def testParserFormatList(self):
"""
This failed for DropBox while working
on #3200
"""
from omero.cli import Parser
p = Parser()
p._format_list([])
p._format_list(["a"])
def main():
parser = Parser()
parser.add_login_arguments()
parser.add_argument("file")
parser.add_argument("object")
ns = parser.parse_args()
cli = CLI()
cli.loadplugins()
client = cli.conn(ns)
try:
screen_metadata(client, ns.file, ns.object)
finally:
cli.close()
def main():
parser = Parser()
parser.add_login_arguments()
parser.add_argument("file")
parser.add_argument("object")
ns = parser.parse_args()
cli = CLI()
cli.loadplugins()
client = cli.conn(ns)
try:
screen_metadata(client, ns.file, ns.object)
finally:
cli.close()
def main():
parser = Parser()
parser.add_login_arguments()
parser.add_argument("--orphans", action="store_true")
parser.add_argument("--unknown", action="store_true")
parser.add_argument("--search", action="store_true")
parser.add_argument("--images", action="store_true")
parser.add_argument("--copy-from", type=long, default=None)
parser.add_argument("--copy-type", default="Image")
parser.add_argument("--copy-to", type=long, default=None)
parser.add_argument("screen", nargs="?")
ns = parser.parse_args()
cli = CLI()
cli.loadplugins()
client = cli.conn(ns)
try:
query = client.sf.getQueryService()
if ns.orphans:
orphans(query)
elif ns.unknown:
unknown(query)
elif ns.search:
search = client.sf.createSearchService()
check_search(query, search)
elif not ns.screen:
stat_screens(query)
else:
if ns.copy_to:
copy(client, ns.copy_from, ns.copy_type, ns.copy_to)
else:
for x in stat_plates(query, ns.screen, ns.images):
print x
finally:
cli.close()
def main():
parser = Parser()
parser.add_login_arguments()
parser.add_argument("--orphans", action="store_true")
parser.add_argument("--unknown", action="store_true")
parser.add_argument("--search", action="store_true")
parser.add_argument("--images", action="store_true")
parser.add_argument("--copy-from", type=long, default=None)
parser.add_argument("--copy-type", default="Image")
parser.add_argument("--copy-to", type=long, default=None)
parser.add_argument("screen", nargs="?")
ns = parser.parse_args()
cli = CLI()
cli.loadplugins()
client = cli.conn(ns)
try:
query = client.sf.getQueryService()
if ns.orphans:
orphans(query)
elif ns.unknown:
unknown(query)
elif ns.search:
search = client.sf.createSearchService()
check_search(query, search)
elif not ns.screen:
stat_screens(query)
else:
if ns.copy_to:
copy(client, ns.copy_from, ns.copy_type, ns.copy_to)
else:
for x in stat_plates(query, ns.screen, ns.images):
print x
finally:
cli.close()
def main():
parser = Parser()
parser.add_login_arguments()
parser.add_argument("--orphans", action="store_true")
parser.add_argument("--unknown", action="store_true")
parser.add_argument("--search", action="store_true")
parser.add_argument("--images", action="store_true")
parser.add_argument("--release",
default="TODO",
help="The name of the release, e.g. 'prod88'")
parser.add_argument(
"--disable-fsusage",
action="store_true",
help=("Disable fs usage file size and counts. "
"Use this flag if the script is taking too long."))
parser.add_argument(
"--format",
default="tsv",
help=(
"Output format, includes 'string', 'csv', 'tsv' (default), and "
"'json'. "
"'tsv' can be appended to the IDR studies.csv file with no further "
"processing. "
"All other formats include headers and totals. "
"'string' is the most human readable (fixed width columns). "))
parser.add_argument("studies",
nargs='*',
help="Studies to be processed, default all (idr*)")
parser.add_argument('-v', '--verbose', action='count', default=0)
ns = parser.parse_args()
levels = [logging.WARNING, logging.INFO, logging.DEBUG]
level = levels[min(len(levels) - 1, ns.verbose)]
logging.basicConfig(level=level,
format="%(asctime)s %(levelname)s %(message)s")
cli = CLI()
cli.loadplugins()
client = cli.conn(ns)
try:
query = client.sf.getQueryService()
if ns.orphans:
orphans(query)
elif ns.unknown:
unknown(query, ns.studies)
elif ns.search:
search = client.sf.createSearchService()
check_search(query, search)
else:
df = stat_top_level(client,
ns.studies,
release=ns.release,
fsusage=(not ns.disable_fsusage),
append_totals=(ns.format != 'tsv'))
print_stats(df, ns.format)
finally:
cli.close()