Whitespace tests for Terms and TypeDefs

OBO.NET.sln

@@ -19,6 +19,7 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "project", "project", "{13CB
 		global.json = global.json
 		LICENSE = LICENSE
 		playground.fsx = playground.fsx
+		playgroundInput.fsx = playgroundInput.fsx
 		README.md = README.md
 		RELEASE_NOTES.md = RELEASE_NOTES.md
 	EndProjectSection

build/TestTasks.fs

@@ -6,6 +6,9 @@ open Fake.DotNet
 open ProjectInfo
 open BasicTasks
 
+
+let standardParams = Fake.DotNet.MSBuild.CliArguments.Create ()
+
 let runTests = BuildTask.create "RunTests" [clean; build] {
     testProjects
     |> Seq.iter (fun testProject ->
@@ -15,14 +18,17 @@ let runTests = BuildTask.create "RunTests" [clean; build] {
                     Logger = Some "console;verbosity=detailed"
                     Configuration = DotNet.BuildConfiguration.fromString configuration
                     NoBuild = true
+                    MSBuildParams = {
+                        standardParams with
+                            DisableInternalBinLog = true
+                    }
             }
         ) testProject
     )
 }
 
 // to do: use this once we have actual tests
 let runTestsWithCodeCov = BuildTask.create "RunTestsWithCodeCov" [clean; build] {
-    let standardParams = Fake.DotNet.MSBuild.CliArguments.Create ()
     testProjects
     |> Seq.iter(fun testProject -> 
         Fake.DotNet.DotNet.test(fun testParams ->
@@ -35,6 +41,7 @@ let runTestsWithCodeCov = BuildTask.create "RunTestsWithCodeCov" [clean; build]
                                 "AltCoverCobertura","../../codeCov.xml"
                                 "AltCoverForce","true"
                             ]
+                            DisableInternalBinLog = true
                     };
                     Logger = Some "console;verbosity=detailed"
             }

playgroundInput.fsx

@@ -0,0 +1,21 @@
+#I "src/OBO.NET/bin/Debug/netstandard2.0"
+#I "src/OBO.NET/bin/Release/netstandard2.0"
+#I "src/OBO.NET.CodeGeneration/bin/Debug/netstandard2.0"
+#I "src/OBO.NET.CodeGeneration/bin/Release/netstandard2.0"
+
+#r "OBO.NET.dll"
+//#r "OBO.NET.CodeGeneration.dll"
+
+#r "nuget: ARCtrl.Core"
+#r "nuget: FSharpAux"
+
+open OBO.NET
+open OBO.NET.DBXref
+open ARCtrl
+open FSharpAux
+//open OBO.NET.CodeGeneration
+
+
+let res = OboOntology.fromFile true @"C:\Repos\CSBiology\OBO.NET\tests\OBO.NET.Tests\References\WhitespaceAfterTerm.obo"
+
+let res2 = OboOntology.fromFile true @"C:\Repos\CSBiology\OBO.NET\tests\OBO.NET.Tests\References\WhitespaceAfterTypeDef.obo"

tests/OBO.NET.Tests/OBO.NET.Tests.fsproj

@@ -9,6 +9,8 @@
   </PropertyGroup>
 
   <ItemGroup>
+    <None Include="References\WhitespaceAfterTypeDef.obo" />
+    <None Include="References\WhitespaceAfterTerm.obo" />
     <None Include="References\IncorrectHeaderTags.obo" />
     <None Include="References\DuplicateHeaderTags.obo" />
     <None Include="references\CorrectHeaderTags.obo" />

tests/OBO.NET.Tests/OboOntology.Tests.fs

@@ -54,15 +54,21 @@ module OboOntologyTests =
             let testFile1Path = Path.Combine(__SOURCE_DIRECTORY__, "References", "CorrectHeaderTags.obo")
             let testFile2Path = Path.Combine(__SOURCE_DIRECTORY__, "References", "IncorrectHeaderTags.obo")
             let testFile3Path = Path.Combine(__SOURCE_DIRECTORY__, "References", "DuplicateHeaderTags.obo")
+            let testFile4Path = Path.Combine(__SOURCE_DIRECTORY__, "References", "WhitespaceAfterTerm.obo")
+            let testFile5Path = Path.Combine(__SOURCE_DIRECTORY__, "References", "WhitespaceAfterTypeDef.obo")
             let testFile1 = try OboOntology.fromFile false testFile1Path |> Some with _ -> None
             let testFile2 = try OboOntology.fromFile false testFile2Path |> Some with _ -> None
             let testFile3 = try OboOntology.fromFile false testFile3Path |> Some with _ -> None
+            let testFile4 = try OboOntology.fromFile false testFile4Path |> Some with _ -> None
+            let testFile5 = try OboOntology.fromFile false testFile5Path |> Some with _ -> None
 
             testList "fromFile" [
                 testCase "can read files" <| fun _ ->
                     Expect.isSome testFile1 $"Could not read testFile1: {testFile1Path}"
                     Expect.isSome testFile2 $"Could not read testFile2: {testFile2Path}"
                     Expect.isSome testFile3 $"Could not read testFile3: {testFile3Path}"
+                    Expect.isSome testFile4 $"Could not read testFile4: {testFile4Path}"
+                    Expect.isSome testFile5 $"Could not read testFile5: {testFile5Path}"
                 testCase "reads correct headers correctly" <| fun _ ->
                     let formatVersionActual                                 = Option.map (fun o -> o.FormatVersion)                                 testFile1
                     let dataVersionActual                                   = Option.map (fun o -> o.DataVersion)                                   testFile1 |> Option.flatten
@@ -129,6 +135,10 @@ module OboOntologyTests =
                 testCase "reads Typedefs correctly" <| fun _ ->
                     let typedefsExpected = List.init 2 (fun i -> OboTypeDef.Create($"Test:000{i + 3}", "", "")) |> Some
                     Expect.equal (Option.map (fun o -> o.TypeDefs) testFile1) typedefsExpected "Terms did not match"
+                testCase "reads Terms with whitespace correctly" <| fun _ ->
+                    Expect.equal testFile4.Value.Terms.Length 4 "Number of terms did not match"
+                testCase "reads TypeDefs with whitespace correctly" <| fun _ ->
+                    Expect.equal testFile5.Value.TypeDefs.Length 4 "Number of typedefs did not match"
             ]
 
             let testOntology = OboOntology.Create([testTerm1; testTerm2; testTerm3; testTerm4; testTerm5], [], "", TreatXrefsAsEquivalents = ["check"])

tests/OBO.NET.Tests/References/WhitespaceAfterTerm.obo

@@ -0,0 +1,43 @@
+format-version: 0.0.1
+data-version: 0.0.1
+ontology: CL
+date: 01:01:1970 00:00
+saved-by: Oliver Maus
+auto-generated-by: TalkGPT
+subsetdef: GO_SLIM "GO Slim"
+subsetdef: GO_BASIC "GO Basic"
+import: http://purl.obolibrary.org/obo/go.owl
+import: http://purl.obolibrary.org/obo/cl.owl
+synonymtypedef: UK_SPELLING "British spelling" EXACT
+synonymtypedef: US_SPELLING "American spelling" EXACT
+idspace: GO urn:lsid:bioontology.org:GO: "gene ontology terms"
+idspace: GO urn:lsid:bioontology.org:GO: "gene ontology types"
+default-relationship-id-prefix: OBO_REL
+id-mapping: part_of OBO_REL:part_of
+id-mapping: has_a OBO_REL:has_a
+remark: test1
+remark: test2
+treat-xrefs-as-equivalent: CL 
+treat-xrefs-as-equivalent: GO 
+treat-xrefs-as-genus-differentia: CL part_of NCBITaxon:7955 
+treat-xrefs-as-genus-differentia: CL part_of NCBITaxon:7956 
+treat-xrefs-as-relationship: MA homologous_to
+treat-xrefs-as-relationship: MA analogous_to
+treat-xrefs-as-is_a: CL 
+treat-xrefs-as-is_a: GO 
+relax-unique-identifier-assumption-for-namespace: my_combined_ontology 
+relax-unique-identifier-assumption-for-namespace: my_combined_ontology2
+relax-unique-label-assumption-for-namespace: my_combined_ontology 
+relax-unique-label-assumption-for-namespace: my_combined_ontology2
+
+[Term] 
+id: Test:0001
+
+[Term]     
+id: Test:0002
+
+[Term]	
+id: Test:0003
+
+[Term]
+id: Test:0004

tests/OBO.NET.Tests/References/WhitespaceAfterTypeDef.obo

@@ -0,0 +1,43 @@
+format-version: 0.0.1
+data-version: 0.0.1
+ontology: CL
+date: 01:01:1970 00:00
+saved-by: Oliver Maus
+auto-generated-by: TalkGPT
+subsetdef: GO_SLIM "GO Slim"
+subsetdef: GO_BASIC "GO Basic"
+import: http://purl.obolibrary.org/obo/go.owl
+import: http://purl.obolibrary.org/obo/cl.owl
+synonymtypedef: UK_SPELLING "British spelling" EXACT
+synonymtypedef: US_SPELLING "American spelling" EXACT
+idspace: GO urn:lsid:bioontology.org:GO: "gene ontology terms"
+idspace: GO urn:lsid:bioontology.org:GO: "gene ontology types"
+default-relationship-id-prefix: OBO_REL
+id-mapping: part_of OBO_REL:part_of
+id-mapping: has_a OBO_REL:has_a
+remark: test1
+remark: test2
+treat-xrefs-as-equivalent: CL 
+treat-xrefs-as-equivalent: GO 
+treat-xrefs-as-genus-differentia: CL part_of NCBITaxon:7955 
+treat-xrefs-as-genus-differentia: CL part_of NCBITaxon:7956 
+treat-xrefs-as-relationship: MA homologous_to
+treat-xrefs-as-relationship: MA analogous_to
+treat-xrefs-as-is_a: CL 
+treat-xrefs-as-is_a: GO 
+relax-unique-identifier-assumption-for-namespace: my_combined_ontology 
+relax-unique-identifier-assumption-for-namespace: my_combined_ontology2
+relax-unique-label-assumption-for-namespace: my_combined_ontology 
+relax-unique-label-assumption-for-namespace: my_combined_ontology2
+
+[Typedef] 
+id: Test:0001
+
+[Typedef]     
+id: Test:0002
+
+[Typedef]	
+id: Test:0003
+
+[Typedef]
+id: Test:0004