update upstream dependencies, add tests for a package with CQCHookEnd…

…point

src/ARCExpect/ARCExpect.fsproj

@@ -34,6 +34,6 @@
     <PackageReference Include="OBO.NET" Version="[0.4.2]" />
     <PackageReference Include="AnyBadge.NET" Version="[2.0.0]" />
     <PackageReference Include="FSharp.SystemTextJson" Version="[1.3.13]" />
-    <PackageReference Include="AVPRIndex" Version="[0.1.1]" />
+    <PackageReference Include="AVPRIndex" Version="[0.1.3]" />
   </ItemGroup>
 </Project>

src/ARCExpect/RELEASE_NOTES.md

@@ -1,3 +1,7 @@
+### 3.0.1 - (Released 2024-04-30)
+
+Update pinned dependencies
+
 ### 3.0.0 - (Released 2024-04-30)
 
 Remove separate `CQCHookEndpoint` because it is now directly contained in package metadata.

src/ARCValidationPackages/ARCValidationPackages.fsproj

@@ -22,8 +22,8 @@
   <ItemGroup>
     <PackageReference Include="Fake.DotNet.Cli" Version="[6.0.0]" />
     <PackageReference Include="FsHttp" Version="[14.5.0]" />
-	<PackageReference Include="AVPRIndex" Version="[0.1.1]" />
-    <PackageReference Include="AVPRClient" Version="[0.0.5]" />
+    <PackageReference Include="AVPRIndex" Version="[0.1.3]" />
+    <PackageReference Include="AVPRClient" Version="[0.0.9]" />
   </ItemGroup>
 
 </Project>

src/ARCValidationPackages/RELEASE_NOTES.md

@@ -1,4 +1,8 @@
-### 4.0.0 - (Released 2024-04-30)
+### 4.0.1 - (Released 2024-04-30)
+
+Update pinned dependencies
+
+### 4.0.0 - (Released 2024-04-30)
 
 Update to AVPRIndex v0.1.1 and AVPRClient v0.0.5
 

tests/ARCValidationPackages.Tests/AVPRAPITests.fs

@@ -13,27 +13,34 @@ let token = get_gh_api_token()
 [<Tests>]
 let ``AVPRAPI tests`` = 
     testList "AVPR API tests" [
-        test "getRepositoryContent returns correct content" {
-            let vp = AVPR.api.GetPackageByNameAndVersion "test" "3.0.0"
-            let script =
-                vp.PackageContent
-                |> Encoding.UTF8.GetString
-            Expect.equal 
-                (script.ReplaceLineEndings())
-                ReferenceObjects.testScriptContentAVPR
-                $"repository content was not correct{System.Environment.NewLine}{script}"
-        }
-        test "getPackageIndex contains test script" {
+        testList "GetPackageByNameAndVersion" [
+            test "test_3_0_0" {
+                let vp = AVPR.api.GetPackageByNameAndVersion "test" "3.0.0"
+                Expect.AVPRClient.validationPackageEqual vp ReferenceObjects.AVPRClientDomain.ValidationPackage.testPackage_3_0_0
+            }
+            test "test_5_0_0 - CQCHookEndpoint addition" {
+                let vp = AVPR.api.GetPackageByNameAndVersion "test" "5.0.0"
+                let script =
+                    vp.PackageContent
+                    |> Encoding.UTF8.GetString
+                Expect.equal 
+                    (script.ReplaceLineEndings("\n"))
+                    ReferenceObjects.testScriptContentAVPR_test_5_0_0
+                    $"repository content was not correct{System.Environment.NewLine}{script}"
+            }
+
+        ]
+        test "GetAllPackages contains a test package" {
             let indexedPackages = AVPR.api.GetAllPackages()
             Expect.isTrue (indexedPackages |> Array.exists (fun package -> package.Name = "test")) "package index did not contain test script"
         }
-        test "getScriptContent returns correct content" {
+        test "downloadPackageScript test_3_0_0" {
             Expect.equal 
                 (
                     AVPR.api.downloadPackageScript( "test", "3.0.0")
-                    |> fun content -> content.ReplaceLineEndings()
+                    |> fun content -> content.ReplaceLineEndings("\n")
                 )
-                ReferenceObjects.testScriptContentAVPR
+                ReferenceObjects.testScriptContentAVPR_test_3_0_0
                 "script content was not correct"
         }
     ]

tests/ARCValidationPackages.Tests/ConfigTests.fs

@@ -12,7 +12,7 @@ open TestUtils
 [<Tests>]
 let ``Config tests`` = 
     testSequenced (
-        testList "Config tests" [
+        testList "Domain Tests.Config tests" [
 
             let testConfig =
                 Config.create(

tests/ARCValidationPackages.Tests/DefaultsTests.fs

@@ -13,7 +13,7 @@ open TestUtils
 [<Tests>]
 let ``Defaults tests`` =
     testSequenced (
-        testList "Defaults tests" [
+        testList "Domain Tests.Defaults tests" [
             test "config folder path is correct" {
                 Expect.equal 
                     (Defaults.CONFIG_FOLDER()) 

tests/ARCValidationPackages.Tests/GitHubAPITests.fs

@@ -37,7 +37,7 @@ let ``GitHubAPI tests`` =
                     response
                     |> fun json -> (json?content).GetString()
                     |> fun content -> Convert.FromBase64String(content)
-                    |> fun bytes -> Encoding.UTF8.GetString(bytes).ReplaceLineEndings()
+                    |> fun bytes -> Encoding.UTF8.GetString(bytes).ReplaceLineEndings("\n")
                 )
                 ReferenceObjects.testScriptContent
                 $"repository content was not correct{System.Environment.NewLine}{response}"
@@ -48,7 +48,7 @@ let ``GitHubAPI tests`` =
         }
         test "getPackageIndex contains test script" {
             let indexedPackages = GitHubAPI.getPackageIndex(?Token = token)
-            Expect.isTrue (indexedPackages |> Array.exists (fun package -> package.RepoPath = "StagingArea/test/[email protected]")) "package index did not contain test script"
+            Expect.isTrue (indexedPackages |> Array.exists (fun package -> package.RepoPath = "./StagingArea/test/[email protected]")) "package index did not contain test script"
         }
         test "getScriptContent terminates" {
             GitHubAPI.downloadPackageScript(
@@ -64,7 +64,7 @@ let ``GitHubAPI tests`` =
                         "StagingArea/test/[email protected]",
                         ?Token = token
                     )
-                    |> fun content -> content.ReplaceLineEndings()
+                    |> fun content -> content.ReplaceLineEndings("\n")
                 )
                 ReferenceObjects.testScriptContent
                 "script content was not correct"

tests/ARCValidationPackages.Tests/PackageCacheTests.fs

@@ -11,7 +11,7 @@ open System.Collections.Generic
 
 [<Tests>]
 let tests =
-    testSequenced (testList "PackageCache tests" [
+    testSequenced (testList "Domain Tests.PackageCache tests" [
 
         test "createFromPackageList"  {
             Expect.packageCacheEqual 

tests/ARCValidationPackages.Tests/ReferenceObjects.fs

@@ -52,9 +52,9 @@ validationCases
 |> Execute.ValidationPipeline(
     basePath = System.Environment.CurrentDirectory,
     packageName = "test"
-)"""                        .ReplaceLineEndings()
+)"""                        .ReplaceLineEndings("\n")
 
-let testScriptContentAVPR = """(*
+let testScriptContentAVPR_test_3_0_0 = """(*
 ---
 Name: test
 MajorVersion: 3
@@ -96,7 +96,53 @@ validationCases
 |> Execute.ValidationPipeline(
     basePath = System.Environment.CurrentDirectory,
     packageName = "test"
-)"""                            .ReplaceLineEndings()
+)"""                                    .ReplaceLineEndings("\n")
+
+let testScriptContentAVPR_test_5_0_0 = "let [<Literal>]PACKAGE_METADATA = \"\"\"(*
+---
+Name: test
+MajorVersion: 5
+MinorVersion: 0
+PatchVersion: 0
+Publish: true
+Summary: this package is here for testing purposes only.
+Description: this package is here for testing purposes only.
+Authors:
+  - FullName: John Doe
+    Email: [email protected]
+    Affiliation: University of Nowhere
+    AffiliationLink: https://nowhere.edu
+  - FullName: Jane Doe
+    Email: [email protected]
+    Affiliation: University of Somewhere
+    AffiliationLink: https://somewhere.edu
+Tags:
+  - Name: validation
+  - Name: my-package
+  - Name: thing
+ReleaseNotes: Use ARCExpect v3
+CQCHookEndpoint: https://avpr.nfdi4plants.org
+---
+*)\"\"\"
+
+printfn \"If you can read this in your console, you successfully executed test package v5.0.0!\" 
+
+#r \"nuget: ARCExpect, 3.0.0\"
+
+open ARCExpect
+open Expecto
+let test_package =
+    Setup.ValidationPackage(
+        metadata = Setup.Metadata(PACKAGE_METADATA),
+        CriticalValidationCases = [
+            test \"yes\" {Expect.equal 1 1 \"yes\"}
+        ]
+    )
+
+test_package
+|> Execute.ValidationPipeline(
+    basePath = System.Environment.CurrentDirectory
+)"                                          .ReplaceLineEndings("\n")
 
 let testValidationPackage1 =
     CachedValidationPackage.create(
@@ -157,4 +203,37 @@ let testScriptPath = "fixtures/testScript.fsx"
 let testScriptArgsPath = "fixtures/testScriptArgs.fsx"
 
 let testScriptPackage = CachedValidationPackage.create("testScript", testDate1, testScriptPath, ValidationPackageMetadata())
-let testScriptArgsPackage = CachedValidationPackage.create("testScriptArgs", testDate1, testScriptArgsPath, ValidationPackageMetadata())
+let testScriptArgsPackage = CachedValidationPackage.create("testScriptArgs", testDate1, testScriptArgsPath, ValidationPackageMetadata())
+
+module AVPRClientDomain =
+    module ValidationPackage =
+        let testPackage_3_0_0 = AVPRClient.ValidationPackage(
+            Name = "test",
+            MajorVersion = 3,
+            MinorVersion = 0,
+            PatchVersion = 0,
+            Summary = "this package is here for testing purposes only.",
+            Description = "this package is here for testing purposes only.",
+            Authors = [|
+                AVPRClient.Author(
+                    FullName = "John Doe",
+                    Email = "[email protected]",
+                    Affiliation = "University of Nowhere",
+                    AffiliationLink = "https://nowhere.edu"
+                )
+                AVPRClient.Author(
+                    FullName = "Jane Doe",
+                    Email = "[email protected]",
+                    Affiliation = "University of Somewhere",
+                    AffiliationLink = "https://somewhere.edu"
+                )
+            |],
+            Tags = [|
+                AVPRClient.OntologyAnnotation(Name = "validation", TermAccessionNumber = "", TermSourceREF = "")
+                AVPRClient.OntologyAnnotation(Name = "my-package", TermAccessionNumber = "", TermSourceREF = "")
+                AVPRClient.OntologyAnnotation(Name = "thing", TermAccessionNumber = "", TermSourceREF = "")
+            |],
+            ReleaseNotes = "add authors and tags for further testing",
+            PackageContent = System.Text.Encoding.UTF8.GetBytes testScriptContentAVPR_test_3_0_0,
+            CQCHookEndpoint = ""
+    )

tests/ARCValidationPackages.Tests/TestUtils.fs

@@ -62,6 +62,39 @@ module Expect =
         Expect.sequenceEqual expectedKeysSorted actualKeysSorted $"Keys were not equal."
         Expect.sequenceEqual zippedValuesActual zippedValuesExpected "Values were not equal."
 
+    module AVPRClient =
+
+        let authorEqual (actual:AVPRClient.Author) (expected:AVPRClient.Author) =
+            Expect.equal actual.FullName expected.FullName "AVPRClient.Author Name not equal"
+            Expect.equal actual.Email expected.Email "AVPRClient.Author Email not equal"
+            Expect.equal actual.Affiliation expected.Affiliation "AVPRClient.Author Affiliation not equal"
+            Expect.equal actual.AffiliationLink expected.AffiliationLink "AVPRClient.Author AffiliationLink not equal"
+
+        let ontologyAnnotationTagEqual (actual:AVPRClient.OntologyAnnotation) (expected:AVPRClient.OntologyAnnotation) =
+            Expect.equal actual.Name expected.Name "AVPRClient.OntologyAnnotation Name not equal"
+            Expect.equal actual.TermAccessionNumber expected.TermAccessionNumber "AVPRClient.OntologyAnnotation TermAccessionNumber not equal"
+            Expect.equal actual.TermSourceREF expected.TermSourceREF "AVPRClient.OntologyAnnotation TermSourceREF not equal"
+
+        let validationPackageEqual (actual: AVPRClient.ValidationPackage) (expected:AVPRClient.ValidationPackage) =
+            Expect.equal actual.Name expected.Name "AVPRClient.ValidationPackage Name not equal"
+            Expect.equal actual.Summary expected.Summary "AVPRClient.ValidationPackage Summary not equal"
+            Expect.equal actual.MajorVersion expected.MajorVersion "AVPRClient.ValidationPackage MajorVersion not equal"
+            Expect.equal actual.MinorVersion expected.MinorVersion "AVPRClient.ValidationPackage MinorVersion not equal"
+            Expect.equal actual.PatchVersion expected.PatchVersion "AVPRClient.ValidationPackage PatchVersion not equal"
+            Expect.equal actual.ReleaseNotes expected.ReleaseNotes "AVPRClient.ValidationPackage ReleaseNotes not equal"
+            Expect.equal actual.CQCHookEndpoint expected.CQCHookEndpoint "AVPRClient.ValidationPackage CQCHookEndpoint not equal"
+
+            Seq.zip actual.Authors expected.Authors 
+            |> Seq.iter (fun (actual, expected) -> authorEqual actual expected)
+
+            Seq.zip actual.Tags expected.Tags
+            |> Seq.iter (fun (actual, expected) -> ontologyAnnotationTagEqual actual expected)
+
+            Expect.sequenceEqual expected.Tags expected.Tags "AVPRClient.ValidationPackage Tags not equal"
+            Expect.sequenceEqual expected.PackageContent expected.PackageContent "AVPRClient.ValidationPackage PackageContent not equal"
+
+
+
 module Result =
 
     let okValue = function

tests/arc-validate.Tests/CLITests/ValidateCommandTests.fs

@@ -141,9 +141,9 @@ let ``ValidateCommand CLI Tests`` =
                         (get_gh_api_token())
                     ) [
                         "Package script exists in avpr cache after running package install test" ,  
-                            fun tool args proc -> Expect.isTrue (File.Exists(Path.Combine(expected_package_cache_folder_path_release, "test@3.0.0.fsx")))  (ErrorMessage.withCLIDiagnostics "package file was not installed at expected location" tool args )
+                            fun tool args proc -> Expect.isTrue (File.Exists(Path.Combine(expected_package_cache_folder_path_release, "test@5.0.0.fsx")))  (ErrorMessage.withCLIDiagnostics "package file was not installed at expected location" tool args )
                         "Package script does not exist in preview cache after running package install test" ,  
-                            fun tool args proc -> Expect.isFalse (File.Exists(Path.Combine(expected_package_cache_folder_path_preview, "test@3.0.0.fsx")))  (ErrorMessage.withCLIDiagnostics "package file was not installed at expected location" tool args )
+                            fun tool args proc -> Expect.isFalse (File.Exists(Path.Combine(expected_package_cache_folder_path_preview, "test@5.0.0.fsx")))  (ErrorMessage.withCLIDiagnostics "package file was not installed at expected location" tool args )
 
                     ]
                 yield! 
@@ -158,7 +158,7 @@ let ``ValidateCommand CLI Tests`` =
                         "Console output does not indicate that package is not installed" , 
                             fun tool args proc -> Expect.isFalse (proc.Result.Output.Contains("Package test not installed. You can run run arc-validate package install ")) (ErrorMessage.withProcessDiagnostics "incorrect console output" proc tool args )
                         "Console Output is correct" ,
-                            fun tool args proc -> Expect.isTrue (proc.Result.Output.Contains("If you can read this in your console, you successfully executed test package v3.0.0!")) (ErrorMessage.withProcessDiagnostics "incorrect console output" proc tool args )
+                            fun tool args proc -> Expect.isTrue (proc.Result.Output.Contains("If you can read this in your console, you successfully executed test package v5.0.0!")) (ErrorMessage.withProcessDiagnostics "incorrect console output" proc tool args )
                         ]
                 ])
         ])