def testChgrp11109(self):
"""
Place a plate in a single screen and attempt to move it.
"""
# One user in two groups
client, user = self.new_client_and_user(perms=PRIVATE)
admin = client.sf.getAdminService()
target_grp = self.new_group([user], perms=PRIVATE)
target_gid = target_grp.id.val
admin.getEventContext() # Refresh
update = client.sf.getUpdateService()
plate = PlateI()
plate.name = rstring("testChgrp11109")
screen = ScreenI()
screen.name = rstring("testChgrp11109")
link = screen.linkPlate(plate)
link = update.saveAndReturnObject(link)
# Now chgrp, should succeed
chgrp = Chgrp2(targetObjects={"Plate": [link.child.id.val]},
groupId=target_gid)
self.doSubmit(chgrp, client)
# Check that the links have been destroyed
query = client.sf.getQueryService()
with pytest.raises(omero.ValidationException):
query.get("ScreenPlateLink", link.id.val, {"omero.group": "-1"})
def testChgrp11109(self):
"""
Place a plate in a single screen and attempt to move it.
"""
# One user in two groups
client, user = self.new_client_and_user(perms=PRIVATE)
admin = client.sf.getAdminService()
target_grp = self.new_group([user], perms=PRIVATE)
target_gid = target_grp.id.val
admin.getEventContext() # Refresh
update = client.sf.getUpdateService()
plate = PlateI()
plate.name = rstring("testChgrp11109")
screen = ScreenI()
screen.name = rstring("testChgrp11109")
link = screen.linkPlate(plate)
link = update.saveAndReturnObject(link)
# Now chgrp, should succeed
chgrp = Chgrp2(
targetObjects={"Plate": [link.child.id.val]}, groupId=target_gid)
self.doSubmit(chgrp, client)
# Check that the links have been destroyed
query = client.sf.getQueryService()
with pytest.raises(omero.ValidationException):
query.get("ScreenPlateLink", link.id.val, {"omero.group": "-1"})
def screen_plate_run_well(request, itest, update_service):
"""
Returns a new OMERO Screen, linked Plate, linked Well, linked WellSample,
linked Image populate by an L{test.integration.library.ITest} instance and
linked PlateAcquisition with all required fields set.
"""
screen = ScreenI()
screen.name = rstring(itest.uuid())
plate = PlateI()
plate.name = rstring(itest.uuid())
# Well A10 (will have two WellSamples)
well_a = WellI()
well_a.row = rint(0)
well_a.column = rint(9)
# Well A11 (will not have a WellSample)
well_b = WellI()
well_b.row = rint(0)
well_b.column = rint(10)
ws_a = WellSampleI()
image_a = itest.new_image(name=itest.uuid())
ws_a.image = image_a
ws_b = WellSampleI()
image_b = itest.new_image(name=itest.uuid())
ws_b.image = image_b
plate_acquisition = PlateAcquisitionI()
plate_acquisition.plate = plate
ws_a.plateAcquisition = plate_acquisition
ws_b.plateAcquisition = plate_acquisition
well_a.addWellSample(ws_a)
well_a.addWellSample(ws_b)
plate.addWell(well_a)
plate.addWell(well_b)
screen.linkPlate(plate)
return update_service.saveAndReturnObject(screen)
def screen_plates(self, user1):
"""Return Screen with Plates and an orphaned Plate."""
# Create and name all the objects
screen = ScreenI()
screen.name = rstring('screen')
for i in range(5):
plate1 = PlateI()
plate1.name = rstring('Plate%s' % i)
screen.linkPlate(plate1)
# Create single orphaned Plate
plate = PlateI()
plate.name = rstring('plate')
screen = get_update_service(user1).saveAndReturnObject(screen)
plate = get_update_service(user1).saveAndReturnObject(plate)
# Add well to first plate
plates = screen.linkedPlateList()
plates.sort(cmp_name_insensitive)
plate_id = plates[0].id.val
well = WellI()
well.column = rint(0)
well.row = rint(0)
well.plate = PlateI(plate_id, False)
image = self.create_test_image(size_x=5,
size_y=5,
session=user1[0].getSession())
ws = WellSampleI()
ws.image = ImageI(image.id, False)
ws.well = well
well.addWellSample(ws)
well = get_update_service(user1).saveAndReturnObject(well)
return screen, plate
def screen_plate_run_well(self):
"""
Returns a new OMERO Screen, linked Plate, linked Well, linked
WellSample, linked Image populate by an
L{test.integration.library.ITest} instance and
linked PlateAcquisition with all required fields set.
"""
screen = ScreenI()
screen.name = rstring(self.uuid())
plate = PlateI()
plate.name = rstring(self.uuid())
# Well A10 (will have two WellSamples)
well_a = WellI()
well_a.row = rint(0)
well_a.column = rint(9)
# Well A11 (will not have a WellSample)
well_b = WellI()
well_b.row = rint(0)
well_b.column = rint(10)
ws_a = WellSampleI()
image_a = self.new_image(name=self.uuid())
ws_a.image = image_a
ws_b = WellSampleI()
image_b = self.new_image(name=self.uuid())
ws_b.image = image_b
plate_acquisition = PlateAcquisitionI()
plate_acquisition.plate = plate
ws_a.plateAcquisition = plate_acquisition
ws_b.plateAcquisition = plate_acquisition
well_a.addWellSample(ws_a)
well_a.addWellSample(ws_b)
plate.addWell(well_a)
plate.addWell(well_b)
screen.linkPlate(plate)
return self.update.saveAndReturnObject(screen)
def screen_plate(self):
"""
Returns a new OMERO Screen and linked Plate with required fields set.
"""
screen = ScreenI()
screen.name = rstring(self.uuid())
plate = PlateI()
plate.name = rstring(self.uuid())
screen.linkPlate(plate)
return self.update.saveAndReturnObject(screen)
def user_screens(self, user1):
"""Create screens belonging to user1."""
screens = []
for i in range(5):
screen = ScreenI()
screen.name = rstring('Screen%s' % i)
screens.append(screen)
screens = get_update_service(user1).saveAndReturnArray(screens)
screens.sort(cmp_name_insensitive)
return screens
def user_screens(self, user1):
"""Create screens belonging to user1."""
screens = []
for i in range(5):
screen = ScreenI()
screen.name = rstring('Screen%s' % i)
screens.append(screen)
screens = get_update_service(user1).saveAndReturnArray(screens)
screens.sort(key=lambda x: lower_or_none(unwrap(x.name)))
return screens
def screen_plate(request, itest, update_service):
"""
Returns a new OMERO Screen and linked Plate with required fields set.
"""
screen = ScreenI()
screen.name = rstring(itest.uuid())
plate = PlateI()
plate.name = rstring(itest.uuid())
screen.linkPlate(plate)
return update_service.saveAndReturnObject(screen)
def screen_plate(request, itest, update_service):
"""
Returns a new OMERO Screen and linked Plate with required fields set.
"""
screen = ScreenI()
screen.name = rstring(itest.uuid())
plate = PlateI()
plate.name = rstring(itest.uuid())
screen.linkPlate(plate)
return update_service.saveAndReturnObject(screen)
def screen():
o = ScreenI()
o.id = rlong(4L)
o.name = rstring("the_name")
o.description = rstring("the_description")
o.protocolDescription = rstring("the_protocol_description")
o.protocolIdentifier = rstring("the_protocol_identifier")
o.reagentSetDescription = rstring("the_reagent_set_description")
o.reagentSetIdentifier = rstring("the_reagent_set_identifier")
o.type = rstring("the_type")
return o
def screen():
o = ScreenI()
o.id = rlong(4L)
o.name = rstring('the_name')
o.description = rstring('the_description')
o.protocolDescription = rstring('the_protocol_description')
o.protocolIdentifier = rstring('the_protocol_identifier')
o.reagentSetDescription = rstring('the_reagent_set_description')
o.reagentSetIdentifier = rstring('the_reagent_set_identifier')
o.type = rstring('the_type')
return o
def screen_plate_run(self):
"""
Returns a new OMERO Screen, linked Plate, and linked PlateAcquisition
with all required fields set.
"""
screen = ScreenI()
screen.name = rstring(self.uuid())
plate = PlateI()
plate.name = rstring(self.uuid())
plate_acquisition = PlateAcquisitionI()
plate.addPlateAcquisition(plate_acquisition)
screen.linkPlate(plate)
return self.update.saveAndReturnObject(screen)
def screen_plate_run(request, itest, update_service):
"""
Returns a new OMERO Screen, linked Plate, and linked PlateAcquisition
with all required fields set.
"""
screen = ScreenI()
screen.name = rstring(itest.uuid())
plate = PlateI()
plate.name = rstring(itest.uuid())
plate_acquisition = PlateAcquisitionI()
plate.addPlateAcquisition(plate_acquisition)
screen.linkPlate(plate)
return update_service.saveAndReturnObject(screen)
def create_screen(self, row_count, col_count):
# TODO: remove 5.2 vs 5.3 compatibility
try:
plate = self.importPlates(plateRows=row_count,
plateCols=col_count)[0]
except AttributeError:
plate = self.import_plates(plateRows=row_count,
plateCols=col_count)[0]
plate = self.set_name(plate, "Plate001")
screen = ScreenI()
screen.name = rstring("Screen001")
screen.linkPlate(plate.proxy())
return (self.client.sf.getUpdateService().saveAndReturnObject(screen),
plate)
def create_screen(self, row_count, col_count):
# TODO: remove 5.2 vs 5.3 compatibility
try:
plate = self.importPlates(plateRows=row_count,
plateCols=col_count)[0]
except AttributeError:
plate = self.import_plates(plate_rows=row_count,
plate_cols=col_count)[0]
plate = self.set_name(plate, "Plate001")
screen = ScreenI()
screen.name = rstring("Screen001")
screen.linkPlate(plate.proxy())
return (self.client.sf.getUpdateService().saveAndReturnObject(screen),
plate)
def screen_plate_well(self):
"""
Returns a new OMERO Screen, linked Plate and linked Well with required
fields set.
"""
screen = ScreenI()
screen.name = rstring(self.uuid())
plate = PlateI()
plate.name = rstring(self.uuid())
# Well A10
well = WellI()
well.row = rint(0)
well.column = rint(9)
plate.addWell(well)
screen.linkPlate(plate)
return self.update.saveAndReturnObject(screen)
def screen_plate_well(request, itest, update_service):
"""
Returns a new OMERO Screen, linked Plate and linked Well with required
fields set.
"""
screen = ScreenI()
screen.name = rstring(itest.uuid())
plate = PlateI()
plate.name = rstring(itest.uuid())
# Well A10
well = WellI()
well.row = rint(0)
well.column = rint(9)
plate.addWell(well)
screen.linkPlate(plate)
return update_service.saveAndReturnObject(screen)
def create_screen(self, cli, screen):
"""
Creates screen with name provided if it doesn't exist already.
Returns Screen ID.
"""
conn = self.use_connection(cli, host)
params = self.get_params(conn)
slist = list(conn.getObjects("Screen", attributes={'name': screen}, params=params))
if len(slist) == 0:
print "Creating Screen:", screen
s = ScreenI()
s.name = wrap(screen.encode('ascii','ignore'))
scrId = conn.getUpdateService().saveAndReturnObject(s).id.val
else:
scrId = slist[0].getId()
print "Using Screen:", screen
return scrId
def plates_runs(request, itest, update_service, names):
"""
Returns a four new Plates, and two linked PlateAcquisitions with required
fields set and with names that can be used to exercise sorting semantics.
"""
plates = [PlateI(), PlateI(), PlateI(), PlateI()]
for index, plate in enumerate(plates):
plate.name = rstring(names[index])
plate_acquisitions = [PlateAcquisitionI(), PlateAcquisitionI()]
for plate_acquisition in plate_acquisitions:
plate.addPlateAcquisition(plate_acquisition)
# Non-orphaned Plate to catch issues with queries where non-orphaned
# plates are included in the results.
screen = ScreenI()
screen.name = rstring(itest.uuid())
plate = PlateI()
plate.name = rstring(itest.uuid())
screen.linkPlate(plate)
update_service.saveAndReturnObject(screen)
return update_service.saveAndReturnArray(plates)
def plates_runs(request, itest, update_service, names):
"""
Returns a four new Plates, and two linked PlateAcquisitions with required
fields set and with names that can be used to exercise sorting semantics.
"""
plates = [PlateI(), PlateI(), PlateI(), PlateI()]
for index, plate in enumerate(plates):
plate.name = rstring(names[index])
plate_acquisitions = [PlateAcquisitionI(), PlateAcquisitionI()]
for plate_acquisition in plate_acquisitions:
plate.addPlateAcquisition(plate_acquisition)
# Non-orphaned Plate to catch issues with queries where non-orphaned
# plates are included in the results.
screen = ScreenI()
screen.name = rstring(itest.uuid())
plate = PlateI()
plate.name = rstring(itest.uuid())
screen.linkPlate(plate)
update_service.saveAndReturnObject(screen)
return update_service.saveAndReturnArray(plates)
def screens_different_users(self):
"""
Returns two new OMERO Screens created by different users with
required fields set.
"""
client = self.conn.c
group = self.conn.getGroupFromContext()._obj
screens = list()
# User that has already been created by the "client" fixture
user, name = self.user_and_name(client)
self.add_experimenters(group, [user])
for name in (rstring(self.uuid()), rstring(self.uuid())):
client, user = self.new_client_and_user(group=group)
try:
screen = ScreenI()
screen.name = name
update_service = client.getSession().getUpdateService()
screens.append(update_service.saveAndReturnObject(screen))
finally:
client.closeSession()
return screens
def screens_different_users(request, itest, conn):
"""
Returns two new OMERO Screens created by different users with
required fields set.
"""
client = conn.c
group = conn.getGroupFromContext()._obj
screens = list()
# User that has already been created by the "client" fixture
user, name = itest.user_and_name(client)
itest.add_experimenters(group, [user])
for name in (rstring(itest.uuid()), rstring(itest.uuid())):
client, user = itest.new_client_and_user(group=group)
try:
screen = ScreenI()
screen.name = name
update_service = client.getSession().getUpdateService()
screens.append(update_service.saveAndReturnObject(screen))
finally:
client.closeSession()
return screens
def testListParentsSPW(self):
"""Test listParents() for Image in WellSample"""
client, exp = self.new_client_and_user()
conn = BlitzGateway(client_obj=client)
# setup SPW-WS-Img...
s = ScreenI()
s.name = wrap('ScreenA')
p = PlateI()
p.name = wrap('PlateA')
s.linkPlate(p)
w = WellI()
w.column = wrap(0)
w.row = wrap(0)
p.addWell(w)
s = client.sf.getUpdateService().saveAndReturnObject(s)
p = s.linkedPlateList()[0]
w = p.copyWells()[0]
i = self.make_image(name="SPW listParents", client=client)
ws = WellSampleI()
ws.image = i
ws.well = WellI(w.id.val, False)
w.addWellSample(ws)
ws = client.sf.getUpdateService().saveAndReturnObject(ws)
# Traverse from Image -> Screen
image = conn.getObject("Image", i.id.val)
wellSample = image.listParents()[0]
well = wellSample.listParents()[0]
assert well.id == w.id.val
plate = well.listParents()[0]
assert plate.id == p.id.val
screen = plate.listParents()[0]
assert screen.id == s.id.val
# Screen has no parent
assert len(screen.listParents()) == 0
def create_screen(self, cli, screen):
"""
Creates screen with name provided if it doesn't exist already.
Returns Screen ID.
"""
sessionId = cli._event_context.sessionUuid
conn = BlitzGateway(host='localhost')
conn.connect(sUuid = sessionId)
params = omero.sys.Parameters()
params.theFilter = omero.sys.Filter()
params.theFilter.ownerId = wrap(conn.getUser().getId())
slist = list(conn.getObjects("Screen", attributes={'name': screen}, params=params))
if len(slist) == 0:
print "Creating Screen:", screen
s = ScreenI()
s.name = wrap(screen.encode('ascii','ignore'))
scrId = conn.getUpdateService().saveAndReturnObject(s).id.val
else:
scrId = slist[0].getId()
print "Using Screen:", screen
return scrId
def screen(self):
"""Returns a new OMERO Screen with required fields set."""
screen = ScreenI()
screen.name = rstring(self.uuid())
return self.update.saveAndReturnObject(screen)
def screen(request, itest, update_service):
"""Returns a new OMERO Screen with required fields set."""
screen = ScreenI()
screen.name = rstring(itest.uuid())
return update_service.saveAndReturnObject(screen)
def screen(request, itest, update_service):
"""Returns a new OMERO Screen with required fields set."""
screen = ScreenI()
screen.name = rstring(itest.uuid())
return update_service.saveAndReturnObject(screen)
