From 275323c95a1e350196fef61169bba030ba45288f Mon Sep 17 00:00:00 2001 From: Heinrich Lukas Weil Date: Wed, 2 Aug 2023 12:28:09 +0400 Subject: [PATCH] add first experimental version of arc.getWriteContracts --- src/ARCtrl/ARCtrl.fs | 69 +++++++++++++++++++++++++++++++- src/FileSystem/FileSystemTree.fs | 35 +++++++++++++++- 2 files changed, 102 insertions(+), 2 deletions(-) diff --git a/src/ARCtrl/ARCtrl.fs b/src/ARCtrl/ARCtrl.fs index d8b31fec..5cda26c8 100644 --- a/src/ARCtrl/ARCtrl.fs +++ b/src/ARCtrl/ARCtrl.fs @@ -3,7 +3,7 @@ open FileSystem open Contract open ISA - +open FsSpreadsheet open Fable.Core module ARCAux = @@ -163,6 +163,73 @@ You could initialized your ARC with `ARC.fromFilePaths` or run `yourArc.addFSFro ) {this with ISA = Some investigation} + + static member updateFileSystemTree(arc) = + match arc.ISA,arc.FileSystem with + | Some inv,_ -> + let studyNames,assayNames = + inv.Studies + |> Seq.fold (fun (studyNames,assayNames) s -> + Array.append studyNames [|s.Identifier|], + Array.append assayNames (s.Assays |> Seq.map (fun a -> a.Identifier) |> Array.ofSeq) + + ) ([||],[||]) + let workflows = FileSystemTree.createWorkflowsFolder [||] + let runs = FileSystemTree.createRunsFolder [||] + let assays = FileSystemTree.createAssaysFolder (assayNames |> Array.map FileSystemTree.initAssayFolder) + let studies = FileSystemTree.createStudiesFolder (studyNames |> Array.map FileSystemTree.initStudyFolder) + let investigation = FileSystemTree.createFile "isa.investigation.xlsx" + let tree = FileSystemTree.createFolder(inv.Identifier, [|investigation;assays;studies;workflows;runs|]) + let fs = FileSystem.create(tree) + ARC.create(inv,fs = fs) + | _ -> + let workflows = FileSystemTree.createWorkflowsFolder [||] + let runs = FileSystemTree.createRunsFolder [||] + let assays = FileSystemTree.createAssaysFolder [||] + let studies = FileSystemTree.createStudiesFolder [||] + let tree = FileSystemTree.createFolder(Identifier.createMissingIdentifier(), [|assays;studies;workflows;runs|]) + let fs = FileSystem.create(tree) + ARC.create(fs = fs) + + + /// + /// This function creates the ARC-model from fullfilled READ contracts. The necessary READ contracts can be created with `ARC.getReadContracts`. + /// + /// The fullfilled READ contracts. + /// If this flag is set true, the function will print any missing/found assays/studies to the console. *Default* = false + member this.getWriteContracts () = + let arc = ARC.updateFileSystemTree this + let workbooks = System.Collections.Generic.Dictionary() + match arc.ISA with + | Some inv -> + workbooks.Add ("isa.investigation.xlsx", (DTOType.ISA_Investigation, ISA.Spreadsheet.ArcInvestigation.toFsWorkbook inv)) + inv.Studies + |> Seq.iter (fun s -> + workbooks.Add ( + Path.combineMany[|"studies";s.Identifier;"isa.study.xlsx"|], + (DTOType.ISA_Study, ISA.Spreadsheet.ArcStudy.toFsWorkbook s)) + s.Assays + |> Seq.iter (fun a -> + workbooks.Add ( + Path.combineMany[|"assays";a.Identifier;"isa.assay.xlsx"|], + (DTOType.ISA_Assay, ISA.Spreadsheet.ArcAssay.toFsWorkbook a)) + ) + ) + | None -> printfn "ARC contains no ISA part." + match arc.FileSystem with + | Some fs -> + fs.Tree.ToFilePaths(true) + |> Array.map (fun fp -> + match Dictionary.tryGet fp workbooks with + | Some (dto,wb) -> Contract.createCreate(fp,dto,DTO.Spreadsheet wb) + | None -> Contract.createCreate(fp, DTOType.PlainText, DTO.Text "") + + ) + | None -> + printfn "ARC contains no FileSystem part." + [||] + + //-Pseudo code-// //// Option 1 //let fs, readcontracts = ARC.FSFromFilePaths filepaths diff --git a/src/FileSystem/FileSystemTree.fs b/src/FileSystem/FileSystemTree.fs index acaf6f3e..8ee02fd7 100644 --- a/src/FileSystem/FileSystemTree.fs +++ b/src/FileSystem/FileSystemTree.fs @@ -112,4 +112,37 @@ type FileSystemTree = loop this static member filter (predicate: string -> bool) = - fun (tree: FileSystemTree) -> tree.Filter predicate \ No newline at end of file + fun (tree: FileSystemTree) -> tree.Filter predicate + + + + static member initAssayFolder(assayName : string) = + let dataset = FileSystemTree.createFolder("dataset", [|FileSystemTree.createFile ".gitkeep"|]) + let protocols = FileSystemTree.createFolder("protocols", [|FileSystemTree.createFile ".gitkeep"|]) + let readme = FileSystemTree.createFile "README.md" + let assayFile = FileSystemTree.createFile "isa.assay.xlsx" + FileSystemTree.createFolder(assayName, [|dataset; protocols; assayFile; readme|]) + + static member initStudyFolder(studyName : string) = + let resources = FileSystemTree.createFolder("resources", [|FileSystemTree.createFile ".gitkeep"|]) + let protocols = FileSystemTree.createFolder("protocols", [|FileSystemTree.createFile ".gitkeep"|]) + let readme = FileSystemTree.createFile "README.md" + let studyFile = FileSystemTree.createFile "isa.study.xlsx" + FileSystemTree.createFolder(studyName, [|resources; protocols; studyFile; readme|]) + + static member initInvestigationFile() = + FileSystemTree.createFile "isa.investigation.xlsx" + + + static member createAssaysFolder(assays : FileSystemTree array) = + FileSystemTree.createFolder("assays", Array.append [|FileSystemTree.createFile ".gitkeep"|] assays) + + static member createStudiesFolder(studies : FileSystemTree array) = + FileSystemTree.createFolder("studies", Array.append [|FileSystemTree.createFile ".gitkeep"|] studies) + + static member createWorkflowsFolder(workflows : FileSystemTree array) = + FileSystemTree.createFolder("assays", Array.append [|FileSystemTree.createFile ".gitkeep"|] workflows) + + static member createRunsFolder(runs : FileSystemTree array) = + FileSystemTree.createFolder("runs", Array.append [|FileSystemTree.createFile ".gitkeep"|] runs) +