def doSubmit(self, request, client, test_should_pass=True):
"""
Performs the request waits on completion and checks that the
result is not an error.
"""
sf = client.sf
prx = sf.submit(request)
assert not State.FAILURE in prx.getStatus().flags
cb = CmdCallbackI(client, prx)
cb.loop(20, 500)
assert prx.getResponse() != None
status = prx.getStatus()
rsp = prx.getResponse()
if test_should_pass:
if isinstance(rsp, ERR):
assert False,\
"Found ERR when test_should_pass==true: %s (%s) params=%s" %\
(rsp.category, rsp.name, rsp.parameters)
assert not State.FAILURE in prx.getStatus().flags
else:
if isinstance(rsp, OK):
assert False, "Found OK when test_should_pass==false: %s" % rsp
assert State.FAILURE in prx.getStatus().flags
return rsp
def doChange(gateway, obj_type, obj_ids, group_id, container_id=None,
test_should_pass=True, return_complete=True):
"""
Performs the change-group action, waits on completion and checks that the
result is not an error.
"""
prx = gateway.chgrpObjects(obj_type, obj_ids, group_id, container_id)
if not return_complete:
return prx
cb = CmdCallbackI(gateway.c, prx)
try:
for i in range(10):
cb.loop(20, 500)
if prx.getResponse() is not None:
break
assert prx.getResponse() is not None
prx.getStatus()
rsp = prx.getResponse()
if test_should_pass:
assert not isinstance(rsp, ERR), \
"Found ERR when test_should_pass==true: %s (%s) params=%s" \
% (rsp.category, rsp.name, rsp.parameters)
assert State.FAILURE not in prx.getStatus().flags
else:
assert not isinstance(rsp, OK), \
"Found OK when test_should_pass==false: %s" % rsp
assert State.FAILURE in prx.getStatus().flags
return rsp
finally:
cb.close(True)
def doSubmit(self, request, client, test_should_pass=True,
omero_group=None):
"""
Performs the request waits on completion and checks that the
result is not an error.
"""
sf = client.sf
if omero_group is not None:
prx = sf.submit(request, {'omero.group': str(omero_group)})
else:
prx = sf.submit(request)
assert State.FAILURE not in prx.getStatus().flags
cb = CmdCallbackI(client, prx)
cb.loop(20, 500)
assert prx.getResponse() is not None
rsp = prx.getResponse()
if test_should_pass:
if isinstance(rsp, ERR):
assert False,\
"Found ERR when test_should_pass==true: %s (%s) params=%s" %\
(rsp.category, rsp.name, rsp.parameters)
assert State.FAILURE not in prx.getStatus().flags
else:
if isinstance(rsp, OK):
assert False, "Found OK when test_should_pass==false: %s" % rsp
assert State.FAILURE in prx.getStatus().flags
return rsp
def doSubmit(self, request, client, test_should_pass=True):
"""
Performs the request waits on completion and checks that the
result is not an error.
"""
sf = client.sf
prx = sf.submit(request)
self.assertFalse(State.FAILURE in prx.getStatus().flags)
cb = CmdCallbackI(client, prx)
cb.loop(20, 500)
self.assertNotEqual(prx.getResponse(), None)
status = prx.getStatus()
rsp = prx.getResponse()
if test_should_pass:
if isinstance(rsp, ERR):
self.fail("Found ERR when test_should_pass==true: %s (%s) params=%s" % (rsp.category, rsp.name, rsp.parameters))
self.assertFalse(State.FAILURE in prx.getStatus().flags)
else:
if isinstance(rsp, OK):
self.fail("Found OK when test_should_pass==false: %s", rsp)
self.assertTrue(State.FAILURE in prx.getStatus().flags)
return rsp
def doChange(self, group_id, permissions, test_should_pass=True, return_complete=True):
"""
Performs the chmod action, waits on completion and checks that the
result is not an error.
"""
prx = self.gateway.chmodGroup(group_id, permissions)
if not return_complete:
return prx
cb = CmdCallbackI(self.gateway.c, prx)
cb.loop(20, 500) # This fails (see #8439). Can comment out this line and
# try a different way of waiting for result - This never completes...
import time
rsp = prx.getResponse()
i = 0
while (rsp is None):
time.sleep(10)
rsp = prx.getResponse()
i += 1
print "rsp", i, rsp
self.assertNotEqual(rsp, None)
status = prx.getStatus()
if test_should_pass:
if isinstance(rsp, ERR):
self.fail("Found ERR when test_should_pass==true: %s (%s) params=%s" % (rsp.category, rsp.name, rsp.parameters))
self.assertFalse(State.FAILURE in prx.getStatus().flags)
else:
if isinstance(rsp, OK):
self.fail("Found OK when test_should_pass==false: %s", rsp)
self.assertTrue(State.FAILURE in prx.getStatus().flags)
return rsp
def doSubmit(self, request, client, test_should_pass=True):
"""
Performs the request waits on completion and checks that the
result is not an error.
"""
sf = client.sf
prx = sf.submit(request)
self.assertFalse(State.FAILURE in prx.getStatus().flags)
cb = CmdCallbackI(client, prx)
cb.loop(20, 500)
self.assertNotEqual(prx.getResponse(), None)
status = prx.getStatus()
rsp = prx.getResponse()
if test_should_pass:
if isinstance(rsp, ERR):
self.fail(
"Found ERR when test_should_pass==true: %s (%s) params=%s"
% (rsp.category, rsp.name, rsp.parameters))
self.assertFalse(State.FAILURE in prx.getStatus().flags)
else:
if isinstance(rsp, OK):
self.fail("Found OK when test_should_pass==false: %s", rsp)
self.assertTrue(State.FAILURE in prx.getStatus().flags)
return rsp
def doChange(self, obj_type, obj_id, group_id, test_should_pass=True, return_complete=True):
"""
Performs the change-group action, waits on completion and checks that the
result is not an error.
"""
prx = self.gateway.chgrpObject(obj_type, obj_id, group_id)
if not return_complete:
return prx
cb = CmdCallbackI(self.gateway.c, prx)
for i in range(10):
cb.loop(20, 500)
if prx.getResponse() != None:
break
self.assertNotEqual(prx.getResponse(), None)
status = prx.getStatus()
rsp = prx.getResponse()
if test_should_pass:
if isinstance(rsp, ERR):
self.fail("Found ERR when test_should_pass==true: %s (%s) params=%s" % (rsp.category, rsp.name, rsp.parameters))
self.assertFalse(State.FAILURE in prx.getStatus().flags)
else:
if isinstance(rsp, OK):
self.fail("Found OK when test_should_pass==false: %s", rsp)
self.assertTrue(State.FAILURE in prx.getStatus().flags)
return rsp
def testChgrpImage(self):
# Data Setup
img = self.new_image()
img = self.update.saveAndReturnObject(img)
# New method
chgrp = omero.cmd.Chgrp2(targetObjects={'Image': [img.id.val]})
handle = self.sf.submit(chgrp)
cb = CmdCallbackI(self.client, handle)
cb.loop(20, 750)
# Check Data
self.query.get("Image", img.id.val)
def assertImport(self, client, proc, folder):
hashes = self.upload_folder(proc, folder)
handle = proc.verifyUpload(hashes)
cb = CmdCallbackI(client, handle)
rsp = self.assertPasses(cb)
assert 1 == len(rsp.pixels)
return rsp
def testImport(self):
import time
s1 = time.time()
client = self.new_client()
mrepo = self.get_managed_repo(client)
folder = create_path(folder=True)
for x in range(200):
name = "%s.unknown" % x
(folder / name).touch()
paths = folder.files()
proc = mrepo.importPaths(paths)
hashes = self.upload_folder(proc, folder)
handle = proc.verifyUpload(hashes)
req = handle.getRequest()
fs = req.activity.getParent()
cb = CmdCallbackI(client, handle)
self.assert_error(cb, loops=200)
delete = omero.cmd.Delete2()
delete.targetObjects = {'Fileset': [fs.id.val]}
s2 = time.time()
print s2 - s1,
t1 = time.time()
client.submit(delete, loops=200)
t2 = time.time()
print " ", t2 - t1,
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 testChgrpImage(self):
# One user in two groups
client, exp = self.new_client_and_user()
update = client.sf.getUpdateService()
query = client.sf.getQueryService()
# Data Setup
img = self.new_image()
img = update.saveAndReturnObject(img)
# New method
chgrp = omero.cmd.Chgrp(type="/Image", id=img.id.val, options=None)
handle = client.sf.submit(chgrp)
cb = CmdCallbackI(client, handle)
cb.loop(20, 750)
# Check Data
query.get("Image", img.id.val)
def testChgrpImage(self):
# One user in two groups
client, exp = self.new_client_and_user()
update = client.sf.getUpdateService()
query = client.sf.getQueryService()
# Data Setup
img = self.new_image()
img = update.saveAndReturnObject(img)
# New method
chgrp = omero.cmd.Chgrp(type="/Image", id=img.id.val, options=None)
handle = client.sf.submit(chgrp)
cb = CmdCallbackI(client, handle)
cb.loop(20, 750)
# Check Data
query.get("Image", img.id.val)
def doSubmit(self,
request,
client,
test_should_pass=True,
omero_group=None):
"""
Performs the request(s), waits on completion and checks that the
result is not an error. The request can either be a single command
or a list of commands. If the latter then the request list will be
wrapped in a DoAll.
"""
if isinstance(request, list):
request = DoAll(request)
sf = client.sf
if omero_group is not None:
prx = sf.submit(request, {'omero.group': str(omero_group)})
else:
prx = sf.submit(request)
assert State.FAILURE not in prx.getStatus().flags
cb = CmdCallbackI(client, prx)
cb.loop(20, 500)
assert prx.getResponse() is not None
rsp = prx.getResponse()
if test_should_pass:
if isinstance(rsp, ERR):
assert False, (
"Found ERR when test_should_pass==true: %s (%s) params=%s"
% (rsp.category, rsp.name, rsp.parameters))
assert State.FAILURE not in prx.getStatus().flags
else:
if isinstance(rsp, OK):
assert False, ("Found OK when test_should_pass==false: %s" %
rsp)
assert State.FAILURE in prx.getStatus().flags
return rsp
def deleteRoi(self, roi_id):
"""
Delete the given ROI
:param roi: an ROI object
:type roi: `omero.model.Roi`
"""
from omero.callbacks import CmdCallbackI # @UnresolvedImport
handle = self.conn.deleteObjects("Roi", [roi_id],
deleteAnns=True,
deleteChildren=True)
callback = CmdCallbackI(self.conn.c, handle)
while not callback.block(500):
if self.args.verbose:
print_date(".", newline=False, incl_date=False)
time.sleep(2)
callback.close(True)
def doChange(self,
group_id,
permissions,
test_should_pass=True,
return_complete=True):
"""
Performs the chmod action, waits on completion and checks that the
result is not an error.
"""
prx = self.gateway.chmodGroup(group_id, permissions)
if not return_complete:
return prx
cb = CmdCallbackI(self.gateway.c, prx)
cb.loop(20,
500) # This fails (see #8439). Can comment out this line and
# try a different way of waiting for result - This never completes...
import time
rsp = prx.getResponse()
i = 0
while (rsp is None):
time.sleep(10)
rsp = prx.getResponse()
i += 1
print "rsp", i, rsp
self.assertNotEqual(rsp, None)
status = prx.getStatus()
if test_should_pass:
if isinstance(rsp, ERR):
self.fail(
"Found ERR when test_should_pass==true: %s (%s) params=%s"
% (rsp.category, rsp.name, rsp.parameters))
self.assertFalse(State.FAILURE in prx.getStatus().flags)
else:
if isinstance(rsp, OK):
self.fail("Found OK when test_should_pass==false: %s", rsp)
self.assertTrue(State.FAILURE in prx.getStatus().flags)
return rsp
def raw(self, command, args, client=None):
if client == None:
client = self.client
mrepo = self.getManagedRepo(self.client)
obj = mrepo.root()
sha = obj.hash.val
raw_access = omero.grid.RawAccessRequest()
raw_access.repoUuid = sha
raw_access.command = command
raw_access.args = args
handle = client.sf.submit(raw_access)
return CmdCallbackI(client, handle)
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 doChange(self, obj_type, obj_ids, group_id, container_id=None, test_should_pass=True, return_complete=True):
"""
Performs the change-group action, waits on completion and checks that the
result is not an error.
"""
prx = self.gateway.chgrpObjects(obj_type, obj_ids, group_id, container_id)
if not return_complete:
return prx
cb = CmdCallbackI(self.gateway.c, prx)
try:
for i in range(10):
cb.loop(20, 500)
if prx.getResponse() != None:
break
self.assertNotEqual(prx.getResponse(), None)
status = prx.getStatus()
rsp = prx.getResponse()
if test_should_pass:
if isinstance(rsp, ERR):
self.fail("Found ERR when test_should_pass==true: %s (%s) params=%s" % (rsp.category, rsp.name, rsp.parameters))
self.assertFalse(State.FAILURE in prx.getStatus().flags)
else:
if isinstance(rsp, OK):
self.fail("Found OK when test_should_pass==false: %s", rsp)
self.assertTrue(State.FAILURE in prx.getStatus().flags)
return rsp
finally:
cb.close(True)
def wait_on_callback(self, conn, proxy, test_should_pass=True):
"""
Handles callback on proxy handle and checks that the
result is not an error.
"""
cb = CmdCallbackI(conn.c, proxy)
try:
for i in range(10):
cb.loop(20, 500)
if proxy.getResponse() is not None:
break
assert proxy.getResponse() is not None
proxy.getStatus()
rsp = proxy.getResponse()
if test_should_pass:
assert not isinstance(rsp, ERR)
assert State.FAILURE not in proxy.getStatus().flags
else:
assert not isinstance(rsp, OK)
assert State.FAILURE in proxy.getStatus().flags
return rsp
finally:
cb.close(True)
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 doSubmit(self, request, client, test_should_pass=True, omero_group=None):
"""
Performs the request(s), waits on completion and checks that the
result is not an error. The request can either be a single command
or a list of commands. If the latter then the request list will be
wrapped in a DoAll.
"""
if isinstance(request, list):
request = DoAll(request)
sf = client.sf
if omero_group is not None:
prx = sf.submit(request, {"omero.group": str(omero_group)})
else:
prx = sf.submit(request)
assert State.FAILURE not in prx.getStatus().flags
cb = CmdCallbackI(client, prx)
cb.loop(20, 500)
assert prx.getResponse() is not None
rsp = prx.getResponse()
if test_should_pass:
if isinstance(rsp, ERR):
assert False, "Found ERR when test_should_pass==true: %s (%s) params=%s" % (
rsp.category,
rsp.name,
rsp.parameters,
)
assert State.FAILURE not in prx.getStatus().flags
else:
if isinstance(rsp, OK):
assert False, "Found OK when test_should_pass==false: %s" % rsp
assert State.FAILURE in prx.getStatus().flags
return rsp
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
def doChange(gateway,
obj_type,
obj_ids,
group_id,
container_id=None,
test_should_pass=True,
return_complete=True):
"""
Performs the change-group action, waits on completion and checks that the
result is not an error.
"""
prx = gateway.chgrpObjects(obj_type, obj_ids, group_id, container_id)
if not return_complete:
return prx
cb = CmdCallbackI(gateway.c, prx)
try:
for i in range(10):
cb.loop(20, 500)
if prx.getResponse() != None:
break
assert prx.getResponse() is not None
status = prx.getStatus()
rsp = prx.getResponse()
if test_should_pass:
assert not isinstance(rsp, ERR),\
"Found ERR when test_should_pass==true: %s (%s) params=%s" \
% (rsp.category, rsp.name, rsp.parameters)
assert State.FAILURE not in prx.getStatus().flags
else:
assert not isinstance(rsp, OK),\
"Found OK when test_should_pass==false: %s" % rsp
assert State.FAILURE in prx.getStatus().flags
return rsp
finally:
cb.close(True)
