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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 | ||
open ControlledVocabulary | ||
module <name> = | ||
""" | ||
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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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<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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51
tests/OBO.NET.CodeGeneration.Tests/CodeGeneration.Tests.fs
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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 System.IO | ||
open type System.Environment | ||
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module CodeGenerationTests = | ||
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let refObo = OboOntology.fromFile false (Path.Combine(__SOURCE_DIRECTORY__, "References/ReferenceOboFile.obo")) | ||
let refSF = File.ReadAllText (Path.Combine(__SOURCE_DIRECTORY__, "References/ReferenceSourceFile.fs")) | ||
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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 = refSF.ReplaceLineEndings() | ||
let actual = (CodeGeneration.toSourceCode "Investigation" refObo).ReplaceLineEndings() | ||
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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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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tests/OBO.NET.CodeGeneration.Tests/OBO.NET.CodeGeneration.Tests.fsproj
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<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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