mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-16 21:37:59 +08:00
dd56d0937c
* fix anaconda build * Added link for TKAgg * Add matplotlib to requirements We are pulling it in through scanpy, but since we are importing it directly we should include it explicitly
113 lines
4.2 KiB
Python
113 lines
4.2 KiB
Python
import sys
|
|
import click
|
|
import logging
|
|
from os.path import splitext, basename
|
|
import webbrowser
|
|
|
|
from server.app.util.errors import ScanpyFileError
|
|
|
|
|
|
@click.command()
|
|
@click.argument("data", metavar="<data file>", type=click.Path(exists=True, file_okay=True, dir_okay=False))
|
|
@click.option("--layout", "-l", type=click.Choice(["umap", "tsne"]), default="umap", show_default=True,
|
|
help="Method for layout.")
|
|
@click.option("--diffexp", "-d", type=click.Choice(["ttest"]), default="ttest", show_default=True,
|
|
help="Method for differential expression.")
|
|
@click.option("--title", "-t", help="Title to display (if omitted will use file name).", metavar="")
|
|
@click.option("--verbose", "-v", is_flag=True, default=False, show_default=True,
|
|
help="Provide verbose output, including warnings and all server requests.")
|
|
@click.option("--debug", "-d", is_flag=True, default=False, show_default=True,
|
|
help="Run in debug mode.")
|
|
@click.option("--open", "-o", "open_browser", is_flag=True, default=False, show_default=True,
|
|
help="Open the web browser after launch.")
|
|
@click.option("--port", "-p", help="Port to run server on.", metavar="", default=5005, show_default=True)
|
|
@click.option("--obs-names", default=None, metavar="", help="Name of annotation field to use for observations.")
|
|
@click.option("--var-names", default=None, metavar="", help="Name of annotation to use for variables.")
|
|
@click.option("--listen-all", is_flag=True, default=False, show_default=True,
|
|
help="Bind to all interfaces (this makes the server accessible beyond this computer).")
|
|
@click.option("--max-category-items", default=100, metavar="", show_default=True,
|
|
help="Limits the number of categorical annotation items displayed.")
|
|
def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
|
|
open_browser, port, listen_all, max_category_items):
|
|
"""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.
|
|
|
|
Examples:
|
|
|
|
> cellxgene launch example_dataset/pbmc3k.h5ad --title pbmc3k
|
|
|
|
> cellxgene launch <your data file> --title <your title>"""
|
|
|
|
# Startup message
|
|
click.echo("[cellxgene] Starting the CLI...")
|
|
|
|
# Import Flask app
|
|
from server.app.app import app
|
|
|
|
# Argument checking
|
|
name, extension = splitext(data)
|
|
if extension != ".h5ad":
|
|
raise click.FileError(basename(data), hint="file type must be .h5ad")
|
|
|
|
if debug:
|
|
verbose = True
|
|
open_browser = False
|
|
|
|
if not verbose:
|
|
sys.tracebacklimit = 0
|
|
|
|
if not title:
|
|
file_parts = splitext(basename(data))
|
|
title = file_parts[0]
|
|
|
|
if listen_all:
|
|
host = "0.0.0.0"
|
|
else:
|
|
host = "127.0.0.1"
|
|
|
|
# Setup app
|
|
cellxgene_url = f"http://{host}:{port}"
|
|
api_base = f"{cellxgene_url}/api/"
|
|
|
|
app.config.update(
|
|
DATASET_TITLE=title,
|
|
CXG_API_BASE=api_base
|
|
)
|
|
|
|
if not verbose:
|
|
log = logging.getLogger("werkzeug")
|
|
log.setLevel(logging.ERROR)
|
|
|
|
click.echo(f"[cellxgene] Loading data from {basename(data)}, this may take awhile...")
|
|
|
|
# Fix for anaconda python. matplotlib typically expects python to be installed as a framework TKAgg is usually
|
|
# available and fixes this issue. See https://matplotlib.org/faq/virtualenv_faq.html
|
|
import matplotlib as mpl
|
|
mpl.use('TkAgg')
|
|
from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
|
|
|
|
args = {
|
|
"layout": layout,
|
|
"diffexp": diffexp,
|
|
"max_category_items": max_category_items,
|
|
"obs_names": obs_names,
|
|
"var_names": var_names
|
|
}
|
|
|
|
try:
|
|
app.data = ScanpyEngine(data, args)
|
|
except ScanpyFileError as e:
|
|
raise click.ClickException(f"{e}")
|
|
|
|
if 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.")
|
|
|
|
app.run(host=host, debug=debug, port=port, threaded=True)
|