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 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
