def connect(**kwargs):
if "conn" not in kwargs or kwargs["conn"] is None:
kwargs["conn"] = tools.connect_to_omero(kwargs["uname"], kwargs["passwd"])
err = None
for i in xrange(3): # try to connect 3 times
try:
kwargs["dataset"] = tools.get_dataset(kwargs["conn"], os.path.dirname(kwargs["path"]))
except Exception, e:
close_session(**kwargs)
kwargs["conn"] = tools.connect_to_omero(kwargs["uname"], kwargs["passwd"])
err = e
continue
err = None
break
def import_to_omero(path, pattern=None, ignores=None):
ignore_pattern = re.compile("|".join(construct(ignores, r".*/\..*")))
result = {}
connects = {}
info("path: %s" % path)
for dpath, fname in search_files(path, pattern, ignore_pattern):
fullpath = os.path.join(dpath, fname)
info('checking for "%s"' % fullpath)
if not os.access(fullpath, os.R_OK):
continue
owner = get_owner(fullpath)
if owner not in connects:
passwd = getPassword(owner)
if passwd is None:
continue
connects[owner] = tools.connect_to_omero(owner, passwd)
obj, is_completed = import_file(fullpath, owner, passwd, connects[owner])
if not is_completed:
continue
# result[fullpath] = obj
if "ERROR" not in obj or "ERRNO" not in obj["ERROR"] or obj["ERROR"]["ERRNO"] != errno.EEXIST:
print '"%s": %s' % (fullpath, json.dumps(obj))
for uname, conn in connects:
close_session(conn=conn)
return result
def main():
pattern = re.compile('^(.*)\R3D.zs$')
for user, passwd in users:
conn = omero_tools.connect_to_omero(user, passwd)
for image in omero_tools.get_images(conn):
if re.match(pattern, image.getName()):
print '#' * 50
print 'from: %s' % image.getName()
to_name = re.sub(pattern, r'\1R3D_D3D.dv.zs', image.getName())
image.setName(to_name)
image.save()
print 'to : %s' % image.getName()
conn._closeSession()
