Commits on Feb 18, 2024

1. ShellJob: Detect and prevent filename clashes …

   So far, no validation was performed on the filenames of input nodes that
   would be written to the working directory that could overlap with files
   written by the plugin itself, such as `stdout` and `stderr`. This could
   lead to unexpected results and often calculations failing completely.
   
   For example, if a `SinglefileData` would be written to the working
   directory with the filename `stdout`, most likely because the `filename`
   attribute of the node was set to this, then this would be overwritten by
   the redirection of the stdout, which is redirected to the file `stdout`
   by default.
   
   A distinction is made between clashes that happen "implicitly", meaning
   the filename of the `SinglefileData` or `FolderData` just happen to
   overlap, compared to "explicitly" where the user specifies a conflicting
   filename in the `filenames` input. In the latter case, an exception is
   raised during the validation. In the former case, the target filename is
   automatically changed to a unique filename to resolve the naming issue.
   This solution is chosen because this will happen often in normal use
   cases of `aiida-shell`. For example, if a command is run whose stdout is
   captured, it will be stored as a `SinglefileData` with the name
   `stdout`. If this in turn is used as an input for a next command, this
   filename will clash as `stdout` is a reserved name. This would force the
   user to manually correct the problem by defining an alternative name in
   `filenames`. Since this will occur so often, it is better to have the
   plugin automatically solve this conflict.
   
   There is a special case for the `FolderData` where an object contained
   within it overlaps with a reserved filename. In this case, the strategy
   mentioned above of automatically renaming won't work because the writing
   of the contents is not done by the plugin but by the engine. Instead, an
   exception is raised. Unfortunately, this is not done in the input
   validation and so this will result in an excepted process. However, it
   is currently not possible to put this logic in the input validation as
   this would require significant refactoring.

   

   sphuber committed Feb 18, 2024
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