diff --git a/ARCtrl.NET.sln b/ARCtrl.Querymodel.sln similarity index 66% rename from ARCtrl.NET.sln rename to ARCtrl.Querymodel.sln index b56f1b0..e3c2842 100644 --- a/ARCtrl.NET.sln +++ b/ARCtrl.Querymodel.sln @@ -15,10 +15,6 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution RELEASE_NOTES.md = RELEASE_NOTES.md EndProjectSection EndProject -Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.NET", "src\ARCtrl.NET\ARCtrl.NET.fsproj", "{A6324D54-1D9A-4EE8-BD57-FEB59132821B}" -EndProject -Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.NET.Tests", "tests\ARCtrl.NET.Tests\ARCtrl.NET.Tests.fsproj", "{74227D27-9ED9-45CC-BF80-1569C80719F7}" -EndProject Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.QueryModel", "src\ARCtrl.QueryModel\ARCtrl.QueryModel.fsproj", "{1927F72B-180E-49C7-A189-96176E6067D3}" EndProject Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Querymodel.Tests", "tests\ARCtrl.Querymodel.Tests\ARCtrl.Querymodel.Tests.fsproj", "{3907F71F-1F36-4164-A53A-68DBCB5DC22E}" @@ -45,30 +41,6 @@ Global {E7F453CD-BCCA-42EF-96A2-C74B9A09A593}.Release|x64.Build.0 = Release|Any CPU {E7F453CD-BCCA-42EF-96A2-C74B9A09A593}.Release|x86.ActiveCfg = Release|Any CPU {E7F453CD-BCCA-42EF-96A2-C74B9A09A593}.Release|x86.Build.0 = Release|Any CPU - {A6324D54-1D9A-4EE8-BD57-FEB59132821B}.Debug|Any CPU.ActiveCfg = Debug|Any CPU - {A6324D54-1D9A-4EE8-BD57-FEB59132821B}.Debug|Any CPU.Build.0 = Debug|Any CPU - {A6324D54-1D9A-4EE8-BD57-FEB59132821B}.Debug|x64.ActiveCfg = Debug|Any CPU - {A6324D54-1D9A-4EE8-BD57-FEB59132821B}.Debug|x64.Build.0 = Debug|Any CPU - {A6324D54-1D9A-4EE8-BD57-FEB59132821B}.Debug|x86.ActiveCfg = Debug|Any CPU - {A6324D54-1D9A-4EE8-BD57-FEB59132821B}.Debug|x86.Build.0 = Debug|Any CPU - {A6324D54-1D9A-4EE8-BD57-FEB59132821B}.Release|Any CPU.ActiveCfg = Release|Any CPU - {A6324D54-1D9A-4EE8-BD57-FEB59132821B}.Release|Any CPU.Build.0 = Release|Any CPU - {A6324D54-1D9A-4EE8-BD57-FEB59132821B}.Release|x64.ActiveCfg = Release|Any CPU - {A6324D54-1D9A-4EE8-BD57-FEB59132821B}.Release|x64.Build.0 = Release|Any CPU - {A6324D54-1D9A-4EE8-BD57-FEB59132821B}.Release|x86.ActiveCfg = Release|Any CPU - {A6324D54-1D9A-4EE8-BD57-FEB59132821B}.Release|x86.Build.0 = Release|Any CPU - {74227D27-9ED9-45CC-BF80-1569C80719F7}.Debug|Any CPU.ActiveCfg = Debug|Any CPU - {74227D27-9ED9-45CC-BF80-1569C80719F7}.Debug|Any CPU.Build.0 = Debug|Any CPU - {74227D27-9ED9-45CC-BF80-1569C80719F7}.Debug|x64.ActiveCfg = Debug|Any CPU - {74227D27-9ED9-45CC-BF80-1569C80719F7}.Debug|x64.Build.0 = Debug|Any CPU - {74227D27-9ED9-45CC-BF80-1569C80719F7}.Debug|x86.ActiveCfg = Debug|Any CPU - {74227D27-9ED9-45CC-BF80-1569C80719F7}.Debug|x86.Build.0 = Debug|Any CPU - {74227D27-9ED9-45CC-BF80-1569C80719F7}.Release|Any CPU.ActiveCfg = Release|Any CPU - {74227D27-9ED9-45CC-BF80-1569C80719F7}.Release|Any CPU.Build.0 = Release|Any CPU - {74227D27-9ED9-45CC-BF80-1569C80719F7}.Release|x64.ActiveCfg = Release|Any CPU - {74227D27-9ED9-45CC-BF80-1569C80719F7}.Release|x64.Build.0 = Release|Any CPU - {74227D27-9ED9-45CC-BF80-1569C80719F7}.Release|x86.ActiveCfg = Release|Any CPU - {74227D27-9ED9-45CC-BF80-1569C80719F7}.Release|x86.Build.0 = Release|Any CPU {1927F72B-180E-49C7-A189-96176E6067D3}.Debug|Any CPU.ActiveCfg = Debug|Any CPU {1927F72B-180E-49C7-A189-96176E6067D3}.Debug|Any CPU.Build.0 = Debug|Any CPU {1927F72B-180E-49C7-A189-96176E6067D3}.Debug|x64.ActiveCfg = Debug|Any CPU diff --git a/README.md b/README.md index 5794cb5..9f02d46 100644 --- a/README.md +++ b/README.md @@ -1,45 +1,38 @@ -# ARCtrl.NET +# ARCtrl.Querymodel -Nuget +> [!NOTE] +> Filesystem Access has been implemented in ARCtrl since v2.3.0, even transpilable to JS and Python. ARCtrl.NET is therefore deprecated and this repository hosts only ARCtrl.Querymodel. -This library functions as an IO wrapper for the [ARCtrl](https://github.com/nfdi4plants/ARCtrl) library in .NET. + +Nuget + +Adds querying functionality to the core [ARCtrl](https://github.com/nfdi4plants/ARCtrl) package in .NET. The documentation for the actual functions for manipulating the ARC datamodel can be found [here](https://github.com/nfdi4plants/ARCtrl/tree/main/docs/scripts_fsharp). ## Usage ```fsharp -#r "nuget: ARCtrl.NET" - -open ARCtrl.NET open ARCtrl +open ARCtrl.QueryModel +open ARCtrl.ISA +let i = ArcInvestigation("Dummy Investigation") -let arcPath = "" - -let arc = ARC.load(arcPath) - -let isa = arc.ISA.Value - -isa.InitStudy("MyStudy") +i.ArcTables.Values().WithName("Dummy Header").First.ValueText -arc.Write(arcPath) +i.GetAssay("Dummy Assay").LastSamples ``` ## Development -`./build.cmd runtests` - -## ARCtrl.Querymodel +#### Requirements -```fsharp -open ARCtrl -open ARCtrl.QueryModel -open ARCtrl.ISA +- [.NET SDK](https://dotnet.microsoft.com/en-us/download) + - verify with `dotnet --version` (Tested with 7.0.306) -let i = ArcInvestigation("Dummy Investigation") +#### Local Setup -i.ArcTables.Values().WithName("Dummy Header").First.ValueText +- Setup dotnet tools `dotnet tool restore` -i.GetAssay("Dummy Assay").LastSamples -``` +- Verify correct setup with `./build.cmd runtests` ✨ \ No newline at end of file diff --git a/build/ProjectInfo.fs b/build/ProjectInfo.fs index b3b1209..2b3425f 100644 --- a/build/ProjectInfo.fs +++ b/build/ProjectInfo.fs @@ -6,7 +6,7 @@ let project = "ARCtrl.NET" let testProjects = [ - "tests/ARCtrl.NET.Tests/ARCtrl.NET.Tests.fsproj" + //"tests/ARCtrl.NET.Tests/ARCtrl.NET.Tests.fsproj" "tests/ARCtrl.Querymodel.Tests/ARCtrl.Querymodel.Tests.fsproj" ] diff --git a/src/ARCtrl.NET/ARCtrl.NET.fsproj b/src/ARCtrl.NET/ARCtrl.NET.fsproj deleted file mode 100644 index fcd2574..0000000 --- a/src/ARCtrl.NET/ARCtrl.NET.fsproj +++ /dev/null @@ -1,46 +0,0 @@ - - - - netstandard2.1 - true - 3390;$(WarnOn) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nfdi4plants, Lukas Weil - Library for easy handling of ARC folders and files with file access in .NET. - MIT - - F# FSharp dotnet .Net bioinformatics biology datascience metadata investigation study assay ISA XLSX ARC IO ARCtrl - https://github.com/nfdi4plants/ARCtrl.NET - https://github.com/nfdi4plants/ARCtrl.NET - git - - diff --git a/src/ARCtrl.NET/Arc.fs b/src/ARCtrl.NET/Arc.fs deleted file mode 100644 index fe04a18..0000000 --- a/src/ARCtrl.NET/Arc.fs +++ /dev/null @@ -1,82 +0,0 @@ -namespace ARCtrl.NET - -open ARCtrl -open Contract - -[] -module ARCExtensions = - - type ARC with - - member this.Write(arcPath) = - this.GetWriteContracts() - |> Array.iter (Contract.fulfillWriteContract arcPath) - - static member load (arcPath : string) = - let paths = Path.getAllFilePaths arcPath - let arc = ARC.fromFilePaths paths - - let contracts = arc.GetReadContracts() - - let fulFilledContracts = - contracts - |> Array.map (fulfillReadContract arcPath) - - arc.SetISAFromContracts(fulFilledContracts) - arc - - ///// Initializes the ARC-specific folder structure. - //let initFolders (arcPath) = - // subFolderPaths - // |> List.iter (fun n -> - // let dp = Path.Combine(arcPath,n) - // let dir = Directory.CreateDirectory(dp) - // File.Create(Path.Combine(dir.FullName, ".gitkeep")).Close() - // ) - - /// Initializes the ARC-specific git repository. - static member initGit(workDir,?repositoryAddress : string,?branch : string) = - - let log = Logging.createLogger "ArcInitGitLog" - - log.Trace("Init Git repository") - - let branch = branch |> Option.defaultValue "main" - - try - - GitHelper.executeGitCommand workDir $"init -b {branch}" - - log.Trace("Add remote repository") - match repositoryAddress with - | None -> () - | Some remote -> - GitHelper.executeGitCommand workDir $"remote add origin {remote}" - //GitHelper.executeGitCommand workDir $"branch -u origin/{branch} {branch}" - - with - | e -> - - log.Error($"Git could not be set up. Please try installing Git cli and run `arc git init`.\n\t{e}") - - ///// Initializes the ARC-specific folder structure, investigation file and git repository. - //let init (workDir : string) (identifier : string) (repositoryAddress : string option) (branch : string option) = - - // let log = Logging.createLogger "ArcInitLog" - - // log.Info("Start Arc Init") - - // log.Trace("Create Directory") - - // Directory.CreateDirectory workDir |> ignore - - // log.Trace("Initiate folder structure") - - // initFolders workDir - - // log.Trace("Initiate investigation file") - - // let inv = ISADotNet.Investigation.create(Identifier=identifier) - // Investigation.write workDir inv - - // initGit workDir repositoryAddress branch diff --git a/src/ARCtrl.NET/Assay.fs b/src/ARCtrl.NET/Assay.fs deleted file mode 100644 index 6b293f1..0000000 --- a/src/ARCtrl.NET/Assay.fs +++ /dev/null @@ -1,86 +0,0 @@ -namespace ARCtrl.NET - -open ARCtrl -open ARCtrl -open ARCtrl.Spreadsheet -open FsSpreadsheet -open FsSpreadsheet.Net -open System.IO - -module Assay = - - - - module AssayFolder = - - /// Checks if an assay folder exists in the ARC. - let exists (arc : string) (identifier : string) = - - Path.Combine([|arc;ARCtrl.ArcPathHelper.AssaysFolderName;identifier|]) - |> System.IO.Directory.Exists - - - let readByFileName (arc : string) (assayFileName : string) = - Path.Combine([|arc;assayFileName|]).Replace(@"\","/") - |> FsWorkbook.fromXlsxFile - |> ArcAssay.fromFsWorkbook - - - let readByIdentifier (arc : string) (identifier : string) = - Helper.Identifier.Assay.fileNameFromIdentifier identifier - |> readByFileName arc - - //let tryReadFromFolder (folderPath : string) = - // try - // readFromFolder folderPath |> Some - // with | _ -> None - - //let tryReadByFileName (arc : string) (assayFileName : string) = - // try - // readByFileName arc assayFileName |> Some - // with | _ -> None - - //let tryReadByName (arc : string) (assayName : string) = - // try - // readByName arc assayName |> Some - // with | _ -> None - - //let writeToFolder (folderPath : string) (contacts : Person list) (assay : Assay) = - // let ap = Path.Combine (folderPath,assayFileName) - // AssayFile.Assay.toFile ap contacts assay - - //let write (arc : string) (contacts : Person list) (assay : Assay) = - // if assay.FileName.IsNone then - // failwith "Cannot write assay to arc, as it has no filename" - // let ap = Path.Combine ([|arc;"assays";assay.FileName.Value|]) - // AssayFile.Assay.toFile ap contacts assay - - - //let add (arc : string) (assay : ArcAssay) = - - // if assay.FileName.IsNone then - // failwith "Given assay does not contain filename" - - // let assayIdentifier = identifierFromFileName assay.FileName.Value - - // if AssayFolder.exists arc assayIdentifier then - // printfn $"Assay folder with identifier {assayIdentifier} already exists." - // else - // subFolderPaths - // |> List.iter (fun n -> - // let dp = Path.Combine([|arc;rootFolderName;assayIdentifier;n|]) - // let dir = Directory.CreateDirectory(dp) - // File.Create(Path.Combine(dir.FullName, ".gitkeep")).Close() - // ) - - // let assayFilePath = Path.Combine([|arc;rootFolderName;assay.FileName.Value|]) - - // AssayFile.Assay.toFile assayFilePath [] assay - - - //let init (arc : string) (assayName : string) = - - // let assay = Assay.create(FileName = nameToFileName assayName) - - // init arc assay - diff --git a/src/ARCtrl.NET/Contract.fs b/src/ARCtrl.NET/Contract.fs deleted file mode 100644 index cf7afe0..0000000 --- a/src/ARCtrl.NET/Contract.fs +++ /dev/null @@ -1,49 +0,0 @@ -module ARCtrl.NET.Contract - -open ARCtrl.Contract -open FsSpreadsheet -open FsSpreadsheet.Net - -let fulfillReadContract basePath (c : Contract) = - let log = Logging.createLogger("ReadContractHandler") - match c.DTOType with - | Some DTOType.ISA_Assay - | Some DTOType.ISA_Investigation - | Some DTOType.ISA_Study -> - let path = System.IO.Path.Combine(basePath, c.Path) - let wb = FsWorkbook.fromXlsxFile path |> box |> DTO.Spreadsheet - {c with DTO = Some wb} - | Some DTOType.PlainText -> - let path = System.IO.Path.Combine(basePath, c.Path) - let text = System.IO.File.ReadAllText(path) |> DTO.Text - {c with DTO = Some text} - | _ -> - log.Info(sprintf "Contract %s is not an ISA contract" c.Path) - c - -let fulfillWriteContract basePath (c : Contract) = - let log = Logging.createLogger("WriteContractHandler") - match c.DTO with - | Some (DTO.Spreadsheet wb) -> - let path = System.IO.Path.Combine(basePath, c.Path) - Path.ensureDirectory path - FsWorkbook.toXlsxFile path (wb :?> FsWorkbook) - | Some (DTO.Text t) -> - let path = System.IO.Path.Combine(basePath, c.Path) - Path.ensureDirectory path - System.IO.File.WriteAllText(path,t) - | None -> - let path = System.IO.Path.Combine(basePath, c.Path) - Path.ensureDirectory path - System.IO.File.Create(path).Close() - | _ -> - log.Info(sprintf "Contract %s is not an ISA contract" c.Path) - -//let fulfillExecuteContract basePath (c : Contract) = -// let log = Logging.createLogger("ExecuteContractHandler") -// match c.DTO with -// | Some (DTO.CLITool tool) -> -// let path = System.IO.Path.Combine(basePath, c.Path) -// Path.ensureDirectory path -// FsWorkbook.toFile path (wb :?> FsWorkbook) -// | _ -> log.Info(sprintf "Contract %O is not an Execute contract" c) \ No newline at end of file diff --git a/src/ARCtrl.NET/Converter.fs b/src/ARCtrl.NET/Converter.fs deleted file mode 100644 index 8833269..0000000 --- a/src/ARCtrl.NET/Converter.fs +++ /dev/null @@ -1,40 +0,0 @@ -namespace ARCtrl.NET.Converter - -//open ISADotNet -//open ISADotNet.QueryModel -//open FsSpreadsheet.DSL -//open LitXml -//open JsonDSL -//open System.Text.Json - -//type ARCconverter = -//| ARCtoCSV of (QInvestigation -> QStudy -> QAssay -> SheetEntity) -//| ARCtoTSV of (QInvestigation -> QStudy -> QAssay -> SheetEntity) -//| ARCtoXLSX of (QInvestigation -> QStudy -> QAssay -> SheetEntity) -//| ARCtoXML of (QInvestigation -> QStudy -> QAssay -> LitXml.XmlPart) -//| ARCtoJSON of (QInvestigation -> QStudy -> QAssay -> JEntity) - -// member this.ConvertCSV(i,s,a) = -// match this with -// | ARCtoCSV f -> f i s a -// | _ -> failwith "could not convert to csv" - -// member this.ConvertTSV(i,s,a) = -// match this with -// | ARCtoTSV f -> f i s a -// | _ -> failwith "could not convert to tsv" - -// member this.ConvertXLSX(i,s,a) = -// match this with -// | ARCtoXLSX f -> f i s a -// | _ -> failwith "could not convert to xlsx" - -// member this.ConvertXML(i,s,a) = -// match this with -// | ARCtoXML f -> f i s a -// | _ -> failwith "could not convert to xml" - -// member this.ConvertJsn(i,s,a) = -// match this with -// | ARCtoJSON f -> f i s a -// | _ -> failwith "could not convert to xml" diff --git a/src/ARCtrl.NET/GitHelper.fs b/src/ARCtrl.NET/GitHelper.fs deleted file mode 100644 index 09b3d4e..0000000 --- a/src/ARCtrl.NET/GitHelper.fs +++ /dev/null @@ -1,135 +0,0 @@ -namespace ARCtrl.NET - -open System.Diagnostics -open System.Runtime.InteropServices -open System.IO - -module GitHelper = - - /// Executes Git command and returns git output. - let executeGitCommandWithResponse (repoDir : string) (command : string) = - - let log = Logging.createLogger "ExecuteGitCommandLog" - - log.Trace($"Run git {command}") - - let procStartInfo = - ProcessStartInfo( - WorkingDirectory = repoDir, - RedirectStandardOutput = true, - RedirectStandardError = true, - UseShellExecute = false, - FileName = "git", - Arguments = command - ) - - let outputs = System.Collections.Generic.List() - let outputHandler (_sender:obj) (args:DataReceivedEventArgs) = - if (args.Data = null |> not) then - if args.Data.ToLower().Contains ("error") then - log.Error($"GIT: {args.Data}") - elif args.Data.ToLower().Contains ("trace") then - log.Trace($"GIT: {args.Data}") - else - outputs.Add(args.Data) - log.Info($"GIT: {args.Data}") - - let errorHandler (_sender:obj) (args:DataReceivedEventArgs) = - if (args.Data = null |> not) then - let msg = args.Data.ToLower() - if msg.Contains ("error") || msg.Contains ("fatal") then - log.Error($"GIT: {args.Data}") - elif msg.Contains ("trace") then - log.Trace($"GIT: {args.Data}") - else - outputs.Add(args.Data) - log.Info($"GIT: {args.Data}") - - let p = new Process(StartInfo = procStartInfo) - - p.OutputDataReceived.AddHandler(DataReceivedEventHandler outputHandler) - p.ErrorDataReceived.AddHandler(DataReceivedEventHandler errorHandler) - p.Start() |> ignore - p.BeginOutputReadLine() - p.BeginErrorReadLine() - p.WaitForExit() - outputs - - /// Executes Git command. - let executeGitCommand (repoDir : string) (command : string) = - - executeGitCommandWithResponse repoDir command |> ignore - - let formatRepoString username pass (url : string) = - let comb = username + ":" + pass + "@" - url.Replace("https://","https://" + comb) - - let setLocalEmail (dir : string) (email : string) = - executeGitCommand dir (sprintf "config user.email \"%s\"" email) - - let tryGetLocalEmail (dir : string) = - let r = executeGitCommandWithResponse dir "config --local --get user.email" - if r.Count = 0 then None - else Some r.[0] - - let setGlobalEmail (email : string) = - executeGitCommand "" (sprintf "config --global user.email \"%s\"" email) - - let tryGetGlobalEmail () = - let r = executeGitCommandWithResponse "" "config --global --get user.email" - if r.Count = 0 then None - else Some r.[0] - - let setLocalName (dir : string) (name : string) = - executeGitCommand dir (sprintf "config user.name \"%s\"" name) - - let tryGetLocalName (dir : string) = - let r = executeGitCommandWithResponse dir "config --local --get user.name" - if r.Count = 0 then None - else Some r.[0] - - let setGlobalName (name : string) = - executeGitCommand "" (sprintf "config --global user.name \"%s\"" name) - - let tryGetGlobalName () = - let r = executeGitCommandWithResponse "" "config --global --get user.name" - if r.Count = 0 then None - else Some r.[0] - - let clone dir url = - executeGitCommand dir (sprintf "clone %s" url) - - let noLFSConfig = "-c \"filter.lfs.smudge = git-lfs smudge --skip -- %f\" -c \"filter.lfs.process = git-lfs filter-process --skip\"" - - let cloneNoLFS dir url = - executeGitCommand dir (sprintf "clone %s %s" noLFSConfig url) - - let add dir = - executeGitCommand dir "add ." - - let commit dir message = - executeGitCommand dir (sprintf "commit -m \"%s\"" message) - - let push dir = - executeGitCommand dir "push" - - /// Set containing all the paths and path rules that should be tracked using git lfs - type LFSRuleSet = Set - - /// Checks the .gitattributes file in the repo for all git lfs paths and path rules - let retrieveLFSRules repoDir : LFSRuleSet = - let gitAttributesFilePath = Path.Combine(repoDir,".gitattributes") - let lfsRulePattern = ".*(?= filter=lfs diff=lfs merge=lfs -text)" - if File.Exists gitAttributesFilePath then - File.ReadAllLines(gitAttributesFilePath) - |> Array.choose (fun l -> - let r = System.Text.RegularExpressions.Regex.Match(l,lfsRulePattern) - if r.Success then - Some r.Value - else None - ) - |> set - else Set.empty - - let containsLFSRule (ruleSet : LFSRuleSet) (path : string) = - ruleSet.Contains path diff --git a/src/ARCtrl.NET/Investigation.fs b/src/ARCtrl.NET/Investigation.fs deleted file mode 100644 index 3c8cea5..0000000 --- a/src/ARCtrl.NET/Investigation.fs +++ /dev/null @@ -1,178 +0,0 @@ -namespace ARCtrl.NET - -//open ISADotNet -//open ISADotNet.XLSX -//open System.IO - -//module Investigation = - -// let investigationFileName = "isa.investigation.xlsx" - -// /// Creates an investigation file in the ARC. -// let write (arcDir : string) (investigation : ISADotNet.Investigation) = - -// let log = Logging.createLogger "InvestigationWriteLog" - -// log.Info("Start Investigation Write") - -// if System.IO.File.Exists(Path.Combine(arcDir,investigationFileName)) then -// log.Error("Investigation file does already exist.") - -// else -// let investigationFilePath = Path.Combine(arcDir,investigationFileName) -// Investigation.toFile investigationFilePath investigation - -// /// Creates an investigation file in the ARC. -// let overWrite (arcDir : string) (investigation : ISADotNet.Investigation) = - -// let log = Logging.createLogger "InvestigationWriteLog" -// log.Info("Start Investigation Write") - -// let investigationFilePath = Path.Combine(arcDir,investigationFileName) - -// if System.IO.File.Exists(investigationFilePath) then -// try -// let cache = File.ReadAllBytes(investigationFilePath) -// File.Delete(investigationFilePath) -// try -// Investigation.toFile investigationFilePath investigation -// with -// | err -> -// File.WriteAllBytes(investigationFilePath,cache) -// log.Error($"Investigation file could not be overwritten: {err.Message}") -// with -// | err -> -// log.Error($"Investigation file could not be overwritten: {err.Message}") -// else -// Investigation.toFile investigationFilePath investigation - -// /// Reads an investigation from the ARC. -// let read (arcDir : string) = - -// let log = Logging.createLogger "InvestigationReadLog" - -// log.Info("Start Investigation Read") - -// if System.IO.File.Exists(Path.Combine(arcDir,investigationFileName)) then -// let investigationFilePath = Path.Combine(arcDir,investigationFileName) -// Investigation.fromFile investigationFilePath - -// else -// log.Error("Investigation file does not exist.") -// raise (System.SystemException()) - -// /// Reads and combines all ISA components of the ARC into the ISA object -// let fromArcFolder (arcDir : string) = -// let log = Logging.createLogger "InvestigationFromArcFolderLog" - -// // read investigation from investigation file -// let ip = Path.Combine(arcDir,investigationFileName).Replace(@"\","/") -// let i = Investigation.fromFile ip - -// // get study list from study files and assay files -// let istudies = -// i.Studies -// |> Option.map (List.map (fun study -> -// //// read study from file -// match study.Identifier with -// | Some id -> -// let studyFromFile = Study.readByIdentifier arcDir id -// let mergedStudy = API.Update.UpdateByExistingAppendLists.updateRecordType study studyFromFile -// // update study assays and contacts with information from assay files -// match study.Assays with -// | Some assays -> -// let scontacts,sassays = -// assays -// |> List.fold (fun (cl,al) assay -> -// match assay.FileName with -// | Some fn -> -// let contactsFromFile,assayFromFile = Assay.readByFileName arcDir assay.FileName.Value -// cl @ contactsFromFile, al @ [assayFromFile] -// | None -> -// log.Warn("Study \'" + id + "\' contains Assay without filename.") -// cl, al @ [assay] -// ) (mergedStudy.Contacts |> Option.defaultValue [],[]) -// {mergedStudy with -// Contacts = Some (scontacts |> List.distinct) -// Assays = Some sassays -// } -// | None -> -// mergedStudy -// | None -> -// log.Warn("Investigation file contains study without identifier.") -// study -// )) - -// // construct complete process list from studies and assays, then update by itself -// let iprocesses = -// istudies -// |> Option.map (List.fold (fun pl study -> -// let sprocesses = study.ProcessSequence |> Option.defaultValue [] -// let aprocesses = -// study.Assays -// |> Option.map (List.fold (fun spl assay -> -// let ap = assay.ProcessSequence |> Option.defaultValue [] -// spl @ ap -// ) [] ) -// |> Option.defaultValue [] -// pl @ sprocesses @ aprocesses -// ) [] ) -// |> Option.defaultValue [] -// let ref = iprocesses |> ProcessSequence.updateByItself - -// // update investigation processes -// let istudies' = -// istudies -// |> Option.map (List.map (fun study -> -// {study with -// Assays = study.Assays |> Option.map (List.map (fun a -> {a with ProcessSequence = a.ProcessSequence |> Option.map (ProcessSequence.updateByRef ref)})) -// ProcessSequence = study.ProcessSequence |> Option.map (ProcessSequence.updateByRef ref) -// } -// )) - -// // fill investigation with information from study files and assay files -// {i with Studies = istudies'} -// |> API.Investigation.update - -// /// Registers an assay to the investigation arc registry -// let registerAssay arcDir studyName (assayName) = - -// let log = Logging.createLogger "RegisterAssayLog" - -// let _, assay = Assay.readByName arcDir assayName - -// let investigation = read arcDir - -// match investigation.Studies with -// | Some studies -> -// match API.Study.tryGetByIdentifier studyName studies with -// | Some study -> -// match study.Assays with -// | Some assays -> -// match Assay.tryReadByName arcDir assayName with -// | Some _ -> -// log.Error($"Assay with the identifier {assayName} already exists in the investigation file.") -// assays -// | None -> -// API.Assay.add assays assay -// | None -> -// [assay] -// |> API.Study.setAssays study -// |> fun s -> API.Study.updateByIdentifier API.Update.UpdateAll s studies -// | None -> -// log.Info($"Study with the identifier {studyName} does not exist yet, creating it now.") -// let study = Study.create(Identifier = studyName, Assays = [assay]) -// Study.init arcDir study -// API.Study.add studies study -// | None -> -// log.Info($"Study with the identifier {studyName} does not exist yet, creating it now.") -// let study = Study.create(Identifier = studyName, Assays = [assay]) -// Study.init arcDir study -// [study] -// |> API.Investigation.setStudies investigation -// |> write arcDir - -// /// Update investigation file with information from the different ISA components of the ARC -// let updateRegistry arcDir = -// fromArcFolder arcDir -// |> overWrite arcDir \ No newline at end of file diff --git a/src/ARCtrl.NET/Logging.fs b/src/ARCtrl.NET/Logging.fs deleted file mode 100644 index b5c3fb3..0000000 --- a/src/ARCtrl.NET/Logging.fs +++ /dev/null @@ -1,39 +0,0 @@ -module ARCtrl.NET.Logging - -open System -open NLog -open NLog.Config -open NLog.Targets -open NLog.Conditions - - -/// Creates a new logger with the given name. Configuration details are obtained from the generateConfig function. -let createLogger (loggerName : string) = - - // new instance of "Logger" with activated config - let logger = LogManager.GetLogger(loggerName) - - logger - -/// Takes a logger and an exception and separates usage and error messages. Usage messages will be printed into the console while error messages will be logged. -let handleExceptionMessage (log : NLog.Logger) (exn : Exception) = - // separate usage message (Argu) and error messages. Error messages shall be logged, usage messages shall not, empty error message shall not appear at all - let isUsageMessage = exn.Message.Contains("USAGE") || exn.Message.Contains("SUBCOMMANDS") - let isErrorMessage = exn.Message.Contains("ERROR") - let isEmptyMessage = exn.Message = "" - match isUsageMessage, isErrorMessage, isEmptyMessage with - | true,true,false -> // exception message contains usage AND error messages - let eMsg, uMsg = - exn.Message.Split(Environment.NewLine) // '\n' leads to parsing problems - |> fun arr -> - arr |> Array.find (fun t -> t.Contains("ERROR")), - arr |> Array.filter (fun t -> t.Contains("ERROR") |> not) |> String.concat "\n" // Argu usage instruction shall not be logged as error - log.Error(eMsg) - printfn "%s" uMsg - | true,false,false -> printfn "%s" exn.Message // exception message contains usage message but NO error message - | false,false,true -> () // empty error message - | _ -> log.Error(exn) // everything else will be a non-empty error message - -/// Checks if a message (string) is empty and if it is not, applies a logging function to it. -let checkNonLog s (logging : string -> unit) = if s <> "" then logging s - \ No newline at end of file diff --git a/src/ARCtrl.NET/Path.fs b/src/ARCtrl.NET/Path.fs deleted file mode 100644 index 58da8a0..0000000 --- a/src/ARCtrl.NET/Path.fs +++ /dev/null @@ -1,27 +0,0 @@ -module ARCtrl.NET.Path - -open System.IO - -let ensureDirectory (filePath : string) = - let file = new System.IO.FileInfo(filePath); - file.Directory.Create() - -/// Return the absolute path relative to the directoryPath -let makeRelative directoryPath (path : string) = - if directoryPath = "." || directoryPath = "/" || directoryPath = "" then path - else - if path.StartsWith(directoryPath) then - path.Substring(directoryPath.Length) - else path - -let standardizeSlashes (path : string) = - path.Replace("\\","/") - -let getAllFilePaths (directoryPath : string) = - let rec allFiles dirs = - if Seq.isEmpty dirs then Seq.empty else - seq { yield! dirs |> Seq.collect Directory.EnumerateFiles - yield! dirs |> Seq.collect Directory.EnumerateDirectories |> allFiles } - - allFiles [directoryPath] |> Seq.toArray - |> Array.map (makeRelative directoryPath >> standardizeSlashes) diff --git a/src/ARCtrl.NET/Run.fs b/src/ARCtrl.NET/Run.fs deleted file mode 100644 index 80ba1ae..0000000 --- a/src/ARCtrl.NET/Run.fs +++ /dev/null @@ -1,6 +0,0 @@ -namespace ARCtrl.NET - -module Run = - - let rootFolderName = "runs" - diff --git a/src/ARCtrl.NET/Study.fs b/src/ARCtrl.NET/Study.fs deleted file mode 100644 index d7a59a5..0000000 --- a/src/ARCtrl.NET/Study.fs +++ /dev/null @@ -1,245 +0,0 @@ -namespace ARCtrl.NET - -//open ISADotNet -//open ISADotNet.XLSX -//open System.IO - - -//module Study = - -// let rootFolderName = "studies" - -// let studyFileName = "isa.study.xlsx" - -// let subFolderPaths = -// ["resources";"protocol"] - -// module StudyFolder = - -// /// Checks if a Study folder exists in the ARC. -// let exists (arc : string) (identifier : string) = -// Path.Combine([|arc;rootFolderName;identifier|]) -// |> System.IO.Directory.Exists - -// /// Returns the Study identifiers of the Study Files located in each Study's folder of a given path to an ARC. -// let findStudyIdentifiers arcDir = -// let log = Logging.createLogger "findStudyIdentifiersLog" -// let studiesPath = Path.Combine(arcDir, rootFolderName) -// try -// let studyFolders = Directory.GetDirectories studiesPath -// studyFolders -// |> Array.collect ( -// fun sf -> -// let studyIdentifier = (DirectoryInfo sf).Name -// Directory.GetFiles sf -// |> Array.choose (fun s -> -// if s.EndsWith "isa.study.xlsx" then -// Some studyIdentifier -// elif s.EndsWith "_isa.study.xlsx" then -// log.Warn $"The Study File of Study {studyIdentifier} has a deprecated File Name: {s}" -// Some studyIdentifier -// else -// None -// ) -// ) -// with e -> -// log.Error e.Message -// [||] - -// let readFromFolder (arc : string) (folderPath : string) = -// let sp = Path.Combine(folderPath,studyFileName).Replace(@"\","/") -// let study = StudyFile.Study.fromFile sp -// match study.Assays with -// | Some assays -> -// let contacts,ps,assays = -// assays -// |> List.fold (fun (contacts,processSequence,assays) a -> -// let c,a = Assay.readByFileName arc a.FileName.Value -// contacts @ c, processSequence @ (a.ProcessSequence |> Option.defaultValue []), assays @ [a] -// ) (study.Contacts |> Option.defaultValue [],study.ProcessSequence |> Option.defaultValue [],[]) -// let ref = ps |> ProcessSequence.updateByItself -// let updatedAssays = -// assays -// |> List.map (fun a -> -// {a with ProcessSequence = a.ProcessSequence |> Option.map (ProcessSequence.updateByRef ref)} -// ) -// {study with -// ProcessSequence = study.ProcessSequence |> Option.map (ProcessSequence.updateByRef ref) -// Assays = Some updatedAssays -// Contacts = Option.fromValueWithDefault [] (contacts |> List.distinct) -// } -// | None -> -// {study with ProcessSequence = study.ProcessSequence |> Option.map ProcessSequence.updateByItself} - -// let readByIdentifier (arc : string) (studyIdentifier : string) = -// Path.Combine ([|arc;rootFolderName;studyIdentifier|]) -// |> readFromFolder arc - -// /// Writes a study to the given folder. Fails, if the file already exists -// let writeToFolder (folderPath : string) (study : Study) = - -// let log = Logging.createLogger "StudyWriteLog" - -// log.Info("Start Study Write") - -// let studyFilePath = Path.Combine (folderPath,studyFileName) - -// if System.IO.File.Exists(studyFilePath) then -// log.Error("Study file does already exist.") - -// else -// StudyFile.Study.toFile studyFilePath study - -// /// Writes a study to the given folder. Overwrites it, if the file already exists -// let overWriteToFolder (folderPath : string) (study : Study) = - -// let log = Logging.createLogger "StudyWriteLog" -// log.Info("Start Study Write") - -// let studyFilePath = Path.Combine (folderPath,studyFileName) - -// if System.IO.File.Exists(studyFilePath) then -// try -// let cache = File.ReadAllBytes(studyFilePath) -// File.Delete(studyFilePath) -// try -// StudyFile.Study.toFile studyFilePath study -// with -// | err -> -// File.WriteAllBytes(studyFilePath,cache) -// log.Error($"Study file could not be overwritten: {err.Message}") -// with -// | err -> -// log.Error($"Study file could not be overwritten: {err.Message}") -// else -// StudyFile.Study.toFile studyFilePath study - -// /// Writes a study to the arc. Fails, if the file already exists -// let write (arc : string) (study : Study) = - -// let log = Logging.createLogger "StudyWriteLog" - -// log.Info("Start Study Write") - -// if study.FileName.IsNone then -// log.Error("Cannot write study to arc, as it has no filename") -// else - -// let studyFilePath = Path.Combine ([|arc;rootFolderName;study.FileName.Value|]) - -// if System.IO.File.Exists(studyFilePath) then -// log.Error("Study file does already exist.") - -// else -// StudyFile.Study.toFile studyFilePath study - -// /// Writes a study to the arc. Overwrites it, if the file already exists -// let overWrite (arc : string) (study : Study) = -// let log = Logging.createLogger "StudyWriteLog" - -// log.Info("Start Study Write") - -// if study.FileName.IsNone then -// log.Error("Cannot write study to arc, as it has no filename") -// else -// let studyFilePath = Path.Combine ([|arc;rootFolderName;study.FileName.Value|]) -// if System.IO.File.Exists(studyFilePath) then -// try -// let cache = File.ReadAllBytes(studyFilePath) -// File.Delete(studyFilePath) -// try -// StudyFile.Study.toFile studyFilePath study -// with -// | err -> -// File.WriteAllBytes(studyFilePath,cache) -// log.Error($"Study file could not be overwritten: {err.Message}") -// with -// | err -> -// log.Error($"Study file could not be overwritten: {err.Message}") -// else -// StudyFile.Study.toFile studyFilePath study - -// let init (arc : string) (study : Study) = - -// if study.Identifier.IsNone || study.FileName.IsNone then -// failwith "Given study does not contain identifier or filename" - -// let studyIdentifier = study.Identifier.Value - -// if StudyFolder.exists arc studyIdentifier then -// printfn $"Study folder with identifier {studyIdentifier} already exists." -// else -// subFolderPaths -// |> List.iter (fun n -> -// let dp = Path.Combine([|arc;rootFolderName;studyIdentifier;n|]) -// let dir = Directory.CreateDirectory(dp) -// File.Create(Path.Combine(dir.FullName, ".gitkeep")).Close() -// ) - -// let studyFilePath = Path.Combine([|arc;rootFolderName;study.FileName.Value|]) - -// StudyFile.Study.toFile studyFilePath study - - -// let initFromName (arc : string) (studyName : string) = - -// let studyFileName = Path.Combine(studyName,studyFileName).Replace(@"\","/") - -// let study = Study.create(FileName = studyFileName, Identifier = studyName) - -// init arc study - -// /// Takes the path to an ARC and lists all study identifiers registered in this ARC's investigation file. -// let list (arcDir : string) = - -// let log = Logging.createLogger "StudyListLog" - -// log.Info("Start Study List") - -// (* the following part is _not nice_: The functionality for this already exists in Investigation.fs. Unfortunately, Investigation.fs is compiled *AFTER* -// Study.fs and, thus, we cannot use functions from there. Moving Study.fs after Investigation.fs in compilation order also does not work due to -// Investigation.fs using functions from Study.fs. -// If someone finds a solution for this F#-specific compilation problem, feel free to fix :) *) -// let investigationFilePath = Path.Combine(arcDir, "isa.investigation.xlsx") -// log.Trace($"InvestigationFile: {investigationFilePath}") -// let investigation = Investigation.fromFile investigationFilePath -// // end of part - -// let studyFileIdentifiers = set (StudyFolder.findStudyIdentifiers arcDir) - -// let studyIdentifiers = -// investigation.Studies -// |> Option.defaultValue [] -// |> List.choose (fun s -> -// match s.Identifier with -// | None | Some "" -> -// log.Warn("Study does not have identifier") -// None -// | Some i -> Some i -// ) -// |> set - -// let onlyRegistered = Set.difference studyIdentifiers studyFileIdentifiers -// let onlyInitialized = Set.difference studyFileIdentifiers studyIdentifiers -// let combined = Set.union studyIdentifiers studyFileIdentifiers - -// if not onlyRegistered.IsEmpty then -// log.Warn("The ARC contains following registered studies that have no associated file:") -// onlyRegistered -// |> Seq.iter ((sprintf "%s") >> log.Warn) -// log.Info($"You can init the study file using \"arc s init\"") - -// if not onlyInitialized.IsEmpty then -// log.Warn("The ARC contains study files with the following identifiers not registered in the investigation:") -// onlyInitialized -// |> Seq.iter ((sprintf "%s") >> log.Warn) -// log.Info($"You can register the study using \"arc s register\"") - -// if combined.IsEmpty then -// log.Error("The ARC does not contain any studies.") - -// combined -// |> Seq.map (fun identifier -> -// //log.Debug(sprintf "Study: %s" identifier) -// sprintf "Study: %s" identifier -// ) \ No newline at end of file diff --git a/src/ARCtrl.NET/Workflow.fs b/src/ARCtrl.NET/Workflow.fs deleted file mode 100644 index 540e9d9..0000000 --- a/src/ARCtrl.NET/Workflow.fs +++ /dev/null @@ -1,6 +0,0 @@ -namespace ARCtrl.NET - -module Workflow = - - let rootFolderName = "workflows" - diff --git a/src/ARCtrl.QueryModel/ARCtrl.QueryModel.fsproj b/src/ARCtrl.QueryModel/ARCtrl.QueryModel.fsproj index d9f0ffc..4ba7c82 100644 --- a/src/ARCtrl.QueryModel/ARCtrl.QueryModel.fsproj +++ b/src/ARCtrl.QueryModel/ARCtrl.QueryModel.fsproj @@ -27,7 +27,7 @@ - + diff --git a/src/ARCtrl.QueryModel/ArcTables.fs b/src/ARCtrl.QueryModel/ArcTables.fs index b9c0570..3cb6993 100644 --- a/src/ARCtrl.QueryModel/ArcTables.fs +++ b/src/ARCtrl.QueryModel/ArcTables.fs @@ -709,16 +709,16 @@ module ArcTables = ArcTables.getFinalOutputsBy (fun (io : IOType) -> io.isData) this /// One Node of an ISA Process Sequence (Source, Sample, Data) - type QNode(Name : string, IOType : IOType, ?ParentProcessSequence : ArcTables) = + type QNode(name : string, ioType : IOType, ?parentProcessSequence : ArcTables) = /// Returns the process sequence in which the node appears - member this.ParentProcessSequence = ParentProcessSequence |> Option.defaultValue (ArcTables(ResizeArray [])) + member this.ParentProcessSequence = parentProcessSequence |> Option.defaultValue (ArcTables(ResizeArray [])) /// Identifying name of the node - member this.Name = Name + member this.Name = name /// Type of node (source, sample, data, raw data ...) - member this.IOType : IOType = IOType + member this.IOType : IOType = ioType interface System.IEquatable with member this.Equals other = other.Name.Equals this.Name diff --git a/tests/ARCtrl.NET.Tests/ARCtrl.NET.Tests.fsproj b/tests/ARCtrl.NET.Tests/ARCtrl.NET.Tests.fsproj deleted file mode 100644 index e07d1b4..0000000 --- a/tests/ARCtrl.NET.Tests/ARCtrl.NET.Tests.fsproj +++ /dev/null @@ -1,32 +0,0 @@ - - - - Exe - net8.0 - false - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/ARCtrl.NET.Tests/Arc.fs b/tests/ARCtrl.NET.Tests/Arc.fs deleted file mode 100644 index e3b980b..0000000 --- a/tests/ARCtrl.NET.Tests/Arc.fs +++ /dev/null @@ -1,155 +0,0 @@ -module Arc.Tests - -open Expecto -open ARCtrl.NET -open System.IO -open ARCtrl - -let testInputFolder = System.IO.Path.Combine(__SOURCE_DIRECTORY__,@"TestObjects") -let testOutputFolder = System.IO.Path.Combine(__SOURCE_DIRECTORY__,@"TestResults") - -let testLoad = - - testList "Load" [ - testCase "simpleARC" (fun () -> - let p = System.IO.Path.Combine(testInputFolder,"ARC_SimpleARC") - let result = ARC.load(p) - - Expect.isSome result.ISA "Should contain an ISA part" - Expect.isNone result.CWL "Should not contain a CWL part" - - let isa = result.ISA.Value - Expect.equal isa.StudyCount 1 "Should contain 1 study" - Expect.equal isa.AssayCount 1 "Should contain 1 assay" - Expect.equal isa.RegisteredStudies.Count 1 "Should contain 1 registered study" - - let s = isa.Studies.[0] - Expect.equal s.RegisteredAssayCount 1 "Should contain 1 registered assay" - Expect.equal s.TableCount 3 "Study should contain 3 tables" - - let a = s.RegisteredAssays.[0] - Expect.equal a.TableCount 4 "Assay should contain 4 tables" - - ) - ] - - -let testWrite = - - testList "Write" [ - testCase "empty" (fun () -> - let p = System.IO.Path.Combine(testOutputFolder,"ARC_Write_Empty") - let a = ARC() - a.Write(p) - - let expectedPaths = - [ - "/isa.investigation.xlsx"; - "/assays/.gitkeep"; - "/studies/.gitkeep"; - "/runs/.gitkeep"; - "/workflows/.gitkeep" - ] - |> List.sort - - - let paths = - Path.getAllFilePaths p - |> Array.sort - - Expect.sequenceEqual paths expectedPaths "Files were not created correctly." - ) - testCase "SimpleARC" (fun () -> - let p = Path.Combine(testOutputFolder,"ARC_Write_SimpleARC") - let arc = ARC() - - let i = ArcInvestigation("MyInvestigation") - let studyName = "MyStudy" - let s = ArcStudy(studyName) - i.AddRegisteredStudy(s) - let assayName = "MyAssay" - let a = ArcAssay(assayName) - s.AddRegisteredAssay(a) - arc.ISA <- Some i - arc.UpdateFileSystem() - arc.Write(p) - - let expectedPaths = - [ - "/isa.investigation.xlsx"; - "/studies/.gitkeep"; - $"/studies/{studyName}/isa.study.xlsx" - $"/studies/{studyName}/README.md" - $"/studies/{studyName}/protocols/.gitkeep"; - $"/studies/{studyName}/resources/.gitkeep"; - "/assays/.gitkeep"; - $"/assays/{assayName}/isa.assay.xlsx" - $"/assays/{assayName}/README.md" - $"/assays/{assayName}/protocols/.gitkeep" - $"/assays/{assayName}/dataset/.gitkeep" - "/runs/.gitkeep"; - "/workflows/.gitkeep" - ] - |> List.sort - - - let paths = - Path.getAllFilePaths p - |> Array.sort - - Expect.sequenceEqual paths expectedPaths "Files were not created correctly." - ) - testCase "LoadSimpleARCAndAddAssay" (fun () -> - let p = System.IO.Path.Combine(testOutputFolder,"ARC_Write_SimpleARC") - let arc = ARC.load(p) - - let i = arc.ISA.Value - - let existingStudyName = "MyStudy" - let existingAssayName = "MyAssay" - - let assayName = "YourAssay" - i.InitAssay(assayName) |> ignore - arc.ISA <- Some i - - arc.UpdateFileSystem() - arc.Write(p) - - let expectedPaths = - [ - "/isa.investigation.xlsx"; - "/studies/.gitkeep"; - $"/studies/{existingStudyName}/isa.study.xlsx" - $"/studies/{existingStudyName}/README.md" - $"/studies/{existingStudyName}/protocols/.gitkeep"; - $"/studies/{existingStudyName}/resources/.gitkeep"; - "/assays/.gitkeep"; - $"/assays/{existingAssayName}/isa.assay.xlsx" - $"/assays/{existingAssayName}/README.md" - $"/assays/{existingAssayName}/protocols/.gitkeep" - $"/assays/{existingAssayName}/dataset/.gitkeep" - $"/assays/{assayName}/isa.assay.xlsx" - $"/assays/{assayName}/README.md" - $"/assays/{assayName}/protocols/.gitkeep" - $"/assays/{assayName}/dataset/.gitkeep" - "/runs/.gitkeep"; - "/workflows/.gitkeep" - ] - |> List.sort - - - let paths = - Path.getAllFilePaths p - |> Array.sort - - Expect.sequenceEqual paths expectedPaths "Files were not created correctly." - ) - |> testSequenced - ] - -[] -let main = - testList "ARC_Tests" [ - testLoad - testWrite - ] \ No newline at end of file diff --git a/tests/ARCtrl.NET.Tests/AssayTests.fs b/tests/ARCtrl.NET.Tests/AssayTests.fs deleted file mode 100644 index 769612e..0000000 --- a/tests/ARCtrl.NET.Tests/AssayTests.fs +++ /dev/null @@ -1,14 +0,0 @@ -module AssayTests - -open Expecto -open System.Text.Json - -//[] -let testComponentCasting = - - testList "Test" [ - testCase "WillFail" (fun () -> - Expect.isTrue true "Test if the test will test." - - ) - ] \ No newline at end of file diff --git a/tests/ARCtrl.NET.Tests/Contract.fs b/tests/ARCtrl.NET.Tests/Contract.fs deleted file mode 100644 index b1b6c9a..0000000 --- a/tests/ARCtrl.NET.Tests/Contract.fs +++ /dev/null @@ -1,107 +0,0 @@ -module Contract.Tests - -open ARCtrl.NET.Contract -open ARCtrl.Contract -open Expecto -open System.IO -open FsSpreadsheet -open FsSpreadsheet.Net - -let testInputFolder = System.IO.Path.Combine(__SOURCE_DIRECTORY__,@"TestObjects/Contracts") -let testOutputFolder = System.IO.Path.Combine(__SOURCE_DIRECTORY__,@"TestResults/Contracts") - -let testRead = - - testList "Read" [ - testCase "TextFile" (fun () -> - let fileName = "TestReadMe.txt" - let contract = Contract.createRead(fileName,DTOType.PlainText) - let dto = DTO.Text "This is a test" - let expected = - {contract with DTO = Some dto} - let result = fulfillReadContract testInputFolder contract - Expect.equal result expected $"Text was not read correctly" - ) - testCase "XLSXFile" (fun () -> - let fileName = "TestWorkbook.xlsx" - let contract = Contract.createRead(fileName,DTOType.ISA_Study) - let result = fulfillReadContract testInputFolder contract - let dto = Expect.wantSome result.DTO "DTO was not read correctly" - Expect.isTrue dto.isSpreadsheet "DTO was not read correctly" - let wb = dto.AsSpreadsheet() :?> FsSpreadsheet.FsWorkbook - let ws = Expect.wantSome (wb.TryGetWorksheetByName "TestSheet") "Workbook does not contain worksheet" - let row1 = Expect.wantSome (ws.TryGetRowValuesAt 1) "Worksheet does not contain row 1" - let row1AsInts = row1 |> Seq.map (string >> int) - let expected = [1;2;3] - Expect.sequenceEqual row1AsInts expected "Worksheet does not contain correct values" - let row2 = Expect.wantSome (ws.TryGetRowValuesAt 2) "Worksheet does not contain row 2" - let expected = ["A";"B";"C"] |> Seq.map box - Expect.sequenceEqual row2 expected "Worksheet does not contain correct values" - ) - ] - - -let testWrite = - - testList "Write" [ - testCase "TextFileEmpty" (fun () -> - let fileName = "TestEmpty.txt" - let contract = Contract.createCreate(fileName,DTOType.PlainText) - - fulfillWriteContract testOutputFolder contract - - let filePath = Path.Combine(testOutputFolder,fileName) - Expect.isTrue (System.IO.File.Exists filePath) $"File {filePath} was not created" - Expect.equal (File.ReadAllText filePath) "" $"File {filePath} was not empty" - ) - testCase "TextFile" (fun () -> - - let testText = "This is a test" - let fileName = "TestReadMe.txt" - let dto = DTO.Text testText - let contract = Contract.createCreate(fileName,DTOType.PlainText,dto) - - fulfillWriteContract testOutputFolder contract - - let filePath = Path.Combine(testOutputFolder,fileName) - Expect.isTrue (System.IO.File.Exists filePath) $"File {filePath} was not created" - Expect.equal (File.ReadAllText filePath) testText $"File {filePath} was not empty" - ) - testCase "XLSXFile" (fun () -> - - let worksheetName = "TestSheet" - let testWB = new FsWorkbook() - let testSheet = testWB.InitWorksheet (worksheetName) - testSheet.Row(1).Item(1).Value <- "A1" - testSheet.Row(1).Item(2).Value <- "B1" - testSheet.Row(1).Item(3).Value <- "C1" - let fileName = "TestWorkbook.xlsx" - let dto = DTO.Spreadsheet testWB - let contract = Contract.createCreate(fileName,DTOType.ISA_Assay,dto) - - fulfillWriteContract testOutputFolder contract - - let filePath = Path.Combine(testOutputFolder,fileName) - - let wb = FsWorkbook.fromXlsxFile filePath - let ws = Expect.wantSome (wb.TryGetWorksheetByName worksheetName) "Workbook does not contain worksheet" - let row1 = Expect.wantSome (ws.TryGetRowValuesAt 1) "Worksheet does not contain row 1" - let expected = ["A1";"B1";"C1"] |> Seq.map box - Expect.sequenceEqual row1 expected "Worksheet does not contain correct values" - ) - ] - -let testExecute = - - testList "Write" [ - testCase "Implement" (fun () -> - Expect.isTrue false "ImplementTest" - ) - ] - -[] -let main = - testList "ContractTests" [ - testRead - testWrite - ] diff --git a/tests/ARCtrl.NET.Tests/Main.fs b/tests/ARCtrl.NET.Tests/Main.fs deleted file mode 100644 index 224049e..0000000 --- a/tests/ARCtrl.NET.Tests/Main.fs +++ /dev/null @@ -1,14 +0,0 @@ -module arcIO.NET.Tests - -open Expecto - - -let all = testSequenced <| testList "All" [ - Path.Tests.main - Arc.Tests.main - ] - -[] -let main argv = - - Tests.runTestsWithCLIArgs [] argv all diff --git a/tests/ARCtrl.NET.Tests/Path.fs b/tests/ARCtrl.NET.Tests/Path.fs deleted file mode 100644 index b480aa7..0000000 --- a/tests/ARCtrl.NET.Tests/Path.fs +++ /dev/null @@ -1,30 +0,0 @@ -module Path.Tests - -open Expecto -open ARCtrl.NET -open System.Text.Json - - -let getAllFilePaths = - - testList "GetAllFilePaths" [ - testCase "simple" (fun () -> - let p = System.IO.Path.Combine(__SOURCE_DIRECTORY__,@"TestObjects\Path_findSubPaths") - let result = Path.getAllFilePaths p - let expected = - [ - "/File1.txt" - "/File2.csv" - "/SubFolder/File3.xlsx" - "/SubFolder/SubSubFolder/File4" - ] - Expect.sequenceEqual result expected "File Paths were not found correctly." - - ) - ] - -[] -let main = - testList "PathTests" [ - getAllFilePaths - ] diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/.arc/.gitkeep b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/.arc/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/.gitkeep b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/README.md b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/README.md deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/.gitkeep b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/proteomics_result.csv b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/proteomics_result.csv deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample1.raw b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample1.raw deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample2.raw b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample2.raw deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample3.raw b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample3.raw deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample4.raw b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample4.raw deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample5.raw b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample5.raw deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample6.raw b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample6.raw deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample7.raw b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/sample7.raw deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/table.csv b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/table.csv deleted file mode 100644 index a3c13b4..0000000 --- a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/dataset/table.csv +++ /dev/null @@ -1,651 +0,0 @@ -Index,value_1,quant_1,value_2,quant_2,value_3,quant_3,value_4,quant_4,value_5,quant_5,value_6,quant_6 -0,20.60917636,2.366800063,31.76575111,2.51972112,31.239141,2.994118452,38.54463269,2.235910104,26.74437584,3.351820025,18.87709616,3.408542256 -1,20.2667511,3.45287336,10.44136185,3.04179784,24.76736657,2.912656477,36.16958385,3.430737189,24.20981945,3.122776939,-5.253242754,2.186538738 -2,17.36828141,3.73863731,25.9790139,3.498130345,28.59307579,3.049276271,39.80151617,2.05657019,13.29576986,3.752299254,31.94888467,3.28870028 -3,9.917464634,3.41392671,22.41344542,3.811982726,27.02827473,2.871323801,27.91095666,3.401721228,31.75968784,3.099053447,22.38381643,2.944344071 -4,41.79881325,3.479405118,27.03382081,3.496490729,16.14388422,2.811865235,45.12616701,3.004925209,43.44154067,3.512141495,13.92163384,3.265526505 -5,17.14758253,2.286495209,33.79567127,2.848821097,29.53447225,3.594532936,41.29957184,3.208352043,18.97964211,2.943254771,7.00021151,3.023056376 -6,39.36514967,2.623481095,43.34430733,3.253270352,37.65244428,3.340323609,15.02595487,3.174360915,59.08649438,3.116179827,32.12707181,3.128946216 -7,24.67531734,3.005013639,21.14050562,2.909298401,27.58292887,3.076099914,25.44390985,2.409556765,24.41151962,3.80626409,34.54725553,3.632621756 -8,24.36182152,3.188425192,24.96747128,3.491500103,36.83422896,3.653180394,28.5746082,3.036992103,22.66157764,2.908729803,36.05784788,1.696238827 -9,8.17927182,3.152130596,6.865294845,2.739631151,28.26505134,2.672745865,32.78770943,3.04109728,24.51318045,3.405063636,47.01077115,2.836521016 -10,23.89515294,3.061123404,18.68652245,2.455147043,46.97485465,3.68918597,26.88184583,3.358516996,24.70883965,3.448101321,25.28267201,2.277448641 -11,19.23462713,3.178167021,42.25565794,3.544084566,5.496309228,2.40837214,19.26703661,3.665371223,15.46755864,2.933841019,35.49115953,3.39372516 -12,29.2464254,3.009975576,32.23685962,2.482772452,21.89530136,3.218307613,4.223189095,2.770498673,20.16137388,2.692457687,42.99818546,3.643681991 -13,21.92369808,3.447973514,11.59162699,3.480650329,33.96074837,2.95468097,19.57986705,3.766877677,41.12660294,3.427034792,21.62259742,3.443194242 -14,15.96474227,3.061203691,23.06283077,3.42444171,25.98426886,3.576125139,21.49532558,2.224421571,16.28495731,2.972966931,13.2045675,2.700833556 -15,25.24765674,3.554892466,32.56730516,3.622277772,36.53095697,3.228979032,28.31952741,3.184153175,39.41000706,2.983383051,23.43532653,1.420588925 -16,24.81316281,3.490788584,16.67112529,3.191237197,24.12307012,3.96816438,45.98150201,3.235178562,22.57703174,2.711702377,27.44075624,3.513032992 -17,44.08286738,3.296324853,18.88658857,3.322930292,31.38405354,3.816661909,32.82428929,3.430822911,26.80402725,3.415673275,25.13325396,3.413904541 -18,23.85666276,3.128851776,32.22763419,2.796953488,45.17888136,2.756213389,23.53408123,3.294350412,30.5549607,3.450311441,36.13674601,3.013595846 -19,34.51145393,3.206745385,41.50326891,2.810570405,24.80342829,3.360357476,12.10297986,3.552163786,28.30342187,3.521498551,14.3955304,1.440841411 -20,22.10854005,3.33854044,17.60659316,3.424198717,34.15457895,2.157162526,34.50498387,3.123786212,23.43427294,3.082016061,13.6249119,2.782179131 -21,34.44765198,3.596613648,38.87198488,3.438231695,36.46154941,3.249408847,22.95215379,2.510152553,21.83809641,3.394245845,40.94563426,3.025732545 -22,36.63022387,3.342592993,30.39640632,3.783198972,19.3636592,3.096327448,11.91082904,3.496797366,21.38293085,3.171900024,39.08628238,3.795622852 -23,27.07855567,3.812380691,29.81001463,3.442106021,24.2599697,3.400543914,32.57173186,3.376729351,34.720929,2.450155236,32.95509159,2.951217781 -24,22.22450547,2.517942833,26.18650541,2.703049593,17.47141535,2.888110621,16.94781063,3.220523464,28.08883401,3.589119865,20.19751678,3.468856947 -25,33.72343818,3.40174576,36.4584919,3.002611613,17.03641428,3.917758498,18.21973668,3.800800816,35.31534639,2.747726586,33.30657157,3.206567311 -26,5.968099441,3.564184284,12.08788366,3.098450762,7.836571927,3.036421686,34.10008403,2.597896214,43.63721942,3.046321677,35.00081181,3.078246621 -27,25.10825562,3.464433432,10.11000141,3.488205519,21.47266954,2.904994286,12.40850104,3.788932017,21.18601112,3.89148464,6.737994176,3.140522503 -28,18.09333759,3.091071068,8.746817871,3.920155065,23.83582285,2.822370744,18.86604924,2.98091841,23.35955583,2.706377418,24.52094976,3.22691115 -29,32.46633105,2.96197856,39.91942193,3.540263057,30.88271643,3.167635665,25.90363595,3.293508694,28.87080505,2.599489549,24.63950169,2.641400212 -30,16.42492898,2.478240228,27.54774241,3.288378368,30.0514856,3.39623439,24.46778634,3.322674114,16.11623232,3.16791363,23.45238495,3.07292471 -31,28.65125637,2.730139646,15.42732978,3.132744456,19.20841752,3.31213107,27.70768989,2.702571278,30.94306601,3.711177291,33.11773628,2.907266827 -32,24.37799414,3.20804831,29.56041526,-0.139610586,35.55479845,2.561175589,34.8445276,3.128937581,35.35928363,3.273098852,17.78099675,1.905911827 -33,10.62230927,3.57999766,32.77317909,3.021654271,16.3030726,2.45668172,48.46767452,3.073207712,21.01321527,3.446959753,32.77150279,3.682618207 -34,12.91389117,3.140340926,15.80994609,2.611820081,42.25851995,2.329097582,31.67511374,2.346430502,20.76910847,2.948779825,33.22470367,2.164800454 -35,27.86699924,3.266887331,26.19448085,3.507437752,32.9002868,3.435957211,27.49728144,3.590400923,16.09384527,3.651085597,29.38498699,3.135808778 -36,16.88605519,3.033284474,41.64243863,3.137665504,31.76601668,2.716378366,29.70541284,3.217272992,45.74884088,3.543674858,36.65948256,3.612869186 -37,15.0610888,3.185101951,37.17574998,3.469305554,33.52091805,3.811023275,29.66945732,3.135192666,42.38030763,2.874206516,15.66452908,0.907097635 -38,39.97363659,3.161315695,16.91937791,2.919056752,9.462822931,3.050492712,15.88427824,3.518612497,34.20252776,3.493428981,14.16181464,3.226026909 -39,41.02812418,2.7732624,15.49724184,3.339399641,25.10294484,3.172906446,22.19257601,3.211969462,6.408272032,3.377294413,20.46460527,3.452143893 -40,30.32795224,3.164217484,28.62777628,3.265322128,9.782081539,3.137228273,38.40777842,2.566254383,-2.222074486,2.923678288,26.84180022,3.523434988 -41,14.36828159,3.185506125,32.07611361,3.093838885,40.63067086,3.501549851,9.876755777,2.945255426,36.11385625,3.477409392,35.80878946,2.687730366 -42,13.58762729,2.157281252,25.68178319,3.231361083,13.21044936,3.42830451,46.72279919,3.295394239,27.192841,2.58739696,14.91534661,3.398582762 -43,23.60292601,3.334716637,20.82039889,2.953515827,22.9105469,1.818206004,11.6841137,3.940747875,34.83013908,3.682339562,8.413412527,2.471014773 -44,11.60949513,3.370558791,7.901267537,2.867029199,13.21794599,3.02310825,26.55403753,3.766376009,30.28063738,3.639710454,18.77319768,2.132998026 -45,30.85285523,3.885913232,17.8196691,3.30602411,36.31386084,2.614818494,25.61119166,2.830339215,21.63804018,3.371687267,37.37272672,2.922609494 -46,22.18392142,2.907889902,42.7494121,3.241511504,11.36263677,3.14685158,10.51442268,1.956598932,26.33190565,3.578230526,-2.141454626,3.236098167 -47,31.39044542,3.292671329,29.36012387,3.013594008,19.52291834,3.721420879,10.94551141,2.564235116,27.8600769,2.812409683,18.82904191,3.220421478 -48,34.18387858,2.971870442,11.33280692,3.047066451,20.22455315,2.470675753,3.86911054,3.413816634,23.17444279,4.002321378,21.67512609,3.270079298 -49,17.51376691,3.525339312,29.10956717,3.209998305,18.14863463,3.203169991,19.47956295,3.499029799,2.485149349,3.257298875,44.70375408,3.136744084 -50,42.42865019,1.540684066,33.8419035,3.858634073,20.85350494,3.642711487,38.91303268,2.905148645,22.86078214,3.568857086,28.96181033,3.23001123 -51,19.36794077,3.510032185,10.56607062,3.553945851,-3.400625654,2.794294148,14.20105364,3.129057971,30.52039566,3.593830626,25.33870781, -52,27.85046482,3.093063513,22.4250409,3.701695639,20.51736138,3.339693961,24.36326823,3.280961733,17.01715142,3.365392568,25.34764749,3.070516736 -53,30.51969923,3.575569491,10.05280118,3.508819867,27.33943807,3.268660906,27.0037118,2.920648215,29.34444463,2.800734318,27.79686163,3.04729657 -54,34.01123534,3.39749369,21.4975815,1.837559879,20.9064718,1.884919731,42.1166379,2.883840013,31.90331739,3.335654809,15.94613387,2.898350014 -55,24.75862805,3.770533208,19.08595675,3.362855987,16.04172404,3.681986875,22.31341188,2.291727097,22.71995232,3.166936989,25.42921429,3.47937379 -56,29.86505997,3.501184957,27.4337937,3.706565484,28.83529093,2.796550164,26.09004881,3.861491003,22.08929576,2.752441598,17.51996755,3.554385189 -57,21.08232857,3.445537308,17.63939421,3.271286888,12.99554996,3.269942836,29.69342553,3.422760002,24.43867487,2.40741653,23.81017339,3.027190552 -58,17.1029576,3.213781085,32.60447497,2.716184911,22.59376774,2.870465518,36.17899884,2.909668345,20.01299958,2.927544236,25.10559119,3.826869463 -59,22.32883761,3.584126606,26.05486915,2.333320991,17.78441137,2.623281348,32.54735663,3.705331891,10.09909231,2.752045112,22.30082692,4.021415767 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b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/protocols/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/protocols/extractionProtocol.txt b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/protocols/extractionProtocol.txt deleted file mode 100644 index 41de6e7..0000000 --- a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/assays/measurement1/protocols/extractionProtocol.txt +++ /dev/null @@ -1,3 +0,0 @@ -- centrifuge again -- discard the supernate -- solve the pellet in buffer chemical X \ No newline at end of file diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/isa.investigation.xlsx b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/isa.investigation.xlsx deleted file mode 100644 index f6c25d3..0000000 Binary files a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/isa.investigation.xlsx and /dev/null differ diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/runs/.gitkeep b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/runs/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/.gitkeep b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/README.md b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/README.md deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/isa.study.xlsx b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/isa.study.xlsx deleted file mode 100644 index 321ce55..0000000 Binary files a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/isa.study.xlsx and /dev/null differ diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/protocols/.gitkeep b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/protocols/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/.gitkeep b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample1_e36ca6b8-19ba-4504-aa82-d4781765873d.png b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample1_e36ca6b8-19ba-4504-aa82-d4781765873d.png deleted file mode 100644 index 369be75..0000000 Binary files a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample1_e36ca6b8-19ba-4504-aa82-d4781765873d.png and /dev/null differ diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample2_714ca2b7-22b7-4f69-b83d-9165f624da25.png b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample2_714ca2b7-22b7-4f69-b83d-9165f624da25.png deleted file mode 100644 index bf11050..0000000 Binary files a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample2_714ca2b7-22b7-4f69-b83d-9165f624da25.png and /dev/null differ diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample3_66fac760-acc7-4ed4-ba21-2cb67fa36e4d.png b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample3_66fac760-acc7-4ed4-ba21-2cb67fa36e4d.png deleted file mode 100644 index dfa265d..0000000 Binary files a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample3_66fac760-acc7-4ed4-ba21-2cb67fa36e4d.png and /dev/null differ diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample4_cba5f40c-fc05-44d6-a589-b0e3dafaeefe.png b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample4_cba5f40c-fc05-44d6-a589-b0e3dafaeefe.png deleted file mode 100644 index 8bb7def..0000000 Binary files a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample4_cba5f40c-fc05-44d6-a589-b0e3dafaeefe.png and /dev/null differ diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample5_84c37b60-2342-4226-a36c-4b8dfe84ebe9.png b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample5_84c37b60-2342-4226-a36c-4b8dfe84ebe9.png deleted file mode 100644 index cfb9823..0000000 Binary files a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample5_84c37b60-2342-4226-a36c-4b8dfe84ebe9.png and /dev/null differ diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample6_208df064-4b1c-4da0-a1f8-6412e1fb2284.png b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample6_208df064-4b1c-4da0-a1f8-6412e1fb2284.png deleted file mode 100644 index e5c5c41..0000000 Binary files a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/studies/experiment1_material/resources/Sample6_208df064-4b1c-4da0-a1f8-6412e1fb2284.png and /dev/null differ diff --git a/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/workflows/.gitkeep b/tests/ARCtrl.NET.Tests/TestObjects/ARC_SimpleARC/workflows/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/Contracts/TestReadMe.txt b/tests/ARCtrl.NET.Tests/TestObjects/Contracts/TestReadMe.txt deleted file mode 100644 index 793aa68..0000000 --- a/tests/ARCtrl.NET.Tests/TestObjects/Contracts/TestReadMe.txt +++ /dev/null @@ -1 +0,0 @@ -This is a test \ No newline at end of file diff --git a/tests/ARCtrl.NET.Tests/TestObjects/Contracts/TestWorkbook.xlsx b/tests/ARCtrl.NET.Tests/TestObjects/Contracts/TestWorkbook.xlsx deleted file mode 100644 index dfc1e46..0000000 Binary files a/tests/ARCtrl.NET.Tests/TestObjects/Contracts/TestWorkbook.xlsx and /dev/null differ diff --git a/tests/ARCtrl.NET.Tests/TestObjects/Path_findSubPaths/File1.txt b/tests/ARCtrl.NET.Tests/TestObjects/Path_findSubPaths/File1.txt deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/Path_findSubPaths/File2.csv b/tests/ARCtrl.NET.Tests/TestObjects/Path_findSubPaths/File2.csv deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/Path_findSubPaths/SubFolder/File3.xlsx b/tests/ARCtrl.NET.Tests/TestObjects/Path_findSubPaths/SubFolder/File3.xlsx deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.NET.Tests/TestObjects/Path_findSubPaths/SubFolder/SubSubFolder/File4 b/tests/ARCtrl.NET.Tests/TestObjects/Path_findSubPaths/SubFolder/SubSubFolder/File4 deleted file mode 100644 index e69de29..0000000 diff --git a/tests/ARCtrl.Querymodel.Tests/ARCtrl.Querymodel.Tests.fsproj b/tests/ARCtrl.Querymodel.Tests/ARCtrl.Querymodel.Tests.fsproj index 86126e9..42246e3 100644 --- a/tests/ARCtrl.Querymodel.Tests/ARCtrl.Querymodel.Tests.fsproj +++ b/tests/ARCtrl.Querymodel.Tests/ARCtrl.Querymodel.Tests.fsproj @@ -16,11 +16,7 @@ - - - - diff --git a/tests/ARCtrl.Querymodel.Tests/TestARC.fs b/tests/ARCtrl.Querymodel.Tests/TestARC.fs index d568f1b..5600bbc 100644 --- a/tests/ARCtrl.Querymodel.Tests/TestARC.fs +++ b/tests/ARCtrl.Querymodel.Tests/TestARC.fs @@ -3,7 +3,6 @@ open Expecto open System.Text.Json open ARCtrl -open ARCtrl.NET open ARCtrl.Process open ARCtrl.QueryModel let testArcPath = __SOURCE_DIRECTORY__ + @"\TestObjects\TestArc"