script_hashes, style_hashes = WSGIServer.load_static_csp_hashes(app)
script_hashes += WSGIServer.compute_inline_scp_hashes(app, app_config)
return (script_hashes, style_hashes)
try:
app_config = AppConfig()
has_config = False
# config file: look first for "config.yaml" in the current working directory
config_file = "config.yaml"
config_location = DataLocator(config_file)
if config_location.exists():
with config_location.local_handle() as lh:
logging.info(f"Configuration from {config_file}")
app_config.update_from_config_file(lh)
has_config = True
else:
# config file: second, use the CXG_CONFIG_FILE
config_file = os.getenv("CXG_CONFIG_FILE")
if config_file:
region_name = discover_s3_region_name(config_file)
config_location = DataLocator(config_file, region_name)
if config_location.exists():
with config_location.local_handle() as lh:
logging.info(f"Configuration from {config_file}")
app_config.update_from_config_file(lh)
has_config = True
else:
logging.critical(f"Configuration file not found {config_file}")
def launch(
datapath,
dataroot,
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>"""
# TODO Examples to provide when "--dataroot" is unhidden
# > cellxgene launch --dataroot example-dataset/
#
# > cellxgene launch --dataroot <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,
multi_dataset__dataroot=dataroot,
adaptor__anndata_adaptor__backed=backed,
)
cli_config.update_default_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.default_dataset_config.changes_from_default()
changes = {key: val for key, val, _ in diff}
app_config.update_default_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(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