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protomoprep not updating symlinks #1092

Open leginonbot opened 6 months ago

leginonbot commented 6 months ago

Author Name: Scott Stagg (Scott Stagg) Original Redmine Issue: 1092, https://emg.nysbc.org/redmine/issues/1092 Original Date: 2010-12-16 Original Assignee: Scott Stagg

We had a weird bug here at FSU where protomoprep was not updating symlinks when preparing files for protomo. It seems to be a problem with python, not this program. The easiest work around was to force the user to erase old folders before running protomo again. This should be revisited at a later date

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2011-01-05T20:02:52Z

code reviewed. I also added codes in appionlib/apProtomo.py setProtomoDir function to remove existing subdirectories on the first (0) cycle of protomo alignment in case that we have the same problem here in r15222.

Scott, please review my code. it doesn't look like I can test protomoprep.py here since 09feb18c_006.prexg is hard-coded in it. Please test that yourself.

By the way, can your problem be that the old link is not removed first? I see that protomoprep.py does not remove old links before linking. I know that I can not modify links in shell script, either.

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2011-01-05T20:03:34Z

see apProtomo.py function linkImageFiles for what I did there.