def check(self):
from omero.cli import CLI
from omero.gateway import BlitzGateway
cli = CLI()
cli.loadplugins()
cli.onecmd('login -q')
try:
gateway = BlitzGateway(client_obj=cli.get_client())
for experiment in self.m["experiments"]:
self.check_object(gateway, experiment, "Project")
for experiment in self.m["screens"]:
self.check_object(gateway, experiment, "Screen")
if "map" in self.m:
if self.m["experiments"]:
study_type = "Project"
else:
study_type = "Screen"
self.check_object(gateway, self.m, study_type)
finally:
if cli:
cli.close()
gateway.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 check(obj):
from omero.cli import CLI
from omero.gateway import BlitzGateway
cli = CLI()
cli.loadplugins()
cli.onecmd('login')
try:
gateway = BlitzGateway(client_obj=cli.get_client())
remote_obj = gateway.getObject(
obj.type, attributes={"name": obj.name})
errors = []
if remote_obj.description != obj.description:
errors.append("current:%s\nexpected:%s" % (
remote_obj.description, obj.description))
for al in remote_obj._getAnnotationLinks(
ns="openmicroscopy.org/omero/client/mapAnnotation"):
mapValue = al.child.mapValue
kv_pairs = [(m.name, m.value) for m in mapValue]
for i in range(len(kv_pairs)):
if kv_pairs[i] != obj.map[i]:
errors.append(
"current:%s\nexpected:%s" % (kv_pairs[i], obj.map[i]))
if not errors:
log.info("No annotations mismatch detected")
else:
for e in errors:
log.info("Found some annotations mismatch")
print e
finally:
if cli:
cli.close()
gateway.close()
def check(self):
from omero.cli import CLI
from omero.gateway import BlitzGateway
cli = CLI()
cli.loadplugins()
cli.onecmd('login -q')
try:
gateway = BlitzGateway(client_obj=cli.get_client())
for experiment in self.m["experiments"]:
self.check_object(gateway, experiment, "Project")
for experiment in self.m["screens"]:
self.check_object(gateway, experiment, "Screen")
if "map" in self.m:
if self.m["experiments"]:
study_type = "Project"
else:
study_type = "Screen"
self.check_object(gateway, self.m, study_type)
finally:
if cli:
cli.close()
gateway.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()
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 check(self, update=False):
from omero.cli import CLI
from omero.gateway import BlitzGateway
cli = CLI()
cli.loadplugins()
cli.onecmd('login -q')
try:
gateway = BlitzGateway(client_obj=cli.get_client())
self.check_study(gateway, update=update)
finally:
if cli:
cli.close()
gateway.close()
def run(studyfile, targetstr):
try:
# `omero shell --login` automatically creates the client object
session = client.getSession()
cli = None
except NameError:
cli = CLI()
cli.loadplugins()
cli.onecmd('login')
session = cli.get_client().getSession()
try:
us = session.getUpdateService()
target = ProxyStringType()(targetstr)
with open(studyfile) as f:
rowkvs = get_pairs(f)
links = create_map_annotation([target], rowkvs, ns)
ids = us.saveAndReturnIds(links)
print 'Created MapAnnotation links: %s' % ids
finally:
if cli:
cli.close()
for ds in project.listChildren():
for img in ds.listChildren():
channels = img.getChannels(noRE=True)
lc = channels[channel_index].getLogicalChannel()
lc.setName(channel_name)
lc.save()
if len(sys.argv) < 4:
printusage()
else:
channel_index = int(sys.argv[1])
channel_name = sys.argv[2]
target = sys.argv[3].split(':')
if target[0] == 'Project':
project_id = int(target[1])
else:
printusage()
cli = CLI()
cli.loadplugins()
cli.onecmd('login -q')
try:
conn = BlitzGateway(client_obj=cli.get_client())
rename(conn, project_id, channel_index, channel_name)
finally:
if cli:
cli.close()
conn.close()
