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 plate(request, itest, update_service):
"""
Returns a new OMERO Plate with all required fields set.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
return update_service.saveAndReturnObject(plate)
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 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 plate(self):
"""
Returns a new OMERO Plate with all required fields set.
"""
plate = PlateI()
plate.name = rstring(self.uuid())
return self.update.saveAndReturnObject(plate)
def plate(request, itest, update_service):
"""
Returns a new OMERO Plate with all required fields set.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
return update_service.saveAndReturnObject(plate)
def plate_run(request, itest, update_service):
"""
Returns a new OMERO Plate and linked PlateAcquisition with all required
fields set.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
plate_acquisition = PlateAcquisitionI()
plate.addPlateAcquisition(plate_acquisition)
return update_service.saveAndReturnObject(plate)
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 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 plate_run(self):
"""
Returns a new OMERO Plate and linked PlateAcquisition with all
required fields set.
"""
plate = PlateI()
plate.name = rstring(self.uuid())
plate_acquisition = PlateAcquisitionI()
plate.addPlateAcquisition(plate_acquisition)
return self.update.saveAndReturnObject(plate)
def plate_run(request, itest, update_service):
"""
Returns a new OMERO Plate and linked PlateAcquisition with all required
fields set.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
plate_acquisition = PlateAcquisitionI()
plate.addPlateAcquisition(plate_acquisition)
return update_service.saveAndReturnObject(plate)
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 plate_wells(itest, well_grid_factory, plate_well_coords, update_service):
"""
Returns a new OMERO Plate, linked Wells, linked WellSamples, and linked
Images populated by an L{omeroweb.testlib.IWebTest} instance.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
wells = well_grid_factory(plate_well_coords)
for well in wells:
plate.addWell(well)
return update_service.saveAndReturnObject(plate)
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 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 create_plate_wells(self, user1, rows, cols, plateacquisitions=1):
"""Return Plate with Wells."""
updateService = get_update_service(user1)
plate = PlateI()
plate.name = rstring('plate')
plate = updateService.saveAndReturnObject(plate)
# PlateAcquisitions for plate
plate_acqs = []
for p in range(plateacquisitions):
plate_acq = PlateAcquisitionI()
plate_acq.name = rstring('plateacquisition_%s' % p)
plate_acq.description = rstring('plateacquisition_description')
plate_acq.maximumFieldCount = rint(3)
plate_acq.startTime = rtime(1)
plate_acq.endTime = rtime(2)
plate_acq.plate = PlateI(plate.id.val, False)
plate_acq = updateService.saveAndReturnObject(plate_acq)
plate_acqs.append(plate_acq)
# Create Wells for plate
ref_frame = UnitsLength.REFERENCEFRAME
for row in range(rows):
for col in range(cols):
# create Well
well = WellI()
well.column = rint(col)
well.row = rint(row)
well.plate = PlateI(plate.id.val, False)
# Only wells in first Column have well-samples etc.
if col == 0:
# Have 3 images/well-samples per plateacquisition
# (if no plateacquisitions, create 3 well-samples without)
for p in range(max(1, plateacquisitions)):
for i in range(3):
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
ws.posX = LengthI(i * 10, ref_frame)
ws.posY = LengthI(i, ref_frame)
if p < len(plate_acqs):
ws.setPlateAcquisition(
PlateAcquisitionI(plate_acqs[p].id.val,
False))
well.addWellSample(ws)
updateService.saveObject(well)
return plate
def plate_wells_with_description(itest, well_grid_factory, update_service):
"""
Creates a plate with a single well containing an image with a description.
Returns the plate and the description in a map.
"""
description = "test description"
plate = PlateI()
plate.name = rstring(itest.uuid())
# Simple grid: one well with one image
[well] = well_grid_factory({(0, 0): 1})
well.copyWellSamples()[0].image.description = rstring(description)
plate.addWell(well)
plate = update_service.saveAndReturnObject(plate)
return {'plate': plate, 'description': description}
def plate_wells(itest, well_grid_factory, update_service):
"""
Returns a new OMERO Plate, linked Wells, linked WellSamples, and linked
Images populated by an L{weblibrary.IWebTest} instance.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
# Well A10 has two WellSamples
# Well A11 has no WellSamples
# Well D3 has one WellSample
wells = well_grid_factory({(0, 9): 2, (0, 10): 0, (3, 2): 1})
for well in wells:
plate.addWell(well)
return update_service.saveAndReturnObject(plate)
def plate_wells(itest, well_grid_factory, update_service):
"""
Returns a new OMERO Plate, linked Wells, linked WellSamples, and linked
Images populated by an L{weblibrary.IWebTest} instance.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
# Well A10 has two WellSamples
# Well A11 has no WellSamples
# Well D3 has one WellSample
wells = well_grid_factory({(0, 9): 2, (0, 10): 0, (3, 2): 1})
for well in wells:
plate.addWell(well)
return update_service.saveAndReturnObject(plate)
def plate_wells_with_description(itest, well_grid_factory, update_service):
"""
Creates a plate with a single well containing an image with a description.
Returns the plate and the description in a map.
"""
description = "test description"
plate = PlateI()
plate.name = rstring(itest.uuid())
# Simple grid: one well with one image
[well] = well_grid_factory({(0, 0): 1})
well.copyWellSamples()[0].image.description = rstring(description)
plate.addWell(well)
plate = update_service.saveAndReturnObject(plate)
return {'plate': plate,
'description': description}
def plate_wells_with_acq_date(itest, well_grid_factory, update_service):
"""
Creates a plate with a single well containing an image with both an
acquisition date set as well as a creation event with a date. Returns the
plate and the acquisition date in a map.
"""
acq_date = (time.time() - 60 * 60 * 24) * 1000
plate = PlateI()
plate.name = rstring(itest.uuid())
# Simple grid: one well with one image
[well] = well_grid_factory({(0, 0): 1})
well.copyWellSamples()[0].image.acquisitionDate = rtime(int(acq_date))
plate.addWell(well)
plate = update_service.saveAndReturnObject(plate)
return {'plate': plate, 'acq_date': int(acq_date / 1000)}
def plate_wells_with_acq_date(itest, well_grid_factory, update_service):
"""
Creates a plate with a single well containing an image with both an
acquisition date set as well as a creation event with a date. Returns the
plate and the acquisition date in a map.
"""
acq_date = (time.time() - 60 * 60 * 24) * 1000
plate = PlateI()
plate.name = rstring(itest.uuid())
# Simple grid: one well with one image
[well] = well_grid_factory({(0, 0): 1})
well.copyWellSamples()[0].image.acquisitionDate = rtime(int(acq_date))
plate.addWell(well)
plate = update_service.saveAndReturnObject(plate)
return {'plate': plate,
'acq_date': int(acq_date / 1000)}
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 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 plate_wells_with_no_acq_date(itest, well_grid_factory, update_service,
conn):
"""
Creates a plate with a single well containing an image with no acquisition
date set. Returns the plate and the time from the creation event in a map.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
# Simple grid: one well with one image
[well] = well_grid_factory({(0, 0): 1})
plate.addWell(well)
well.copyWellSamples()[0].image.acquisitionDate = None
plate = update_service.saveAndReturnObject(plate)
image = plate.copyWells()[0].copyWellSamples()[0].image
creation_date = image.details.creationEvent.time
return {'plate': plate,
'creation_date': creation_date.val / 1000}
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 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 full_plate_wells(itest, update_service):
"""
Returns a full OMERO Plate, linked Wells, linked WellSamples, and linked
Images populated by an L{weblibrary.IWebTest} instance.
"""
lett = map(chr, range(ord('A'), ord('Z')+1))
plate = PlateI()
plate.name = rstring(itest.uuid())
for row in range(8):
for column in range(12):
well = WellI()
well.row = rint(row)
well.column = rint(column)
ws = WellSampleI()
image = itest.new_image(name=lett[row]+str(column))
ws.image = image
well.addWellSample(ws)
plate.addWell(well)
return update_service.saveAndReturnObject(plate)
def full_plate_wells(itest, update_service):
"""
Returns a full OMERO Plate, linked Wells, linked WellSamples, and linked
Images populated by an L{weblibrary.IWebTest} instance.
"""
lett = map(chr, range(ord('A'), ord('Z') + 1))
plate = PlateI()
plate.name = rstring(itest.uuid())
for row in range(8):
for column in range(12):
well = WellI()
well.row = rint(row)
well.column = rint(column)
ws = WellSampleI()
image = itest.new_image(name=lett[row] + str(column))
ws.image = image
well.addWellSample(ws)
plate.addWell(well)
return update_service.saveAndReturnObject(plate)
def createPlate(self, rowCount, colCount):
uuid = self.ctx.sessionUuid
def createWell(row, column):
well = WellI()
well.row = rint(row)
well.column = rint(column)
ws = WellSampleI()
image = self.new_image(name=uuid)
ws.image = image
well.addWellSample(ws)
return well
plate = PlateI()
plate.name = rstring("TestPopulateMetadata%s" % uuid)
for row in range(rowCount):
for col in range(colCount):
well = createWell(row, col)
plate.addWell(well)
return self.client.sf.getUpdateService().saveAndReturnObject(plate)
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 createPlate(self, rowCount, colCount):
uuid = self.ctx.sessionUuid
def createWell(row, column):
well = WellI()
well.row = rint(row)
well.column = rint(column)
ws = WellSampleI()
image = self.new_image(name=uuid)
ws.image = image
well.addWellSample(ws)
return well
plate = PlateI()
plate.name = rstring("TestPopulateMetadata%s" % uuid)
for row in range(rowCount):
for col in range(colCount):
well = createWell(row, col)
plate.addWell(well)
return self.client.sf.getUpdateService().saveAndReturnObject(plate)
def plates_different_users(self):
"""
Returns two new OMERO Plates created by different users with
required fields set.
"""
client = self.conn.c
group = self.conn.getGroupFromContext()._obj
plates = 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:
plate = PlateI()
plate.name = name
update_service = client.getSession().getUpdateService()
plates.append(update_service.saveAndReturnObject(plate))
finally:
client.closeSession()
return plates
def plate(request, gatewaywrapper):
"""Creates a Plate."""
gatewaywrapper.loginAsAuthor()
gw = gatewaywrapper.gateway
update_service = gw.getUpdateService()
plate = PlateI()
plate.name = rstring(uuid())
for well_index in range(3):
well = WellI()
well.row = rint(well_index**2)
well.column = rint(well_index**3)
for well_sample_index in range(2):
well_sample = WellSampleI()
image = ImageI()
image.name = rstring('%s_%d' % (uuid(), well_sample_index))
image.acquisitionDate = rtime(0)
well_sample.image = image
well.addWellSample(well_sample)
plate.addWell(well)
plate_id, = update_service.saveAndReturnIds([plate])
return gw.getObject('Plate', plate_id)
def plates_different_users(request, itest, conn):
"""
Returns two new OMERO Plates created by different users with
required fields set.
"""
client = conn.c
group = conn.getGroupFromContext()._obj
plates = 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:
plate = PlateI()
plate.name = name
update_service = client.getSession().getUpdateService()
plates.append(update_service.saveAndReturnObject(plate))
finally:
client.closeSession()
return plates
def plate(request, gatewaywrapper):
"""Creates a Plate."""
gatewaywrapper.loginAsAuthor()
gw = gatewaywrapper.gateway
update_service = gw.getUpdateService()
plate = PlateI()
plate.name = rstring(uuid())
for well_index in range(3):
well = WellI()
well.row = rint(well_index**2)
well.column = rint(well_index**3)
for well_sample_index in range(2):
well_sample = WellSampleI()
image = ImageI()
image.name = rstring('%s_%d' % (uuid(), well_sample_index))
image.acquisitionDate = rtime(0)
well_sample.image = image
well.addWellSample(well_sample)
plate.addWell(well)
plate_id, = update_service.saveAndReturnIds([plate])
return gw.getObject('Plate', plate_id)
def image_well_plate(self):
"""
Returns a new OMERO Project, linked Dataset and linked Image populated
by an L{test.integration.library.ITest} instance with required fields
set.
"""
plate = PlateI()
plate.name = rstring(self.uuid())
plate = self.update.saveAndReturnObject(plate)
well = WellI()
well.plate = plate
well = self.update.saveAndReturnObject(well)
image = self.new_image(name=self.uuid())
ws = WellSampleI()
ws.image = image
ws.well = well
well.addWellSample(ws)
ws = self.update.saveAndReturnObject(ws)
return plate, well, ws.image
def image_well_plate(self):
"""
Returns a new OMERO Project, linked Dataset and linked Image populated
by an L{test.integration.library.ITest} instance with required fields
set.
"""
plate = PlateI()
plate.name = rstring(self.uuid())
plate = self.update.saveAndReturnObject(plate)
well = WellI()
well.plate = plate
well = self.update.saveAndReturnObject(well)
image = self.new_image(name=self.uuid())
ws = WellSampleI()
ws.image = image
ws.well = well
well.addWellSample(ws)
ws = self.update.saveAndReturnObject(ws)
return plate, well, ws.image
def plate_well_table(itest, well_grid_factory, update_service, conn):
"""
Returns a new OMERO Plate, linked Wells, linked WellSamples, and linked
Images populated by an L{weblibrary.IWebTest} instance.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
# Well A1 has one WellSample
plate.addWell(well_grid_factory({(0, 0): 1})[0])
plate = update_service.saveAndReturnObject(plate)
col1 = WellColumn('Well', '', [])
col2 = StringColumn('TestColumn', '', 64, [])
columns = [col1, col2]
tablename = "plate_well_table_test:%s" % str(random())
table = conn.c.sf.sharedResources().newTable(1, tablename)
table.initialize(columns)
wellIds = [w.id.val for w in plate.copyWells()]
print "WellIds", wellIds
data1 = WellColumn('Well', '', wellIds)
data2 = StringColumn('TestColumn', '', 64, ["foobar"])
data = [data1, data2]
table.addData(data)
table.close()
orig_file = table.getOriginalFile()
fileAnn = FileAnnotationI()
fileAnn.ns = rstring('openmicroscopy.org/omero/bulk_annotations')
fileAnn.setFile(OriginalFileI(orig_file.id.val, False))
fileAnn = conn.getUpdateService().saveAndReturnObject(fileAnn)
link = PlateAnnotationLinkI()
link.setParent(PlateI(plate.id.val, False))
link.setChild(FileAnnotationI(fileAnn.id.val, False))
update_service.saveAndReturnObject(link)
return plate, wellIds
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 run(username, password, plate_id, host, port):
"""Run the script."""
# Create connection to training server
conn = BlitzGateway(username, password, host=host, port=port)
conn.connect()
# Create connection to IDR server
# NB: conn.connect() not working on IDR. Do it like this
idr_client = omero.client(host="idr.openmicroscopy.org", port=4064)
idr_client.createSession('public', 'public')
idr_conn = BlitzGateway(client_obj=idr_client)
# The plate we want to copy from IDR
idr_plate = idr_conn.getObject("Plate", plate_id)
plate_name = idr_plate.getName()
update_service = conn.getUpdateService()
plate = PlateI()
plate.name = rstring(plate_name)
plate = update_service.saveAndReturnObject(plate)
for idr_well in idr_plate.listChildren():
print("Well", idr_well.id, 'row', idr_well.row, 'col', idr_well.column)
# For each Well, get image and clone locally...
new_imgs = []
for idr_wellsample in idr_well.listChildren():
idr_image = idr_wellsample.getImage()
print("Image", idr_image.id)
image = copy_image(conn, idr_image)
new_imgs.append(image)
# link to Plate...
add_images_to_plate(update_service, plate, new_imgs,
idr_well.row, idr_well.column)
conn.close()
idr_conn.close()
def test_plate(self):
"""Tests label methods for Plate and Well."""
name = u'plate_∞'
cols = 4
rows = 3
obj = PlateI()
obj.name = rstring(name)
plate = MockConnection(obj).getObject("Plate", 1)
assert plate.getName() == name.encode('utf8')
plate._gridSize = {'rows': rows, 'columns': cols}
assert plate.getColumnLabels() == [c for c in range(1, cols + 1)]
assert plate.getRowLabels() == ['A', 'B', 'C']
well_obj = WellI()
well_obj.column = rint(1)
well_obj.row = rint(2)
class MockWell(WellWrapper):
def getParent(self):
return plate
well = MockWell(None, well_obj)
assert well.getWellPos() == "C2"
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 plate_wells_with_no_acq_date(itest, well_grid_factory, update_service,
conn):
"""
Creates a plate with a single well containing an image with no acquisition
date set. Returns the plate and the time from the creation event in a map.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
# Simple grid: one well with one image
[well] = well_grid_factory({(0, 0): 1})
plate.addWell(well)
well.copyWellSamples()[0].image.acquisitionDate = None
plate = update_service.saveAndReturnObject(plate)
image = plate.copyWells()[0].copyWellSamples()[0].image
creation_date = image.details.creationEvent.time
return {'plate': plate, 'creation_date': creation_date.val / 1000}
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 update_table(self, columns):
"""Updates the OmeroTables instance backing our results."""
# Create a new OMERO table to store our measurement results
sr = self.service_factory.sharedResources()
name = self.get_name()
self.table = sr.newTable(1, '/%s.r5' % name)
if self.table is None:
raise MeasurementError(
"Unable to create table: %s" % name)
# Retrieve the original file corresponding to the table for the
# measurement, link it to the file annotation representing the
# umbrella measurement run, link the annotation to the plate from
# which it belongs and save the file annotation.
table_original_file = self.table.getOriginalFile()
table_original_file_id = table_original_file.id.val
log.info("Created new table: %d" % table_original_file_id)
unloaded_o_file = OriginalFileI(table_original_file_id, False)
self.file_annotation.file = unloaded_o_file
unloaded_plate = PlateI(self.analysis_ctx.plate_id, False)
plate_annotation_link = PlateAnnotationLinkI()
plate_annotation_link.parent = unloaded_plate
plate_annotation_link.child = self.file_annotation
plate_annotation_link = \
self.update_service.saveAndReturnObject(plate_annotation_link)
self.file_annotation = plate_annotation_link.child
t0 = int(time.time() * 1000)
self.table.initialize(columns)
log.debug("Table init took %sms" % (int(time.time() * 1000) - t0))
t0 = int(time.time() * 1000)
column_report = dict()
for column in columns:
column_report[column.name] = len(column.values)
log.debug("Column report: %r" % column_report)
self.table.addData(columns)
self.table.close()
log.info("Table update took %sms" % (int(time.time() * 1000) - t0))
def plate_well_table(itest, well_grid_factory, update_service, conn):
"""
Returns a new OMERO Plate, linked Wells, linked WellSamples, and linked
Images populated by an L{omeroweb.testlib.IWebTest} instance.
"""
plate = PlateI()
plate.name = rstring(itest.uuid())
# Well A1 has one WellSample
plate.addWell(well_grid_factory({(0, 0): 1})[0])
plate = update_service.saveAndReturnObject(plate)
col1 = WellColumn('Well', '', [])
col2 = StringColumn('TestColumn', '', 64, [])
columns = [col1, col2]
tablename = "plate_well_table_test:%s" % str(random())
table = conn.c.sf.sharedResources().newTable(1, tablename)
table.initialize(columns)
wellIds = [w.id.val for w in plate.copyWells()]
print("WellIds", wellIds)
data1 = WellColumn('Well', '', wellIds)
data2 = StringColumn('TestColumn', '', 64, ["foobar"])
data = [data1, data2]
table.addData(data)
orig_file = table.getOriginalFile()
table.close()
fileAnn = FileAnnotationI()
fileAnn.ns = rstring('openmicroscopy.org/omero/bulk_annotations')
fileAnn.setFile(OriginalFileI(orig_file.id.val, False))
fileAnn = conn.getUpdateService().saveAndReturnObject(fileAnn)
link = PlateAnnotationLinkI()
link.setParent(PlateI(plate.id.val, False))
link.setChild(FileAnnotationI(fileAnn.id.val, False))
update_service.saveAndReturnObject(link)
return plate, wellIds
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 screen_with_plates(screen):
for plate_id in range(5, 7):
o = PlateI()
o.id = rlong(plate_id)
o.name = rstring('plate_name_%d' % plate_id)
o.description = rstring('plate_description_%d' % plate_id)
o.columnNamingConvention = rstring('number')
o.rowNamingConvention = rstring('letter')
o.columns = rint(12)
o.rows = rint(8)
o.defaultSample = rint(0)
o.externalIdentifier = rstring('external_identifier_%d' % plate_id)
o.status = rstring('status_%d' % plate_id)
o.wellOriginX = LengthI(0.1, UnitsLength.REFERENCEFRAME)
o.wellOriginY = LengthI(1.1, UnitsLength.REFERENCEFRAME)
screen.linkPlate(o)
for well_id in range(7, 9):
well = WellI()
well.id = rlong(well_id)
well.column = rint(2)
well.row = rint(1)
well.externalDescription = \
rstring('external_description_%d' % well_id)
well.externalIdentifier = \
rstring('external_identifier_%d' % well_id)
well.type = rstring('the_type')
well.alpha = rint(0)
well.red = rint(255)
well.green = rint(0)
well.blue = rint(0)
well.status = rstring('the_status')
o.addWell(well)
plateacquisition = PlateAcquisitionI()
plateacquisition.id = rlong(well_id)
plateacquisition.name = rstring(
'plateacquisition_name_%d' % well_id)
plateacquisition.description = rstring(
'plateacquisition_description_%d' % well_id)
plateacquisition.maximumFieldCount = rint(1)
plateacquisition.startTime = rtime(1L)
plateacquisition.endTime = rtime(2L)
for wellsample_id in range(9, 11):
wellsample = WellSampleI()
wellsample.setPlateAcquisition(plateacquisition)
wellsample.id = rlong(wellsample_id)
wellsample.posX = LengthI(1.0, UnitsLength.REFERENCEFRAME)
wellsample.posY = LengthI(2.0, UnitsLength.REFERENCEFRAME)
wellsample.timepoint = rtime(1L)
wellsample.image = create_image(1L)
well.addWellSample(wellsample)
return screen
def screen_with_plates(screen):
for plate_id in range(5, 7):
o = PlateI()
o.id = rlong(plate_id)
o.name = rstring("plate_name_%d" % plate_id)
o.description = rstring("plate_description_%d" % plate_id)
o.columnNamingConvention = rstring("number")
o.rowNamingConvention = rstring("letter")
o.columns = rint(12)
o.rows = rint(8)
o.defaultSample = rint(0)
o.externalIdentifier = rstring("external_identifier_%d" % plate_id)
o.status = rstring("status_%d" % plate_id)
o.wellOriginX = LengthI(0.1, UnitsLength.REFERENCEFRAME)
o.wellOriginY = LengthI(1.1, UnitsLength.REFERENCEFRAME)
screen.linkPlate(o)
return screen
