[23.0] Fix upload paramfile handling (for real user setups) #16504
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bernt-matthias
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the paramfile is created by `galaxy.tools.actions.upload_common.create_paramfile()` and stored in `database/tmp/upload_params_TMPNAME` with mode 600 (it's created with tmpfile, i.e. the mode is independent of the used umask). `galaxy.jobs.MinimalJobWrapper.__prepare_upload_paramfile()` copies this file to the jow working dir. Without the change `ToolEvaluator.build_param_dict()` sets the paramfile to the file in the jow working dir, but it is overwritten immediately by the value in `incoming`.
nsoranzo
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Aug 2, 2023
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the paramfile is created by
galaxy.tools.actions.upload_common.create_paramfile()and stored indatabase/tmp/upload_params_TMPNAMEwith mode 600 (it's created with tmpfile, i.e. the mode is independent of the used umask).galaxy.jobs.MinimalJobWrapper.__prepare_upload_paramfile()copies this file to the jow working dir.Without the change
ToolEvaluator.build_param_dict()sets the paramfile to the file in the jow working dir, but it is overwritten immediately by the value inincoming.The original implementation should make no difference for non-real user setups, but real user setups break because the users can't read the paramfile in
database/tmp/.I noticed this for an upload to a library (which apparently still uses the old upload tool and not data fetch).
Was thinking if its possible to fix the value in incoming, or just use a config file from the start. But I was unsure how and went for the quick and dirty fix.
I'm targeting 23.0 because it's the release I'm currently using.
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