def get_config(self, **kwargs): file_name = self.custom_app_config( dataset_datapath=H5AD_FIXTURE, config_file_name=self.config_file_name, **kwargs ) config = AppConfig() config.update_from_config_file(file_name) return config
def test_get_dataset_config_returns_dataset_config_for_single_datasets(self): datapath = f"{FIXTURES_ROOT}/1e4dfec4-c0b2-46ad-a04e-ff3ffb3c0a8f.h5ad" file_name = self.custom_app_config(dataset_datapath=datapath, config_file_name=self.config_file_name) config = AppConfig() config.update_from_config_file(file_name) self.assertEqual(config.get_dataset_config(), config.dataset_config)
def test_aws_secrets_manager(self, mock_get_secret_key): mock_get_secret_key.return_value = { "flask_secret_key": "mock_flask_secret_key", } configfile = self.custom_external_config( aws_secrets_manager_region="us-west-2", aws_secrets_manager_secrets=[ dict( name="my_secret", values=[ dict(key="flask_secret_key", path=["server", "app", "flask_secret_key"], required=True), ], ) ], config_file_name="secret_external_config.yaml", ) app_config = AppConfig() app_config.update_from_config_file(configfile) app_config.server_config.single_dataset__datapath = f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad" app_config.complete_config() self.assertEqual(app_config.server_config.app__flask_secret_key, "mock_flask_secret_key")
def test_configfile_with_specialization(self): # test that per_dataset_config config load the default config, then the specialized config with tempfile.TemporaryDirectory() as tempdir: configfile = os.path.join(tempdir, "config.yaml") with open(configfile, "w") as fconfig: config = """ server: single_dataset: datapath: fake_datapath dataset: user_annotations: enable: false type: local_file_csv local_file_csv: file: fake_file directory: fake_dir """ fconfig.write(config) app_config = AppConfig() app_config.update_from_config_file(configfile) test_config = app_config.dataset_config # test config from default self.assertEqual(test_config.user_annotations__type, "local_file_csv") self.assertEqual( test_config.user_annotations__local_file_csv__file, "fake_file")
def test_handle_embeddings__checks_data_file_types(self): file_name = self.custom_app_config( embedding_names=["name1", "name2"], enable_reembedding="true", dataset_datapath=f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad", anndata_backed="true", config_file_name=self.config_file_name, ) config = AppConfig() config.update_from_config_file(file_name) config.server_config.complete_config(self.context) with self.assertRaises(ConfigurationError): config.dataset_config.handle_embeddings()
def test_config_for_single_dataset(self): file_name = self.custom_app_config( config_file_name="single_dataset.yml", dataset_datapath=f"{H5AD_FIXTURE}") config = AppConfig() config.update_from_config_file(file_name) config.server_config.handle_single_dataset(self.context) file_name = self.custom_app_config( config_file_name="single_dataset_with_about.yml", about="www.cziscience.com", dataset_datapath=f"{H5AD_FIXTURE}", ) config = AppConfig() config.update_from_config_file(file_name) with self.assertRaises(ConfigurationError): config.server_config.handle_single_dataset(self.context)
def test_configfile_no_server_section(self): # test a config file without a dataset section with tempfile.TemporaryDirectory() as tempdir: configfile = os.path.join(tempdir, "config.yaml") with open(configfile, "w") as fconfig: config = """ dataset: user_annotations: enable: false """ fconfig.write(config) app_config = AppConfig() app_config.update_from_config_file(configfile) server_changes = app_config.server_config.changes_from_default() dataset_changes = app_config.dataset_config.changes_from_default() self.assertEqual(server_changes, []) self.assertEqual(dataset_changes, [("user_annotations__enable", False, True)])
def test_handle_data_locator_works_for_default_types( self, mock_discover_region_name): mock_discover_region_name.return_value = None # Default config self.assertEqual( self.config.server_config.data_locator__s3__region_name, None) # hard coded config = self.get_config() self.assertEqual(config.server_config.data_locator__s3__region_name, "us-east-1") # incorrectly formatted datapath = "s3://shouldnt/work" file_name = self.custom_app_config( dataset_datapath=datapath, config_file_name=self.config_file_name, data_locater_region_name="true") config = AppConfig() config.update_from_config_file(file_name) with self.assertRaises(ConfigurationError): config.server_config.handle_data_locator()
def launch( datapath, verbose, debug, open_browser, port, host, embedding, obs_names, var_names, max_category_items, disable_custom_colors, diffexp_lfc_cutoff, title, scripts, about, disable_annotations, annotations_file, annotations_dir, backed, disable_diffexp, experimental_annotations_ontology, experimental_annotations_ontology_obo, experimental_enable_reembedding, config_file, dump_default_config, ): """Launch the cellxgene data viewer. This web app lets you explore single-cell expression data. Data must be in a format that cellxgene expects. Read the "getting started" guide to learn more: https://chanzuckerberg.github.io/cellxgene/getting-started.html Examples: > cellxgene launch example-dataset/pbmc3k.h5ad --title pbmc3k > cellxgene launch <your data file> --title <your title> > cellxgene launch <url>""" if dump_default_config: print(default_config) sys.exit(0) # Startup message click.echo("[cellxgene] Starting the CLI...") # app config app_config = AppConfig() server_config = app_config.server_config try: if config_file: app_config.update_from_config_file(config_file) # Determine which config options were give on the command line. # Those will override the ones provided in the config file (if provided). cli_config = AppConfig() cli_config.update_server_config( app__verbose=verbose, app__debug=debug, app__host=host, app__port=port, app__open_browser=open_browser, single_dataset__datapath=datapath, single_dataset__title=title, single_dataset__about=about, single_dataset__obs_names=obs_names, single_dataset__var_names=var_names, adaptor__anndata_adaptor__backed=backed, ) cli_config.update_dataset_config( app__scripts=scripts, user_annotations__enable=not disable_annotations, user_annotations__local_file_csv__file=annotations_file, user_annotations__local_file_csv__directory=annotations_dir, user_annotations__ontology__enable= experimental_annotations_ontology, user_annotations__ontology__obo_location= experimental_annotations_ontology_obo, presentation__max_categories=max_category_items, presentation__custom_colors=not disable_custom_colors, embeddings__names=embedding, embeddings__enable_reembedding=experimental_enable_reembedding, diffexp__enable=not disable_diffexp, diffexp__lfc_cutoff=diffexp_lfc_cutoff, ) diff = cli_config.server_config.changes_from_default() changes = {key: val for key, val, _ in diff} app_config.update_server_config(**changes) diff = cli_config.dataset_config.changes_from_default() changes = {key: val for key, val, _ in diff} app_config.update_dataset_config(**changes) # process the configuration # any errors will be thrown as an exception. # any info messages will be passed to the messagefn function. def messagefn(message): click.echo("[cellxgene] " + message) # Use a default secret if one is not provided if not server_config.app__flask_secret_key: app_config.update_server_config( app__flask_secret_key="SparkleAndShine") app_config.complete_config(messagefn) except (ConfigurationError, DatasetAccessError) as e: raise click.ClickException(e) handle_scripts(scripts) # create the server server = CliLaunchServer(app_config) if not server_config.app__verbose: log = logging.getLogger("werkzeug") log.setLevel(logging.ERROR) cellxgene_url = f"http://{app_config.server_config.app__host}:{app_config.server_config.app__port}" if server_config.app__open_browser: click.echo( f"[cellxgene] Launching! Opening your browser to {cellxgene_url} now." ) webbrowser.open(cellxgene_url) else: click.echo( f"[cellxgene] Launching! Please go to {cellxgene_url} in your browser." ) click.echo("[cellxgene] Type CTRL-C at any time to exit.") if not server_config.app__verbose: f = open(os.devnull, "w") sys.stdout = f try: server.app.run( host=server_config.app__host, debug=server_config.app__debug, port=server_config.app__port, threaded=not server_config.app__debug, use_debugger=False, use_reloader=False, ) except OSError as e: if e.errno == errno.EADDRINUSE: raise click.ClickException( "Port is in use, please specify an open port using the --port flag." ) from e raise