def redo_compare_all_releases(self):
"""
When problems in release comparisons are discovered, use this
function in manual mode to recompute the release difference table.
"""
all_releases = self.list_all_releases(self.motif_type)
for i in xrange(len(all_releases)):
release = all_releases[i]
c1 = MotifCollection(release=release,type=self.motif_type)
for j in xrange((i+1),len(all_releases)):
print '%s vs %s' % (all_releases[i], all_releases[j])
c2 = MotifCollection(release=all_releases[j],type=self.motif_type)
logging.info('Comparing %s and %s' % (c1.release, c2.release))
A = Uploader(ensembles=MotifCollectionMerger(c1,c2),
upload_mode='release_diff',
motif_type=self.motif_type)
A.import_release()
# set direct parent flag
if j == i+1:
a = session.query(Release_diff).filter(Release_diff.release_id1==release)\
.filter(Release_diff.release_id2==all_releases[j])\
.first()
a.direct_parent = 1;
session.merge(a)
session.commit()
def import_motif_release(self):
"""
"""
c1 = MotifCollection(file=self.f['MotifList'], type=self.motif_type)
c2 = MotifCollection(release='latest', type=self.motif_type)
A = Uploader(ensembles=MotifCollectionMerger(c1,c2),
mode=self.config['release_mode']['motifs'], #'minor',
description=self.f['description'],
files=self.f,
motif_type=self.motif_type)
A.import_release()
def compare_all_releases(self):
"""
"""
all_releases = self.list_all_releases(self.motif_type)
if len(all_releases) <= 2:
return
all_releases = all_releases[2:]
c1 = MotifCollection(release='latest',type=self.motif_type)
for release in all_releases:
c2 = MotifCollection(release=release,type=self.motif_type)
logging.info('Comparing %s and %s' % (c1.release, c2.release))
A = Uploader(ensembles=MotifCollectionMerger(c1,c2),
upload_mode='release_diff',
motif_type=self.motif_type)
A.import_release()
def main(argv):
"""
"""
try:
opts, args = getopt.getopt(argv, "t:r:h", ['help','type'])
except getopt.GetoptError:
usage()
sys.exit(2)
motif_type = None
release_to_remove = None
for opt, arg in opts:
if opt in ('-h', '--help'):
usage()
sys.exit()
elif opt in ('-t', '--type'):
motif_type = arg
elif opt in ('-r'):
release_to_remove = arg
if motif_type is None:
usage()
print 'Please specify motif type: il, hl, j3, j4 etc'
sys.exit(2)
if release_to_remove is not None:
print 'Are you sure you want to delete %s release %s?. Press c to continue or q to abort.' \
% (motif_type, release_to_remove)
pdb.set_trace()
U = Uploader(motif_type=motif_type)
U.remove_release(release_to_remove)
logging.info('Release %s removed successfully' % release_to_remove)
return
L = MotifLoader(motif_type=motif_type)
L.start_logging()
# L.redo_compare_all_releases() # use in manual mode only
L.import_data()
L.send_report()