More fixes for scripts run.command() in 0.3.16 #922
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The intent of this function is to get a script to halt processing until a particular file not only exists, but a valid file handle can be acquired. This can therefore be used in cases where e.g. network-based file systems may introduce a race condition within a script, or SGE may by used to execute a particular function but script execution immediately continues as soon as the jobs are sent. Since this hopefully fixes issues encountered in the 5ttgen fsl script due to the use of SGE by the FSL script run_first_all, SGE has now been re-enabled.
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Following on from discussion in #920.
I thought that perhaps there was some sort of network file system race condition that was causing the annoying
standard_space_roimissing file issue in5ttgen fsl(hence functionfile.waitFor()). It now appears as though it'sshnot finding the script, yet giving a 0 return code. Differences insubprocessbetween Python versions may have contributed to the prior confusion in diagnosing - on top of thesherror message not being found until the-debugoption was used.Independently of the
standard_space_roiissue, this function can also be used to wait for therun_first_alloutput rather than globally disabling SGE.Need to confirm that this still works on Windows.