FileSystemTree additions and Payload detection #189
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@@ -242,7 +242,108 @@ type ARC(?isa : ISA.ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSyste | |
| let fsCopy = _fs.Copy() | ||
| new ARC(?isa = isaCopy, ?cwl = _cwl, fs = fsCopy) | ||
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| /// <summary> | ||
| /// Returns the FileSystemTree of the ARC with only the registered files and folders included. | ||
| /// </summary> | ||
| /// <param name="IgnoreHidden">Wether or not to ignore hidden files and folders starting with '.'. If true, no hidden files are included in the result. (default: true)</param> | ||
| member this.GetRegisteredPayload(?IgnoreHidden:bool) = | ||
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| let isaCopy = _isa |> Option.map (fun i -> i.Copy()) // not sure if needed, but let's be safe | ||
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| let registeredStudies = | ||
| isaCopy | ||
| |> Option.map (fun isa -> isa.Studies.ToArray()) // to-do: isa.RegisteredStudies | ||
| |> Option.defaultValue [||] | ||
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| let registeredAssays = | ||
| registeredStudies | ||
| |> Array.map (fun s -> s.Assays.ToArray()) // to-do: s.RegisteredAssays | ||
| |> Array.concat | ||
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| let includeRootFiles : Set<string> = | ||
| set [ | ||
| Path.InvestigationFileName | ||
| Path.READMEFileName | ||
| ] | ||
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| let includeStudyFiles = | ||
| registeredStudies | ||
| |> Array.map (fun s -> | ||
| let studyFoldername = $"{Path.StudiesFolderName}/{s.Identifier}" | ||
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| set [ | ||
| yield $"{studyFoldername}/{Path.StudyFileName}" | ||
| yield $"{studyFoldername}/{Path.READMEFileName}" | ||
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| //just allow any constructed path from cell values. there may be occasions where this includes wrong files, but its good enough for now. | ||
| for table in s.Tables do | ||
| for kv in table.Values do | ||
| let textValue = kv.Value.ToFreeTextCell().AsFreeText | ||
| yield textValue // from arc root | ||
| yield $"{studyFoldername}/{Path.StudiesResourcesFolderName}/{textValue}" // from study root > resources | ||
| yield $"{studyFoldername}/{Path.StudiesProtocolsFolderName}/{textValue}" // from study root > protocols | ||
| ] | ||
| ) | ||
| |> Set.unionMany | ||
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| let includeAssayFiles = | ||
| registeredAssays | ||
| |> Array.map (fun a -> | ||
| let assayFoldername = $"{Path.AssaysFolderName}/{a.Identifier}" | ||
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| set [ | ||
| yield $"{assayFoldername}/{Path.AssayFileName}" | ||
| yield $"{assayFoldername}/{Path.READMEFileName}" | ||
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| //just allow any constructed path from cell values. there may be occasions where this includes wrong files, but its good enough for now. | ||
| for table in a.Tables do | ||
| for kv in table.Values do | ||
| let textValue = kv.Value.ToFreeTextCell().AsFreeText | ||
|
There was a problem hiding this comment. @Freymaurer @HLWeil is this the way to access a cells text? If that's the case, I suggest we add a convenience function for this There was a problem hiding this comment. Yup just tested it out. This definitely needs some convenience function. |
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| yield textValue // from arc root | ||
| yield $"{assayFoldername}/{Path.AssayDatasetFolderName}/{textValue}" // from assay root > dataset | ||
| yield $"{assayFoldername}/{Path.AssayProtocolsFolderName}/{textValue}" // from assay root > protocols | ||
| ] | ||
| ) | ||
| |> Set.unionMany | ||
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| let includeFiles = Set.unionMany [includeRootFiles; includeStudyFiles; includeAssayFiles] | ||
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| let ignoreHidden = defaultArg IgnoreHidden true | ||
| let fsCopy = _fs.Copy() // not sure if needed, but let's be safe | ||
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| fsCopy.Tree | ||
| |> FileSystemTree.toFilePaths() | ||
| |> Array.filter (fun p -> | ||
| p.StartsWith(Path.WorkflowsFolderName) | ||
| || p.StartsWith(Path.RunsFolderName) | ||
| || includeFiles.Contains(p) | ||
| ) | ||
| |> FileSystemTree.fromFilePaths | ||
| |> fun tree -> if ignoreHidden then tree |> FileSystemTree.filterFiles (fun n -> not (n.StartsWith("."))) else Some tree | ||
| |> Option.bind (fun tree -> if ignoreHidden then tree |> FileSystemTree.filterFolders (fun n -> not (n.StartsWith("."))) else Some tree) | ||
| |> Option.defaultValue (FileSystemTree.fromFilePaths [||]) | ||
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| /// <summary> | ||
| /// Returns the FileSystemTree of the ARC with only and folders included that are considered additional payload. | ||
| /// </summary> | ||
| /// <param name="IgnoreHidden">Wether or not to ignore hidden files and folders starting with '.'. If true, no hidden files are included in the result. (default: true)</param> | ||
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| member this.GetAdditionalPayload(?IgnoreHidden:bool) = | ||
| let ignoreHidden = defaultArg IgnoreHidden true | ||
| let registeredPayload = | ||
| this.GetRegisteredPayload() | ||
| |> FileSystemTree.toFilePaths() | ||
| |> set | ||
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| _fs.Copy().Tree | ||
| |> FileSystemTree.toFilePaths() | ||
| |> Array.filter (fun p -> not (registeredPayload.Contains(p))) | ||
| |> FileSystemTree.fromFilePaths | ||
| |> fun tree -> if ignoreHidden then tree |> FileSystemTree.filterFiles (fun n -> not (n.StartsWith("."))) else Some tree | ||
| |> Option.bind (fun tree -> if ignoreHidden then tree |> FileSystemTree.filterFolders (fun n -> not (n.StartsWith("."))) else Some tree) | ||
| |> Option.defaultValue (FileSystemTree.fromFilePaths [||]) | ||
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| //-Pseudo code-// | ||
| //// Option 1 | ||
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As far as I see it, this is not needed. But we definitely need structural equality functions @Freymaurer. So functions like this here can be tested for doing no change to the ARC itself.
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then i guess it is better to leave it for now