mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-15 20:57:56 +08:00
213 lines
6.6 KiB
Python
213 lines
6.6 KiB
Python
import errno
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import functools
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import logging
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from os import devnull
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from os.path import splitext, basename, getsize
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import sys
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import warnings
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import webbrowser
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import click
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from server.app.app import Server
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from server.app.util.errors import ScanpyFileError
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from server.app.util.utils import custom_format_warning
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from server.utils.utils import find_available_port, is_port_available
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# anything bigger than this will generate a special message
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BIG_FILE_SIZE_THRESHOLD = 100 * 2 ** 20 # 100MB
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def common_args(func):
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"""
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Decorator to contain CLI args that will be common to both CLI and GUI: title and engine args.
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"""
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@click.option("--title", "-t", help="Title to display (if omitted will use file name).")
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@click.option(
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"--layout",
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"-l",
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default=[],
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multiple=True,
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show_default=True,
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help="Layout name, eg, 'umap'."
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)
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@click.option("--obs-names", default=None, metavar="", help="Name of annotation field to use for observations.")
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@click.option("--var-names", default=None, metavar="", help="Name of annotation to use for variables.")
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@click.option(
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"--max-category-items",
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default=1000,
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metavar="",
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show_default=True,
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help="Categories with more distinct values than this will not be displayed.",
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)
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@click.option(
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"--diffexp-lfc-cutoff",
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default=0.01,
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show_default=True,
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help="Relative expression cutoff used when selecting top N differentially expressed genes",
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)
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@functools.wraps(func)
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def wrapper(*args, **kwargs):
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return func(*args, **kwargs)
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return wrapper
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def parse_engine_args(layout, obs_names, var_names, max_category_items, diffexp_lfc_cutoff):
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return {
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"layout": layout,
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"max_category_items": max_category_items,
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"diffexp_lfc_cutoff": diffexp_lfc_cutoff,
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"obs_names": obs_names,
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"var_names": var_names,
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}
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@click.command()
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@click.argument("data", metavar="<data file>", type=click.Path(exists=True, file_okay=True, dir_okay=False))
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@click.option(
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"--verbose",
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"-v",
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is_flag=True,
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default=False,
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show_default=True,
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help="Provide verbose output, including warnings and all server requests.",
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)
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@click.option("--debug", is_flag=True, default=False, show_default=True, help="Run in debug mode.")
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@click.option(
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"--open",
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"-o",
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"open_browser",
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is_flag=True,
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default=False,
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show_default=True,
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help="Open the web browser after launch.",
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)
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@click.option("--port", "-p", help="Port to run server on, if not specified cellxgene will find an available port.",
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metavar="", show_default=True)
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@click.option("--host", default="127.0.0.1", help="Host IP address")
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@click.option(
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"--scripts",
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default=[],
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multiple=True,
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help="Additional script files to include in html page",
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show_default=True,
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)
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@common_args
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def launch(
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data,
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verbose,
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debug,
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open_browser,
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port,
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host,
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layout,
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obs_names,
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var_names,
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max_category_items,
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diffexp_lfc_cutoff,
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title,
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scripts
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):
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"""Launch the cellxgene data viewer.
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This web app lets you explore single-cell expression data.
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Data must be in a format that cellxgene expects, read the
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"getting started" guide.
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Examples:
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> cellxgene launch example_dataset/pbmc3k.h5ad --title pbmc3k
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> cellxgene launch <your data file> --title <your title>"""
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e_args = parse_engine_args(layout, obs_names, var_names, max_category_items, diffexp_lfc_cutoff)
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# Startup message
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click.echo("[cellxgene] Starting the CLI...")
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# Argument checking
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name, extension = splitext(data)
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if extension != ".h5ad":
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raise click.FileError(basename(data), hint="file type must be .h5ad")
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if debug:
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verbose = True
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open_browser = False
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else:
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warnings.formatwarning = custom_format_warning
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if not verbose:
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sys.tracebacklimit = 0
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if scripts:
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click.echo(r"""
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/ / /\ \ \__ _ _ __ _ __ (_)_ __ __ _
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\ \/ \/ / _` | '__| '_ \| | '_ \ / _` |
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\ /\ / (_| | | | | | | | | | | (_| |
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\/ \/ \__,_|_| |_| |_|_|_| |_|\__, |
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|___/
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The --scripts flag is intended for developers to include google analytics etc. You could be opening yourself to a
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security risk by including the --scripts flag. Make sure you trust the scripts that you are including.
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""")
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scripts_pretty = ", ".join(scripts)
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click.confirm(f"Are you sure you want to inject these scripts: {scripts_pretty}?", abort=True)
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if not title:
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file_parts = splitext(basename(data))
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title = file_parts[0]
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if port:
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if debug:
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raise click.ClickException("--port and --debug may not be used together (try --verbose for error logging).")
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if not is_port_available(host, int(port)):
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raise click.ClickException(
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f"The port selected {port} is in use, please specify an open port using the --port flag."
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)
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else:
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port = find_available_port(host)
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# Setup app
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cellxgene_url = f"http://{host}:{port}"
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# Import Flask app
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server = Server()
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server.create_app()
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server.app.config.update(SCRIPTS=scripts)
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if not verbose:
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log = logging.getLogger("werkzeug")
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log.setLevel(logging.ERROR)
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file_size = getsize(data)
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# if a big file, let the user know it may take a while to load.
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if file_size > BIG_FILE_SIZE_THRESHOLD:
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click.echo(f"[cellxgene] Loading data from {basename(data)}, this may take awhile...")
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else:
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click.echo(f"[cellxgene] Loading data from {basename(data)}.")
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from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
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try:
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server.attach_data(ScanpyEngine(data, e_args), title=title)
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except ScanpyFileError as e:
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raise click.ClickException(f"{e}")
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if open_browser:
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click.echo(f"[cellxgene] Launching! Opening your browser to {cellxgene_url} now.")
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webbrowser.open(cellxgene_url)
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else:
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click.echo(f"[cellxgene] Launching! Please go to {cellxgene_url} in your browser.")
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click.echo("[cellxgene] Type CTRL-C at any time to exit.")
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if not verbose:
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f = open(devnull, "w")
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sys.stdout = f
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try:
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server.app.run(host=host, debug=debug, port=port, threaded=True, use_debugger=False)
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except OSError as e:
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if e.errno == errno.EADDRINUSE:
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raise click.ClickException("Port is in use, please specify an open port using the --port flag.") from e
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raise
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