mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Daniel Blankenberg
ed964dd043
will prevent Galaxy from deleting the file when the dataset is purged. Copies of datasets (such as when sharing a
history), no longer copy file contents.
Database changes required:
CREATE TABLE dataset_filename (
id INTEGER NOT NULL,
create_time TIMESTAMP DEFAULT current_timestamp,
update_time TIMESTAMP DEFAULT current_timestamp,
filename TEXT,
extra_files_path TEXT,
readonly BOOLEAN,
PRIMARY KEY (id)
);
ALTER TABLE dataset ADD filename_id INTEGER;
95 lines
3.3 KiB
Python
95 lines
3.3 KiB
Python
#!/usr/bin/env python2.4
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#Dan Blankenberg
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"""
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Allows dataset cleanup.
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"""
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import sys, os, time, ConfigParser
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from optparse import OptionParser
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import galaxy.app
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def main():
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parser = OptionParser()
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parser.add_option("-d", "--days", dest="days", action="store", type="int", help="number of days (30)", default=30)
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parser.add_option("-a", "--abandon", action="store_true", dest="abandon", default=False, help="abandon old, unowned (userless) histories")
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parser.add_option("-p", "--purge", action="store_true", dest="purge", default=False, help="purge old deleted datasets")
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(options, args) = parser.parse_args()
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ini_file = args[0]
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if not (options.purge ^ options.abandon):
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parser.print_help()
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sys.exit(0)
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conf_parser = ConfigParser.ConfigParser({'here':os.getcwd()})
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conf_parser.read(ini_file)
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configuration = {}
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for key, value in conf_parser.items("app:main"): configuration[key] = value
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app = galaxy.app.UniverseApplication( global_conf = ini_file, **configuration )
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msg = None
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if options.purge:
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msg = purge(app, options.days)
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elif options.abandon:
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msg = abandon(app, options.days)
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app.shutdown()
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if msg:
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print
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print "Number of days buffered: %i" % options.days
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print msg
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sys.exit(0)
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def abandon( app, days ):
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""" Abandons userless histories older than specified number of days """
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histories_no_users = []
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history_count = 0
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for row in app.model.History.table.select().execute():
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try:
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int(row.user_id)
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except:
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history = app.model.History.get(row.id)
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now = time.time()
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last = time.mktime( time.strptime( history.update_time.strftime('%a %b %d %H:%M:%S %Y') ))
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diff = (now - last) /3600/24 # days
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if diff>days:
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histories_no_users.append(row.id)
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if history.deleted: continue #we don't add to history delete count, but we do want to be able to make sure datasets associated with deleted histories are really deleted
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history.deleted = True
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history_count += 1
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dataset_count = 0
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for row in app.model.Dataset.table.select().execute():
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if row.history_id in histories_no_users:
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#delete dataset
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data = app.model.Dataset.get(row.id)
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if data.deleted: continue
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data.deleted = True
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dataset_count += 1
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try:
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app.model.flush()
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except:
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pass
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msg = 'deleted %d abandoned histories with %d total datasets' % ( history_count, dataset_count )
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return msg
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def purge( app, days ):
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""" Purges deleted datasets older than specified number of days """
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count = 0
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now = time.time()
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for row in list(app.model.Dataset.table.select().execute()):
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data = app.model.Dataset.get(row.id)
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if data.deleted and not data.purged:
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last = time.mktime( time.strptime( data.update_time.strftime('%a %b %d %H:%M:%S %Y') ))
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diff = (now - last) /3600/24 # days
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if diff>days:
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data.purge()
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data.flush()
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count += 1
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try:
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app.model.flush()
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except:
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pass
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msg = 'Purged %d datasets' % count
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return msg
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if __name__ == "__main__":
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main() |