Merge pull request #155 from nfdi4plants/arcctrl_alpha

Prepare for arctrl alpha release
nfdi4plants · Aug 3, 2023 · 160d6df · 160d6df
2 parents a9c24c9 + 9cfbb0c
commit 160d6df
Show file tree

Hide file tree

Showing 154 changed files with 272 additions and 278 deletions.
diff --git a/ARCtrl.sln b/ARCtrl.sln
@@ -16,9 +16,9 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution
 		RELEASE_NOTES.md = RELEASE_NOTES.md
 	EndProjectSection
 EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "CWL", "src\CWL\CWL.fsproj", "{1CD34A01-D19A-441F-8F3D-6EF69D9DDA8D}"
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.CWL", "src\CWL\ARCtrl.CWL.fsproj", "{1CD34A01-D19A-441F-8F3D-6EF69D9DDA8D}"
 EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "FileSystem", "src\FileSystem\FileSystem.fsproj", "{F47E23C3-8415-4725-9E85-57271694DEB3}"
+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
@@ -76,13 +76,14 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "Build", "build\Build.fsproj
 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
 EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA", "src\ISA\ISA\ISA.fsproj", "{67CF6725-6AC0-47FB-A725-6DC2192713B5}"
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ISA", "src\ISA\ISA\ARCtrl.ISA.fsproj", "{67CF6725-6AC0-47FB-A725-6DC2192713B5}"
 EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Json", "src\ISA\ISA.Json\ISA.Json.fsproj", "{2CA397B2-0220-49A3-AD79-2F9F53633EC1}"
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ISA.Json", "src\ISA\ISA.Json\ARCtrl.ISA.Json.fsproj", "{2CA397B2-0220-49A3-AD79-2F9F53633EC1}"
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tests", "tests", "{64B34A6E-318D-4E6E-9262-CE52C9B85A38}"
 EndProject
@@ -92,7 +93,7 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Tests", "tests\ISA\ISA.
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Json.Tests", "tests\ISA\ISA.Json.Tests\ISA.Json.Tests.fsproj", "{04789F17-3DC2-4A09-848D-376E5D269740}"
 EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Spreadsheet", "src\ISA\ISA.Spreadsheet\ISA.Spreadsheet.fsproj", "{07C7942E-FC34-4C27-82C1-6B2972654BA7}"
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ISA.Spreadsheet", "src\ISA\ISA.Spreadsheet\ARCtrl.ISA.Spreadsheet.fsproj", "{07C7942E-FC34-4C27-82C1-6B2972654BA7}"
 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
@@ -115,7 +116,7 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl", "src\ARCtrl\ARCtrl
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Tests", "tests\ARCtrl\ARCtrl.Tests.fsproj", "{801247D5-7EE5-49C8-AB26-F822A415BA49}"
 EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "Contract", "src\Contract\Contract.fsproj", "{1945EE8A-F105-43A9-91C9-8C4422B9873E}"
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Contract", "src\Contract\ARCtrl.Contract.fsproj", "{1945EE8A-F105-43A9-91C9-8C4422B9873E}"
 EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution

diff --git a/playground/KevinF.fsx b/playground/KevinF.fsx
@@ -15,7 +15,7 @@
 let [<Literal>] rootPath = @"C:\Users\Kevin\Desktop\TestARC"
 open Contract
 open ARCtrl
-open FileSystem
+open ARCtrl.FileSystem
 
 module ARC_IO =
     open FsSpreadsheet
@@ -45,10 +45,10 @@ let myarc = ARC_IO.initExistingARC(rootPath)
 
 let newArcPath = System.IO.Path.Combine(__SOURCE_DIRECTORY__, "TestArc") 
 
-open ISA
+open ARCtrl.ISA
 open FsSpreadsheet
 open FsSpreadsheet.ExcelIO
-open ISA.Spreadsheet
+open ARCtrl.ISA.Spreadsheet
 
 module WriteContracts =
 

diff --git a/playground/testScript.fsx b/playground/testScript.fsx
@@ -10,8 +10,8 @@
 #r "ISA.dll"
 
 open ARC
-open FileSystem
-open ISA
+open ARCtrl.FileSystem
+open ARCtrl.ISA
 open System.IO
 
 let arcPath = Path.Combine(__SOURCE_DIRECTORY__, "testArc")

diff --git a/src/ARCtrl/ARCtrl.fs b/src/ARCtrl/ARCtrl.fs
@@ -1,8 +1,8 @@
 namespace ARCtrl
 
-open FileSystem
-open Contract
-open ISA
+open ARCtrl.FileSystem
+open ARCtrl.Contract
+open ARCtrl.ISA
 open FsSpreadsheet
 open Fable.Core
 
@@ -11,18 +11,18 @@ module ARCAux =
     // No idea where to move this
     let getArcAssaysFromContracts (contracts: Contract []) = 
         contracts 
-        |> Array.choose Contracts.ArcAssay.tryFromContract
+        |> Array.choose ARCtrl.Contract.ArcAssay.tryFromContract
         |> Array.map (fun x -> x :?> FsWorkbook |> ISA.Spreadsheet.ArcAssay.fromFsWorkbook)
 
     // No idea where to move this
     let getArcStudiesFromContracts (contracts: Contract []) =
         contracts 
-        |> Array.choose Contracts.ArcStudy.tryFromContract
+        |> Array.choose Contract.ArcStudy.tryFromContract
         |> Array.map (fun x -> x :?> FsWorkbook |> ISA.Spreadsheet.ArcStudy.fromFsWorkbook)
 
     let getArcInvestigationFromContracts (contracts: Contract []) =
         contracts 
-        |> Array.choose Contracts.ArcInvestigation.tryFromContract
+        |> Array.choose Contract.ArcInvestigation.tryFromContract
         |> Array.exactlyOne 
         |> fun x -> x :?> FsWorkbook |> ISA.Spreadsheet.ArcInvestigation.fromFsWorkbook
 
@@ -151,7 +151,7 @@ type ARC(?isa : ISA.ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSyste
 
     // to-do: function that returns read contracts based on a list of paths.
     member this.GetReadContracts () =
-        fs.Tree.ToFilePaths() |> Array.choose Contracts.ARCtrl.tryISAReadContractFromPath 
+        fs.Tree.ToFilePaths() |> Array.choose Contract.ARC.tryISAReadContractFromPath 
 
     /// <summary>
     /// This function creates the ARC-model from fullfilled READ contracts. The necessary READ contracts can be created with `ARC.getReadContracts`.

diff --git a/src/ARCtrl/ARCtrl.fsproj b/src/ARCtrl/ARCtrl.fsproj
@@ -21,12 +21,12 @@
   </ItemGroup>
 
   <ItemGroup>
-    <ProjectReference Include="..\Contract\Contract.fsproj" />
-    <ProjectReference Include="..\CWL\CWL.fsproj" />
-    <ProjectReference Include="..\FileSystem\FileSystem.fsproj" />
-    <ProjectReference Include="..\ISA\ISA\ISA.fsproj" />
-    <ProjectReference Include="..\ISA\ISA.Json\ISA.Json.fsproj" />
-    <ProjectReference Include="..\ISA\ISA.Spreadsheet\ISA.Spreadsheet.fsproj" />
+    <ProjectReference Include="..\Contract\ARCtrl.Contract.fsproj" />
+    <ProjectReference Include="..\CWL\ARCtrl.CWL.fsproj" />
+    <ProjectReference Include="..\FileSystem\ARCtrl.FileSystem.fsproj" />
+    <ProjectReference Include="..\ISA\ISA\ARCtrl.ISA.fsproj" />
+    <ProjectReference Include="..\ISA\ISA.Json\ARCtrl.ISA.Json.fsproj" />
+    <ProjectReference Include="..\ISA\ISA.Spreadsheet\ARCtrl.ISA.Spreadsheet.fsproj" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/ARCtrl/Contracts/Contracts.ARCtrl.fs b/src/ARCtrl/Contracts/Contracts.ARCtrl.fs
@@ -1,11 +1,10 @@
-module Contracts.ARCtrl 
+module ARCtrl.Contract.ARC
 
 open ARCtrl.Path
-open Contract
 
-open Contracts.ArcInvestigation
-open Contracts.ArcAssay
-open Contracts.ArcStudy
+open ARCtrl.Contract.ArcInvestigation
+open ARCtrl.Contract.ArcAssay
+open ARCtrl.Contract.ArcStudy
 
 // Assumptions: 
 // 1. All ISA .xlsx files MUST have the same names, either "isa.investigation.xlsx", "isa.assay.xlsx" or "isa.study.xlsx"

diff --git a/src/ARCtrl/Contracts/Contracts.ArcAssay.fs b/src/ARCtrl/Contracts/Contracts.ArcAssay.fs
@@ -1,6 +1,4 @@
-module Contracts.ArcAssay
-
-open Contract
+module ARCtrl.Contract.ArcAssay
 
 let tryFromContract (c:Contract) =
     match c with

diff --git a/src/ARCtrl/Contracts/Contracts.ArcInvestigation.fs b/src/ARCtrl/Contracts/Contracts.ArcInvestigation.fs
@@ -1,6 +1,4 @@
-module Contracts.ArcInvestigation
-
-open Contract
+module ARCtrl.Contract.ArcInvestigation
 
 let tryFromContract (c:Contract) =
     match c with

diff --git a/src/ARCtrl/Contracts/Contracts.ArcStudy.fs b/src/ARCtrl/Contracts/Contracts.ArcStudy.fs
@@ -1,6 +1,4 @@
-module Contracts.ArcStudy
-
-open Contract
+module ARCtrl.Contract.ArcStudy
 
 let tryFromContract (c:Contract) =
     match c with

diff --git a/src/ARCtrl/FileSystemTree.fs b/src/ARCtrl/FileSystemTree.fs
@@ -1,6 +1,6 @@
 module ARCtrl.FileSystemTree
 
-open FileSystem
+open ARCtrl.FileSystem
 
 let createGitKeepFile() = 
     FileSystemTree.createFile ARCtrl.Path.GitKeepFileName

diff --git a/src/ARCtrl/Path.fs b/src/ARCtrl/Path.fs
@@ -1,7 +1,7 @@
 module ARCtrl.Path
 
-open ISA
-open FileSystem
+open ARCtrl.ISA
+open ARCtrl.FileSystem
 
 // Files
 let [<Literal>] GitKeepFileName = ".gitkeep" 

diff --git a/src/CWL/CWL.fsproj → src/CWL/ARCtrl.CWL.fsproj b/src/CWL/CWL.fsproj → src/CWL/ARCtrl.CWL.fsproj
diff --git a/src/CWL/Library.fs b/src/CWL/Library.fs
@@ -1,3 +1,3 @@
-namespace CWL
+namespace ARCtrl.CWL
 
 type CWL = unit
diff --git a/src/Contract/Contract.fsproj → src/Contract/ARCtrl.Contract.fsproj b/src/Contract/Contract.fsproj → src/Contract/ARCtrl.Contract.fsproj
diff --git a/src/Contract/Contract.fs b/src/Contract/Contract.fs
@@ -1,4 +1,4 @@
-namespace Contract
+namespace ARCtrl.Contract
 
 open Fable.Core
 open FsSpreadsheet

diff --git a/src/FileSystem/FileSystem.fsproj → src/FileSystem/ARCtrl.FileSystem.fsproj b/src/FileSystem/FileSystem.fsproj → src/FileSystem/ARCtrl.FileSystem.fsproj
diff --git a/src/FileSystem/Commit.fs b/src/FileSystem/Commit.fs
@@ -1,4 +1,4 @@
-namespace FileSystem
+namespace ARCtrl.FileSystem
 
 open Fable.Core
 

diff --git a/src/FileSystem/FileSystem.fs b/src/FileSystem/FileSystem.fs
@@ -1,4 +1,4 @@
-namespace FileSystem
+namespace ARCtrl.FileSystem
 
 open Fable.Core
 

diff --git a/src/FileSystem/FileSystemTree.fs b/src/FileSystem/FileSystemTree.fs
@@ -1,4 +1,4 @@
-namespace FileSystem
+namespace ARCtrl.FileSystem
 
 open Fable.Core
 

diff --git a/src/ISA/ISA.Json/ISA.Json.fsproj → src/ISA/ISA.Json/ARCtrl.ISA.Json.fsproj b/src/ISA/ISA.Json/ISA.Json.fsproj → src/ISA/ISA.Json/ARCtrl.ISA.Json.fsproj
@@ -31,14 +31,14 @@
     <PackageReference Include="Thoth.Json" Version="10.1.0" />
     <PackageReference Include="Thoth.Json.Net" Version="11.0.0" />
   </ItemGroup>
-  <ItemGroup>
-    <ProjectReference Include="..\ISA\ISA.fsproj" />
-  </ItemGroup>
 
   <!-- Add source files to "fable" folder in Nuget package -->
   <ItemGroup>
   	<Content Include="*.fsproj; **\*.fs; **\*.fsi" PackagePath="fable\" />
   </ItemGroup>
+  <ItemGroup>
+    <ProjectReference Include="..\ISA\ARCtrl.ISA.fsproj" />
+  </ItemGroup>
   <ItemGroup>
     <PackageReference Update="FSharp.Core" Version="6.0.7" />
   </ItemGroup>

diff --git a/src/ISA/ISA.Json/Assay.fs b/src/ISA/ISA.Json/Assay.fs
@@ -1,11 +1,11 @@
-namespace ISA.Json
+namespace ARCtrl.ISA.Json
 
 #if FABLE_COMPILER
 open Thoth.Json
 #else
 open Thoth.Json.Net
 #endif
-open ISA
+open ARCtrl.ISA
 open System.IO
 
 module AssayMaterials = 

diff --git a/src/ISA/ISA.Json/Comment.fs b/src/ISA/ISA.Json/Comment.fs
@@ -1,12 +1,12 @@
-namespace ISA.Json
+namespace ARCtrl.ISA.Json
 
 
 #if FABLE_COMPILER
 open Thoth.Json
 #else
 open Thoth.Json.Net
 #endif
-open ISA
+open ARCtrl.ISA
 open System.IO
 
 module Comment = 

diff --git a/src/ISA/ISA.Json/ConverterOptions.fs b/src/ISA/ISA.Json/ConverterOptions.fs
@@ -1,4 +1,4 @@
-namespace ISA.Json
+namespace ARCtrl.ISA.Json
 
 type ConverterOptions() = 
 

diff --git a/src/ISA/ISA.Json/Data.fs b/src/ISA/ISA.Json/Data.fs
@@ -1,11 +1,11 @@
-namespace ISA.Json
+namespace ARCtrl.ISA.Json
 
 #if FABLE_COMPILER
 open Thoth.Json
 #else
 open Thoth.Json.Net
 #endif
-open ISA
+open ARCtrl.ISA
 open System.IO
 
 module DataFile = 

diff --git a/src/ISA/ISA.Json/Decode.fs b/src/ISA/ISA.Json/Decode.fs
@@ -1,4 +1,4 @@
-namespace ISA.Json
+namespace ARCtrl.ISA.Json
 
 #if FABLE_COMPILER
 open Thoth.Json
@@ -7,7 +7,7 @@ open Thoth.Json.Net
 open Newtonsoft.Json.Linq
 #endif
 
-open ISA
+open ARCtrl.ISA
 open Fable.Core
 
 module GDecode =

diff --git a/src/ISA/ISA.Json/Factor.fs b/src/ISA/ISA.Json/Factor.fs
@@ -1,11 +1,11 @@
-namespace ISA.Json
+namespace ARCtrl.ISA.Json
 
 #if FABLE_COMPILER
 open Thoth.Json
 #else
 open Thoth.Json.Net
 #endif
-open ISA
+open ARCtrl.ISA
 open System.IO
 
 module Value = 

diff --git a/src/ISA/ISA.Json/GEncode.fs b/src/ISA/ISA.Json/GEncode.fs
@@ -1,4 +1,4 @@
-namespace ISA.Json
+namespace ARCtrl.ISA.Json
 
 #if FABLE_COMPILER
 open Thoth.Json
@@ -26,7 +26,7 @@ module GEncode =
         property
         |> Option.bind (fun property -> 
             match FSharp.Reflection.FSharpValue.GetRecordField (object,property) with
-            | ISA.Aux.Update.SomeObj o -> 
+            | ARCtrl.ISA.Aux.Update.SomeObj o -> 
                 Some o
             | o when isNull o -> 
                 None

diff --git a/src/ISA/ISA.Json/Investigation.fs b/src/ISA/ISA.Json/Investigation.fs
@@ -1,11 +1,11 @@
-namespace ISA.Json
+namespace ARCtrl.ISA.Json
 
 #if FABLE_COMPILER
 open Thoth.Json
 #else
 open Thoth.Json.Net
 #endif
-open ISA
+open ARCtrl.ISA
 open System.IO
 
 module Investigation =

diff --git a/src/ISA/ISA.Json/JsonSchemaValidation.fs b/src/ISA/ISA.Json/JsonSchemaValidation.fs
@@ -1,4 +1,4 @@
-namespace ISA.Validation
+namespace ARCtrl.ISA.Validation
 
 module JSchema = 
 

diff --git a/src/ISA/ISA.Json/Material.fs b/src/ISA/ISA.Json/Material.fs
@@ -1,11 +1,11 @@
-namespace ISA.Json
+namespace ARCtrl.ISA.Json
 
 #if FABLE_COMPILER
 open Thoth.Json
 #else
 open Thoth.Json.Net
 #endif
-open ISA
+open ARCtrl.ISA
 open System.IO
 
 

diff --git a/src/ISA/ISA.Json/Ontology.fs b/src/ISA/ISA.Json/Ontology.fs
@@ -1,11 +1,11 @@
-namespace ISA.Json
+namespace ARCtrl.ISA.Json
 
 #if FABLE_COMPILER
 open Thoth.Json
 #else
 open Thoth.Json.Net
 #endif
-open ISA
+open ARCtrl.ISA
 open System.IO
 
 module AnnotationValue =