Merge pull request #216 from nfdi4plants/developer_issues2

Issues

build/PackageTasks.fs

@@ -1,7 +1,5 @@
 module PackageTasks
 
-open ProjectInfo
-
 open MessagePrompts
 open BasicTasks
 open TestTasks
@@ -18,91 +16,81 @@ let private replaceCommitLink input =
     Regex.Replace(input,commitLinkPattern,"")
 
 let packDotNet = BuildTask.create "PackDotNet" [clean; build; runTests] {
-    if promptYesNo (sprintf "creating stable package with version %s OK?" stableVersionTag ) 
+    if promptYesNo (sprintf "[NUGET] creating stable package with version %s OK?" ProjectInfo.stableVersionTag ) 
         then
             !! "src/**/*.*proj"
             -- "src/bin/*"
             |> Seq.iter (Fake.DotNet.DotNet.pack (fun p ->
                 let msBuildParams =
                     {p.MSBuildParams with 
                         Properties = ([
-                            "Version",stableVersionTag
-                            "PackageReleaseNotes",  (release.Notes |> List.map replaceCommitLink |> String.concat "\r\n" )
+                            "Version", ProjectInfo.stableVersionTag
+                            "PackageReleaseNotes",  (ProjectInfo.release.Notes |> List.map replaceCommitLink |> String.concat "\r\n" )
                         ] @ p.MSBuildParams.Properties)
                     }
                 {
                     p with 
                         MSBuildParams = msBuildParams
-                        OutputPath = Some pkgDir
+                        OutputPath = Some ProjectInfo.pkgDir
                 }
             ))
     else failwith "aborted"
 }
 
 let packDotNetPrerelease = BuildTask.create "PackDotNetPrerelease" [setPrereleaseTag; clean; build; (*runTests*)] {
-    if promptYesNo (sprintf "package tag will be %s OK?" prereleaseTag )
+    if promptYesNo (sprintf "[NUGET] package tag will be %s OK?" ProjectInfo.prereleaseTag )
         then 
             !! "src/**/*.*proj"
             -- "src/bin/*"
             |> Seq.iter (Fake.DotNet.DotNet.pack (fun p ->
                         let msBuildParams =
                             {p.MSBuildParams with 
                                 Properties = ([
-                                    "Version", prereleaseTag
-                                    "PackageReleaseNotes",  (release.Notes |> List.map replaceCommitLink  |> String.toLines )
+                                    "Version", ProjectInfo.prereleaseTag
+                                    "PackageReleaseNotes",  (ProjectInfo.release.Notes |> List.map replaceCommitLink  |> String.toLines )
                                 ] @ p.MSBuildParams.Properties)
                             }
                         {
                             p with 
-                                VersionSuffix = Some prereleaseSuffix
-                                OutputPath = Some pkgDir
+                                VersionSuffix = Some ProjectInfo.prereleaseSuffix
+                                OutputPath = Some ProjectInfo.pkgDir
                                 MSBuildParams = msBuildParams
                         }
             ))
     else
         failwith "aborted"
 }
 
-let packJS = BuildTask.create "PackJS" [clean; build; runTests] {
-    if promptYesNo (sprintf "creating stable package with version %s OK?" stableVersionTag ) 
-        then
-            Fake.JavaScript.Npm.run "bundlejs" (fun o -> o)
-            Fake.IO.File.readAsString "build/release_package.json"
-            |> Fake.IO.File.writeString false "dist/js/package.json"
-
-            Fake.IO.File.readAsString "README.md"
-            |> Fake.IO.File.writeString false "dist/js/README.md"
-
-            "" // "fable-library.**/**"
-            |> Fake.IO.File.writeString false "dist/js/fable_modules/.npmignore"
-
-            Fake.JavaScript.Npm.exec "pack" (fun o ->
-                { o with
-                    WorkingDirectory = "./dist/js/"
-                })
-    else failwith "aborted"
-}
-
-
-let packJSPrerelease = BuildTask.create "PackJSPrerelease" [setPrereleaseTag; clean; build; runTests] {
-    if promptYesNo (sprintf "package tag will be %s OK?" prereleaseTag ) then
+module BundleJs =
+    let bundle (versionTag: string) =
         Fake.JavaScript.Npm.run "bundlejs" (fun o -> o)
-
+        GenerateIndexJs.ARCtrl_generate ProjectInfo.npmPkgDir
         Fake.IO.File.readAsString "build/release_package.json"
         |> fun t ->
-            let t = t.Replace(stableVersionTag, prereleaseTag)
-            Fake.IO.File.writeString false "dist/js/package.json" t
+            let t = t.Replace(ProjectInfo.stableVersionTag, versionTag)
+            Fake.IO.File.writeString false $"{ProjectInfo.npmPkgDir}/package.json" t
 
         Fake.IO.File.readAsString "README.md"
-        |> Fake.IO.File.writeString false "dist/js/README.md"
+        |> Fake.IO.File.writeString false $"{ProjectInfo.npmPkgDir}/README.md"
 
         "" // "fable-library.**/**"
-        |> Fake.IO.File.writeString false "dist/js/fable_modules/.npmignore"
+        |> Fake.IO.File.writeString false $"{ProjectInfo.npmPkgDir}/fable_modules/.npmignore"
 
         Fake.JavaScript.Npm.exec "pack" (fun o ->
             { o with
-                WorkingDirectory = "./dist/js/"
+                WorkingDirectory = ProjectInfo.npmPkgDir
             })
+
+let packJS = BuildTask.create "PackJS" [clean; build; runTests] {
+    if promptYesNo (sprintf "[NPM] creating stable package with version %s OK?" ProjectInfo.stableVersionTag ) 
+        then
+            BundleJs.bundle ProjectInfo.stableVersionTag
+    else failwith "aborted"
+}
+
+let packJSPrerelease = BuildTask.create "PackJSPrerelease" [setPrereleaseTag; clean; build; runTests] {
+    if promptYesNo (sprintf "[NPM] package tag will be %s OK?" ProjectInfo.prereleaseTag ) then
+        BundleJs.bundle ProjectInfo.prereleaseTag
     else failwith "aborted"
     }
 

build/ProjectInfo.fs

@@ -31,7 +31,7 @@ let gitHome = $"https://github.com/{gitOwner}"
 let projectRepo = $"https://github.com/{gitOwner}/{project}"
 
 let pkgDir = "dist/pkg"
-let npmPkgDir = "dist/js"
+let npmPkgDir = "./dist/js"
 
 // Create RELEASE_NOTES.md if not existing. Or "release" would throw an error.
 Fake.Extensions.Release.ReleaseNotes.ensure()

src/ARCtrl/ARCtrl.fs → src/ARCtrl/ARC.fs

@@ -64,6 +64,7 @@ type ARC(?isa : ISA.ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSyste
         with get() = _isa
         and set(newISA : ArcInvestigation option) =
             _isa <- newISA
+            this.UpdateFileSystem()
 
     member this.CWL 
         with get() = cwl
@@ -225,8 +226,8 @@ type ARC(?isa : ISA.ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSyste
             )
 
         | None -> 
+            //printfn "ARC contains no ISA part."
             workbooks.Add (Path.InvestigationFileName, (DTOType.ISA_Investigation, ISA.Spreadsheet.ArcInvestigation.toFsWorkbook (ArcInvestigation.create(Identifier.MISSING_IDENTIFIER))))
-            printfn "ARC contains no ISA part."
 
         // Iterates over filesystem and creates a write contract for every file. If possible, include DTO.       
         _fs.Tree.ToFilePaths(true)
@@ -355,6 +356,9 @@ type ARC(?isa : ISA.ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSyste
         |> Option.bind (fun tree -> if ignoreHidden then tree |> FileSystemTree.filterFolders (fun n -> not (n.StartsWith("."))) else Some tree)
         |> Option.defaultValue (FileSystemTree.fromFilePaths [||])
 
+    static member DefaultContracts = Map<string,Contract> [|
+        ARCtrl.Contract.Git.gitignoreFileName, ARCtrl.Contract.Git.gitignoreContract
+    |]
 
 //-Pseudo code-//
 //// Option 1

src/ARCtrl/ARCtrl.fsproj

@@ -34,7 +34,7 @@
     <Compile Include="Templates\Template.Spreadsheet.fs" />
     <Compile Include="Templates\Template.Web.fs" />
     <None Include="README.md" />
-    <Compile Include="ARCtrl.fs" />
+    <Compile Include="ARC.fs" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\Contract\ARCtrl.Contract.fsproj" />

src/ARCtrl/Templates/Template.Json.fs

@@ -105,12 +105,12 @@ module Template =
             )
         )
 
-    let decodeFromString (jsonString: string) =
+    let fromJsonString (jsonString: string) =
         match Decode.fromString decode jsonString with
         | Ok template   -> template
         | Error exn     -> failwithf "Error. Given json string cannot be parsed to Template: %A" exn
 
-    let encodeToString (spaces: int) (template:Template) =
+    let toJsonString (spaces: int) (template:Template) =
         Encode.toString spaces (encode template)
 
 module Templates =
@@ -125,12 +125,12 @@ module Templates =
         let d = Decode.dict Template.decode
         Decode.fromString d
 
-    let decodeFromString (jsonString: string) =
+    let fromJsonString (jsonString: string) =
         match decode jsonString with
         | Ok templateMap    -> templateMap
         | Error exn         -> failwithf "Error. Given json string cannot be parsed to Templates map: %A" exn
 
-    let encodeToString (spaces: int) (templateList: (string*Template) []) =
+    let toJsonString (spaces: int) (templateList: (string*Template) []) =
         Encode.toString spaces (encode templateList)
 
 
@@ -140,4 +140,4 @@ module Extension =
     type Template with
         member this.ToJson(?spaces: int) =
             let spaces = defaultArg spaces 0
-            Template.encodeToString(spaces)
+            Template.toJsonString(spaces)

src/ARCtrl/Templates/Template.Web.fs

@@ -10,7 +10,7 @@ let getTemplates(url: string option) =
     let url = defaultArg url defaultURL
     async {
         let! jsonString = ARCtrl.WebRequest.downloadFile url
-        let mapResult = Json.Templates.decodeFromString jsonString
+        let mapResult = Json.Templates.fromJsonString jsonString
         return mapResult
     }
 

src/FileSystem/DefaultGitignore.fs

@@ -1,5 +1,8 @@
 module ARCtrl.FileSystem.DefaultGitignore
 
+/// <summary>
+/// A string containing the default .gitignore file content.
+/// </summary>
 let dgi = """# ----- macos rules -----
 # taken from https://github.com/github/gitignore/blob/main/Global/macOS.gitignore
 # General

src/ISA/ISA.Json/Assay.fs

@@ -37,13 +37,13 @@ module Assay =
 
     let encoder (options : ConverterOptions) (oa : obj) = 
         [
-            if options.SetID then "@id", GEncode.string (oa :?> Assay |> genID)
-                else GEncode.tryInclude "@id" GEncode.string (oa |> GEncode.tryGetPropertyValue "ID")
-            if options.IncludeType then "@type", GEncode.string "Assay"
-            GEncode.tryInclude "filename" GEncode.string (oa |> GEncode.tryGetPropertyValue "FileName")
+            if options.SetID then "@id", GEncode.toJsonString (oa :?> Assay |> genID)
+                else GEncode.tryInclude "@id" GEncode.toJsonString (oa |> GEncode.tryGetPropertyValue "ID")
+            if options.IncludeType then "@type", GEncode.toJsonString "Assay"
+            GEncode.tryInclude "filename" GEncode.toJsonString (oa |> GEncode.tryGetPropertyValue "FileName")
             GEncode.tryInclude "measurementType" (OntologyAnnotation.encoder options) (oa |> GEncode.tryGetPropertyValue "MeasurementType")
             GEncode.tryInclude "technologyType" (OntologyAnnotation.encoder options) (oa |> GEncode.tryGetPropertyValue "TechnologyType")
-            GEncode.tryInclude "technologyPlatform" GEncode.string (oa |> GEncode.tryGetPropertyValue "TechnologyPlatform")
+            GEncode.tryInclude "technologyPlatform" GEncode.toJsonString (oa |> GEncode.tryGetPropertyValue "TechnologyPlatform")
             GEncode.tryInclude "dataFiles" (Data.encoder options) (oa |> GEncode.tryGetPropertyValue "DataFiles")
             GEncode.tryInclude "materials" (AssayMaterials.encoder options) (oa |> GEncode.tryGetPropertyValue "Materials")
             GEncode.tryInclude "characteristicCategories" (MaterialAttribute.encoder options) (oa |> GEncode.tryGetPropertyValue "CharacteristicCategories")
@@ -71,10 +71,10 @@ module Assay =
             }
         )
 
-    let fromString (s:string) = 
-        GDecode.fromString (decoder (ConverterOptions())) s
+    let fromJsonString (s:string) = 
+        GDecode.fromJsonString (decoder (ConverterOptions())) s
 
-    let toString (p:Assay) = 
+    let toJsonString (p:Assay) = 
         encoder (ConverterOptions()) p
         |> Encode.toString 2
 
@@ -95,11 +95,11 @@ module ArcAssay =
 
     open Assay
 
-    let fromString (s:string) = 
-        GDecode.fromString (decoder (ConverterOptions())) s
+    let fromJsonString (s:string) = 
+        GDecode.fromJsonString (decoder (ConverterOptions())) s
         |> ArcAssay.fromAssay
 
-    let toString (a:ArcAssay) = 
+    let toJsonString (a:ArcAssay) = 
         encoder (ConverterOptions()) (a.ToAssay())
         |> Encode.toString 2
 

src/ISA/ISA.Json/Comment.fs

@@ -22,11 +22,11 @@ module Comment =
 
     let encoder (options : ConverterOptions) (comment : obj) = 
         [
-            if options.SetID then "@id", GEncode.string (comment :?> Comment |> genID)
-                else GEncode.tryInclude "@id" GEncode.string (comment |> GEncode.tryGetPropertyValue "ID")
-            if options.IncludeType then "@type", GEncode.string "Comment"
-            GEncode.tryInclude "name" GEncode.string (comment |> GEncode.tryGetPropertyValue "Name")
-            GEncode.tryInclude "value" GEncode.string (comment |> GEncode.tryGetPropertyValue "Value")
+            if options.SetID then "@id", GEncode.toJsonString (comment :?> Comment |> genID)
+                else GEncode.tryInclude "@id" GEncode.toJsonString (comment |> GEncode.tryGetPropertyValue "ID")
+            if options.IncludeType then "@type", GEncode.toJsonString "Comment"
+            GEncode.tryInclude "name" GEncode.toJsonString (comment |> GEncode.tryGetPropertyValue "Name")
+            GEncode.tryInclude "value" GEncode.toJsonString (comment |> GEncode.tryGetPropertyValue "Value")
         ]
         |> GEncode.choose
         |> Encode.object
@@ -40,10 +40,10 @@ module Comment =
             }
         )
 
-    let fromString (s:string)  = 
-        GDecode.fromString (decoder (ConverterOptions())) s
+    let fromJsonString (s:string)  = 
+        GDecode.fromJsonString (decoder (ConverterOptions())) s
 
-    let toString (c:Comment) = 
+    let toJsonString (c:Comment) = 
         encoder (ConverterOptions()) c
         |> Encode.toString 2