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Code Issues Packages Projects Releases Wiki Activity

Launch validation (#414)

Browse Source 
* WIP

* Cleanup

* Validation

* typo

* Max category limit 100 -> 500
This commit is contained in:
Charlotte Weaver
2018-11-07 13:01:13 -08:00
committed by GitHub
parent a9189017c7
commit 7d5c054b90
10 changed files with 204 additions and 141 deletions
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server/cli/launch.py
+42 -33
View File
@@ -1,31 +1,32 @@
import sys
import click
import logging
from os.path import splitext, basename
import webbrowser
from os.path import splitext, basename
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.')
@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.
@@ -40,15 +41,15 @@ def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
> cellxgene launch <your data file> --title <your title>"""
# Startup message
click.echo('[cellxgene] Starting the CLI...')
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 extension != ".h5ad":
raise click.FileError(basename(data), hint="file type must be .h5ad")
if debug:
verbose = True
@@ -62,9 +63,9 @@ def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
title = file_parts[0]
if listen_all:
host = '0.0.0.0'
host = "0.0.0.0"
else:
host = '127.0.0.1'
host = "127.0.0.1"
# Setup app
cellxgene_url = f"http://{host}:{port}"
@@ -76,24 +77,32 @@ def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
)
if not verbose:
log = logging.getLogger('werkzeug')
log = logging.getLogger("werkzeug")
log.setLevel(logging.ERROR)
click.echo(f'[cellxgene] Loading data from {basename(data)}, this may take awhile...')
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}
args = {
"layout": layout,
"diffexp": diffexp,
"max_category_items": max_category_items,
"obs_names": obs_names,
"var_names": var_names
}
app.data = ScanpyEngine(data, args)
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.')
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(f"[cellxgene] Launching! Please go to {cellxgene_url} in your browser.")
click.echo('[cellxgene] Type CTRL-C at any time to exit.')
click.echo("[cellxgene] Type CTRL-C at any time to exit.")
app.run(host=host, debug=debug, port=port, threaded=True)