I'm trying to use the built-in cleanup scripts (instead of my own), came across
a possible bug:
1. When running "delete_datasets.sh", the "info_only" flag is ignored.
This is evident by running it twice with "-i" and getting different results
(the second time - no datasets are deleted).
2. When running "purge_datasets.sh" with the "info_only" flag, no information
is printed at all, making it impossible to know what would be purged without
the "-i" flag.
The only way to see what is purged is actually purging the datasets (kind of
defeats the purpose of "info only").
I think the attached patch fixes both issues.
3. The relevant wiki page
says about "delete_datasets.sh": "The purge_datasets.sh script will need to be
run afterwards to remove the base datasets from disk."
But the example on the wiki page (and in the script) has "-r" - so the files
are actually deleted from the disk by "delete_datasets.sh".
Does one still need to run "purge_datasets.sh" if used "-r" with
4. If I accidentally run "purge_datasets.sh" without "-r" = is there a way to
delete the stale files ?
if not, perhaps the script should require either "-i" or "-r" to avoid such
cases (or provide another cleanup script?)
comments are welcomed,
--- /localdata1/gordon/tmp/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py 2011-07-01 16:35:22.128341199 -0400
+++ ./scripts/cleanup_datasets/cleanup_datasets.py 2011-07-01 17:04:44.004707711 -0400
@@ -411,10 +411,13 @@ def _delete_dataset( dataset, app, remov
app.sa_session.add( metadata_file )
print "%s" % metadata_file.file_name
- print "Deleting dataset id", dataset.id
- dataset.deleted = True
- app.sa_session.add( dataset )
+ if not info_only:
+ print "Deleting dataset id", dataset.id
+ dataset.deleted = True
+ app.sa_session.add( dataset )
+ print "Dataset %i will be deleted (without 'info_only' mode)" % ( dataset.id )
def _purge_dataset( app, dataset, remove_from_disk, info_only = False ):
@@ -433,6 +436,8 @@ def _purge_dataset( app, dataset, remove
dataset.purged = True
app.sa_session.add( dataset )
+ print "Dataset %i will be purged (without 'info_only' mode)" % (dataset.id)
print "This dataset (%i) is not purgable, the file (%s) will not be removed.\n" % ( dataset.id, dataset.file_name )
except OSError, exc:
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: