def test_url_http(self):
url = "http://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad"
locator = DataLocator(url)
config = AppConfig()
config.update(**self.args)
data = AnndataAdaptor(locator, config)
self.stdAsserts(data)
def data_with_tmp_annotations(ext: MatrixDataType, annotations_fixture=False):
tmp_dir = tempfile.mkdtemp()
annotations_file = path.join(tmp_dir, "test_annotations.csv")
if annotations_fixture:
shutil.copyfile(
f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-annotations.csv",
annotations_file)
args = {
"embeddings__names": ["umap"],
"presentation__max_categories": 100,
"single_dataset__obs_names": None,
"single_dataset__var_names": None,
"diffexp__lfc_cutoff": 0.01,
}
fname = {
MatrixDataType.H5AD: f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
MatrixDataType.CXG: "test/test_datasets/pbmc3k.cxg",
}[ext]
data_locator = DataLocator(fname)
config = AppConfig()
config.update(**args)
config.update(single_dataset__datapath=data_locator.path)
config.complete_config()
data = MatrixDataLoader(data_locator.abspath()).open(config)
annotations = AnnotationsLocalFile(None, annotations_file)
return data, tmp_dir, annotations
def test_posix_file(self):
locator = DataLocator("../example-dataset/pbmc3k.h5ad")
config = AppConfig()
config.update(**self.args)
config.update(single_dataset__datapath=locator.path)
config.complete_config()
data = AnndataAdaptor(locator, config)
self.stdAsserts(data)
def test_update(self):
c = AppConfig()
c.update(server__verbose=True, multi_dataset__dataroot="datadir")
v = c.changes_from_default()
self.assertCountEqual(v,
[("server__verbose", True, False),
("multi_dataset__dataroot", "datadir", None)]),
def app_config(data_locator, backed=False):
args = {
"embeddings__names": ["umap", "tsne", "pca"],
"presentation__max_categories": 100,
"single_dataset__obs_names": None,
"single_dataset__var_names": None,
"diffexp__lfc_cutoff": 0.01,
"adaptor__anndata_adaptor__backed": backed,
"single_dataset__datapath": data_locator,
"limits__diffexp_cellcount_max": None,
"limits__column_request_max": None,
}
config = AppConfig()
config.update(**args)
config.complete_config()
return config
app_config.update_from_config_file(lh)
else:
logging.critical(f"Configuration file not found {config_file}")
sys.exit(1)
else:
# no config file specified, try "config.yaml" in the current working directory
config_file = "config.yaml"
config_location = DataLocator(config_file)
if config_location.exists():
with config_location.local_handle() as lh:
logging.info(f"Configuration from {config_file}")
app_config.update_from_config_file(lh)
if dataroot:
logging.info(f"Configuration from CXG_DATAROOT")
app_config.update(multi_dataset__dataroot=dataroot)
if secret_name:
if secret_region_name is None:
secret_region_name = discover_s3_region_name(
app_config.multi_dataset__dataroot)
if not secret_region_name:
logging.error(
f"Expected to discover the s3 region name from {app_config.multi_dataset__dataroot}"
)
flask_secret_key = get_flask_secret_key(secret_region_name,
secret_name)
app_config.update(server__flask_secret_key=flask_secret_key)
# features are unsupported in the current hosted server
app_config.update(
def setUp(self):
self.data_file = DataLocator(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
config = AppConfig()
config.update(single_dataset__datapath=self.data_file.path)
config.complete_config()
self.data = AnndataAdaptor(self.data_file, config)
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()
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__verbose=verbose,
server__debug=debug,
server__host=host,
server__port=port,
server__scripts=scripts,
server__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,
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,
adaptor__anndata_adaptor__backed=backed,
)
diff = cli_config.changes_from_default()
changes = {}
for key, val, defval in diff:
changes[key] = val
app_config.update(**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 app_config.server__flask_secret_key:
app_config.update(server__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 app_config.server__verbose:
log = logging.getLogger("werkzeug")
log.setLevel(logging.ERROR)
cellxgene_url = f"http://{app_config.server__host}:{app_config.server__port}"
if app_config.server__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 app_config.server__verbose:
f = open(devnull, "w")
sys.stdout = f
try:
server.app.run(
host=app_config.server__host,
debug=app_config.server__debug,
port=app_config.server__port,
threaded=not app_config.server__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