mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-15 20:57:56 +08:00
b284e6f820
* launch option changes * more CLI help improvements * change plot help * additional changes requested * change metavars for options and subcommand
328 lines
11 KiB
Python
328 lines
11 KiB
Python
import errno
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import functools
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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 sys
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import warnings
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import webbrowser
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from urllib.parse import urlparse
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import click
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from server.app.app import Server
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from server.app.util.errors import ScanpyFileError
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from server.app.util.utils import custom_format_warning
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from server.utils.utils import find_available_port, is_port_available, sort_options
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from server.app.util.data_locator import DataLocator
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# anything bigger than this will generate a special message
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BIG_FILE_SIZE_THRESHOLD = 100 * 2 ** 20 # 100MB
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def common_args(func):
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"""
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Decorator to contain CLI args that will be common to both CLI and GUI: title and engine args.
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"""
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@click.option(
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"--title",
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"-t",
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metavar="<text>",
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help="Title to display. If omitted will use file name.")
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@click.option(
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"--about",
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metavar="<URL>",
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help="URL providing more information about the dataset "
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"(hint: must be a fully specified absolute URL).")
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@click.option(
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"--embedding",
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"-e",
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default=[],
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multiple=True,
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show_default=False,
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metavar="<text>",
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help="Embedding name, eg, 'umap'. Repeat option for multiple embeddings. Defaults to all."
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)
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@click.option(
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"--obs-names",
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"-obs",
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default=None,
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metavar="<text>",
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help="Name of annotation field to use for observations. If not specified cellxgene will use the the obs index.")
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@click.option(
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"--var-names",
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"-var",
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default=None,
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metavar="<text>",
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help="Name of annotation to use for variables. If not specified cellxgene will use the the var index.")
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@click.option(
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"--max-category-items",
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default=1000,
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metavar="<integer>",
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show_default=True,
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help="Will not display categories with more distinct values than specified.",)
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@click.option(
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"--diffexp-lfc-cutoff",
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"-de",
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default=0.01,
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show_default=True,
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metavar="<float>",
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help="Minimum log fold change threshold for differential expression.",)
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@click.option(
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"--experimental-label-file",
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default=None,
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show_default=True,
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multiple=False,
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metavar="<path>",
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help="CSV file containing user annotations; will be overwritten. Created if does not exist.",)
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@click.option(
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"--backed",
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"-b",
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is_flag=True,
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default=False,
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show_default=False,
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help="Load data in file-backed mode. This may save memory, but may result in slower overall performance.")
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@click.option(
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"--disable-diffexp",
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is_flag=True,
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default=False,
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show_default=False,
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help="Disable on-demand differential expression.")
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@functools.wraps(func)
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def wrapper(*args, **kwargs):
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return func(*args, **kwargs)
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return wrapper
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def parse_engine_args(embedding, obs_names, var_names, max_category_items,
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diffexp_lfc_cutoff, experimental_label_file, backed,
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disable_diffexp):
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return {
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"layout": embedding,
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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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"label_file": experimental_label_file,
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"backed": backed,
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"disable_diffexp": disable_diffexp
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}
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@sort_options
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@click.command(short_help="Launch the cellxgene data viewer. "
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"Run `cellxgene launch --help` for more information.",
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options_metavar="<options>",)
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@click.argument("data", nargs=1, metavar="<path to data file>", required=True)
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@click.option(
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"--verbose",
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"-v",
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is_flag=True,
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default=False,
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show_default=True,
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help="Provide verbose output, including warnings and all server requests.",)
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@click.option(
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"--debug",
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"-d",
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is_flag=True,
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default=False,
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show_default=True,
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help="Run in debug mode. This is helpful for cellxgene developers, "
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"or when you want more information about an error condition.",)
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@click.option(
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"--open",
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"-o",
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"open_browser",
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is_flag=True,
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default=False,
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show_default=True,
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help="Open web browser after launch.",)
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@click.option(
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"--port",
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"-p",
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metavar="<port>",
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show_default=True,
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help="Port to run server on. If not specified cellxgene will find an available port.",)
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@click.option(
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"--host",
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metavar="<IP address>",
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default="127.0.0.1",
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show_default=False,
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help="Host IP address. By default cellxgene will use localhost (e.g. 127.0.0.1).")
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@click.option(
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"--scripts",
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"-s",
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default=[],
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multiple=True,
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metavar="<text>",
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help="Additional script files to include in HTML page. If not specified, "
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"no additional script files will be included.",
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show_default=False,)
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@click.help_option("--help", "-h", help="Show this message and exit.")
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@common_args
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def launch(
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data,
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verbose,
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debug,
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open_browser,
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port,
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host,
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embedding,
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obs_names,
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var_names,
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max_category_items,
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diffexp_lfc_cutoff,
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title,
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scripts,
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about,
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experimental_label_file,
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backed,
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disable_diffexp
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):
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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.
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Read the "getting started" guide to learn more:
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https://chanzuckerberg.github.io/cellxgene/getting-started.html
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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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> cellxgene launch <url>"""
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e_args = parse_engine_args(embedding, obs_names, var_names, max_category_items,
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diffexp_lfc_cutoff, experimental_label_file, backed,
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disable_diffexp)
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try:
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data_locator = DataLocator(data)
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except RuntimeError as re:
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raise click.ClickException(f"Unable to access data at {data}. {str(re)}")
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# Startup message
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click.echo("[cellxgene] Starting the CLI...")
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# Argument checking
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if data_locator.islocal():
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# if data locator is local, apply file system conventions and other "cheap"
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# validation checks. If a URI, defer until we actually fetch the data and
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# try to read it. Many of these tests don't make sense for URIs (eg, extension-
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# based typing).
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if not data_locator.exists():
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raise click.FileError(data, hint="file does not exist")
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if not data_locator.isfile():
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raise click.FileError(data, hint="data is not a file")
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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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else:
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warnings.formatwarning = custom_format_warning
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if not verbose:
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sys.tracebacklimit = 0
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if scripts:
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click.echo(r"""
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/ / /\ \ \__ _ _ __ _ __ (_)_ __ __ _
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\ \/ \/ / _` | '__| '_ \| | '_ \ / _` |
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\ /\ / (_| | | | | | | | | | | (_| |
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\/ \/ \__,_|_| |_| |_|_|_| |_|\__, |
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|___/
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The --scripts flag is intended for developers to include google analytics etc. You could be opening yourself to a
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security risk by including the --scripts flag. Make sure you trust the scripts that you are including.
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""")
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scripts_pretty = ", ".join(scripts)
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click.confirm(f"Are you sure you want to inject these scripts: {scripts_pretty}?", abort=True)
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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 port:
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if debug:
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raise click.ClickException("--port and --debug may not be used together (try --verbose for error logging).")
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if not is_port_available(host, int(port)):
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raise click.ClickException(
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f"The port selected {port} is in use, please specify an open port using the --port flag."
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)
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else:
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port = find_available_port(host)
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if experimental_label_file:
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lf_name, lf_ext = splitext(experimental_label_file)
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if lf_ext and lf_ext != ".csv":
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raise click.FileError(basename(experimental_label_file), hint="label file type must be .csv")
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if about:
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def url_check(url):
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try:
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result = urlparse(url)
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if all([result.scheme, result.netloc]):
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return True
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else:
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return False
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except ValueError:
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return False
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if not url_check(about):
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raise click.ClickException("Must provide an absolute URL for --about. (Example format: http://example.com)")
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# Setup app
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cellxgene_url = f"http://{host}:{port}"
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# Import Flask app
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server = Server()
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server.create_app()
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server.app.config.update(SCRIPTS=scripts)
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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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file_size = data_locator.size() if data_locator.islocal() else 0
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# if a big file, let the user know it may take a while to load.
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if file_size > BIG_FILE_SIZE_THRESHOLD:
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click.echo(f"[cellxgene] Loading data from {basename(data)}, this may take a while...")
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else:
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click.echo(f"[cellxgene] Loading data from {basename(data)}.")
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from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
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try:
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server.attach_data(ScanpyEngine(data_locator, e_args), title=title, about=about)
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except ScanpyFileError as e:
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raise click.ClickException(f"{e}")
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if not disable_diffexp and server.app.data.config['diffexp_may_be_slow']:
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click.echo(f"[cellxgene] CAUTION: due to the size of your dataset, "
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f"running differential expression may take longer or fail.")
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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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try:
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server.app.run(host=host, debug=debug, port=port, threaded=False if debug else True, use_debugger=False)
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except OSError as e:
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if e.errno == errno.EADDRINUSE:
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raise click.ClickException("Port is in use, please specify an open port using the --port flag.") from e
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raise
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