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| Original file line number | Diff line number | Diff line change |
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| @@ -1,106 +1,107 @@ | ||
|  | ||
| Microsoft Visual Studio Solution File, Format Version 12.00 | ||
| # Visual Studio Version 17 | ||
| VisualStudioVersion = 17.0.31903.59 | ||
| MinimumVisualStudioVersion = 10.0.40219.1 | ||
| Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tests", "tests", "{2EB71559-9BE4-4E02-9763-9092876D1E4A}" | ||
| EndProject | ||
| Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "sln", "sln", "{CE1B84FD-33DE-48E4-A97A-A4BDC34E08F0}" | ||
| ProjectSection(SolutionItems) = preProject | ||
| .gitignore = .gitignore | ||
| .github\workflows\build-and-test.yml = .github\workflows\build-and-test.yml | ||
| build.cmd = build.cmd | ||
| build.sh = build.sh | ||
| global.json = global.json | ||
| codeGenTestScript.fsx = codeGenTestScript.fsx | ||
| LICENSE = LICENSE | ||
| package.json = package.json | ||
| playground.fsx = playground.fsx | ||
| .github\workflows\publish-docs.yml = .github\workflows\publish-docs.yml | ||
| README.md = README.md | ||
| RELEASE_NOTES.md = RELEASE_NOTES.md | ||
| EndProjectSection | ||
| EndProject | ||
| Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "src", "src", "{67DA0DCC-75F4-4F30-91C3-309A48B13D49}" | ||
| EndProject | ||
| Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ControlledVocabulary", "src\ControlledVocabulary\ControlledVocabulary.fsproj", "{F8E5EFC0-C74B-4C3C-BC22-7A5286A31DF6}" | ||
| EndProject | ||
| Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ControlledVocabulary.Tests", "tests\ControlledVocabulary.Tests\ControlledVocabulary.Tests.fsproj", "{2CBEE59D-07E4-460E-8B97-9267965D3F46}" | ||
| EndProject | ||
| Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "build", "build", "{3DB2A5F4-23F6-4A06-9AE5-CEAC0707735B}" | ||
| ProjectSection(SolutionItems) = preProject | ||
| build.cmd = build.cmd | ||
| build.sh = build.sh | ||
| global.json = global.json | ||
| EndProjectSection | ||
| EndProject | ||
| Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "Build", "build\Build.fsproj", "{ED24D0E3-BA79-4F6D-9A30-D05FF4EBAFDB}" | ||
| EndProject | ||
| Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCTokenization", "src\ARCTokenization\ARCTokenization.fsproj", "{24D99DC2-DF18-45A3-B444-B60351F131DB}" | ||
| EndProject | ||
| Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCTokenization.Tests", "tests\ARCTokenization.Tests\ARCTokenization.Tests.fsproj", "{30177EF1-3980-4FFE-9B49-90B75DCEBDA3}" | ||
| EndProject | ||
| Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "docs", "docs", "{551D4715-5ECD-4CAB-8A4A-41E246F4A7B5}" | ||
| ProjectSection(SolutionItems) = preProject | ||
| docs\index.ipynb = docs\index.ipynb | ||
| EndProjectSection | ||
| EndProject | ||
| Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ARCTokenization", "ARCTokenization", "{699C5B9A-EA4B-4D25-B05D-16CA14320CFB}" | ||
| ProjectSection(SolutionItems) = preProject | ||
| docs\ARCTokenization\Introduction.ipynb = docs\ARCTokenization\Introduction.ipynb | ||
| EndProjectSection | ||
| EndProject | ||
| Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ControlledVocabulary", "ControlledVocabulary", "{524F5156-C079-4AEF-822E-F01DAE6874AA}" | ||
| ProjectSection(SolutionItems) = preProject | ||
| docs\ControlledVocabulary\CvParam.ipynb = docs\ControlledVocabulary\CvParam.ipynb | ||
| docs\ControlledVocabulary\Introduction.ipynb = docs\ControlledVocabulary\Introduction.ipynb | ||
| EndProjectSection | ||
| EndProject | ||
| Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = ".ci", ".ci", "{4805A6D8-8D85-48F5-8902-57CECF872AE6}" | ||
| ProjectSection(SolutionItems) = preProject | ||
| .github\workflows\build-and-test.yml = .github\workflows\build-and-test.yml | ||
| .github\workflows\publish-docs.yml = .github\workflows\publish-docs.yml | ||
| EndProjectSection | ||
| EndProject | ||
| Global | ||
| GlobalSection(SolutionConfigurationPlatforms) = preSolution | ||
| Debug|Any CPU = Debug|Any CPU | ||
| Release|Any CPU = Release|Any CPU | ||
| EndGlobalSection | ||
| GlobalSection(ProjectConfigurationPlatforms) = postSolution | ||
| {F8E5EFC0-C74B-4C3C-BC22-7A5286A31DF6}.Debug|Any CPU.ActiveCfg = Debug|Any CPU | ||
| {F8E5EFC0-C74B-4C3C-BC22-7A5286A31DF6}.Debug|Any CPU.Build.0 = Debug|Any CPU | ||
| {F8E5EFC0-C74B-4C3C-BC22-7A5286A31DF6}.Release|Any CPU.ActiveCfg = Release|Any CPU | ||
| {F8E5EFC0-C74B-4C3C-BC22-7A5286A31DF6}.Release|Any CPU.Build.0 = Release|Any CPU | ||
| {2CBEE59D-07E4-460E-8B97-9267965D3F46}.Debug|Any CPU.ActiveCfg = Debug|Any CPU | ||
| {2CBEE59D-07E4-460E-8B97-9267965D3F46}.Debug|Any CPU.Build.0 = Debug|Any CPU | ||
| {2CBEE59D-07E4-460E-8B97-9267965D3F46}.Release|Any CPU.ActiveCfg = Release|Any CPU | ||
| {2CBEE59D-07E4-460E-8B97-9267965D3F46}.Release|Any CPU.Build.0 = Release|Any CPU | ||
| {ED24D0E3-BA79-4F6D-9A30-D05FF4EBAFDB}.Debug|Any CPU.ActiveCfg = Debug|Any CPU | ||
| {ED24D0E3-BA79-4F6D-9A30-D05FF4EBAFDB}.Debug|Any CPU.Build.0 = Debug|Any CPU | ||
| {ED24D0E3-BA79-4F6D-9A30-D05FF4EBAFDB}.Release|Any CPU.ActiveCfg = Release|Any CPU | ||
| {ED24D0E3-BA79-4F6D-9A30-D05FF4EBAFDB}.Release|Any CPU.Build.0 = Release|Any CPU | ||
| {24D99DC2-DF18-45A3-B444-B60351F131DB}.Debug|Any CPU.ActiveCfg = Debug|Any CPU | ||
| {24D99DC2-DF18-45A3-B444-B60351F131DB}.Debug|Any CPU.Build.0 = Debug|Any CPU | ||
| {24D99DC2-DF18-45A3-B444-B60351F131DB}.Release|Any CPU.ActiveCfg = Release|Any CPU | ||
| {24D99DC2-DF18-45A3-B444-B60351F131DB}.Release|Any CPU.Build.0 = Release|Any CPU | ||
| {30177EF1-3980-4FFE-9B49-90B75DCEBDA3}.Debug|Any CPU.ActiveCfg = Debug|Any CPU | ||
| {30177EF1-3980-4FFE-9B49-90B75DCEBDA3}.Debug|Any CPU.Build.0 = Debug|Any CPU | ||
| {30177EF1-3980-4FFE-9B49-90B75DCEBDA3}.Release|Any CPU.ActiveCfg = Release|Any CPU | ||
| {30177EF1-3980-4FFE-9B49-90B75DCEBDA3}.Release|Any CPU.Build.0 = Release|Any CPU | ||
| EndGlobalSection | ||
| GlobalSection(SolutionProperties) = preSolution | ||
| HideSolutionNode = FALSE | ||
| EndGlobalSection | ||
| GlobalSection(NestedProjects) = preSolution | ||
| {F8E5EFC0-C74B-4C3C-BC22-7A5286A31DF6} = {67DA0DCC-75F4-4F30-91C3-309A48B13D49} | ||
| {2CBEE59D-07E4-460E-8B97-9267965D3F46} = {2EB71559-9BE4-4E02-9763-9092876D1E4A} | ||
| {ED24D0E3-BA79-4F6D-9A30-D05FF4EBAFDB} = {3DB2A5F4-23F6-4A06-9AE5-CEAC0707735B} | ||
| {24D99DC2-DF18-45A3-B444-B60351F131DB} = {67DA0DCC-75F4-4F30-91C3-309A48B13D49} | ||
| {30177EF1-3980-4FFE-9B49-90B75DCEBDA3} = {2EB71559-9BE4-4E02-9763-9092876D1E4A} | ||
| {699C5B9A-EA4B-4D25-B05D-16CA14320CFB} = {551D4715-5ECD-4CAB-8A4A-41E246F4A7B5} | ||
| {524F5156-C079-4AEF-822E-F01DAE6874AA} = {551D4715-5ECD-4CAB-8A4A-41E246F4A7B5} | ||
| EndGlobalSection | ||
| GlobalSection(ExtensibilityGlobals) = postSolution | ||
| SolutionGuid = {933E3470-7D09-4F22-A056-2407458B9600} | ||
| EndGlobalSection | ||
| EndGlobal |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| #I "src/ControlledVocabulary/bin/Debug/netstandard2.0" | ||
| #I "src/ControlledVocabulary/bin/Release/netstandard2.0" | ||
| #r "ControlledVocabulary.dll" | ||
| #I "src/ARCTokenization/bin/Debug/netstandard2.0" | ||
| #I "src/ARCTokenization/bin/Release/netstandard2.0" | ||
| #r "ARCTokenization.dll" | ||
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| #r "nuget: OBO.NET" | ||
| #r "nuget: FSharpAux" | ||
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| open ControlledVocabulary | ||
| open ARCTokenization | ||
| open OBO.NET | ||
| open FSharpAux | ||
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| [<Literal>] | ||
| let baseString = """module INVSMO = | ||
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| """ | ||
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| let onto = OboOntology.fromFile false @"C:\Repos\nfdi4plants\ARCTokenization\src\ARCTokenization\structural_ontologies\investigation_metadata_structural_ontology.obo" | ||
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| let toUnderscoredName (term : OboTerm) = | ||
| term.Name | ||
| |> String.replace " " "_" | ||
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| let toTermSourceRef (term : OboTerm) = | ||
| term.Id | ||
| |> String.takeWhile ((<>) ':') | ||
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| let toCodeString (term : OboTerm) = | ||
| $" let {toUnderscoredName term} = CvTerm.create(\"{term.Id}\", \"{term.Name}\", \"{toTermSourceRef term}\"){System.Environment.NewLine}{System.Environment.NewLine}" | ||
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| toCodeString onto.Terms.Head | ||
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| let toSourceCode (onto : OboOntology) = | ||
| let concattedSingleValues = String.init onto.Terms.Length (fun i -> $"{toCodeString onto.Terms[i]}") | ||
| $"{baseString}{concattedSingleValues}" | ||
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| toSourceCode onto | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,5 @@ | ||
| #r "nuget: FSharpAux" | ||
| //#r "nuget: FsOboParser" | ||
| #r "nuget: OBO.NET" | ||
| #r "nuget: FsSpreadsheet.ExcelIO, 4.1.0" | ||
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@@ -11,7 +12,9 @@ | |
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| open FsSpreadsheet | ||
| open FsSpreadsheet.ExcelIO | ||
| //open FsOboParser | ||
| open OBO.NET | ||
| //open FsSpreadsheet.DSL | ||
| open ControlledVocabulary | ||
| open type ControlledVocabulary.ParamBase | ||
| open ARCTokenization | ||
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@@ -47,6 +50,12 @@ let its = Investigation.parseMetadataSheetsFromTokens() afts | |
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| let ot = List.head Terms.InvestigationMetadata.ontology.Terms | ||
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| ARCTokenization.StructuralOntology.CodeGeneration.toCodeString ot | ||
| CodeGeneration.toSourceCode "Investigation" Terms.InvestigationMetadata.ontology | ||
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| System.IO.Directory.GetCurrentDirectory() | ||
| let fakePath = CvParam(cvTerm = AFSO.``File Path``, v = System.IO.Directory.GetCurrentDirectory() + "/tests/ARCTokenization.Tests/Fixtures/correct/investigation_simple.xlsx") | ||
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@@ -124,7 +133,7 @@ let expectedTermValuesSimple = | |
| [""] | ||
| [""] | ||
| [""] | ||
| [""; "Maus"; "Keider"; "müller"; "oih"] | ||
|
There was a problem hiding this comment. you seriously need to fix your encoding problems 😆 |
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| [""; "Oliver"; "andreas"] | ||
| [""; "L. I."; "C."] | ||
| [""; "[email protected]"] | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| namespace ARCTokenization.StructuralOntology | ||
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| open ControlledVocabulary | ||
| open OBO.NET | ||
| open FSharpAux | ||
| open type System.Environment | ||
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| /// Functions to generate F# source code from OBO files. | ||
| 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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| /// 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 {toUnderscoredName term} = 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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Please stop committing test scripts to repos. Pls refactor anything relevant to actual unit tests or do not commit it at all.