fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-23 21:28:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

Apply yapf to python files

Browse Source
This commit is contained in:
Matt Weiden
2019-12-19 15:20:41 -08:00
parent 42a8d45bd7
commit cdca128a01
43 changed files with 1143 additions and 678 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/cli/cli.py
+4 -5
View File
@@ -10,11 +10,10 @@ from .prepare import prepare
context_settings=dict(max_content_width=85,
help_option_names=['-h', '--help']))
@click.help_option("--help", "-h", help="Show this message and exit.")
@click.version_option(
version="0.13.0",
prog_name="cellxgene",
message="[%(prog)s] Version %(version)s",
help="Show the software version and exit.")
@click.version_option(version="0.13.0",
prog_name="cellxgene",
message="[%(prog)s] Version %(version)s",
help="Show the software version and exit.")
def cli():
pass
server/cli/launch.py
+124 -90
View File
@@ -17,7 +17,7 @@ from server.utils.utils import find_available_port, is_port_available, sort_opti
from server.app.util.data_locator import DataLocator
# 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):
@@ -25,16 +25,14 @@ 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",
metavar="<text>",
help="Title to display. If omitted will use file name.")
@click.option(
"--about",
metavar="<URL>",
help="URL providing more information about the dataset "
"(hint: must be a fully specified absolute URL).")
@click.option("--title",
"-t",
metavar="<text>",
help="Title to display. If omitted will use file name.")
@click.option("--about",
metavar="<URL>",
help="URL providing more information about the dataset "
"(hint: must be a fully specified absolute URL).")
@click.option(
"--embedding",
"-e",
@@ -42,69 +40,80 @@ def common_args(func):
multiple=True,
show_default=False,
metavar="<text>",
help="Embedding name, eg, 'umap'. Repeat option for multiple embeddings. Defaults to all."
help=
"Embedding name, eg, 'umap'. Repeat option for multiple embeddings. Defaults to all."
)
@click.option(
"--obs-names",
"-obs",
default=None,
metavar="<text>",
help="Name of annotation field to use for observations. If not specified cellxgene will use the the obs index.")
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=None,
metavar="<text>",
help="Name of annotation to use for variables. If not specified cellxgene will use the the var index.")
help=
"Name of annotation to use for variables. If not specified cellxgene will use the the var index."
)
@click.option(
"--max-category-items",
default=1000,
metavar="<integer>",
show_default=True,
help="Will not display categories with more distinct values than specified.",)
help=
"Will not display categories with more distinct values than specified.",
)
@click.option(
"--diffexp-lfc-cutoff",
"-de",
default=0.01,
show_default=True,
metavar="<float>",
help="Minimum log fold change threshold for differential expression.",)
@click.option(
"--experimental-annotations",
is_flag=True,
default=False,
show_default=True,
help="Enable user annotation of data."
help="Minimum log fold change threshold for differential expression.",
)
@click.option("--experimental-annotations",
is_flag=True,
default=False,
show_default=True,
help="Enable user annotation of data.")
@click.option(
"--experimental-annotations-file",
default=None,
show_default=True,
multiple=False,
metavar="<path>",
help="CSV file to initialize editing of existing annotations; will be altered in-place. "
"Incompatible with --annotations-output-dir.",)
help=
"CSV file to initialize editing of existing annotations; will be altered in-place. "
"Incompatible with --annotations-output-dir.",
)
@click.option(
"--experimental-annotations-output-dir",
default=None,
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-input-file.",)
help=
"Directory of where to save output annotations; filename will be specified in the application. "
"Incompatible with --annotations-input-file.",
)
@click.option(
"--backed",
"-b",
is_flag=True,
default=False,
show_default=False,
help="Load data in file-backed mode. This may save memory, but may result in slower overall performance.")
@click.option(
"--disable-diffexp",
is_flag=True,
default=False,
show_default=False,
help="Disable on-demand differential expression.")
help=
"Load data in file-backed mode. This may save memory, but may result in slower overall performance."
)
@click.option("--disable-diffexp",
is_flag=True,
default=False,
show_default=False,
help="Disable on-demand differential expression.")
@functools.wraps(func)
def wrapper(*args, **kwargs):
return func(*args, **kwargs)
@@ -112,9 +121,11 @@ def common_args(func):
return wrapper
def parse_engine_args(embedding, obs_names, var_names, max_category_items, diffexp_lfc_cutoff,
experimental_annotations, experimental_annotations_file,
experimental_annotations_output_dir, backed, disable_diffexp):
def parse_engine_args(embedding, obs_names, var_names, max_category_items,
diffexp_lfc_cutoff, experimental_annotations,
experimental_annotations_file,
experimental_annotations_output_dir, backed,
disable_diffexp):
annotations_file = experimental_annotations_file if experimental_annotations else None
annotations_output_dir = experimental_annotations_output_dir if experimental_annotations else None
return {
@@ -132,9 +143,11 @@ def parse_engine_args(embedding, obs_names, var_names, max_category_items, diffe
@sort_options
@click.command(short_help="Launch the cellxgene data viewer. "
"Run `cellxgene launch --help` for more information.",
options_metavar="<options>",)
@click.command(
short_help="Launch the cellxgene data viewer. "
"Run `cellxgene launch --help` for more information.",
options_metavar="<options>",
)
@click.argument("data", nargs=1, metavar="<path to data file>", required=True)
@click.option(
"--verbose",
@@ -142,7 +155,8 @@ def parse_engine_args(embedding, obs_names, var_names, max_category_items, diffe
is_flag=True,
default=False,
show_default=True,
help="Provide verbose output, including warnings and all server requests.",)
help="Provide verbose output, including warnings and all server requests.",
)
@click.option(
"--debug",
"-d",
@@ -150,7 +164,8 @@ def parse_engine_args(embedding, obs_names, var_names, max_category_items, diffe
default=False,
show_default=True,
help="Run in debug mode. This is helpful for cellxgene developers, "
"or when you want more information about an error condition.",)
"or when you want more information about an error condition.",
)
@click.option(
"--open",
"-o",
@@ -158,19 +173,24 @@ def parse_engine_args(embedding, obs_names, var_names, max_category_items, diffe
is_flag=True,
default=False,
show_default=True,
help="Open web browser after launch.",)
help="Open web browser after launch.",
)
@click.option(
"--port",
"-p",
metavar="<port>",
show_default=True,
help="Port to run server on. If not specified cellxgene will find an available port.",)
help=
"Port to run server on. If not specified cellxgene will find an available port.",
)
@click.option(
"--host",
metavar="<IP address>",
default="127.0.0.1",
show_default=False,
help="Host IP address. By default cellxgene will use localhost (e.g. 127.0.0.1).")
help=
"Host IP address. By default cellxgene will use localhost (e.g. 127.0.0.1)."
)
@click.option(
"--scripts",
"-s",
@@ -178,31 +198,15 @@ def parse_engine_args(embedding, obs_names, var_names, max_category_items, diffe
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,)
"no additional script files will be included.",
show_default=False,
)
@click.help_option("--help", "-h", help="Show this message and exit.")
@common_args
def launch(
data,
verbose,
debug,
open_browser,
port,
host,
embedding,
obs_names,
var_names,
max_category_items,
diffexp_lfc_cutoff,
title,
scripts,
about,
experimental_annotations,
experimental_annotations_file,
experimental_annotations_output_dir,
backed,
disable_diffexp
):
def launch(data, verbose, debug, open_browser, port, host, embedding, obs_names,
var_names, max_category_items, diffexp_lfc_cutoff, title, scripts,
about, experimental_annotations, experimental_annotations_file,
experimental_annotations_output_dir, backed, disable_diffexp):
"""Launch the cellxgene data viewer.
This web app lets you explore single-cell expression data.
Data must be in a format that cellxgene expects.
@@ -217,17 +221,17 @@ def launch(
> cellxgene launch <url>"""
e_args = parse_engine_args(embedding, obs_names, var_names, max_category_items,
diffexp_lfc_cutoff,
e_args = parse_engine_args(embedding, obs_names, var_names,
max_category_items, diffexp_lfc_cutoff,
experimental_annotations,
experimental_annotations_file,
experimental_annotations_output_dir,
backed,
experimental_annotations_output_dir, backed,
disable_diffexp)
try:
data_locator = DataLocator(data)
except RuntimeError as re:
raise click.ClickException(f"Unable to access data at {data}. {str(re)}")
raise click.ClickException(
f"Unable to access data at {data}. {str(re)}")
# Startup message
click.echo("[cellxgene] Starting the CLI...")
@@ -244,7 +248,8 @@ def launch(
raise click.FileError(data, hint="data is not a file")
name, extension = splitext(data)
if extension != ".h5ad":
raise click.FileError(basename(data), hint="file type must be .h5ad")
raise click.FileError(basename(data),
hint="file type must be .h5ad")
if debug:
verbose = True
@@ -266,7 +271,9 @@ def launch(
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)
click.confirm(
f"Are you sure you want to inject these scripts: {scripts_pretty}?",
abort=True)
if not title:
file_parts = splitext(basename(data))
@@ -274,7 +281,9 @@ def launch(
if port:
if debug:
raise click.ClickException("--port and --debug may not be used together (try --verbose for error logging).")
raise click.ClickException(
"--port and --debug may not be used together (try --verbose for error logging)."
)
if not is_port_available(host, int(port)):
raise click.ClickException(
f"The port selected {port} is in use, please specify an open port using the --port flag."
@@ -284,27 +293,36 @@ def launch(
if not experimental_annotations:
if experimental_annotations_file is not None:
click.echo("Warning: --experimental-annotations-file ignored as --annotations not enabled.")
click.echo(
"Warning: --experimental-annotations-file ignored as --annotations not enabled."
)
if experimental_annotations_output_dir is not None:
click.echo("Warning: --experimental-annotations-output-dir ignored as --annotations not enabled.")
click.echo(
"Warning: --experimental-annotations-output-dir ignored as --annotations not enabled."
)
else:
if experimental_annotations_file is not None and experimental_annotations_output_dir is not None:
raise click.ClickException("--experimental-annotations-file and --experimental-annotations-output-dir "
"may not be used together.")
raise click.ClickException(
"--experimental-annotations-file and --experimental-annotations-output-dir "
"may not be used together.")
if experimental_annotations_file is not None:
lf_name, lf_ext = splitext(experimental_annotations_file)
if lf_ext and lf_ext != ".csv":
raise click.FileError(basename(experimental_annotations_file), hint="annotation file type must be .csv")
raise click.FileError(basename(experimental_annotations_file),
hint="annotation file type must be .csv")
if experimental_annotations_output_dir is not None and not isdir(experimental_annotations_output_dir):
if experimental_annotations_output_dir is not None and not isdir(
experimental_annotations_output_dir):
try:
mkdir(experimental_annotations_output_dir)
except OSError:
raise click.ClickException("Unable to create directory specified by "
"--experimental-annotations-output-dir")
raise click.ClickException(
"Unable to create directory specified by "
"--experimental-annotations-output-dir")
if about:
def url_check(url):
try:
result = urlparse(url)
@@ -316,7 +334,9 @@ def launch(
return False
if not url_check(about):
raise click.ClickException("Must provide an absolute URL for --about. (Example format: http://example.com)")
raise click.ClickException(
"Must provide an absolute URL for --about. (Example format: http://example.com)"
)
# Setup app
cellxgene_url = f"http://{host}:{port}"
@@ -335,14 +355,18 @@ def launch(
# if a big file, let the user know it may take a while to load.
if file_size > BIG_FILE_SIZE_THRESHOLD:
click.echo(f"[cellxgene] Loading data from {basename(data)}, this may take a while...")
click.echo(
f"[cellxgene] Loading data from {basename(data)}, this may take a while..."
)
else:
click.echo(f"[cellxgene] Loading data from {basename(data)}.")
from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
try:
server.attach_data(ScanpyEngine(data_locator, e_args), title=title, about=about)
server.attach_data(ScanpyEngine(data_locator, e_args),
title=title,
about=about)
except ScanpyFileError as e:
raise click.ClickException(f"{e}")
@@ -351,10 +375,14 @@ def launch(
f"running differential expression may take longer or fail.")
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.")
@@ -363,8 +391,14 @@ def launch(
sys.stdout = f
try:
server.app.run(host=host, debug=debug, port=port, threaded=False if debug else True, use_debugger=False)
server.app.run(host=host,
debug=debug,
port=port,
threaded=False if debug else True,
use_debugger=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 click.ClickException(
"Port is in use, please specify an open port using the --port flag."
) from e
raise
server/cli/prepare.py
+90 -47
View File
@@ -8,9 +8,11 @@ from server.utils.utils import sort_options
@sort_options
@click.command(short_help="Preprocess data for use with cellxgene. "
"Run `cellxgene prepare --help` for more information.",
options_metavar="<options>",)
@click.command(
short_help="Preprocess data for use with cellxgene. "
"Run `cellxgene prepare --help` for more information.",
options_metavar="<options>",
)
@click.argument("data", nargs=1, metavar="<path to data file>", required=True)
@click.option(
"--embedding",
@@ -29,43 +31,66 @@ from server.utils.utils import sort_options
help="Preprocessing to run.",
show_default=True,
)
@click.option("--output", "-o", default="", help="Save a new file to filename.", metavar="<filename>")
@click.option("--plotting", "-p", default=False, is_flag=True, help="Generate plots.", show_default=True)
@click.option("--sparse", default=False, is_flag=True, help="Force sparsity.", show_default=True)
@click.option("--overwrite", default=False, is_flag=True, help="Allow file overwriting.", show_default=True)
@click.option("--set-obs-names", default="", help="Named field to set as index for obs.", metavar="<name>")
@click.option("--set-var-names", default="", help="Named field to set as index for var.", metavar="<name>")
@click.option("--skip-qc", default=False, is_flag=True,
help="Do not run quality control metrics. By default cellxgene runs them "
"(saved to adata.obs and adata.var; see scanpy.pp.calculate_qc_metrics for details).")
@click.option("--output",
"-o",
default="",
help="Save a new file to filename.",
metavar="<filename>")
@click.option("--plotting",
"-p",
default=False,
is_flag=True,
help="Generate plots.",
show_default=True)
@click.option("--sparse",
default=False,
is_flag=True,
help="Force sparsity.",
show_default=True)
@click.option("--overwrite",
default=False,
is_flag=True,
help="Allow file overwriting.",
show_default=True)
@click.option("--set-obs-names",
default="",
help="Named field to set as index for obs.",
metavar="<name>")
@click.option("--set-var-names",
default="",
help="Named field to set as index for var.",
metavar="<name>")
@click.option(
"--make-obs-names-unique",
default=True,
"--skip-qc",
default=False,
is_flag=True,
help="Ensure obs index is unique.",
show_default=True
)
@click.option(
"--make-var-names-unique",
default=True,
is_flag=True,
help="Ensure var index is unique.",
show_default=True
help="Do not run quality control metrics. By default cellxgene runs them "
"(saved to adata.obs and adata.var; see scanpy.pp.calculate_qc_metrics for details)."
)
@click.option("--make-obs-names-unique",
default=True,
is_flag=True,
help="Ensure obs index is unique.",
show_default=True)
@click.option("--make-var-names-unique",
default=True,
is_flag=True,
help="Ensure var index is unique.",
show_default=True)
@click.help_option("--help", "-h", help="Show this message and exit.")
def prepare(
data,
embedding,
recipe,
output,
plotting,
sparse,
overwrite,
set_obs_names,
set_var_names,
skip_qc,
make_obs_names_unique,
make_var_names_unique,
data,
embedding,
recipe,
output,
plotting,
sparse,
overwrite,
set_obs_names,
set_var_names,
skip_qc,
make_obs_names_unique,
make_var_names_unique,
):
"""
Preprocess data for use with cellxgene.
@@ -86,8 +111,7 @@ def prepare(
except ImportError:
raise click.ClickException(
"[cellxgene] cellxgene prepare has not been installed. Please run `pip install cellxgene[prepare]` "
"to install the necessary requirements."
)
"to install the necessary requirements.")
# scanpy settings
sc.settings.verbosity = 0
@@ -102,10 +126,11 @@ def prepare(
if not output:
click.echo(
"Warning: No file will be saved, to save the results of cellxgene prepare include "
"--output <filename> to save output to a new file"
)
"--output <filename> to save output to a new file")
if isfile(output) and not overwrite:
raise click.UsageError(f"Cannot overwrite existing file {output}, try using the flag --overwrite")
raise click.UsageError(
f"Cannot overwrite existing file {output}, try using the flag --overwrite"
)
def load_data(data):
if isfile(data):
@@ -115,7 +140,9 @@ def prepare(
elif extension == ".loom":
adata = sc.read_loom(data)
else:
raise click.FileError(data, hint="does not have a valid extension [.h5ad | .loom]")
raise click.FileError(
data,
hint="does not have a valid extension [.h5ad | .loom]")
elif isdir(data):
if not data.endswith(sep):
data += sep
@@ -125,11 +152,15 @@ def prepare(
if not set_obs_names == "":
if set_obs_names not in adata.obs_keys():
raise click.UsageError(f"obs {set_obs_names} not found, options are: {adata.obs_keys()}")
raise click.UsageError(
f"obs {set_obs_names} not found, options are: {adata.obs_keys()}"
)
adata.obs_names = adata.obs[set_obs_names]
if not set_var_names == "":
if set_var_names not in adata.var_keys():
raise click.UsageError(f"var {set_var_names} not found, options are: {adata.var_keys()}")
raise click.UsageError(
f"var {set_var_names} not found, options are: {adata.var_keys()}"
)
adata.var_names = adata.var[set_var_names]
if make_obs_names_unique:
adata.obs_names_make_unique()
@@ -184,12 +215,18 @@ def prepare(
if "umap" in embedding:
sc.tl.umap(adata)
if plotting:
sc.pl.umap(adata, color="louvain", palette=palette, save="_louvain")
sc.pl.umap(adata,
color="louvain",
palette=palette,
save="_louvain")
if "tsne" in embedding:
sc.tl.tsne(adata)
if plotting:
sc.pl.tsne(adata, color="louvain", palette=palette, save="_louvain")
sc.pl.tsne(adata,
color="louvain",
palette=palette,
save="_louvain")
def show_step(item):
if not skip_qc:
@@ -208,13 +245,19 @@ def prepare(
if item is not None:
return names[item.__name__]
steps = [calculate_qc_metrics, make_sparse, run_recipe, run_pca, run_neighbors, run_louvain, run_embedding]
steps = [
calculate_qc_metrics, make_sparse, run_recipe, run_pca, run_neighbors,
run_louvain, run_embedding
]
click.echo(f"[cellxgene] Loading data from {data}, please wait...")
adata = load_data(data)
click.echo("[cellxgene] Beginning preprocessing...")
with click.progressbar(steps, label="[cellxgene] Progress", show_eta=False, item_show_func=show_step) as bar:
with click.progressbar(steps,
label="[cellxgene] Progress",
show_eta=False,
item_show_func=show_step) as bar:
for step in bar:
step(adata)