def setUp(self): AbstractPlateAnalysisCtx.DEFAULT_ORIGINAL_FILE_PROVIDER = \ FromFileOriginalFileProvider original_files = list() # Create our container images and an original file image map images = list() n_images = 0 for row in range(16): for column in range(24): well = WellI(n_images, True) well.column = rint(column) well.row = rint(row) well_sample = WellSampleI(n_images, True) well_sample.well = well image = ImageI(n_images, True) image.addWellSample(well_sample) images.append(image) original_file_image_map = dict() # Our required original file format format = rstring('Companion/InCell') # Create original file representing the result file o = OriginalFileI(1L, True) o.name = rstring(self.RESULT_FILE) o.path = rstring(os.path.join(self.ROOT, self.RESULT_FILE)) o.mimetype = format original_files.append(o) #[1L] = o original_file_image_map[1L] = image sf = TestingServiceFactory() self.analysis_ctx = InCellPlateAnalysisCtx( images, original_files, original_file_image_map, 1L, sf)
def setUp(self): AbstractPlateAnalysisCtx.DEFAULT_ORIGINAL_FILE_PROVIDER = \ FromFileOriginalFileProvider original_files = list() # Create our container images and an original file image map images = list() n_images = 0 for row in range(16): for column in range(24): well = WellI(n_images, True) well.column = rint(column) well.row = rint(row) well_sample = WellSampleI(n_images, True) well_sample.well = well image = ImageI(n_images, True) image.addWellSample(well_sample) images.append(image) original_file_image_map = dict() # Our required original file format format = rstring('Companion/InCell') # Create original file representing the result file o = OriginalFileI(1, True) o.name = rstring(self.RESULT_FILE) o.path = rstring(os.path.join(self.ROOT, self.RESULT_FILE)) o.mimetype = format original_files.append(o) # [1] = o original_file_image_map[1] = image sf = TestingServiceFactory() self.analysis_ctx = InCellPlateAnalysisCtx(images, original_files, original_file_image_map, 1, sf)
def test_file_annotation(self): """Tests AnnotationWrapper methods return strings""" file_name = u'₩€_file_$$' f = OriginalFileI() f.name = rstring(file_name) obj = FileAnnotationI() obj.file = f file_ann = MockConnection(obj).getObject("Annotation", 1) assert file_ann.getFileName() == file_name.encode('utf8')
def create_fileset(): """Creates and returns a Fileset with associated Images.""" fileset = FilesetI() fileset.templatePrefix = rstring("") for image_index in range(2): image = create_image(image_index) for fileset_index in range(2): fileset_entry = FilesetEntryI() fileset_entry.clientPath = rstring("/client/path/filename_%d.ext" % fileset_index) original_file = OriginalFileI() original_file.name = rstring("filename_%d.ext" % fileset_index) original_file.path = rstring("/server/path/") original_file.size = rlong(50L) fileset_entry.originalFile = original_file fileset.addFilesetEntry(fileset_entry) fileset.addImage(image) return fileset
def create_fileset(): """Creates and returns a Fileset with associated Images.""" fileset = FilesetI() fileset.templatePrefix = rstring('') for image_index in range(2): image = create_image(image_index) for fileset_index in range(2): fileset_entry = FilesetEntryI() fileset_entry.clientPath = rstring('/client/path/filename_%d.ext' % fileset_index) original_file = OriginalFileI() original_file.name = rstring('filename_%d.ext' % fileset_index) original_file.path = rstring('/server/path/') original_file.size = rlong(50L) fileset_entry.originalFile = original_file fileset.addFilesetEntry(fileset_entry) fileset.addImage(image) return fileset
def images_with_original_files(request, gatewaywrapper): """Creates Images with associated OriginalFiles.""" gatewaywrapper.loginAsAuthor() gw = gatewaywrapper.gateway update_service = gw.getUpdateService() original_files = list() for original_file_index in range(2): original_file = OriginalFileI() original_file.name = rstring("filename_%d.ext" % original_file_index) original_file.path = rstring("/server/path/") original_file.size = rlong(50L) original_files.append(original_file) images = list() for image_index in range(2): image = create_image(image_index) for original_file in original_files: image.getPrimaryPixels().linkOriginalFile(original_file) images.append(image) image_ids = update_service.saveAndReturnIds(images) return [gw.getObject("Image", image_id) for image_id in image_ids]
def images_with_original_files(request, gatewaywrapper): """Creates Images with associated OriginalFiles.""" gatewaywrapper.loginAsAuthor() gw = gatewaywrapper.gateway update_service = gw.getUpdateService() original_files = list() for original_file_index in range(2): original_file = OriginalFileI() original_file.name = rstring('filename_%d.ext' % original_file_index) original_file.path = rstring('/server/path/') original_file.size = rlong(50L) original_files.append(original_file) images = list() for image_index in range(2): image = create_image(image_index) for original_file in original_files: image.getPrimaryPixels().linkOriginalFile(original_file) images.append(image) image_ids = update_service.saveAndReturnIds(images) return [gw.getObject('Image', image_id) for image_id in image_ids]