Merge pull request #170 from nfdi4plants/filenameAttribute

Throw warning when character length of file name arguments exceed 31

src/ArcCommander/ArgumentProcessing.fs

@@ -28,20 +28,23 @@ module ArgumentProcessing =
             Tooltip     : string
             IsMandatory : bool
             IsFlag      : bool
+            IsFileName  : bool
         }
 
-    let createAnnotatedArgument arg tt mand isFlag = 
+    let createAnnotatedArgument arg tt mand isFlag isFN = 
         {
             Arg = arg
             Tooltip = tt 
             IsMandatory = mand
             IsFlag = isFlag
+            IsFileName = isFN
         }
 
+     // classic forbidden symbols for file names in Windows (which also includes Linux/macOS)
+    let private forbiddenSymbols = [|'/'; '\\'; '"'; '>'; '<'; '?'; '='; '*'; '|'|]
+
     /// Characters that must not occur in file names.
     let private forbiddenChars = 
-        // classic forbidden symbols for file names in Windows (which also includes Linux/macOS)
-        let forbiddenSymbols = [|'/'; '\\'; '"'; '>'; '<'; '?'; '='; '*'; '|'|]
         let controlChars = Array.init 32 (fun i -> char i)
         Array.append controlChars forbiddenSymbols
 
@@ -77,6 +80,12 @@ module ArgumentProcessing =
             log.Error $"Identifier/filename \"{str}\" is a reserved filename. Please choose another one."
             raise (Exception "")
 
+    /// Takes a string and checks if it is longer than 31 chars
+    let private checkForNameLength (str : string) =
+        let log = Logging.createLogger "ArgumentProcessingCheckForFileNameLength"
+        if seq str |> Seq.length |> (<) 31 then
+            log.Warn $"Identifier/filename \"{str}\" is longer than 31 characters, which might cause problems in excel sheets."
+
     /// Returns true if the argument flag of name k was given by the user.
     let containsFlag k (arguments : Map<string,Argument>) =
         let log = Logging.createLogger "ArgumentProcessingContainsFlagLog"
@@ -144,7 +153,7 @@ module ArgumentProcessing =
             | [||] -> 
                 let toolTip = (FSharpValue.MakeUnion (unionCase, [||]) :?> 'T).Usage
                 let value,isFlag = if Map.containsKey unionCase.Name m then Some Flag,true else None,true
-                unionCase.Name,createAnnotatedArgument value toolTip isMandatory isFlag
+                unionCase.Name,createAnnotatedArgument value toolTip isMandatory isFlag isFileAttribute
             | [|c|] when c.PropertyType.Name = "String" -> 
                 let toolTip = (FSharpValue.MakeUnion (unionCase, [|box ""|]) :?> 'T).Usage
                 let value, isFlag = 
@@ -155,13 +164,14 @@ module ArgumentProcessing =
                             if isFileAttribute then
                                 iterForbiddenChars str
                                 checkForReservedFns str
+                                checkForNameLength str
                                 replaceSpace str
                             else str
                         Field adjustedStr
                         |> Some,
                         false
                     | None -> None, false
-                unionCase.Name, createAnnotatedArgument value toolTip isMandatory isFlag
+                unionCase.Name, createAnnotatedArgument value toolTip isMandatory isFlag isFileAttribute
             | _ ->
                 log.Fatal($"Cannot parse argument {unionCase.Name} because its parsing rules were not yet implemented.")
                 raise (Exception(""))
@@ -239,13 +249,20 @@ module ArgumentProcessing =
                     elif arg.IsFlag then
                         sprintf "Remove # below to set flag: %s" arg.Tooltip
                     else sprintf "%s" arg.Tooltip
+                let fileComment =
+                    $"""# FileName: The value of this argument will be used as a file or folder name.
+# FileName: Please refrain from using the following characters: {forbiddenSymbols |> Seq.map string |> String.concat " "}.
+# FileName: Please write a value of length at most 31 characters."""
                 let value = 
                     match arg.Arg with
                     | Some (Flag)           -> sprintf "%s" key
                     | Some (Field v)        -> sprintf "%s:%s" key v
                     | None when arg.IsFlag  -> sprintf "#%s" key
                     | None                  -> sprintf "%s:" key
-                sprintf "#%s\n%s" comment value
+                if arg.IsFileName then
+                    sprintf "#%s\n%s\n%s" comment fileComment value
+                else
+                    sprintf "#%s\n%s" comment value
             )
             |> Array.reduce (fun a b -> a + "\n\n" + b)
             |> sprintf "%s\n\n%s" header
@@ -260,6 +277,7 @@ module ArgumentProcessing =
                     if key.Contains "Identifier" then
                         iterForbiddenChars trValu
                         checkForReservedFns trValu
+                        checkForNameLength trValu
                         replaceSpace trValu
                     else trValu
             match s.Split c with

src/ArcCommander/CLIArguments/AssayArgs.fs

@@ -68,8 +68,8 @@ type AssayUpdateArgs =
 
 /// CLI arguments for interactively editing existing assay metadata.
 type AssayEditArgs = 
-    | [<AltCommandLine("-s")>][<Unique>][<FileNameAttribute>]               StudyIdentifier of study_identifier : string
-    | [<Mandatory>][<AltCommandLine("-a")>][<Unique>][<FileNameAttribute>]  AssayIdentifier of assay_identifier : string
+    | [<AltCommandLine("-s")>][<Unique>][<FileName>]               StudyIdentifier of study_identifier : string
+    | [<Mandatory>][<AltCommandLine("-a")>][<Unique>][<FileName>]  AssayIdentifier of assay_identifier : string
 
     interface IArgParserTemplate with
         member this.Usage =

src/ArcCommander/CLIArguments/InvestigationArgs.fs

@@ -1,13 +1,14 @@
 namespace ArcCommander.CLIArguments
 
 open Argu 
+open ArcCommander.ArgumentProcessing
 
 /// CLI arguments for creating a new investigation file for the arc
 // in the case of investigations 'empty' does not mean empty file but rather an 
 // investigation without studies/assays. To reflect the need for metadata here,
 // this command is called `create` instead of `init`
 type InvestigationCreateArgs = 
-    | [<Mandatory>][<AltCommandLine("-i")>][<Unique>] Identifier of investigation_identifier:string
+    | [<Mandatory>][<AltCommandLine("-i")>][<Unique>][<FileName>] Identifier of investigation_identifier:string
     | [<Unique>] Title of title:string
     | [<Unique>] Description of description:string
     | [<Unique>] SubmissionDate of submission_date:string
@@ -24,7 +25,7 @@ type InvestigationCreateArgs =
 
 /// CLI arguments updating the arc's existing investigation file
 type InvestigationUpdateArgs = 
-    | [<Mandatory>][<AltCommandLine("-i")>][<Unique>] Identifier of investigation_identifier:string
+    | [<Mandatory>][<AltCommandLine("-i")>][<Unique>][<FileName>] Identifier of investigation_identifier:string
     | [<Unique>] Title of title:string
     | [<Unique>] Description of description:string
     | [<Unique>] SubmissionDate of submission_date:string