Code generation #32
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| Original file line number | Diff line number | Diff line change |
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| namespace OBO.NET.CodeGeneration | ||
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| open OBO.NET | ||
| open FSharpAux | ||
| open type System.Environment | ||
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| module CodeGeneration = | ||
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| [<Literal>] | ||
| let baseString = """namespace ARCTokenization.StructuralOntology | ||
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| open ControlledVocabulary | ||
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| module <name> = | ||
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| """ | ||
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| /// Takes an OboTerm and returns its name but with all spaces replaced by underscores. | ||
| let toUnderscoredName (term : OboTerm) = | ||
| term.Name | ||
| |> String.replace " " "_" | ||
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| /// Returns true if a string contains special characters or starts with a number. | ||
| let checkForSpecialCharacters str = | ||
| let spChs = System.Text.RegularExpressions.Regex(@"(^\d|[^a-zA-Z0-9_])") | ||
| (spChs.Match str).Success | ||
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| /// Takes a string and returns it with back ticks ("``") at the beginning and the end. | ||
| let addBackTicks str = | ||
| $"``{str}``" | ||
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| /// Takes an OboTerm and returns its TermSourceRef as string. | ||
| let toTermSourceRef (term : OboTerm) = | ||
| term.Id | ||
| |> String.takeWhile ((<>) ':') | ||
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| /// Takes an OboTerm and transforms it into an F# code string for structural ontology libraries. | ||
| let toCodeString (term : OboTerm) = | ||
| let underscoredName = toUnderscoredName term | ||
| let curatedName = | ||
| if checkForSpecialCharacters underscoredName then | ||
| addBackTicks underscoredName | ||
| else underscoredName | ||
| $" let {curatedName} = CvTerm.create(\"{term.Id}\", \"{term.Name}\", \"{toTermSourceRef term}\"){NewLine}{NewLine}" | ||
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| /// Takes a module name and an OboOntology and returns the F# code of the whole term list for structural ontology libraries. | ||
| let toSourceCode moduleName (onto : OboOntology) = | ||
| let concattedSingleValues = String.init onto.Terms.Length (fun i -> $"{toCodeString onto.Terms[i]}") | ||
| let updatedBaseString = String.replace "<name>" moduleName baseString | ||
| $"{updatedBaseString}{concattedSingleValues}" | ||
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| /// Takes a module name and an OboOntology and writes the ontology's terms as F# code for structural ontology libraries as a source file at the given path. | ||
| let toFile moduleName (onto : OboOntology) path = | ||
| System.IO.File.WriteAllText(path, toSourceCode moduleName onto) | ||
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| /// Takes a module name and the path to an OBO file and writes the ontology's terms as F# code for structural ontology libraries as a source file at the given output path. | ||
| let fromOboFileToSourceFile moduleName inputPath outputPath = | ||
| OboOntology.fromFile false inputPath | ||
| |> fun o -> toFile moduleName o outputPath |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,36 @@ | ||
| <Project Sdk="Microsoft.NET.Sdk"> | ||
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| <PropertyGroup> | ||
| <TargetFramework>netstandard2.0</TargetFramework> | ||
| <GenerateDocumentationFile>true</GenerateDocumentationFile> | ||
| <!-- Optional: Publish the repository URL in the built .nupkg (in the NuSpec <Repository> element) --> | ||
| <PublishRepositoryUrl>true</PublishRepositoryUrl> | ||
| <!-- Optional: Embed source files that are not tracked by the source control manager in the PDB --> | ||
| <EmbedUntrackedSources>true</EmbedUntrackedSources> | ||
| <!-- Optional: Build symbol package (.snupkg) to distribute the PDB containing Source Link --> | ||
| <IncludeSymbols>true</IncludeSymbols> | ||
| <SymbolPackageFormat>snupkg</SymbolPackageFormat> | ||
| </PropertyGroup> | ||
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| <ItemGroup> | ||
| <ProjectReference Include="..\OBO.NET\OBO.NET.fsproj" /> | ||
| </ItemGroup> | ||
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| <ItemGroup> | ||
| <Compile Include="CodeGeneration.fs" /> | ||
| </ItemGroup> | ||
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| <PropertyGroup> | ||
| <Authors>Oliver Maus, F# open source contributors</Authors> | ||
| <Description>An OBO file format to F# source code generator, written in F#.</Description> | ||
| <Summary>An OBO file format to F# source code generator, written in F#.</Summary> | ||
| <PackageLicenseExpression>MIT</PackageLicenseExpression> | ||
| <PackageProjectUrl>https://github.com/CSBiology/OBO.NET</PackageProjectUrl> | ||
| <PackageTags>ontology fsharp file obo codegeneration code generation</PackageTags> | ||
| <RepositoryUrl>https://github.com/CSBiology/OBO.NET</RepositoryUrl> | ||
| <RepositoryType>git</RepositoryType> | ||
| <FsDocsLicenseLink>https://github.com/CSBiology/OBO.NET/blob/main/LICENSE</FsDocsLicenseLink> | ||
| <FsDocsReleaseNotesLink>https://github.com/CSBiology/OBO.NET/blob/main/RELEASE_NOTES.md</FsDocsReleaseNotesLink> | ||
| </PropertyGroup> | ||
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| </Project> |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,56 @@ | ||
| namespace OBO.NET.CodeGeneration.Tests | ||
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| open Expecto | ||
| open OBO.NET | ||
| open OBO.NET.CodeGeneration | ||
| open FSharpAux | ||
| open ARCTokenization.StructuralOntology | ||
| open ARCTokenization.Terms | ||
| open type System.Environment | ||
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| module CodeGenerationTests = | ||
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| let refObo = OboOntology.fromFile false (System.IO.Path.Combine(__SOURCE_DIRECTORY__, "References/ReferenceOboFile.obo")) | ||
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| let toUnderscoredNameTest = | ||
| testList "toUnderscoredName" [ | ||
| testCase "returns correct underscored name" <| fun _ -> | ||
| let expected = "Investigation_Metadata" | ||
| let actual = List.head refObo.Terms |> CodeGeneration.toUnderscoredName | ||
| Expect.equal actual expected "underscored name is not correct" | ||
| ] | ||
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| let toTermSourceRefTest = | ||
| testList "toTermSourceRef" [ | ||
| testCase "returns correct TermSourceRef" <| fun _ -> | ||
| let expected = "INVMSO" | ||
| let actual = List.head refObo.Terms |> CodeGeneration.toTermSourceRef | ||
| Expect.equal actual expected "TermSourceRef is not correct" | ||
| ] | ||
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| let toCodeStringTest = | ||
| testList "toCodeString" [ | ||
| testCase "returns correct F# code" <| fun _ -> | ||
| let expected = $" let Investigation_Metadata = CvTerm.create(\"INVMSO:00000001\", \"Investigation Metadata\", \"INVMSO\"){NewLine}{NewLine}" | ||
| let actual = List.head refObo.Terms |> CodeGeneration.toCodeString | ||
| Expect.equal actual expected "F# code is not correct" | ||
| ] | ||
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| let toSourceCodeTest = | ||
| testList "toSourceCode" [ | ||
| testCase "returns correct source code" <| fun _ -> | ||
| let expected = | ||
| $"namespace ARCTokenization.StructuralOntology{NewLine}{NewLine} open ControlledVocabulary{NewLine}{NewLine} module Investigation ={NewLine}{NewLine} let Investigation_Metadata = CvTerm.create(\"INVMSO:00000001\", \"Investigation Metadata\", \"INVMSO\"){NewLine}{NewLine} let ONTOLOGY_SOURCE_REFERENCE = CvTerm.create(\"INVMSO:00000002\", \"ONTOLOGY SOURCE REFERENCE\", \"INVMSO\"){NewLine}{NewLine} let Term_Source_Name = CvTerm.create(\"INVMSO:00000003\", \"Term Source Name\", \"INVMSO\")" | ||
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There was a problem hiding this comment. here, i would also just parse a fully correct fsharp source file as reference, and check wether the full output is correct. |
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| |> String.replace "\r" "" | ||
| let actual = | ||
| CodeGeneration.toSourceCode "Investigation" refObo | ||
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There was a problem hiding this comment. There is a There was a problem hiding this comment. Oh lol, didn't know about that! 👍🏻😄 |
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| |> String.splitS NewLine | ||
| |> Array.take 11 | ||
| |> String.concat "\n" | ||
| |> String.replace "\r" "" | ||
| Expect.equal actual expected "Source code is not correct" | ||
| ] | ||
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| [<Tests>] | ||
| let all = testList "CodeGeneration" [toUnderscoredNameTest; toTermSourceRefTest; toCodeStringTest; toSourceCodeTest] | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,7 @@ | ||
| open OBO.NET.CodeGeneration.Tests | ||
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| open Expecto | ||
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| [<EntryPoint>] | ||
| let main argv = Tests.runTestsInAssemblyWithCLIArgs [] argv |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,32 @@ | ||
| <Project Sdk="Microsoft.NET.Sdk"> | ||
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| <PropertyGroup> | ||
| <TargetFramework>net6.0</TargetFramework> | ||
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| <IsPackable>false</IsPackable> | ||
| <GenerateProgramFile>false</GenerateProgramFile> | ||
| <IsTestProject>true</IsTestProject> | ||
| </PropertyGroup> | ||
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| <ItemGroup> | ||
| <None Include="references\ReferenceOboFile.obo" /> | ||
| <Compile Include="References\ReferenceSourceFile.fs" /> | ||
| <Compile Include="CodeGeneration.Tests.fs" /> | ||
| <Compile Include="Main.fs" /> | ||
| </ItemGroup> | ||
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| <ItemGroup /> | ||
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| <ItemGroup> | ||
| <ProjectReference Include="..\..\src\OBO.NET\OBO.NET.fsproj" /> | ||
| <ProjectReference Include="..\..\src\OBO.NET.CodeGeneration\OBO.NET.CodeGeneration.fsproj" /> | ||
| <PackageReference Include="Expecto" Version="10.1.0" /> | ||
| <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.5.0" /> | ||
| <PackageReference Include="MSTest.TestAdapter" Version="2.2.10" /> | ||
| <PackageReference Include="MSTest.TestFramework" Version="2.2.10" /> | ||
| <PackageReference Include="coverlet.collector" Version="3.2.0" /> | ||
| <PackageReference Include="YoloDev.Expecto.TestSdk" Version="0.14.1" /> | ||
| <PackageReference Include="ARCTokenization" Version="6.0.0" /> | ||
| </ItemGroup> | ||
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| </Project> |
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i would not use these ontologies but static files in this repo as references for tests