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 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(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 screens(request, itest, update_service, names):
"""
Returns four new OMERO Screens with required fields set and with names
that can be used to exercise sorting semantics.
"""
to_save = [ScreenI(), ScreenI(), ScreenI(), ScreenI()]
for index, screen in enumerate(to_save):
screen.name = rstring(names[index])
return update_service.saveAndReturnArray(to_save)
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 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 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():
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(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 screens_plates(request, itest, update_service, names):
"""
Returns four new OMERO Screens and four linked Plates with required
fields set and with names that can be used to exercise sorting semantics.
"""
screens = [ScreenI(), ScreenI(), ScreenI(), ScreenI()]
for index, screen in enumerate(screens):
screen.name = rstring(names[index])
plates = [PlateI(), PlateI(), PlateI(), PlateI()]
for index, plate in enumerate(plates):
plate.name = rstring(names[index])
screen.linkPlate(plate)
return update_service.saveAndReturnArray(screens)
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 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 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 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 screens_plates_runs(request, itest, update_service):
"""
Returns a two new OMERO Screens, two linked Plates, and two linked
PlateAcquisitions with all required fields set.
"""
screens = [ScreenI(), ScreenI()]
for screen in screens:
screen.name = rstring(itest.uuid())
plates = [PlateI(), PlateI()]
for plate in plates:
plate.name = rstring(itest.uuid())
plate_acquisitions = [PlateAcquisitionI(), PlateAcquisitionI()]
for plate_acquisition in plate_acquisitions:
plate.addPlateAcquisition(plate_acquisition)
screen.linkPlate(plate)
return update_service.saveAndReturnArray(screens)
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 parse_target_object(target_object):
type, id = target_object.split(':')
if 'Dataset' == type:
return DatasetI(long(id), False)
if 'Plate' == type:
return PlateI(long(id), False)
if 'Screen' == type:
return ScreenI(long(id), False)
raise ValueError('Unsupported target object: %s' % target_object)
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(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 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 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 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 populate_metadata(client, conn, script_params):
object_id = int(script_params["IDs"])
file_id = int(script_params["File_ID"])
original_file = get_original_file(conn, script_params["Data_Type"],
object_id, file_id)
provider = DownloadingOriginalFileProvider(conn)
file_handle = provider.get_original_file_data(original_file)
if script_params["Data_Type"] == "Plate":
omero_object = PlateI(int(object_id), False)
else:
omero_object = ScreenI(int(object_id), False)
ctx = ParsingContext(client, omero_object, "")
ctx.parse_from_handle(file_handle)
ctx.write_to_omero()
def populate_metadata(client, conn, script_params):
object_ids = script_params["IDs"]
object_id = object_ids[0]
file_ann_id = None
if "File_Annotation" in script_params:
file_ann_id = long(script_params["File_Annotation"])
data_type = script_params["Data_Type"]
original_file = get_original_file(conn, data_type, object_id, file_ann_id)
provider = DownloadingOriginalFileProvider(conn)
file_handle = provider.get_original_file_data(original_file)
if data_type == "Plate":
omero_object = PlateI(long(object_id), False)
else:
omero_object = ScreenI(long(object_id), False)
ctx = ParsingContext(client, omero_object, "")
ctx.parse_from_handle(file_handle)
ctx.write_to_omero()
return "Table data populated for %s: %s" % (data_type, object_id)
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 project_structure(conn, timestamp, image_fixture):
"""
Project Dataset Image
------- ------- -----
proj ----> ds ----> im0
Screen Plate Well Image
------ ----- ---- -----
screen ----> plate ----> well -----> im1
"""
proj_name = "proj_" + timestamp
proj_id = ezomero.post_project(conn, proj_name)
ds_name = "ds_" + timestamp
ds_id = ezomero.post_dataset(conn, ds_name, project_id=proj_id)
im_name = 'im_' + timestamp
im_id = ezomero.post_image(conn, image_fixture, im_name, dataset_id=ds_id)
update_service = conn.getUpdateService()
# Create Screen
screen_name = "screen_" + timestamp
screen = ScreenWrapper(conn, ScreenI())
screen.setName(screen_name)
screen.save()
screen_id = screen.getId()
# Create Plate
plate_name = "plate_" + timestamp
plate = PlateWrapper(conn, PlateI())
plate.setName(plate_name)
plate.save()
plate_id = plate.getId()
link = ScreenPlateLinkI()
link.setParent(ScreenI(screen_id, False))
link.setChild(PlateI(plate_id, False))
update_service.saveObject(link)
# Create Well
well = WellI()
well.setPlate(PlateI(plate_id, False))
well.setColumn(rint(1))
well.setRow(rint(1))
well.setPlate(PlateI(plate_id, False))
# Create Well Sample with Image
ws = WellSampleI()
im_id1 = ezomero.post_image(conn, image_fixture, "well image")
ws.setImage(ImageI(im_id1, False))
well.addWellSample(ws)
well_obj = update_service.saveAndReturnObject(well)
well_id = well_obj.getId().getValue()
return ({
'proj': proj_id,
'ds': ds_id,
'im': im_id,
'screen': screen_id,
'plate': plate_id,
'well': well_id,
'im1': im_id1
})
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)