def main():
parser = OptionParser(usage=usage)
parser.add_option('-n', '--dryrun', action="store_true", default=False, help="Print actions but do not execute.")
parser.add_option('-v', '--verbose', action="store_true", default=False, help="")
parser.add_option('-x', '--offsetx', type="int", help="")
parser.add_option('-y', '--offsety', type="int", help="")
options, args = parser.parse_args()
# set log level
if options.verbose:
logging.basicConfig(format='%(levelname)s:%(message)s', level=logging.DEBUG)
else:
logging.basicConfig(format='%(levelname)s:%(message)s', level=logging.INFO)
# use offsets if A01 is not the first well imaged
# e.g. it first well is C4, set offsetx = 3, offsety = 2
offsetx = 0
offsety = 0
if options.offsetx:
offsetx = options.offsetx
if options.offsety:
offsety = options.offsety
# When the python script is started, it has own new shell, with a new irods environment
# where the current working directory is ~.
# This command checks the current working directory of the parent shell from the .irodsEnv files.
iutils.icd2ipwd()
ipwd= iutils.ipwd()
target = None
# check if template was given
if len(args) == 0:
parser.error("No target folder given.")
else:
target = args[0]
# check if template is an absolute path
if iquest.collection_exists(ipwd + "/" + target):
target = ipwd + "/" + target
else:
if not iquest.collection_exists(target):
parser.error("Target " + target + " not found.")
logging.info("Target folder " + target)
dataset = createDatasetCode(target)
files = iquest.list_dataobjects_recursive(target)
for f in files:
# for originals and converted hyperstacks
result = reOMEfield.search(f)
if result:
logging.debug(f)
# read Matrix Screener indexes
u = result.group(3)
v = result.group(4)
x = result.group(8)
y = result.group(9)
# apply offsets
u = int(u) + offsetx
v = int(v) + offsety
avu = imeta.AVU(ATTR_DATASET, dataset)
logging.debug('dataset:{0}'.format(dataset))
if not options.dryrun:
imeta.delete(f,avu)
imeta.add(f,avu)
well = createWellCode(u, v)
logging.debug('U:{0}, V:{1}, well:{2}'.format(u, v, well))
avu = imeta.AVU(ATTR_WELL, well)
if not options.dryrun:
imeta.delete(f, avu)
imeta.add(f, avu)
field = createFieldIndex(x, y)
logging.debug("field: " + field)
avu = imeta.AVU(ATTR_FIELD, field)
if not options.dryrun:
imeta.delete(f, avu)
imeta.add(f, avu)
# for original MatrixScreener output
result = reOME.search(f)
if result:
c = result.group(12)
channel = str(int(c))
logging.debug("channel: " + channel)
avu = imeta.AVU(ATTR_CHANNEL, channel)
if not options.dryrun:
imeta.delete(f, avu)
imeta.add(f, avu)
def main():
irods_host = IRODS_DEFAULT_HOST
bisque_host = BISQUE_DEFAULT_HOST
parser = OptionParser(usage=usage)
parser.add_option("-l", "--list", action="store_true", default=False, help="list contents of irods url and exit")
parser.add_option(
"-n", "--dryrun", action="store_true", default=False, help="print actions but do not execute.. sets verbose"
)
parser.add_option("-i", "--irods_host", help="e.g. irods://ida.csc.fi")
parser.add_option("-b", "--bisque_host", help="e.g. https://bisquevm-1.it.helsinki.fi")
parser.add_option("-v", "--verbose", action="store_true", default=False, help="be verbose")
options, args = parser.parse_args()
if len(args) > 0:
irods_data = args.pop(0)
else:
parser.error("No irods data given.")
# set log level
if options.verbose:
logging.basicConfig(format="%(levelname)s:%(message)s", level=logging.DEBUG)
elif options.dryrun:
logging.basicConfig(format="%(levelname)s:%(message)s", level=logging.INFO)
else:
logging.basicConfig(format="%(levelname)s:%(message)s", level=logging.CRITICAL)
# check server URLs
if options.irods_host:
irods_host = options.irods_host
if not irods_host or not irods_host.startswith("irods://"):
parser.error("must include a valid iRODS url i.e. %s" % IRODS_DEFAULT_HOST)
if options.bisque_host:
bisque_host = options.bisque_host
if not bisque_host or not (bisque_host.startswith("http://") or bisque_host.startswith("https://")):
parser.error(
"Invalid Bisque host URL '%s'.\nPlease specify valid HTTP URL i.e. '%s'."
% (bisque_host, BISQUE_DEFAULT_HOST)
)
if bisque_host.startswith("http://"):
logging.warning("Using plain HTTP, passwords will be sent unencrypted.")
DATA_IS_COLLECTION = False
DATA_IS_SINGLE_OBJECT = False
# check if user specified a collection or a single dataobject
DATA_IS_COLLECTION = iquest.collection_exists(irods_data)
if not DATA_IS_COLLECTION:
DATA_IS_SINGLE_OBJECT = iquest.dataobject_exists(irods_data)
# check if the collection or data exists
if not DATA_IS_COLLECTION and not DATA_IS_SINGLE_OBJECT:
# user probably didn't give full path starting from /ZONE/home/...
# try in the current irods directory
irods_data_orig = irods_data
iutils.icd2ipwd()
root = iutils.ipwd()
irods_data = root + "/" + irods_data
DATA_IS_COLLECTION = iquest.collection_exists(irods_data)
if not DATA_IS_COLLECTION:
DATA_IS_SINGLE_OBJECT = iquest.dataobject_exists(irods_data)
if not DATA_IS_COLLECTION and not DATA_IS_SINGLE_OBJECT:
parser.error("File or collection '" + irods_data_orig + "' not found in " + irods_host + ".")
if DATA_IS_COLLECTION:
entries = iquest.list_dataobjects_recursive(irods_data)
else:
entries = []
entries.append(irods_data)
if options.list:
for e in entries:
print e
return
# ask user for bisque username/password
print
print "Please login to Bisque with your University AD username and password."
bisque_user = getpass.getuser()
print "Username:"******"Username/password needs to be provided for uploads.")
bisque = BisqueConnection(bisque_host, bisque_user, bisque_password)
for irods_file in entries:
bisque.register_irods_file(irods_host, irods_file, options.dryrun)