Merge pull request #237 from nfdi4plants/update_arctrl

Update to arctrl.net 1.0.2
nfdi4plants · Jan 25, 2024 · f416507 · f416507
2 parents 8a4bf16 + 3897ff8
commit f416507
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Showing 10 changed files with 34 additions and 9 deletions.
diff --git a/src/ArcCommander/APIs/StudyAPI.fs b/src/ArcCommander/APIs/StudyAPI.fs
@@ -736,13 +736,13 @@ module StudyAPI =
                 |> List.toArray
 
             let existsByName name publications =               
-                OntologyAnnotation.existsByName (AnnotationValue.Text name) (publications |> Array.toList)
+                OntologyAnnotation.existsByName name (publications |> Array.toList)
 
             let tryGetByName name publications =
-                OntologyAnnotation.tryGetByName (AnnotationValue.Text name) (publications |> Array.toList)
+                OntologyAnnotation.tryGetByName name (publications |> Array.toList)
 
             let removeByName name publications =
-                OntologyAnnotation.removeByName (AnnotationValue.Text name) (publications |> Array.toList)
+                OntologyAnnotation.removeByName name (publications |> Array.toList)
                 |> List.toArray
 
         /// Updates an existing design in the ARC investigation study with the given design metadata contained in cliArgs.

diff --git a/src/ArcCommander/ArcCommander.fsproj b/src/ArcCommander/ArcCommander.fsproj
@@ -70,12 +70,13 @@
 
   <!--References-->
   <ItemGroup>
-    <PackageReference Update="FSharp.Core" Version="7.0.401" />
-    <PackageReference Include="ARCtrl.NET" Version="1.0.0-beta.2" />
-    <PackageReference Include="Argu" Version="6.1.1" />
+    <PackageReference Update="FSharp.Core" Version="8.0.101" />
+    <PackageReference Include="ARCtrl.NET" Version="1.0.2" />
+    <PackageReference Include="Argu" Version="6.1.4" />
     <PackageReference Include="Fake.IO.FileSystem" Version="6.0.0" />
     <PackageReference Include="Fake.Tools.Git" Version="6.0.0" />
     <PackageReference Include="FSharp.Data" Version="5.0.2" />
+    <PackageReference Include="FsSpreadsheet" Version="5.1.0" />
     <PackageReference Include="IdentityModel.OidcClient" Version="5.2.1" />
     <PackageReference Include="ini-parser-netstandard" Version="2.5.2" />
     <PackageReference Include="Giraffe" Version="6.0.0" />

diff --git a/src/ArcCommander/ArcConfiguration.fs b/src/ArcCommander/ArcConfiguration.fs
@@ -458,7 +458,7 @@ module ARCExtensions =
     type ARC with
 
         member this.Write(arcPath) = 
-            this.GetWriteContracts()
+            this.GetWriteContracts(false)
             |> Array.iter (myWrite arcPath)
 
         static member load(config : ArcConfiguration) = 

diff --git a/tests/ArcCommander.Tests/ArcCommander.Tests.fsproj b/tests/ArcCommander.Tests/ArcCommander.Tests.fsproj
@@ -23,8 +23,7 @@
     <PackageReference Include="Expecto" Version="10.1.0" />
     <PackageReference Include="YoloDev.Expecto.TestSdk" Version="0.*" />
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.*" />
-    <PackageReference Update="FSharp.Core" Version="7.0.401" />
-    <PackageReference Include="Argu" Version="6.1.1" />
+    <PackageReference Update="FSharp.Core" Version="8.0.101" />
     <PackageReference Include="ini-parser-netstandard" Version="2.5.2" />
   </ItemGroup>
   <ItemGroup>

diff --git a/tests/ArcCommander.Tests/StudyTests.fs b/tests/ArcCommander.Tests/StudyTests.fs
@@ -256,11 +256,16 @@ let testStudyContacts =
     let investigationFilePath = System.IO.Path.Combine([|GeneralConfiguration.getWorkDirectory config;investigationFileName|])         
     let studyIdentifier = "BII-S-1"
 
+    let studyToCopy = System.IO.Path.Combine([|source;"TestFiles";"studies"|])
+    let studyFilePath = System.IO.Path.Combine([|GeneralConfiguration.getWorkDirectory config;"studies"|])      
 
 
     setupArc config
+
     //Copy testInvestigation
     System.IO.File.Copy(investigationToCopy,investigationFilePath,true)
+    //Copy testStudy
+    directoryCopy studyToCopy studyFilePath true
 
     let arc = ARC.load(config)
 

diff --git a/tests/ArcCommander.Tests/TestFiles/assays/a_metabolome/isa.assay.xlsx b/tests/ArcCommander.Tests/TestFiles/assays/a_metabolome/isa.assay.xlsx
diff --git a/tests/ArcCommander.Tests/TestFiles/assays/a_proteome/isa.assay.xlsx b/tests/ArcCommander.Tests/TestFiles/assays/a_proteome/isa.assay.xlsx
diff --git a/tests/ArcCommander.Tests/TestFiles/studies/BII-S-1/isa.study.xlsx b/tests/ArcCommander.Tests/TestFiles/studies/BII-S-1/isa.study.xlsx
diff --git a/tests/ArcCommander.Tests/TestFiles/studies/BII-S-2/isa.study.xlsx b/tests/ArcCommander.Tests/TestFiles/studies/BII-S-2/isa.study.xlsx
diff --git a/tests/ArcCommander.Tests/Utils.fs b/tests/ArcCommander.Tests/Utils.fs
@@ -11,6 +11,26 @@ open ArcCommander
 open ArgumentProcessing
 open Argu
 
+let rec directoryCopy srcPath dstPath copySubDirs =
+
+    if not <| System.IO.Directory.Exists(srcPath) then
+        let msg = System.String.Format("Source directory does not exist or could not be found: {0}", srcPath)
+        raise (System.IO.DirectoryNotFoundException(msg))
+
+    if not <| System.IO.Directory.Exists(dstPath) then
+        System.IO.Directory.CreateDirectory(dstPath) |> ignore
+
+    let srcDir = new System.IO.DirectoryInfo(srcPath)
+
+    for file in srcDir.GetFiles() do
+        let temppath = System.IO.Path.Combine(dstPath, file.Name)
+        file.CopyTo(temppath, true) |> ignore
+
+    if copySubDirs then
+        for subdir in srcDir.GetDirectories() do
+            let dstSubDir = System.IO.Path.Combine(dstPath, subdir.Name)
+            directoryCopy subdir.FullName dstSubDir copySubDirs
+
 type ArcInvestigation with
 
     member this.ContainsStudy(studyIdentifier : string) =