Changes for 1.0.0-alpha2

.config/dotnet-tools.json

@@ -7,6 +7,12 @@
       "commands": [
         "fable"
       ]
+    },
+    "paket": {
+      "version": "7.2.1",
+      "commands": [
+        "paket"
+      ]
     }
   }
 }

.gitignore

@@ -349,9 +349,11 @@ MigrationBackup/
 # Ionide (cross platform F# VS Code tools) working folder
 .ionide/
 
+#Paket dependency manager
+paket-files/
 
 # Custom ignored files
-pkg/
+dist/
 tmp/
 /tests/FileSystem/FileSystem.Tests/js
 /tests/ISA/ISA.Json.Tests/js
@@ -361,3 +363,4 @@ tmp/
 /tests/Python/ARCtrl
 /tests/ARCtrl/js
 /tests/FileSystem/js
+

ARCtrl.sln

@@ -12,6 +12,7 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution
 		.config\dotnet-tools.json = .config\dotnet-tools.json
 		global.json = global.json
 		package.json = package.json
+		paket.dependencies = paket.dependencies
 		README.md = README.md
 		RELEASE_NOTES.md = RELEASE_NOTES.md
 	EndProjectSection
@@ -20,63 +21,12 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.CWL", "src\CWL\ARCtr
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.FileSystem", "src\FileSystem\ARCtrl.FileSystem.fsproj", "{F47E23C3-8415-4725-9E85-57271694DEB3}"
 EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "js", "js", "{A3669129-8963-4F6E-A1D6-C691555EF125}"
-	ProjectSection(SolutionItems) = preProject
-		js\ARC.js = js\ARC.js
-		js\ARCPath.js = js\ARCPath.js
-		js\ARCStrich.js = js\ARCStrich.js
-		test.js = test.js
-	EndProjectSection
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ts", "ts", "{DB179B36-D77B-4340-A6AB-0C9F52882624}"
-	ProjectSection(SolutionItems) = preProject
-		ts\ARC.ts = ts\ARC.ts
-		ts\ARCPath.ts = ts\ARCPath.ts
-		ts\ARCStrich.ts = ts\ARCStrich.ts
-		ts\test.ts = ts\test.ts
-	EndProjectSection
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "CWL", "CWL", "{D55C23D0-6A31-4727-850C-4BE604EE3A25}"
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "FileSystem", "FileSystem", "{6A68446C-46F7-4DEB-BBD1-EE2CBB696EE2}"
-	ProjectSection(SolutionItems) = preProject
-		js\FileSystem\Commit.js = js\FileSystem\Commit.js
-		js\FileSystem\FileSystem.js = js\FileSystem\FileSystem.js
-		js\FileSystem\FileSystemTree.js = js\FileSystem\FileSystemTree.js
-		js\FileSystem\Path.js = js\FileSystem\Path.js
-	EndProjectSection
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ISA", "ISA", "{A4B8D64B-8B9A-4BEC-B56E-7B5E0DE4F823}"
-	ProjectSection(SolutionItems) = preProject
-		js\ISA\Assay.js = js\ISA\Assay.js
-		js\ISA\Investigation.js = js\ISA\Investigation.js
-		js\ISA\Study.js = js\ISA\Study.js
-	EndProjectSection
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ISA", "ISA", "{C3E09F95-660E-49B9-AE59-979BA3E347B8}"
-	ProjectSection(SolutionItems) = preProject
-		ts\ISA\Assay.ts = ts\ISA\Assay.ts
-		ts\ISA\Investigation.ts = ts\ISA\Investigation.ts
-		ts\ISA\Study.ts = ts\ISA\Study.ts
-	EndProjectSection
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "CWL", "CWL", "{8C99A701-CC88-4710-94BD-38843B437621}"
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "FileSystem", "FileSystem", "{49B4F154-3E60-4FAD-9924-9409DAA5DCD6}"
-	ProjectSection(SolutionItems) = preProject
-		ts\FileSystem\Commit.ts = ts\FileSystem\Commit.ts
-		ts\FileSystem\FileSystem.ts = ts\FileSystem\FileSystem.ts
-		ts\FileSystem\FileSystemTree.ts = ts\FileSystem\FileSystemTree.ts
-		ts\FileSystem\Path.ts = ts\FileSystem\Path.ts
-	EndProjectSection
-EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "src", "src", "{6DA2330B-D407-4FB1-AF05-B0184034EC44}"
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "Build", "build\Build.fsproj", "{5EAFB0CD-1168-4FCA-AA61-E96AD6C85819}"
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ISA", "ISA", "{C61B3F43-2255-4585-9110-F8AB74F02654}"
 	ProjectSection(SolutionItems) = preProject
-		src\ISA\ISA\ArcTypes\ArcInvestigation.fs = src\ISA\ISA\ArcTypes\ArcInvestigation.fs
 		src\ISA\package.json = src\ISA\package.json
 		src\ISA\README.md = src\ISA\README.md
 	EndProjectSection
@@ -97,10 +47,6 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ISA.Spreadsheet", "s
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Spreadsheet.Tests", "tests\ISA\ISA.Spreadsheet.Tests\ISA.Spreadsheet.Tests.fsproj", "{656E8DAF-EFCF-472E-91D0-987D09B74523}"
 EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "FileSystem", "FileSystem", "{E36B41EF-DD2A-45EB-912C-E637BBDBFDDE}"
-EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "FileSystem.Tests", "tests\FileSystem\FileSystem.Tests\FileSystem.Tests.fsproj", "{D7397A55-93AE-4165-9E2D-D83A52C22D41}"
-EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "playground", "playground", "{45E972BE-0BFA-4DE3-B84A-D9F13C4E9D08}"
 	ProjectSection(SolutionItems) = preProject
 		playground\KevinF.fsx = playground\KevinF.fsx
@@ -109,6 +55,7 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "playground", "playground",
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "JavaScript", "JavaScript", "{913222CA-261F-49CB-A823-CC7C335F964A}"
 	ProjectSection(SolutionItems) = preProject
+		tests\JavaScript\ISA.Person.js = tests\JavaScript\ISA.Person.js
 		tests\JavaScript\Main.js = tests\JavaScript\Main.js
 	EndProjectSection
 EndProject
@@ -118,6 +65,8 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Tests", "tests\ARCtr
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Contract", "src\Contract\ARCtrl.Contract.fsproj", "{1945EE8A-F105-43A9-91C9-8C4422B9873E}"
 EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "FileSystem.Tests", "tests\FileSystem\FileSystem.Tests.fsproj", "{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -160,10 +109,6 @@ Global
 		{656E8DAF-EFCF-472E-91D0-987D09B74523}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{656E8DAF-EFCF-472E-91D0-987D09B74523}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{656E8DAF-EFCF-472E-91D0-987D09B74523}.Release|Any CPU.Build.0 = Release|Any CPU
-		{D7397A55-93AE-4165-9E2D-D83A52C22D41}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
-		{D7397A55-93AE-4165-9E2D-D83A52C22D41}.Debug|Any CPU.Build.0 = Debug|Any CPU
-		{D7397A55-93AE-4165-9E2D-D83A52C22D41}.Release|Any CPU.ActiveCfg = Release|Any CPU
-		{D7397A55-93AE-4165-9E2D-D83A52C22D41}.Release|Any CPU.Build.0 = Release|Any CPU
 		{9BE5D83D-EA90-4382-A132-174FD158227F}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
 		{9BE5D83D-EA90-4382-A132-174FD158227F}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{9BE5D83D-EA90-4382-A132-174FD158227F}.Release|Any CPU.ActiveCfg = Release|Any CPU
@@ -176,19 +121,17 @@ Global
 		{1945EE8A-F105-43A9-91C9-8C4422B9873E}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{1945EE8A-F105-43A9-91C9-8C4422B9873E}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{1945EE8A-F105-43A9-91C9-8C4422B9873E}.Release|Any CPU.Build.0 = Release|Any CPU
+		{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
 	EndGlobalSection
 	GlobalSection(NestedProjects) = preSolution
 		{1CD34A01-D19A-441F-8F3D-6EF69D9DDA8D} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
 		{F47E23C3-8415-4725-9E85-57271694DEB3} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
-		{D55C23D0-6A31-4727-850C-4BE604EE3A25} = {A3669129-8963-4F6E-A1D6-C691555EF125}
-		{6A68446C-46F7-4DEB-BBD1-EE2CBB696EE2} = {A3669129-8963-4F6E-A1D6-C691555EF125}
-		{A4B8D64B-8B9A-4BEC-B56E-7B5E0DE4F823} = {A3669129-8963-4F6E-A1D6-C691555EF125}
-		{C3E09F95-660E-49B9-AE59-979BA3E347B8} = {DB179B36-D77B-4340-A6AB-0C9F52882624}
-		{8C99A701-CC88-4710-94BD-38843B437621} = {DB179B36-D77B-4340-A6AB-0C9F52882624}
-		{49B4F154-3E60-4FAD-9924-9409DAA5DCD6} = {DB179B36-D77B-4340-A6AB-0C9F52882624}
 		{C61B3F43-2255-4585-9110-F8AB74F02654} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
 		{67CF6725-6AC0-47FB-A725-6DC2192713B5} = {C61B3F43-2255-4585-9110-F8AB74F02654}
 		{2CA397B2-0220-49A3-AD79-2F9F53633EC1} = {C61B3F43-2255-4585-9110-F8AB74F02654}
@@ -197,12 +140,11 @@ Global
 		{04789F17-3DC2-4A09-848D-376E5D269740} = {D1BBD7AE-35C8-498F-BABA-C93FFAE68037}
 		{07C7942E-FC34-4C27-82C1-6B2972654BA7} = {C61B3F43-2255-4585-9110-F8AB74F02654}
 		{656E8DAF-EFCF-472E-91D0-987D09B74523} = {D1BBD7AE-35C8-498F-BABA-C93FFAE68037}
-		{E36B41EF-DD2A-45EB-912C-E637BBDBFDDE} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
-		{D7397A55-93AE-4165-9E2D-D83A52C22D41} = {E36B41EF-DD2A-45EB-912C-E637BBDBFDDE}
 		{913222CA-261F-49CB-A823-CC7C335F964A} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 		{9BE5D83D-EA90-4382-A132-174FD158227F} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
 		{801247D5-7EE5-49C8-AB26-F822A415BA49} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 		{1945EE8A-F105-43A9-91C9-8C4422B9873E} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
+		{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 		SolutionGuid = {1E354DE6-99BA-421E-9EF8-E808B855A85F}

README.md

@@ -1,4 +1,4 @@
-# ARCtrl
+# ARCtrl
 Top level ARC DataModel and API function descriptions.
 
 - [ARCtrl](#arctrl)
@@ -14,7 +14,7 @@ Top level ARC DataModel and API function descriptions.
 
 [ISA README.md](src/ISA/README.md) :books:
 
-[Contracts README.md](src/ArcContract/README.md) :books:
+[Contracts README.md](src/Contract/README.md) :books:
 
 # Jargon/Nomenclature
 
@@ -265,3 +265,13 @@ export class Study extends Record implements IEquatable<Study>, IComparable<Stud
         return new Study(Identifier, Assays);
     }
 ```
+
+## Development
+
+### Setup
+
+1. `dotnet tool restore`
+2. `dotnet paket install`
+3. `npm install`
+
+Verify correct setup with `./build.cmd runtests` ✨

RELEASE_NOTES.md

@@ -1,3 +1,10 @@
+### 1.0.0+4892f43 (Released 2023-8-3)
+* Additions:
+    * Complete overhaul of the API. 
+    * Shifted focus from only ISA to include full ARC. 
+    * Included Fable compilation to Javascript as first citizen design principles. 
+    * No direct filesystem access but contract based IO, which allows language agnostic IO.
+
 ### 0.7.0+ac83329 (Released 2023-1-26)
 * Additions:
     * latest commit #ac83329
@@ -271,22 +278,21 @@
 * Bugfixes:
     * [[#fa4d1c5](https://github.com/nfdi4plants/ISADotNet/commit/fa4d1c50975765e3838fcebe2aa642220938a77e)] fix remove functions fixes #8
 
-### 0.0.4+2f78a5fa - Wednesday, February 03, 2021
+### 0.0.4+2f78a5fa (Released 2023-8-3)
 * Additions:
     * latest commit #2f78a5fa
-	* Add append optional list functionality when updating record types
-	* Add tests
-	* Soften version constraint of FSharp.Core package dependancy
-
-#### 0.0.2 - Thursday, January 21, 2021
+    * 	* Add append optional list functionality when updating record types
+    * 	* Add tests
+    * 	* Soften version constraint of FSharp.Core package dependancy
 
-* Increased the minimum version of the System.Json.Text dependancy
-* Minor additions to the API functions
+### 0.0.2 (Released 2023-8-3)
+    * Increased the minimum version of the System.Json.Text dependancy
+    * Minor additions to the API functions
 
-#### 0.0.1 - Monday, January 11, 2021
+### 0.0.1 (Released 2023-8-3)
+    * Moved Project from nfdi4Plants/ArcCommander
+    * Full ISA Datamodel
+    * Reworked API
+    * ISA XLSX Investigation file parser
+    * Added ISA Json IO
 
-* Moved Project from nfdi4Plants/ArcCommander
-* Full ISA Datamodel
-* Reworked API
-* ISA XLSX Investigation file parser
-* Added ISA Json IO

build.cmd

@@ -1,3 +1,6 @@
 @echo off
+
+dotnet tool restore
+dotnet paket restore
 cls 
 dotnet run --project ./build/build.fsproj %*

build.sh

@@ -3,4 +3,6 @@
 set -eu
 set -o pipefail
 
+dotnet paket restore
+
 dotnet run --project ./build/Build.fsproj "$@"

build/BasicTasks.fs

@@ -20,7 +20,7 @@ let clean = BuildTask.create "Clean" [] {
     ++ "src/**/obj"
     ++ "tests/**/bin"
     ++ "tests/**/obj"
-    ++ "pkg"
+    ++ ProjectInfo.pkgDir
     |> Shell.cleanDirs 
 }
 

build/Build.fsproj

@@ -1,11 +1,11 @@
-<Project Sdk="Microsoft.NET.Sdk">
-
+<?xml version="1.0" encoding="utf-8"?>
+<Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
     <TargetFramework>net6.0</TargetFramework>
     <OutputType>Exe</OutputType>
   </PropertyGroup>
-
   <ItemGroup>
+    <None Include="paket.references" />
     <Compile Include="Helpers.fs" />
     <Compile Include="MessagePrompts.fs" />
     <Compile Include="ProjectInfo.fs" />
@@ -16,7 +16,6 @@
     <Compile Include="ReleaseTasks.fs" />
     <Compile Include="Build.fs" />
   </ItemGroup>
-
   <ItemGroup>
     <PackageReference Include="BlackFox.Fake.BuildTask" Version="0.1.3" />
     <PackageReference Include="Fake.Api.Github" Version="5.23.0-alpha002" />
@@ -27,7 +26,7 @@
     <PackageReference Include="Fake.DotNet.MSBuild" Version="5.23.0-alpha002" />
     <PackageReference Include="Fake.IO.FileSystem" Version="5.23.0-alpha002" />
     <PackageReference Include="Fake.Tools.Git" Version="5.23.0-alpha002" />
-	<PackageReference Include="Fake.Extensions.Release" Version="0.3.0" />
+    <PackageReference Include="Fake.Extensions.Release" Version="0.3.0" />
   </ItemGroup>
-
-</Project>
+  <Import Project="..\.paket\Paket.Restore.targets" />
+</Project>

build/PackageTasks.fs

@@ -17,7 +17,7 @@ let private replaceCommitLink input =
     let commitLinkPattern = @"\[\[#[a-z0-9]*\]\(.*\)\] "
     Regex.Replace(input,commitLinkPattern,"")
 
-let pack = BuildTask.create "Pack" [clean; build; (*runTests*)] {
+let pack = BuildTask.create "Pack" [clean; build; runTests] {
     if promptYesNo (sprintf "creating stable package with version %s OK?" stableVersionTag ) 
         then
             !! "src/**/*.*proj"
@@ -39,7 +39,7 @@ let pack = BuildTask.create "Pack" [clean; build; (*runTests*)] {
     else failwith "aborted"
 }
 
-let packPrerelease = BuildTask.create "PackPrerelease" [setPrereleaseTag; clean; build; runTests] {
+let packPrerelease = BuildTask.create "PackPrerelease" [setPrereleaseTag; clean; build; (*runTests*)] {
     if promptYesNo (sprintf "package tag will be %s OK?" prereleaseTag )
         then 
             !! "src/**/*.*proj"

build/ProjectInfo.fs

@@ -9,7 +9,7 @@ let testProjects =
         "tests/ISA/ISA.Tests"
         "tests/ISA/ISA.Json.Tests"
         "tests/ISA/ISA.Spreadsheet.Tests"
-        "tests/FileSystem/FileSystem.Tests"
+        "tests/FileSystem"
     ]
 
 let solutionFile  = $"{project}.sln"
@@ -22,7 +22,7 @@ let gitHome = $"https://github.com/{gitOwner}"
 
 let projectRepo = $"https://github.com/{gitOwner}/{project}"
 
-let pkgDir = "pkg"
+let pkgDir = "dist/pkg"
 
 // Create RELEASE_NOTES.md if not existing. Or "release" would throw an error.
 Fake.Extensions.Release.ReleaseNotes.ensure()

build/ReleaseTasks.fs

@@ -22,7 +22,7 @@ let createTag = BuildTask.create "CreateTag" [clean; build; runTests; pack] {
         failwith "aborted"
 }
 
-let createPrereleaseTag = BuildTask.create "CreatePrereleaseTag" [setPrereleaseTag; clean; build; runTests; packPrerelease] {
+let createPrereleaseTag = BuildTask.create "CreatePrereleaseTag" [setPrereleaseTag; clean; build (*runTests*); packPrerelease] {
     if promptYesNo (sprintf "tagging branch with %s OK?" prereleaseTag ) then 
         Git.Branches.tag "" prereleaseTag
         Git.Branches.pushTag "" projectRepo prereleaseTag

build/TestTasks.fs

@@ -114,7 +114,7 @@ module RunTests =
         run npm "run testJson" ""
         run npm "run testSpreadsheet" ""
         run npm "run testFS" ""
-        run npm "run testJavaScript" ""
+        run npm "run testjs" ""
     }
 
     let runTestsDotnet = BuildTask.create "runTestsDotnet" [clean; build] {

build/paket.references

@@ -0,0 +1 @@
+FSharp.Core