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_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 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 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_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_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 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 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 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 run():
"""
"""
dataTypes = [rstring("Plate")]
client = scripts.client(
"Manage_Plate_Acquisitions.py",
"Add or remove PlateAcquisition(s) in a given Plate",
scripts.String("Data_Type", optional=False, grouping="1",
description="The data type you want to work with.",
values=dataTypes,
default="Plate"),
scripts.List("IDs", optional=False, grouping="2",
description="List of Plate IDs").ofType(rlong(0)),
scripts.String("Mode", optional=False, grouping="3",
description="Select if you want to add or "
"remove PlateAcquisitions",
values=[rstring("Add"), rstring("Remove")],
default="Add"),
version="0.2",
authors=["Niko Klaric"],
institutions=["Glencoe Software Inc."],
contact="*****@*****.**",
)
try:
scriptParams = {}
for key in client.getInputKeys():
if client.getInput(key):
scriptParams[key] = client.getInput(key, unwrap=True)
connection = BlitzGateway(client_obj=client)
updateService = connection.getUpdateService()
queryService = connection.getQueryService()
processedMessages = []
for plateId in scriptParams["IDs"]:
plateObj = connection.getObject("Plate", plateId)
if plateObj is None:
client.setOutput(
"Message",
rstring("ERROR: No Plate with ID %s" % plateId))
return
if scriptParams["Mode"] == "Add":
plateAcquisitionObj = PlateAcquisitionI()
plateAcquisitionObj.setPlate(PlateI(plateObj.getId(), False))
wellGrid = plateObj.getWellGrid()
for axis in wellGrid:
for wellObj in axis:
wellSampleList = wellObj.copyWellSamples()
plateAcquisitionObj.addAllWellSampleSet(wellSampleList)
plateAcquisitionObj = updateService.saveAndReturnObject(
plateAcquisitionObj)
plateAcquisitionId = plateAcquisitionObj.getId()._val
processedMessages.append(
"Linked new PlateAcquisition with ID %d"
" to Plate with ID %d." % (plateAcquisitionId, plateId))
else:
params = ParametersI()
params.addId(plateId)
queryString = """
FROM PlateAcquisition AS pa
LEFT JOIN FETCH pa.wellSample
LEFT OUTER JOIN FETCH pa.annotationLinks
WHERE pa.plate.id = :id
"""
plateAcquisitionList = queryService.findAllByQuery(
queryString, params, connection.SERVICE_OPTS)
if plateAcquisitionList:
updateList = []
for plate_acquisition in plateAcquisitionList:
for well_sample in plate_acquisition.copyWellSample():
well_sample.setPlateAcquisition(None)
updateList.append(well_sample)
updateService.saveArray(updateList)
plate_acquisition.clearWellSample()
plate_acquisition.clearAnnotationLinks()
plate_acquisition = updateService.saveAndReturnObject(
plate_acquisition)
updateService.deleteObject(plate_acquisition)
processedMessages.append(
"%d PlateAcquisition(s) removed from Plate with ID %d." %
(len(plateAcquisitionList), plateId))
client.setOutput("Message", rstring("No errors. %s" %
" ".join(processedMessages)))
finally:
client.closeSession()
def run():
"""
"""
dataTypes = [rstring("Plate")]
client = scripts.client(
"Manage_Plate_Acquisitions.py",
"Add or remove PlateAcquisition(s) in a given Plate",
scripts.String("Data_Type",
optional=False,
grouping="1",
description="The data type you want to work with.",
values=dataTypes,
default="Plate"),
scripts.List("IDs",
optional=False,
grouping="2",
description="List of Plate IDs").ofType(rlong(0)),
scripts.String("Mode",
optional=False,
grouping="3",
description="Select if you want to add or "
"remove PlateAcquisitions",
values=[rstring("Add"),
rstring("Remove")],
default="Add"),
version="0.2",
authors=["Niko Klaric"],
institutions=["Glencoe Software Inc."],
contact="*****@*****.**",
)
try:
scriptParams = {}
for key in client.getInputKeys():
if client.getInput(key):
scriptParams[key] = client.getInput(key, unwrap=True)
connection = BlitzGateway(client_obj=client)
updateService = connection.getUpdateService()
queryService = connection.getQueryService()
processedMessages = []
for plateId in scriptParams["IDs"]:
plateObj = connection.getObject("Plate", plateId)
if plateObj is None:
client.setOutput(
"Message", rstring("ERROR: No Plate with ID %s" % plateId))
return
if scriptParams["Mode"] == "Add":
plateAcquisitionObj = PlateAcquisitionI()
plateAcquisitionObj.setPlate(PlateI(plateObj.getId(), False))
wellGrid = plateObj.getWellGrid()
for axis in wellGrid:
for wellObj in axis:
wellSampleList = wellObj.copyWellSamples()
plateAcquisitionObj.addAllWellSampleSet(wellSampleList)
plateAcquisitionObj = updateService.saveAndReturnObject(
plateAcquisitionObj)
plateAcquisitionId = plateAcquisitionObj.getId()._val
processedMessages.append(
"Linked new PlateAcquisition with ID %d"
" to Plate with ID %d." % (plateAcquisitionId, plateId))
else:
params = ParametersI()
params.addId(plateId)
queryString = """
FROM PlateAcquisition AS pa
LEFT JOIN FETCH pa.wellSample
LEFT OUTER JOIN FETCH pa.annotationLinks
WHERE pa.plate.id = :id
"""
plateAcquisitionList = queryService.findAllByQuery(
queryString, params, connection.SERVICE_OPTS)
if plateAcquisitionList:
updateList = []
for plate_acquisition in plateAcquisitionList:
for well_sample in plate_acquisition.copyWellSample():
well_sample.setPlateAcquisition(None)
updateList.append(well_sample)
updateService.saveArray(updateList)
plate_acquisition.clearWellSample()
plate_acquisition.clearAnnotationLinks()
plate_acquisition = updateService.saveAndReturnObject(
plate_acquisition)
updateService.deleteObject(plate_acquisition)
processedMessages.append(
"%d PlateAcquisition(s) removed from Plate with ID %d." %
(len(plateAcquisitionList), plateId))
client.setOutput(
"Message", rstring("No errors. %s" % " ".join(processedMessages)))
finally:
client.closeSession()