Using Cleanse to remove deleted files
Posted: Fri Jun 13, 2014 4:00 pm
Hello OME team,
I'm running 5.0.2 on Linux and have just run a test case whereby data are uploaded, then deleted. Server side, I can navigate to the data in the binary repository.
When I run:
I get the following error quite rightly pointing out that there is no Pixels directory
1) Does this need updating now that there's no Pixel directory (circa 5.X.X)?
2) Am I right in assuming that this script should delete orphaned data stored in the fs.repo.path as well as Files/Thumbnails &c.
Thanks!
Dave
I'm running 5.0.2 on Linux and have just run a test case whereby data are uploaded, then deleted. Server side, I can navigate to the data in the binary repository.
When I run:
- Code: Select all
omero admin cleanse --dry-run /data/OMERO.data/
I get the following error quite rightly pointing out that there is no Pixels directory
- Code: Select all
Reconciling OMERO data directory...
/data/OMERO.data/Files
\_ /data/OMERO.data/Files/116 (keep)
\_ /data/OMERO.data/Files/154 (keep)
\_ /data/OMERO.data/Files/157 (keep)
\_ /data/OMERO.data/Files/53 (keep)
\_ /data/OMERO.data/Files/54 (keep)
\_ /data/OMERO.data/Files/151 (keep)
\_ /data/OMERO.data/Files/129 (keep)
\_ /data/OMERO.data/Files/153 (keep)
\_ /data/OMERO.data/Files/152 (keep)
\_ /data/OMERO.data/Files/155 (keep)
\_ /data/OMERO.data/Files/52 (keep)
\_ /data/OMERO.data/Files/128 (keep)
Reconciling OMERO data directory...
/data/OMERO.data/Pixels
Cleansing context: 0 files (0 bytes)
Traceback (most recent call last):
File "/apps/omero/OMERO.server/bin/omero", line 125, in <module>
rv = omero.cli.argv()
File "/apps/omero/OMERO.server/lib/python/omero/cli.py", line 1242, in argv
cli.invoke(args[1:])
File "/apps/omero/OMERO.server/lib/python/omero/cli.py", line 791, in invoke
stop = self.onecmd(line, previous_args)
File "/apps/omero/OMERO.server/lib/python/omero/cli.py", line 860, in onecmd
self.execute(line, previous_args)
File "/apps/omero/OMERO.server/lib/python/omero/cli.py", line 940, in execute
args.func(args)
File "/apps/omero/OMERO.server/lib/python/omero/plugins/admin.py", line 1299, in cleanse
config_service=client.sf.getConfigService())
File "/apps/omero/OMERO.server/lib/python/omero/util/cleanse.py", line 214, in cleanse
cleanser.cleanse(full_path)
File "/apps/omero/OMERO.server/lib/python/omero/util/cleanse.py", line 100, in cleanse
for file in os.listdir(root):
OSError: [Errno 2] No such file or directory: '/data/OMERO.data/Pixels'
1) Does this need updating now that there's no Pixel directory (circa 5.X.X)?
2) Am I right in assuming that this script should delete orphaned data stored in the fs.repo.path as well as Files/Thumbnails &c.
Thanks!
Dave