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 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_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)
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 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_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 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 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 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 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 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 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 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 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 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
