mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-15 20:57:56 +08:00
3bfeadc2b9
* improve HTTP error reporting * generate standards-compatible JSON * add --nan-to-num work-around for non-finite floating point values * lint * update tests * correctly set Infinities to min/max * REAMDE update for --nan-to-num * define constant for repetitive warning message * clarify where NaN errors will occure
119 lines
4.5 KiB
Python
119 lines
4.5 KiB
Python
import sys
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import click
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import logging
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from os import devnull
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from os.path import splitext, basename
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import webbrowser
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from server.app.util.errors import ScanpyFileError
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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("--layout", "-l", type=click.Choice(["umap", "tsne"]), default="umap", show_default=True,
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help="Method for layout.")
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@click.option("--diffexp", "-d", type=click.Choice(["ttest"]), default="ttest", show_default=True,
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help="Method for differential expression.")
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@click.option("--title", "-t", help="Title to display (if omitted will use file name).", metavar="")
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@click.option("--verbose", "-v", is_flag=True, default=False, show_default=True,
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help="Provide verbose output, including warnings and all server requests.")
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@click.option("--debug", "-d", is_flag=True, default=False, show_default=True,
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help="Run in debug mode.")
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@click.option("--open", "-o", "open_browser", is_flag=True, default=False, show_default=True,
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help="Open the web browser after launch.")
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@click.option("--port", "-p", help="Port to run server on.", metavar="", default=5005, show_default=True)
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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("--host", default="127.0.0.1", help="Host IP address")
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@click.option("--max-category-items", default=100, metavar="", show_default=True,
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help="Limits the number of categorical annotation items displayed.")
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@click.option("--diffexp-lfc-cutoff", default=0.01, show_default=True,
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help="Relative expression cutoff used when selecting top N differentially expressed genes")
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@click.option("--nan-to-num", is_flag=True, default=False, show_default=True,
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help="Replace all floating point NaN with zero, and infinities with finite numbers")
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def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
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open_browser, port, host, max_category_items, diffexp_lfc_cutoff,
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nan_to_num):
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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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# Startup message
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click.echo("[cellxgene] Starting the CLI...")
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# Import Flask app
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from server.app.app import app
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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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if not verbose:
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sys.tracebacklimit = 0
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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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# Setup app
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cellxgene_url = f"http://{host}:{port}"
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api_base = f"{cellxgene_url}/api/"
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app.config.update(
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DATASET_TITLE=title,
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CXG_API_BASE=api_base
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)
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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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click.echo(f"[cellxgene] Loading data from {basename(data)}, this may take awhile...")
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# Fix for anaconda python. matplotlib typically expects python to be installed as a framework TKAgg is usually
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# available and fixes this issue. See https://matplotlib.org/faq/virtualenv_faq.html
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import matplotlib as mpl
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mpl.use('TkAgg')
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from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
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args = {
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"layout": layout,
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"diffexp": diffexp,
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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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"nan_to_num": nan_to_num
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}
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try:
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app.data = ScanpyEngine(data, args)
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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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app.run(host=host, debug=debug, port=port, threaded=True)
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