Baseline validation (#93)

* Update to ARCTokenisation 5.0

* add baseline Validation for ARCs

add baseline Validation for ARCs in case no specific validation package is referenced

* Adress the changes requested in #93

- Rename BaselineValidation -> ARCSpecification
- Rename isaLight -> V2_Draft
- Outsource the Expect functions from V2_Draft to the ValidateAPI
- Remove metadata section from ARCSpecification
- Remove the confusing checkForParam function
- Revert unneeded Changes to the arc-validate.fsproj

* Add arc Structure for testing purposes

* Update .gitignore

Add Mac specific DS_Store files

* Add test for ARCSpecification V2_Draft

Add test for ARCSpecification V2_Draft.

* Update ARCSpecification.fs

Fix test path

* Adress changes requested in #93

- Move ARCSpecification into ARCExpect
- Move Tests and relevant test files in respect
- Rename ARCValidate.ARCSpecification. V2_Draft. testCases ->  ARCExpect.ARCSpecification. V2_Draft .validationCases
- Remove internal keyword from V2_Draft modules
- Fixed typos

* Adress changes requested in #93

- Fix Error Message in tests
- Change Usage of Validation Pipeline to its components
- Removed redundant references in fsproj

* Remove redundant code

as seen in #93

.gitignore

@@ -355,3 +355,6 @@ test/arc-validate-results.xml
 !/tests/fixtures/arcs/invenio-test-arc/.gitkeep
 /tmp/watch
 /.fsdocs
+
+# Mac specific files
+**/.DS_Store

src/ARCExpect/ARCExpect.fsproj

@@ -1,10 +1,8 @@
-<Project Sdk="Microsoft.NET.Sdk">
-
+<Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
     <TargetFramework>netstandard2.0</TargetFramework>
     <GenerateDocumentationFile>true</GenerateDocumentationFile>
   </PropertyGroup>
-
   <ItemGroup>
     <None Include="packages.lock.json" />
     <None Include="RELEASE_NOTES.md" />
@@ -23,20 +21,20 @@
     <Compile Include="TopLevelAPI.fs" />
     <Compile Include="Configs\PathConfig.fs" />
     <Compile Include="Configs\ARCConfig.fs" />
+    <Compile Include="ARCSpecification.fs" />
     <Compile Include="TestGeneration\NonCritical\ARCISA.fs" />
     <Compile Include="TestGeneration\Critical\ARCFileSystem.fs" />
     <Compile Include="TestGeneration\Critical\ARCISA.fs" />
   </ItemGroup>
-
   <ItemGroup>
     <PackageReference Include="Expecto" Version="[9.0.4]" />
     <PackageReference Include="FSharpAux" Version="[2.0.0]" />
     <PackageReference Include="FsSpreadsheet" Version="[5.0.2]" />
     <PackageReference Include="FsSpreadsheet.ExcelIO" Version="[5.0.2]" />
-    <PackageReference Include="ARCTokenization" Version="[3.0.0]" />
+    <PackageReference Include="ARCTokenization" Version="[5.0.0]" />
     <PackageReference Include="Graphoscope" Version="[0.6.0-preview.1]" />
     <PackageReference Include="OBO.NET" Version="[0.4.2]" />
     <PackageReference Include="Cytoscape.NET" Version="[0.2.0]" />
     <PackageReference Include="AnyBadge.NET" Version="[2.0.0]" />
   </ItemGroup>
-</Project>
+</Project>

src/arc-validate/APIs/ValidateAPI.fs

@@ -50,6 +50,40 @@ module ValidateAPI =
                 "   - run [green]arc-validate validate -p <your-desired-package-name>[/] to validate agaionst a validation package."
             ]
             |> List.iter AnsiConsole.MarkupLine
+
+            let status = AnsiConsole.Status()
+            let mutable exitCode = ExitCode.Success
+
+            status.Start($"Performing validation against the ARC specification V2_Draft", fun ctx ->
+
+                if verbose then
+
+                    AnsiConsole.MarkupLine("LOG: Running in:")
+                    AnsiConsole.Write(TextPath(Path.GetFullPath(root)))
+                    AnsiConsole.MarkupLine("")
+                    AnsiConsole.MarkupLine($"LOG: running validation against [bold underline green]ARC specification V2_Draft[/].")
+                    AnsiConsole.MarkupLine($"LOG: Output path is:")
+                    AnsiConsole.Write(TextPath(Path.GetFullPath(outPath)))
+                    AnsiConsole.MarkupLine("")
+
+                let cases = ARCSpecification.V2_Draft.validationCases root 
+
+                let outDirBadge = System.IO.Path.Combine(root, "ARC_specification_V2_Draft.svg")
+                let outDirResXml =System.IO.Path.Combine(root, "ARC_specification_V2_Draft.xml")
+
+                let results = ARCExpect.Execute.Validation cases
+
+                results
+                |> Execute.JUnitSummaryCreation(outDirResXml)
+
+                results
+                |> Execute.BadgeCreation(outDirBadge, "ARC specification V2_Draft", "passing", DefaultColor=AnyBadge.NET.Color.GREEN)
+
+                if results.successful then
+                    exitCode <- ExitCode.Success
+                else
+                    exitCode <- ExitCode.CriticalTestFailure
+            )
 
         | Some packageName -> // Validate against a specific package
 

src/arc-validate/arc-validate.fsproj

@@ -1,12 +1,10 @@
-<Project Sdk="Microsoft.NET.Sdk">
-
+<Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
     <OutputType>Exe</OutputType>
     <TargetFramework>net8.0</TargetFramework>
     <!--<PublishSingleFile>true</PublishSingleFile>-->
     <!--<PackAsTool>true</PackAsTool>-->
   </PropertyGroup>
-
   <ItemGroup>
     <None Include="RELEASE_NOTES.md" />
     <Compile Include="BadgeCreation.fs" />
@@ -19,34 +17,30 @@
     <Compile Include="APIs\ValidateAPI.fs" />
     <Compile Include="APIs\ARCValidateAPI.fs" />
     <Compile Include="CommandHandling.fs" />
-    <Compile Include="Program.fs" />    
+    <Compile Include="Program.fs" />
   </ItemGroup>
-
   <ItemGroup>
     <PackageReference Include="Argu" Version="[6.1.4]" />
     <PackageReference Include="Expecto" Version="[9.0.4]" />
     <PackageReference Include="Spectre.Console" Version="0.48.0" />
     <PackageReference Include="Spectre.Console.CLI" Version="0.48.0" />
   </ItemGroup>
-
   <ItemGroup>
     <ProjectReference Include="..\ARCExpect\ARCExpect.fsproj" PackageVersion="[1.0.0, 2.0.0)" />
     <ProjectReference Include="..\ARCValidationPackages\ARCValidationPackages.fsproj" PackageVersion="[1.0.0, 2.0.0)" />
   </ItemGroup>
-
   <Target Name="UseExplicitPackageVersions" BeforeTargets="GenerateNuspec">
     <ItemGroup>
-      <_ProjectReferenceWithExplicitPackageVersion Include="@(ProjectReference->'%(FullPath)')" Condition="'%(ProjectReference.PackageVersion)' != ''" />
-      <_ProjectReferenceWithExactPackageVersion Include="@(ProjectReference->'%(FullPath)')" Condition="'%(ProjectReference.ExactVersion)' == 'true'" />
+      <_ProjectReferenceWithExplicitPackageVersion Include="@(ProjectReference-&gt;'%(FullPath)')" Condition="'%(ProjectReference.PackageVersion)' != ''" />
+      <_ProjectReferenceWithExactPackageVersion Include="@(ProjectReference-&gt;'%(FullPath)')" Condition="'%(ProjectReference.ExactVersion)' == 'true'" />
       <_ProjectReferenceWithReassignedVersion Include="@(_ProjectReferencesWithVersions)" Condition="'%(Identity)' != '' And '@(_ProjectReferenceWithExplicitPackageVersion)' == '@(_ProjectReferencesWithVersions)'">
-        <ProjectVersion>@(_ProjectReferenceWithExplicitPackageVersion->'%(PackageVersion)')</ProjectVersion>
+        <ProjectVersion>@(_ProjectReferenceWithExplicitPackageVersion-&gt;'%(PackageVersion)')</ProjectVersion>
       </_ProjectReferenceWithReassignedVersion>
       <_ProjectReferenceWithReassignedVersion Include="@(_ProjectReferencesWithVersions)" Condition="'%(Identity)' != '' And '@(_ProjectReferenceWithExactPackageVersion)' == '@(_ProjectReferencesWithVersions)'">
-        <ProjectVersion>[@(_ProjectReferencesWithVersions->'%(ProjectVersion)')]</ProjectVersion>
+        <ProjectVersion>@(_ProjectReferenceWithExplicitPackageVersion->'%(PackageVersion)')</ProjectVersion>
       </_ProjectReferenceWithReassignedVersion>
       <_ProjectReferencesWithVersions Remove="@(_ProjectReferenceWithReassignedVersion)" />
       <_ProjectReferencesWithVersions Include="@(_ProjectReferenceWithReassignedVersion)" />
     </ItemGroup>
   </Target>
-
-</Project>
+</Project>

tests/ARCExpect.Tests/ARCExpect.Tests.fsproj

@@ -1,11 +1,9 @@
-<Project Sdk="Microsoft.NET.Sdk">
-
+<Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
     <OutputType>Exe</OutputType>
     <TargetFramework>net8.0</TargetFramework>
     <GenerateProgramFile>false</GenerateProgramFile>
   </PropertyGroup>
-
   <ItemGroup>
     <None Include="fixtures\**" CopyToOutputDirectory="Always" />
     <EmbeddedResource Remove="CLITests\**" />
@@ -19,9 +17,9 @@
     <Compile Include="ParamCollectionTests.fs" />
     <Compile Include="ARCExpectTests.fs" />
     <Compile Include="ARCGraphTests.fs" />
+    <Compile Include="ARCSpecification.fs" />
     <Compile Include="Main.fs" />
   </ItemGroup>
-
   <ItemGroup>
     <PackageReference Include="Expecto" Version="9.*" />
     <PackageReference Include="YoloDev.Expecto.TestSdk" Version="0.*" />
@@ -30,4 +28,4 @@
     <ProjectReference Include="..\..\src\ARCExpect\ARCExpect.fsproj" />
     <ProjectReference Include="..\Common\Common.fsproj" />
   </ItemGroup>
-</Project>
+</Project>

tests/ARCExpect.Tests/ARCGraphTests.fs

@@ -11,6 +11,7 @@ let mockInv =
     let userComment1 = CvParam(Terms.StructuralTerms.userComment, CvValue Terms.StructuralTerms.metadataSectionKey) :> IParam
     let userComment2 = CvParam(Terms.StructuralTerms.userComment, Value "Keywords") :> IParam
     ARCMock.InvestigationMetadataTokens(
+        false,
         Investigation_Identifier = ["ArcPrototype"],
         Investigation_Title = ["ArcPrototype"],
         Investigation_Description = ["A prototypic ARC that implements all specification standards accordingly"],
@@ -35,6 +36,7 @@ let mockInv =
 
 let mockStu =
     ARCMock.StudyMetadataTokens(
+        false,
         Study_Identifier = ["experiment1_material"],
         Study_Title = ["Prototype for experimental data"],
         Study_Description = ["In this a devised study to have an exemplary experimental material description."],
@@ -45,15 +47,16 @@ let mockStu =
 
 let mockAss =
     ARCMock.AssayMetadataTokens(
+        false,
         Assay_File_Name = ["measurement1/isa.assay.xlsx"],
-        Assay_Performer_Last_Name = ["Maus"; "Katz"],
-        Assay_Performer_First_Name = ["Oliver"; "Marius"],
-        Assay_Performer_Mid_Initials = [""; "G."],
-        Assay_Performer_Email = ["maus@nfdi4plants.org"],
-        Assay_Performer_Affiliation = ["RPTU University of Kaiserslautern"],
-        Assay_Performer_Roles = ["research assistant"],
-        Assay_Performer_Roles_Term_Accession_Number = ["http://purl.org/spar/scoro/research-assistant"],
-        Assay_Performer_Roles_Term_Source_REF = ["scoro"]
+        Assay_Person_Last_Name = ["Maus"; "Katz"],
+        Assay_Person_First_Name = ["Oliver"; "Marius"],
+        Assay_Person_Mid_Initials = [""; "G."],
+        Assay_Person_Email = ["maus@nfdi4plants.org"],
+        Assay_Person_Affiliation = ["RPTU University of Kaiserslautern"],
+        Assay_Person_Roles = ["research assistant"],
+        Assay_Person_Roles_Term_Accession_Number = ["http://purl.org/spar/scoro/research-assistant"],
+        Assay_Person_Roles_Term_Source_REF = ["scoro"]
     )
     |> List.concat // use flat list
     |> Seq.map (fun cvp -> cvp :> IParam)

tests/ARCExpect.Tests/ARCSpecification.fs

@@ -0,0 +1,24 @@
+module ARCSpecification
+
+open Expecto
+
+
+[<Tests>]
+let tests =
+    testList "ARCValidationPackage tests" [
+        test "V2_Draft" {
+
+            let testPath: string = @"../../../../fixtures/arcs/testingArc"
+
+            let cases = ARCExpect.ARCSpecification.V2_Draft.validationCases testPath
+
+            let runSummary = ARCExpect.Execute.Validation cases
+
+            //false None (ParseResults<ARCValidate.CLIArguments.ValidateArgs>.Empty)
+            Expect.isTrue
+                runSummary.successful
+                "The validation cases for ARCSpecification.V2_Draft do not validate a structurally correct ARC."
+
+        }
+
+    ]

tests/arc-validate.Tests/arc-validate.Tests.fsproj

@@ -1,11 +1,9 @@
-<Project Sdk="Microsoft.NET.Sdk">
-
+<Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
     <OutputType>Exe</OutputType>
     <TargetFramework>net8.0</TargetFramework>
     <GenerateProgramFile>false</GenerateProgramFile>
   </PropertyGroup>
-
   <ItemGroup>
     <None Include="fixtures\**" CopyToOutputDirectory="Always" />
     <Compile Include="JUnit.fs" />
@@ -16,16 +14,14 @@
     <Compile Include="CLITests/CLITests.fs" />
     <Compile Include="Main.fs" />
   </ItemGroup>
-
   <ItemGroup>
     <PackageReference Include="Expecto" Version="9.*" />
     <PackageReference Include="YoloDev.Expecto.TestSdk" Version="0.*" />
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.*" />
     <PackageReference Update="FSharp.Core" Version="8.*" />
     <PackageReference Include="Fake.Core.Process" Version="6.0.0" />
   </ItemGroup>
-
   <ItemGroup>
     <ProjectReference Include="..\Common\Common.fsproj" />
   </ItemGroup>
-</Project>
+</Project>