Merge pull request #3 from nfdi4plants/tests-Invenio-#1

Add integration tests for testing Invenio package
nfdi4plants · Oct 17, 2024 · 231b5f0 · 231b5f0
2 parents bc949a1 + 364221f
commit 231b5f0
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diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -17,10 +17,18 @@ on:
       - '.github/**'
 
 jobs:
-  build-and-test:
-    name: "Build and test"
-    uses: nfdi4plants/actions-workflows/.github/workflows/build-and-test-solution.yml@main
-    with:
-      solution: ./arc-validation-packages.sln
-      checkout-submodules: true
-      configuration: Release
+  build-and-test-linux:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with: 
+        submodules: true
+    - name: Setup .NET
+      uses: actions/setup-dotnet@v4
+      with:
+        dotnet-version: 8.x.x
+    - name: Run integration test
+      working-directory: ./
+      run: dotnet test -v:normal
diff --git a/arc-validation-packages.sln b/arc-validation-packages.sln
@@ -1,39 +1,41 @@
-
-Microsoft Visual Studio Solution File, Format Version 12.00
-# Visual Studio Version 17
-VisualStudioVersion = 17.0.31903.59
-MinimumVisualStudioVersion = 10.0.40219.1
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ValidationPackages.Tests", "tests\ValidationPackages.Tests.fsproj", "{D9970D1D-9603-4C7A-9252-6A56CBE21062}"
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "sln", "sln", "{55422101-E1FF-4846-B42C-445298D60D5C}"
-	ProjectSection(SolutionItems) = preProject
-		.gitignore = .gitignore
-		global.json = global.json
-		LICENSE = LICENSE
-		README.md = README.md
-	EndProjectSection
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = ".ci", ".ci", "{8CF8F7A6-E0A5-4B72-8FEF-52084354A4CF}"
-	ProjectSection(SolutionItems) = preProject
-		.github\workflows\manage-issues.yml = .github\workflows\manage-issues.yml
-		.github\workflows\run-tests.yml = .github\workflows\run-tests.yml
-	EndProjectSection
-EndProject
-Global
-	GlobalSection(SolutionConfigurationPlatforms) = preSolution
-		Debug|Any CPU = Debug|Any CPU
-		Release|Any CPU = Release|Any CPU
-	EndGlobalSection
-	GlobalSection(ProjectConfigurationPlatforms) = postSolution
-		{D9970D1D-9603-4C7A-9252-6A56CBE21062}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
-		{D9970D1D-9603-4C7A-9252-6A56CBE21062}.Debug|Any CPU.Build.0 = Debug|Any CPU
-		{D9970D1D-9603-4C7A-9252-6A56CBE21062}.Release|Any CPU.ActiveCfg = Release|Any CPU
-		{D9970D1D-9603-4C7A-9252-6A56CBE21062}.Release|Any CPU.Build.0 = Release|Any CPU
-	EndGlobalSection
-	GlobalSection(SolutionProperties) = preSolution
-		HideSolutionNode = FALSE
-	EndGlobalSection
-	GlobalSection(ExtensibilityGlobals) = postSolution
-		SolutionGuid = {761E9831-7AB0-48D9-B549-413DD7A390FF}
-	EndGlobalSection
-EndGlobal
+
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio Version 17
+VisualStudioVersion = 17.0.31903.59
+MinimumVisualStudioVersion = 10.0.40219.1
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ValidationPackages.Tests", "tests\ValidationPackages.Tests.fsproj", "{D9970D1D-9603-4C7A-9252-6A56CBE21062}"
+EndProject
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "sln", "sln", "{55422101-E1FF-4846-B42C-445298D60D5C}"
+	ProjectSection(SolutionItems) = preProject
+		.gitignore = .gitignore
+		global.json = global.json
+		integrationTests_script.fsx = integrationTests_script.fsx
+		LICENSE = LICENSE
+		playground.fsx = playground.fsx
+		README.md = README.md
+	EndProjectSection
+EndProject
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = ".ci", ".ci", "{8CF8F7A6-E0A5-4B72-8FEF-52084354A4CF}"
+	ProjectSection(SolutionItems) = preProject
+		.github\workflows\manage-issues.yml = .github\workflows\manage-issues.yml
+		.github\workflows\run-tests.yml = .github\workflows\run-tests.yml
+	EndProjectSection
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Any CPU = Debug|Any CPU
+		Release|Any CPU = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{D9970D1D-9603-4C7A-9252-6A56CBE21062}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{D9970D1D-9603-4C7A-9252-6A56CBE21062}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{D9970D1D-9603-4C7A-9252-6A56CBE21062}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{D9970D1D-9603-4C7A-9252-6A56CBE21062}.Release|Any CPU.Build.0 = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+	GlobalSection(ExtensibilityGlobals) = postSolution
+		SolutionGuid = {761E9831-7AB0-48D9-B549-413DD7A390FF}
+	EndGlobalSection
+EndGlobal
diff --git a/integrationTests_script.fsx b/integrationTests_script.fsx
@@ -0,0 +1,93 @@
+#r "nuget: Xunit"
+#r "nuget: Fake.DotNet.Cli"
+
+
+open Xunit
+open Fake.Core
+
+open System.Xml
+
+
+let runTool (tool: string) (args: string []) (dir:string) =
+    CreateProcess.fromRawCommand tool args
+    |> CreateProcess.withWorkingDirectory dir
+    |> CreateProcess.redirectOutput
+    |> Proc.run
+
+
+//let result = runTool "dotnet" [|"fsi"; @"C:\Repos\nfdi4plants\arc-validation-packages\validation_packages\invenio\[email protected]"|] @"C:\Repos\nfdi4plants\arc-validation-packages\tests\fixtures\testARC_empty\"
+let result = runTool "dotnet" [|"fsi"; @"C:\Repos\nfdi4plants\arc-validation-packages\validation_packages\invenio\[email protected]"|] @"C:\Repos\nfdi4plants\arc-validation-packages\tests\fixtures\testARC_emptyContactsColumn\"
+
+
+type JUnitResults = {
+    PassedTests: string list
+    FailedTests: string list
+    ErroredTests: string list
+} with
+    static member fromJUnitFile (path:string) =
+        let doc = new XmlDocument()
+        doc.Load(path)
+        let suite = doc.SelectNodes("/testsuites/testsuite[@name='arc-validate']").Item(0);
+        let testCases = suite.SelectNodes("testcase") |> Seq.cast<XmlNode>
+        {
+            PassedTests =
+                testCases
+                |> Seq.filter (fun tc -> tc.SelectNodes("failure").Count = 0)
+                |> Seq.map (fun tc -> tc.Attributes.["name"].Value)
+                |> Seq.toList
+                |> List.sort
+
+            FailedTests =
+                testCases
+                |> Seq.filter (fun tc -> tc.SelectNodes("failure").Count > 0)
+                |> Seq.map (fun tc -> tc.Attributes.["name"].Value)
+                |> Seq.toList
+                |> List.sort
+
+            ErroredTests =
+                testCases
+                |> Seq.filter (fun tc -> tc.SelectNodes("error").Count > 0)
+                |> Seq.map (fun tc -> tc.Attributes.["name"].Value)
+                |> Seq.toList
+                |> List.sort
+        }
+
+    static member getTotalTestCount (res : JUnitResults) =
+        res.ErroredTests.Length + res.FailedTests.Length + res.PassedTests.Length
+
+
+let jUnitRes = JUnitResults.fromJUnitFile @"C:\Repos\nfdi4plants\arc-validation-packages\tests\fixtures\ArcPrototype\.arc-validate-results\[email protected]\validation_report.xml"
+
+null = null
+
+let doc = new XmlDocument()
+doc.Load(@"C:\Repos\nfdi4plants\arc-validation-packages\tests\fixtures\ArcPrototype\.arc-validate-results\[email protected]\validation_report.xml")
+let suite = 
+    doc.SelectNodes("/testsuites/testsuite[@name='arc-validate']").Item(0) 
+    |> fun r -> 
+        if isNull r then
+            doc.SelectNodes("/testsuites/testsuite[@name='fsi']").Item(0)
+        else r
+let testCases = suite.SelectNodes("testcase") |> Seq.cast<XmlNode>
+{
+    PassedTests =
+        testCases
+        |> Seq.filter (fun tc -> tc.SelectNodes("failure").Count = 0)
+        |> Seq.map (fun tc -> tc.Attributes.["name"].Value)
+        |> Seq.toList
+        |> List.sort
+
+    FailedTests =
+        testCases
+        |> Seq.filter (fun tc -> tc.SelectNodes("failure").Count > 0)
+        |> Seq.map (fun tc -> tc.Attributes.["name"].Value)
+        |> Seq.toList
+        |> List.sort
+
+    ErroredTests =
+        testCases
+        |> Seq.filter (fun tc -> tc.SelectNodes("error").Count > 0)
+        |> Seq.map (fun tc -> tc.Attributes.["name"].Value)
+        |> Seq.toList
+        |> List.sort
+}
diff --git a/playground.fsx b/playground.fsx
@@ -0,0 +1,147 @@
+let [<Literal>]PACKAGE_METADATA = """(*
+---
+Name: invenio
+Summary: Validates if the ARC contains the necessary metadata to be publishable via Invenio.
+Description: |
+  Validates if the ARC contains the necessary metadata to be publishable via Invenio.
+  The following metadata is required:
+  - Investigation has title and description
+  - All persons in Investigation Contacts must have a name, last name, affiliation and valid email
+MajorVersion: 3
+MinorVersion: 0
+PatchVersion: 0
+Publish: true
+Authors:
+  - FullName: Oliver Maus
+    Affiliation: DataPLANT
+  - FullName: Christopher Lux
+    Email: [email protected]
+    Affiliation: RPTU Kaiserslautern
+    AffiliationLink: http://rptu.de/startseite
+  - FullName: Lukas Weil
+    Email: [email protected]
+    Affiliation: DataPLANT
+Tags:
+  - Name: ARC
+  - Name: data publication
+ReleaseNotes: |
+  - Fix package passing validation against Investigation file containing only section keys
+---
+*)"""
+
+#r "nuget: ARCExpect, 4.0.1"
+
+open ControlledVocabulary
+open Expecto
+open ARCExpect
+open ARCTokenization
+open ARCTokenization.StructuralOntology
+open System.IO
+
+// Input:
+//let arcDir = Directory.GetCurrentDirectory()
+let arcDir = @"C:\Repos\nfdi4plants\arc-validation-packages\tests\fixtures\ArcPrototype\"
+
+// Values:
+let absoluteDirectoryPaths = FileSystem.parseARCFileSystem arcDir
+
+let investigationMetadata = 
+    absoluteDirectoryPaths
+    |> Investigation.parseMetadataSheetsFromTokens() arcDir 
+    |> List.concat 
+
+#r "nuget: Xunit"
+open Xunit
+
+investigationMetadata 
+|> List.exists (
+    fun ip -> 
+        Param.getCvAccession ip = "INVMSO:00000009" && 
+        Param.getValueAsString ip |> String.isNullOrWhiteSpace |> not && 
+        match Param.getParamValue ip with | CvValue x -> x.Accession = "AGMO:00000001" | _ -> false
+)
+investigationMetadata |> List.filter (fun ip -> Param.getValueAsString ip |> String.isNullOrWhiteSpace |> not && Param.getCvAccession ip = "INVMSO:00000009")
+
+
+
+let expectedTitleCvPExists =
+    investigationMetadata 
+    |> List.exists (
+        fun ip -> 
+            Param.getCvAccession ip = "INVMSO:00000009" && 
+            Param.getValueAsString ip |> String.isNullOrWhiteSpace |> not && 
+            match Param.getParamValue ip with | CvValue x -> x.Accession = "AGMO:00000001" | _ -> false
+    )
+
+Assert.True expectedTitleCvPExists
+
+
+// Validation Cases:
+let cases = 
+    testList INVMSO.``Investigation Metadata``.INVESTIGATION.key.Name [
+        // Investigation has title
+        ARCExpect.validationCase (TestID.Name INVMSO.``Investigation Metadata``.INVESTIGATION.``Investigation Title``.Name) {
+            investigationMetadata
+            |> Validate.ParamCollection.ContainsNonKeyParamWithTerm
+                INVMSO.``Investigation Metadata``.INVESTIGATION.``Investigation Title``
+        }
+        // Investigation has description
+        ARCExpect.validationCase (TestID.Name INVMSO.``Investigation Metadata``.INVESTIGATION.``Investigation Description``.Name) {
+            investigationMetadata
+            |> Validate.ParamCollection.ContainsNonKeyParamWithTerm
+                INVMSO.``Investigation Metadata``.INVESTIGATION.``Investigation Description``
+        }
+        // Investigation has contacts with name, last name, affiliation and email
+        // Investigation Person First Name
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person First Name``.Name} exists") {
+            investigationMetadata
+            |> Validate.ParamCollection.ContainsNonKeyParamWithTerm INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person First Name``
+        }
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person First Name``.Name} is not empty") {
+            investigationMetadata
+            |> Seq.filter (Param.getTerm >> (=) INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person First Name``)
+            |> Seq.iter Validate.Param.ValueIsNotEmpty
+        }
+        // Investigation Person Last Name
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Last Name``.Name} exists") {
+            investigationMetadata
+            |> Validate.ParamCollection.ContainsNonKeyParamWithTerm INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Last Name``
+        }
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Last Name``.Name} is not empty") {
+            investigationMetadata
+            |> Seq.filter (Param.getTerm >> (=) INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Last Name``)
+            |> Seq.iter Validate.Param.ValueIsNotEmpty
+        }
+        // Investigation Person Affiliation
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Affiliation``.Name} exists") {
+            investigationMetadata
+            |> Validate.ParamCollection.ContainsNonKeyParamWithTerm INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Affiliation``
+        }
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Affiliation``.Name} is not empty") {
+            investigationMetadata
+            |> Seq.filter (Param.getTerm >> (=) INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Affiliation``)
+            |> Seq.filter (Param.getValueAsString >> (<>) "Metadata Section Key")
+            |> Seq.iter Validate.Param.ValueIsNotEmpty
+        }
+        // Investigation Person Email
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Email``.Name} exists") {
+        investigationMetadata
+        |> Validate.ParamCollection.ContainsNonKeyParamWithTerm INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Email``
+        }
+        ARCExpect.validationCase (TestID.Name INVMSO.``Investigation Metadata``. ``INVESTIGATION CONTACTS``.``Investigation Person Email``.Name) {
+            investigationMetadata
+            |> Seq.filter (Param.getTerm >> (=) INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Email``)
+            |> Seq.filter (Param.getValueAsString >> (<>) "Metadata Section Key")
+            |> Seq.iter (Validate.Param.ValueMatchesRegex StringValidationPattern.email)
+        }
+    ]
+
+// Execution:
+
+Setup.ValidationPackage(
+    metadata = Setup.Metadata(PACKAGE_METADATA),
+    CriticalValidationCases = [cases]
+)
+|> Execute.ValidationPipeline(
+    basePath = arcDir
+)
diff --git a/tests/GitSubmodulesTests.fs b/tests/GitSubmodulesTests.fs
@@ -3,10 +3,11 @@
 open System
 open System.IO
 open Xunit
+open ValidationPackages.Tests
 
 [<Fact>]
 let ``ArcPrototype commit hash is correct`` () = 
     Assert.Equal(
-        ReferenceObjects.expected_prototype_commit_hash, 
+        ReferenceObjects.General.expected_prototype_commit_hash, 
         TestObjects.prototypeCommitHash
     )