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Code Issues Packages Projects Releases Wiki Activity

GUI UI Elements (#816)

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This commit is contained in:
Charlotte Weaver
2019-06-27 17:30:57 -07:00
committed by GitHub
parent 5effe4bbbb
commit 8afb22a017
15 changed files with 819 additions and 95 deletions
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server/cli/launch.py
+67 -53
View File
@@ -1,4 +1,5 @@
import errno
import functools
import logging
from os import devnull
from os.path import splitext, basename, getsize
@@ -13,22 +14,56 @@ from server.app.util.errors import ScanpyFileError
from server.app.util.utils import custom_format_warning
from server.utils.utils import find_available_port, is_port_available
# anything bigger than this will generate a special message
BIG_FILE_SIZE_THRESHOLD = 100 * 2**20 # 100MB
BIG_FILE_SIZE_THRESHOLD = 100 * 2 ** 20 # 100MB
def common_args(func):
"""
Decorator to contain CLI args that will be common to both CLI and GUI: title and engine args.
"""
@click.option("--title", "-t", help="Title to display (if omitted will use file name).")
@click.option(
"--layout",
"-l",
default=[],
multiple=True,
show_default=True,
help="Layout name, eg, 'umap'."
)
@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(
"--max-category-items",
default=1000,
metavar="",
show_default=True,
help="Categories with more distinct values than this will not be displayed.",
)
@click.option(
"--diffexp-lfc-cutoff",
default=0.01,
show_default=True,
help="Relative expression cutoff used when selecting top N differentially expressed genes",
)
@functools.wraps(func)
def wrapper(*args, **kwargs):
return func(*args, **kwargs)
return wrapper
def parse_engine_args(layout, obs_names, var_names, max_category_items, diffexp_lfc_cutoff):
return {
"layout": layout,
"max_category_items": max_category_items,
"diffexp_lfc_cutoff": diffexp_lfc_cutoff,
"obs_names": obs_names,
"var_names": var_names,
}
@click.command()
@click.argument("data", metavar="<data file>", type=click.Path(exists=True, file_okay=True, dir_okay=False))
@click.option(
"--layout",
"-l",
default=[],
multiple=True,
show_default=True,
help="Layout name, eg, 'umap'."
)
@click.option("--title", "-t", help="Title to display (if omitted will use file name).", metavar="")
@click.option(
"--verbose",
"-v",
@@ -49,22 +84,7 @@ BIG_FILE_SIZE_THRESHOLD = 100 * 2**20 # 100MB
)
@click.option("--port", "-p", help="Port to run server on, if not specified cellxgene will find an available port.",
metavar="", 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("--host", default="127.0.0.1", help="Host IP address")
@click.option(
"--max-category-items",
default=1000,
metavar="",
show_default=True,
help="Categories with more distinct values than this will not be displayed.",
)
@click.option(
"--diffexp-lfc-cutoff",
default=0.01,
show_default=True,
help="Relative expression cutoff used when selecting top N differentially expressed genes",
)
@click.option(
"--scripts",
default=[],
@@ -72,20 +92,21 @@ BIG_FILE_SIZE_THRESHOLD = 100 * 2**20 # 100MB
help="Additional script files to include in html page",
show_default=True,
)
@common_args
def launch(
data,
layout,
title,
verbose,
debug,
obs_names,
var_names,
open_browser,
port,
host,
layout,
obs_names,
var_names,
max_category_items,
diffexp_lfc_cutoff,
scripts,
title,
scripts
):
"""Launch the cellxgene data viewer.
This web app lets you explore single-cell expression data.
@@ -98,6 +119,7 @@ def launch(
> cellxgene launch <your data file> --title <your title>"""
e_args = parse_engine_args(layout, obs_names, var_names, max_category_items, diffexp_lfc_cutoff)
# Startup message
click.echo("[cellxgene] Starting the CLI...")
@@ -112,22 +134,22 @@ def launch(
else:
warnings.formatwarning = custom_format_warning
if scripts:
click.echo(r"""
/ / /\ \ \__ _ _ __ _ __ (_)_ __ __ _
\ \/ \/ / _` | '__| '_ \| | '_ \ / _` |
\ /\ / (_| | | | | | | | | | | (_| |
\/ \/ \__,_|_| |_| |_|_|_| |_|\__, |
|___/
The --scripts flag is intended for developers to include google analytics etc. You could be opening yourself to a
security risk by including the --scripts flag. Make sure you trust the scripts that you are including.
""")
scripts_pretty = ", ".join(scripts)
click.confirm(f"Are you sure you want to inject these scripts: {scripts_pretty}?", abort=True)
if not verbose:
sys.tracebacklimit = 0
if scripts:
click.echo(r"""
/ / /\ \ \__ _ _ __ _ __ (_)_ __ __ _
\ \/ \/ / _` | '__| '_ \| | '_ \ / _` |
\ /\ / (_| | | | | | | | | | | (_| |
\/ \/ \__,_|_| |_| |_|_|_| |_|\__, |
|___/
The --scripts flag is intended for developers to include google analytics etc. You could be opening yourself to a
security risk by including the --scripts flag. Make sure you trust the scripts that you are including.
""")
scripts_pretty = ", ".join(scripts)
click.confirm(f"Are you sure you want to inject these scripts: {scripts_pretty}?", abort=True)
if not title:
file_parts = splitext(basename(data))
title = file_parts[0]
@@ -170,16 +192,8 @@ security risk by including the --scripts flag. Make sure you trust the scripts t
mpl.use("TkAgg")
from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
args = {
"layout": layout,
"max_category_items": max_category_items,
"diffexp_lfc_cutoff": diffexp_lfc_cutoff,
"obs_names": obs_names,
"var_names": var_names,
}
try:
server.attach_data(ScanpyEngine(data, args), title=title)
server.attach_data(ScanpyEngine(data, e_args), title=title)
except ScanpyFileError as e:
raise click.ClickException(f"{e}")