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_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 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