTypes\ArcTables.fs" />
     <Compile Include="ArcTypes\ArcTypes.fs" />
     <Compile Include="ArcTypes\IdentifierSetters.fs" />
-    <Compile Include="Builder\Types.fs" />
-    <Compile Include="Builder\ProcessBuilder.fs" />
-    <Compile Include="Builder\AssayBuilder.fs" />
-    <Compile Include="Builder\Transform.fs" />
     <None Include="../../../build/logo.png" Pack="true" PackagePath="\" />
   </ItemGroup>
   <ItemGroup>