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 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 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 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 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