CLI refactor (#396)

* 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
2026-09-21 15:08:12 +08:00 · 2018-11-02 10:52:50 -04:00
parent 6e46a65c32
commit 0c8a07ac13
11 changed files with 124 additions and 139 deletions
@@ -0,0 +1,12 @@
+import click
+
+from .launch import launch
+
+
+@click.group(name='cellxgene', context_settings=dict(max_content_width=85))
+@click.version_option(version='0.0.1', prog_name='cellxgene', message='[%(prog)s] Version %(version)s')
+def cli():
+    pass
+
+
+cli.add_command(launch)
@@ -0,0 +1,99 @@
+import sys
+import click
+import logging
+import webbrowser
+
+from os.path import splitext, basename
+
+
+@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...')
+
+    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}
+
+    app.data = ScanpyEngine(data, args)
+
+    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)