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Refactor czi_hosted and server into backend directory, pull common code into backend/common, refactor tests (#2102)

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* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
This commit is contained in:
Madison Dunitz
2021-03-26 00:27:07 -05:00
committed by GitHub
parent e6e358ddc8
commit 78c9d24ed4
425 changed files with 734 additions and 5317 deletions
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server/cli/launch.py
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import errno
import functools
import logging
import sys
import webbrowser
import os
import click
from flask_compress import Compress
from flask_cors import CORS
from server.default_config import default_config
from server.app.app import Server
from server.common.config.app_config import AppConfig
from server.common.errors import DatasetAccessError, ConfigurationError
from server.common.utils.utils import sort_options
DEFAULT_CONFIG = AppConfig()
def annotation_args(func):
@click.option(
"--disable-annotations",
is_flag=True,
default=not DEFAULT_CONFIG.default_dataset_config.user_annotations__enable,
show_default=True,
help="Disable user annotation of data.",
)
@click.option(
"--annotations-file",
default=DEFAULT_CONFIG.default_dataset_config.user_annotations__local_file_csv__file,
show_default=True,
multiple=False,
metavar="<path>",
help="CSV file to initialize editing of existing annotations; will be altered in-place. "
"Incompatible with --annotations-dir.",
)
@click.option(
"--annotations-dir",
default=DEFAULT_CONFIG.default_dataset_config.user_annotations__local_file_csv__directory,
show_default=False,
multiple=False,
metavar="<directory path>",
help="Directory of where to save output annotations; filename will be specified in the application. "
"Incompatible with --annotations-file.",
)
@click.option(
"--experimental-annotations-ontology",
is_flag=True,
default=DEFAULT_CONFIG.default_dataset_config.user_annotations__ontology__enable,
show_default=True,
help="When creating annotations, optionally autocomplete names from ontology terms.",
)
@click.option(
"--experimental-annotations-ontology-obo",
default=DEFAULT_CONFIG.default_dataset_config.user_annotations__ontology__obo_location,
show_default=True,
metavar="<path or url>",
help="Location of OBO file defining cell annotation autosuggest terms.",
)
@functools.wraps(func)
def wrapper(*args, **kwargs):
return func(*args, **kwargs)
return wrapper
def config_args(func):
@click.option(
"--max-category-items",
default=DEFAULT_CONFIG.default_dataset_config.presentation__max_categories,
metavar="<integer>",
show_default=True,
help="Will not display categories with more distinct values than specified.",
)
@click.option(
"--disable-custom-colors",
is_flag=True,
default=False,
show_default=False,
help="Disable user-defined category-label colors drawn from source data file.",
)
@click.option(
"--diffexp-lfc-cutoff",
"-de",
default=DEFAULT_CONFIG.default_dataset_config.diffexp__lfc_cutoff,
show_default=True,
metavar="<float>",
help="Minimum log fold change threshold for differential expression.",
)
@click.option(
"--disable-diffexp",
is_flag=True,
default=not DEFAULT_CONFIG.default_dataset_config.diffexp__enable,
show_default=False,
help="Disable on-demand differential expression.",
)
@click.option(
"--embedding",
"-e",
default=DEFAULT_CONFIG.default_dataset_config.embeddings__names,
multiple=True,
show_default=False,
metavar="<text>",
help="Embedding name, eg, 'umap'. Repeat option for multiple embeddings. Defaults to all.",
)
@click.option(
"--experimental-enable-reembedding",
is_flag=True,
default=DEFAULT_CONFIG.default_dataset_config.embeddings__enable_reembedding,
show_default=False,
hidden=True,
help="Enable experimental on-demand re-embedding using UMAP. WARNING: may be very slow.",
)
@functools.wraps(func)
def wrapper(*args, **kwargs):
return func(*args, **kwargs)
return wrapper
def dataset_args(func):
@click.option(
"--obs-names",
"-obs",
default=DEFAULT_CONFIG.server_config.single_dataset__obs_names,
metavar="<text>",
help="Name of annotation field to use for observations. If not specified cellxgene will use the the obs index.",
)
@click.option(
"--var-names",
"-var",
default=DEFAULT_CONFIG.server_config.single_dataset__var_names,
metavar="<text>",
help="Name of annotation to use for variables. If not specified cellxgene will use the the var index.",
)
@click.option(
"--backed",
"-b",
is_flag=True,
default=DEFAULT_CONFIG.server_config.adaptor__anndata_adaptor__backed,
show_default=False,
help="Load anndata in file-backed mode. " "This may save memory, but may result in slower overall performance.",
)
@click.option(
"--title",
"-t",
default=DEFAULT_CONFIG.server_config.single_dataset__title,
metavar="<text>",
help="Title to display. If omitted will use file name.",
)
@click.option(
"--about",
default=DEFAULT_CONFIG.server_config.single_dataset__about,
metavar="<URL>",
help="URL providing more information about the dataset (hint: must be a fully specified absolute URL).",
)
@functools.wraps(func)
def wrapper(*args, **kwargs):
return func(*args, **kwargs)
return wrapper
def server_args(func):
@click.option(
"--debug",
"-d",
is_flag=True,
default=DEFAULT_CONFIG.server_config.app__debug,
show_default=True,
help="Run in debug mode. This is helpful for cellxgene developers, "
"or when you want more information about an error condition.",
)
@click.option(
"--verbose",
"-v",
is_flag=True,
default=DEFAULT_CONFIG.server_config.app__verbose,
show_default=True,
help="Provide verbose output, including warnings and all server requests.",
)
@click.option(
"--port",
"-p",
metavar="<port>",
default=DEFAULT_CONFIG.server_config.app__port,
type=int,
show_default=True,
help="Port to run server on. If not specified cellxgene will find an available port.",
)
@click.option(
"--host",
metavar="<IP address>",
default=DEFAULT_CONFIG.server_config.app__host,
show_default=False,
help="Host IP address. By default cellxgene will use localhost (e.g. 127.0.0.1).",
)
@click.option(
"--scripts",
"-s",
default=DEFAULT_CONFIG.default_dataset_config.app__scripts,
multiple=True,
metavar="<text>",
help="Additional script files to include in HTML page. If not specified, "
"no additional script files will be included.",
show_default=False,
)
@functools.wraps(func)
def wrapper(*args, **kwargs):
return func(*args, **kwargs)
return wrapper
def launch_args(func):
@annotation_args
@config_args
@dataset_args
@server_args
@click.option(
"--dataroot",
default=DEFAULT_CONFIG.server_config.multi_dataset__dataroot,
metavar="<data directory>",
help="Enable cellxgene to serve multiple files. Supply path (local directory or URL)"
" to folder containing H5AD and/or CXG datasets.",
hidden=True,
) # TODO, unhide when dataroot is supported)
@click.argument("datapath", required=False, metavar="<path to data file>")
@click.option(
"--open",
"-o",
"open_browser",
is_flag=True,
default=DEFAULT_CONFIG.server_config.app__open_browser,
show_default=True,
help="Open web browser after launch.",
)
@click.option(
"--config-file",
"-c",
"config_file",
default=None,
show_default=True,
help="Location to yaml file with configuration settings",
)
@click.option(
"--dump-default-config",
"dump_default_config",
is_flag=True,
default=False,
show_default=True,
help="Print default configuration settings and exit",
)
@click.help_option("--help", "-h", help="Show this message and exit.")
@functools.wraps(func)
def wrapper(*args, **kwargs):
return func(*args, **kwargs)
return wrapper
def handle_scripts(scripts):
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)
class CliLaunchServer(Server):
"""
the CLI runs a local web server, and needs to enable a few more features.
"""
def __init__(self, app_config):
super().__init__(app_config)
@staticmethod
def _before_adding_routes(app, app_config):
app.config["COMPRESS_MIMETYPES"] = [
"text/html",
"text/css",
"text/xml",
"application/json",
"application/javascript",
"application/octet-stream",
]
Compress(app)
if app_config.server_config.app__debug:
CORS(app, supports_credentials=True)
@sort_options
@click.command(
short_help="Launch the cellxgene data viewer. " "Run `cellxgene launch --help` for more information.",
options_metavar="<options>",
)
@launch_args
def launch(
datapath,
dataroot,
verbose,
debug,
open_browser,
port,
host,
embedding,
obs_names,
var_names,
max_category_items,
disable_custom_colors,
diffexp_lfc_cutoff,
title,
scripts,
about,
disable_annotations,
annotations_file,
annotations_dir,
backed,
disable_diffexp,
experimental_annotations_ontology,
experimental_annotations_ontology_obo,
experimental_enable_reembedding,
config_file,
dump_default_config,
):
"""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 to learn more:
https://chanzuckerberg.github.io/cellxgene/getting-started.html
Examples:
> cellxgene launch example-dataset/pbmc3k.h5ad --title pbmc3k
> cellxgene launch <your data file> --title <your title>
> cellxgene launch <url>"""
# TODO Examples to provide when "--dataroot" is unhidden
# > cellxgene launch --dataroot example-dataset/
#
# > cellxgene launch --dataroot <url>
if dump_default_config:
print(default_config)
sys.exit(0)
# Startup message
click.echo("[cellxgene] Starting the CLI...")
# app config
app_config = AppConfig()
server_config = app_config.server_config
try:
if config_file:
app_config.update_from_config_file(config_file)
# Determine which config options were give on the command line.
# Those will override the ones provided in the config file (if provided).
cli_config = AppConfig()
cli_config.update_server_config(
app__verbose=verbose,
app__debug=debug,
app__host=host,
app__port=port,
app__open_browser=open_browser,
single_dataset__datapath=datapath,
single_dataset__title=title,
single_dataset__about=about,
single_dataset__obs_names=obs_names,
single_dataset__var_names=var_names,
multi_dataset__dataroot=dataroot,
adaptor__anndata_adaptor__backed=backed,
)
cli_config.update_default_dataset_config(
app__scripts=scripts,
user_annotations__enable=not disable_annotations,
user_annotations__local_file_csv__file=annotations_file,
user_annotations__local_file_csv__directory=annotations_dir,
user_annotations__ontology__enable=experimental_annotations_ontology,
user_annotations__ontology__obo_location=experimental_annotations_ontology_obo,
presentation__max_categories=max_category_items,
presentation__custom_colors=not disable_custom_colors,
embeddings__names=embedding,
embeddings__enable_reembedding=experimental_enable_reembedding,
diffexp__enable=not disable_diffexp,
diffexp__lfc_cutoff=diffexp_lfc_cutoff,
)
diff = cli_config.server_config.changes_from_default()
changes = {key: val for key, val, _ in diff}
app_config.update_server_config(**changes)
diff = cli_config.default_dataset_config.changes_from_default()
changes = {key: val for key, val, _ in diff}
app_config.update_default_dataset_config(**changes)
# process the configuration
# any errors will be thrown as an exception.
# any info messages will be passed to the messagefn function.
def messagefn(message):
click.echo("[cellxgene] " + message)
# Use a default secret if one is not provided
if not server_config.app__flask_secret_key:
app_config.update_server_config(app__flask_secret_key="SparkleAndShine")
app_config.complete_config(messagefn)
except (ConfigurationError, DatasetAccessError) as e:
raise click.ClickException(e)
handle_scripts(scripts)
# create the server
server = CliLaunchServer(app_config)
if not server_config.app__verbose:
log = logging.getLogger("werkzeug")
log.setLevel(logging.ERROR)
cellxgene_url = f"http://{app_config.server_config.app__host}:{app_config.server_config.app__port}"
if server_config.app__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.")
if not server_config.app__verbose:
f = open(os.devnull, "w")
sys.stdout = f
try:
server.app.run(
host=server_config.app__host,
debug=server_config.app__debug,
port=server_config.app__port,
threaded=not server_config.app__debug,
use_debugger=False,
use_reloader=False,
)
except OSError as e:
if e.errno == errno.EADDRINUSE:
raise click.ClickException("Port is in use, please specify an open port using the --port flag.") from e
raise