def write_to_omero(self):
to_delete = {"Annotation": self.mapannids + self.fileannids}
delCmd = omero.cmd.Delete2(targetObjects=to_delete)
handle = self.client.getSession().submit(delCmd)
callback = None
try:
callback = CmdCallbackI(self.client, handle)
loops = max(10, len(self.mapannids) / 10)
delay = 500
callback.loop(loops, delay)
rsp = callback.getResponse()
if isinstance(rsp, omero.cmd.OK):
ndma = len(
rsp.deletedObjects.get(
"ome.model.annotations.MapAnnotation", []))
log.info("Deleted %d MapAnnotation(s)", ndma)
ndfa = len(
rsp.deletedObjects.get(
"ome.model.annotations.FileAnnotation", []))
log.info("Deleted %d FileAnnotation(s)", ndfa)
else:
log.error("Delete failed: %s", rsp)
finally:
if callback:
callback.close(True)
else:
handle.close()
def write_to_omero(self):
to_delete = {"Annotation": self.mapannids + self.fileannids}
delCmd = omero.cmd.Delete2(targetObjects=to_delete)
handle = self.client.getSession().submit(delCmd)
callback = None
try:
callback = CmdCallbackI(self.client, handle)
loops = max(10, len(self.mapannids) / 10)
delay = 500
callback.loop(loops, delay)
rsp = callback.getResponse()
if isinstance(rsp, omero.cmd.OK):
ndma = len(rsp.deletedObjects.get(
"ome.model.annotations.MapAnnotation", []))
log.info("Deleted %d MapAnnotation(s)", ndma)
ndfa = len(rsp.deletedObjects.get(
"ome.model.annotations.FileAnnotation", []))
log.info("Deleted %d FileAnnotation(s)", ndfa)
else:
log.error("Delete failed: %s", rsp)
finally:
if callback:
callback.close(True)
else:
handle.close()
def fs_usage(client, objecttype, objectid):
req = DiskUsage2()
req.targetObjects = {objecttype: [objectid]}
cb = None
handle = None
try:
handle = client.sf.submit(req)
cb = CmdCallbackI(client, handle)
# Wait for finish
while True:
found = cb.block(1000)
if found:
break
rsp = cb.getResponse()
# status = cb.getStatus()
except KeyboardInterrupt:
# If user uses Ctrl-C, then cancel
if handle is not None:
logging.warning("Attempting cancel...")
if handle.cancel():
logging.warning("Cancelled")
else:
logging.warning("Failed to cancel")
finally:
if cb is not None:
cb.close(True) # Close handle
sizebytes = sum(rsp.totalBytesUsed.values())
nfiles = sum(rsp.totalFileCount.values())
return sizebytes, nfiles
def submit(self, req):
import omero
handle = self.client.sf.submit(req)
cb = CmdCallbackI(self.client, handle)
try:
cb.loop(50, 1000)
rsp = cb.getResponse()
if isinstance(rsp, omero.cmd.ERR):
raise Exception(rsp)
return rsp
finally:
cb.close(True)
def submit(self, req):
import omero
handle = self.client.sf.submit(req)
cb = CmdCallbackI(self.client, handle)
try:
cb.loop(50, 1000)
rsp = cb.getResponse()
if isinstance(rsp, omero.cmd.ERR):
raise Exception(rsp)
return rsp
finally:
cb.close(True)
def assert_import(client, proc, files, wait):
"""Wait and check that we imported an image."""
hashes = upload_files(proc, files, client)
print('Hashes:\n %s' % '\n '.join(hashes))
handle = proc.verifyUpload(hashes)
cb = CmdCallbackI(client, handle)
# https://github.com/openmicroscopy/openmicroscopy/blob/v5.4.9/components/blitz/src/ome/formats/importer/ImportLibrary.java#L631
if wait == 0:
cb.close(False)
return None
if wait < 0:
while not cb.block(2000):
sys.stdout.write('.')
sys.stdout.flush()
sys.stdout.write('\n')
else:
cb.loop(wait, 1000)
rsp = cb.getResponse()
if isinstance(rsp, omero.cmd.ERR):
raise Exception(rsp)
assert len(rsp.pixels) > 0
return rsp
