mirror of
https://github.com/chanzuckerberg/cellxgene.git
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0c8a07ac13
* refactor cli to improve ux and enable easy incorporation of prepare as a subcommand * switches to use click, which removes some boilerplate and gets us some improved ux for free * changes the entry point for the cli * changes the name of the browser option to --open and makes the default false
100 lines
3.7 KiB
Python
100 lines
3.7 KiB
Python
import sys
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import click
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import logging
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import webbrowser
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from os.path import splitext, basename
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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('--listen-all', is_flag=True, default=False, show_default=True,
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help='Bind to all interfaces (this makes the server accessible beyond this computer).')
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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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def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
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open_browser, port, listen_all, max_category_items):
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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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if listen_all:
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host = '0.0.0.0'
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else:
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host = '127.0.0.1'
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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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from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
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args = {'layout': layout, 'diffexp': diffexp, 'max_category_items': max_category_items,
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'obs_names': obs_names, 'var_names': var_names}
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app.data = ScanpyEngine(data, args)
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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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app.run(host=host, debug=debug, port=port)
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