fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-27 02:18:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

refactor config to support different config options for datasets in different dataroots. (#1596)

Browse Source 
This will give us the ability to specify different config options for
different dataroots.

the key of the dataroot dictionary is no longer the same as the dataroot_url.
Previously key==dataroot_url, and now those are separated.

Added an "is_multi_dataset" function to simplify logic where it branched on single vs multi.

Simplified the rest.py interface by no longer passing in the user annotations object, since
that can be retrieved from the dataset.
This commit is contained in:
bmccandless
2020-07-10 16:21:40 -07:00
committed by GitHub
parent 13246cb6d1
commit f69d141336
21 changed files with 1021 additions and 710 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/app/app.py
+53 -35
View File
@@ -33,7 +33,7 @@ def _cache_control(always, **cache_kwargs):
@wraps(f)
def wrapper(*args, **kwargs):
response = make_response(f(*args, **kwargs))
if not always and not current_app.app_config.server__generate_cache_control_headers:
if not always and not current_app.app_config.server_config.app__generate_cache_control_headers:
return response
if response.status_code >= 400:
return response
@@ -61,25 +61,31 @@ def cache_control_always(**cache_kwargs):
@webbp.route("/", methods=["GET"])
@cache_control_always(public=True, max_age=0, no_store=True, no_cache=True, must_revalidate=True)
def dataset_index(url_dataroot=None, dataset=None):
config = current_app.app_config
app_config = current_app.app_config
server_config = app_config.server_config
if dataset is None:
if config.single_dataset__datapath:
location = config.single_dataset__datapath
else:
if app_config.is_multi_dataset():
return dataroot_index()
else:
location = server_config.single_dataset__datapath
else:
dataroot = config.multi_dataset__dataroot.get(url_dataroot)
dataroot = None
for key, dataroot_dict in server_config.multi_dataset__dataroot.items():
if dataroot_dict["base_url"] == url_dataroot:
dataroot = dataroot_dict["dataroot"]
break
if dataroot is None:
abort(HTTPStatus.NOT_FOUND)
location = path_join(dataroot, dataset)
scripts = config.server__scripts
inline_scripts = config.server__inline_scripts
dataset_config = app_config.get_dataset_config(url_dataroot)
scripts = dataset_config.app__scripts
inline_scripts = dataset_config.app__inline_scripts
try:
cache_manager = current_app.matrix_data_cache_manager
with cache_manager.data_adaptor(location, config) as data_adaptor:
dataset_title = config.get_title(data_adaptor)
with cache_manager.data_adaptor(url_dataroot, location, app_config) as data_adaptor:
dataset_title = app_config.get_title(data_adaptor)
return render_template(
"index.html", datasetTitle=dataset_title, SCRIPTS=scripts, INLINE_SCRIPTS=inline_scripts
)
@@ -103,11 +109,19 @@ def handle_request_exception(error):
def get_data_adaptor(url_dataroot=None, dataset=None):
config = current_app.app_config
server_config = config.server_config
dataset_key = None
if dataset is None:
datapath = config.single_dataset__datapath
datapath = server_config.single_dataset__datapath
else:
dataroot = config.multi_dataset__dataroot.get(url_dataroot)
dataroot = None
for key, dataroot_dict in server_config.multi_dataset__dataroot.items():
if dataroot_dict["base_url"] == url_dataroot:
dataroot = dataroot_dict["dataroot"]
dataset_key = key
break
if dataroot is None:
raise DatasetAccessError(f"Invalid dataset {url_dataroot}/{dataset}")
datapath = path_join(dataroot, dataset)
@@ -121,7 +135,7 @@ def get_data_adaptor(url_dataroot=None, dataset=None):
return common_rest.abort_and_log(HTTPStatus.BAD_REQUEST, "Invalid dataset NONE", loglevel=logging.INFO)
cache_manager = current_app.matrix_data_cache_manager
return cache_manager.data_adaptor(datapath, config)
return cache_manager.data_adaptor(dataset_key, datapath, config)
def rest_get_data_adaptor(func):
@@ -145,9 +159,12 @@ def dataroot_test_index():
data += "<body><H1>Welcome to cellxgene</H1>"
config = current_app.app_config
server_config = config.server_config
datasets = []
for url_dataroot, dataroot in config.multi_dataset__dataroot.items():
locator = DataLocator(dataroot, region_name=config.data_locator__s3__region_name)
for dataroot_dict in server_config.multi_dataset__dataroot.values():
dataroot = dataroot_dict["dataroot"]
url_dataroot = dataroot_dict["base_url"]
locator = DataLocator(dataroot, region_name=server_config.data_locator__s3__region_name)
for fname in locator.ls():
location = path_join(dataroot, fname)
try:
@@ -171,12 +188,12 @@ def dataroot_test_index():
def dataroot_index():
# Handle the base url for the cellxgene server when running in multi dataset mode
config = current_app.app_config
if not config.multi_dataset__index:
if not config.server_config.multi_dataset__index:
abort(HTTPStatus.NOT_FOUND)
elif config.multi_dataset__index is True:
elif config.server_config.multi_dataset__index is True:
return dataroot_test_index()
else:
return redirect(config.multi_dataset__index)
return redirect(config.server_config.multi_dataset__index)
class DatasetResource(Resource):
@@ -191,33 +208,33 @@ class SchemaAPI(DatasetResource):
@cache_control(public=True, max_age=ONE_WEEK)
@rest_get_data_adaptor
def get(self, data_adaptor):
return common_rest.schema_get(data_adaptor, current_app.annotations)
return common_rest.schema_get(data_adaptor)
class ConfigAPI(DatasetResource):
@cache_control(public=True, max_age=ONE_WEEK)
@rest_get_data_adaptor
def get(self, data_adaptor):
return common_rest.config_get(current_app.app_config, data_adaptor, current_app.annotations)
return common_rest.config_get(current_app.app_config, data_adaptor)
class AnnotationsObsAPI(DatasetResource):
@cache_control(public=True, max_age=ONE_WEEK)
@rest_get_data_adaptor
def get(self, data_adaptor):
return common_rest.annotations_obs_get(request, data_adaptor, current_app.annotations)
return common_rest.annotations_obs_get(request, data_adaptor)
@cache_control(no_store=True)
@rest_get_data_adaptor
def put(self, data_adaptor):
return common_rest.annotations_obs_put(request, data_adaptor, current_app.annotations)
return common_rest.annotations_obs_put(request, data_adaptor)
class AnnotationsVarAPI(DatasetResource):
@cache_control(public=True, max_age=ONE_WEEK)
@rest_get_data_adaptor
def get(self, data_adaptor):
return common_rest.annotations_var_get(request, data_adaptor, current_app.annotations)
return common_rest.annotations_var_get(request, data_adaptor)
class DataVarAPI(DatasetResource):
@@ -290,29 +307,26 @@ class Server:
self.app = Flask(__name__, static_folder="../common/web/static")
self._before_adding_routes(self.app, app_config)
self.app.json_encoder = Float32JSONEncoder
if app_config.server__server_timing_headers:
server_config = app_config.server_config
if server_config.app__server_timing_headers:
ServerTiming(self.app, force_debug=True)
# enable session data
self.app.permanent_session_lifetime = datetime.timedelta(days=50 * 365)
# Config
secret_key = app_config.server__flask_secret_key
secret_key = server_config.app__flask_secret_key
self.app.config.update(SECRET_KEY=secret_key)
self.app.register_blueprint(webbp)
api_version = "/api/v0.2"
if app_config.single_dataset__datapath:
bp_api = Blueprint("api", __name__, url_prefix=api_version)
resources = get_api_resources(bp_api)
self.app.register_blueprint(resources.blueprint)
else:
if app_config.is_multi_dataset():
# NOTE: These routes only allow the dataset to be in the directory
# of the dataroot, and not a subdirectory. We may want to change
# the route format at some point
for url_dataroot in app_config.multi_dataset__dataroot.keys():
for dataroot_dict in server_config.multi_dataset__dataroot.values():
url_dataroot = dataroot_dict["base_url"]
bp_api = Blueprint(
f"api_dataset_{url_dataroot}", __name__, url_prefix=f"/{url_dataroot}/<dataset>" + api_version
)
@@ -321,9 +335,13 @@ class Server:
self.app.add_url_rule(
f"/{url_dataroot}/<dataset>/",
f"dataset_index_{url_dataroot}",
lambda dataset: dataset_index(url_dataroot, dataset),
lambda dataset, url_dataroot=url_dataroot: dataset_index(url_dataroot, dataset),
methods=["GET"],
)
self.app.matrix_data_cache_manager = app_config.matrix_data_cache_manager
self.app.annotations = app_config.user_annotations
else:
bp_api = Blueprint("api", __name__, url_prefix=api_version)
resources = get_api_resources(bp_api)
self.app.register_blueprint(resources.blueprint)
self.app.matrix_data_cache_manager = server_config.matrix_data_cache_manager
self.app.app_config = app_config
server/cli/launch.py
+52 -46
View File
@@ -22,13 +22,13 @@ def annotation_args(func):
@click.option(
"--disable-annotations",
is_flag=True,
default=not DEFAULT_CONFIG.user_annotations__enable,
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.user_annotations__local_file_csv__file,
default=DEFAULT_CONFIG.default_dataset_config.user_annotations__local_file_csv__file,
show_default=True,
multiple=False,
metavar="<path>",
@@ -37,7 +37,7 @@ def annotation_args(func):
)
@click.option(
"--annotations-dir",
default=DEFAULT_CONFIG.user_annotations__local_file_csv__directory,
default=DEFAULT_CONFIG.default_dataset_config.user_annotations__local_file_csv__directory,
show_default=False,
multiple=False,
metavar="<directory path>",
@@ -47,13 +47,13 @@ def annotation_args(func):
@click.option(
"--experimental-annotations-ontology",
is_flag=True,
default=DEFAULT_CONFIG.user_annotations__ontology__enable,
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.user_annotations__ontology__obo_location,
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.",
@@ -68,7 +68,7 @@ def annotation_args(func):
def config_args(func):
@click.option(
"--max-category-items",
default=DEFAULT_CONFIG.presentation__max_categories,
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.",
@@ -83,7 +83,7 @@ def config_args(func):
@click.option(
"--diffexp-lfc-cutoff",
"-de",
default=DEFAULT_CONFIG.diffexp__lfc_cutoff,
default=DEFAULT_CONFIG.default_dataset_config.diffexp__lfc_cutoff,
show_default=True,
metavar="<float>",
help="Minimum log fold change threshold for differential expression.",
@@ -91,14 +91,14 @@ def config_args(func):
@click.option(
"--disable-diffexp",
is_flag=True,
default=not DEFAULT_CONFIG.diffexp__enable,
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.embeddings__names,
default=DEFAULT_CONFIG.default_dataset_config.embeddings__names,
multiple=True,
show_default=False,
metavar="<text>",
@@ -107,7 +107,7 @@ def config_args(func):
@click.option(
"--experimental-enable-reembedding",
is_flag=True,
default=DEFAULT_CONFIG.embeddings__enable_reembedding,
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.",
@@ -123,14 +123,14 @@ def dataset_args(func):
@click.option(
"--obs-names",
"-obs",
default=DEFAULT_CONFIG.single_dataset__obs_names,
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.single_dataset__var_names,
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.",
)
@@ -138,20 +138,20 @@ def dataset_args(func):
"--backed",
"-b",
is_flag=True,
default=DEFAULT_CONFIG.adaptor__anndata_adaptor__backed,
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.single_dataset__title,
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.single_dataset__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).",
)
@@ -167,7 +167,7 @@ def server_args(func):
"--debug",
"-d",
is_flag=True,
default=DEFAULT_CONFIG.server__debug,
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.",
@@ -176,7 +176,7 @@ def server_args(func):
"--verbose",
"-v",
is_flag=True,
default=DEFAULT_CONFIG.server__verbose,
default=DEFAULT_CONFIG.server_config.app__verbose,
show_default=True,
help="Provide verbose output, including warnings and all server requests.",
)
@@ -184,7 +184,7 @@ def server_args(func):
"--port",
"-p",
metavar="<port>",
default=DEFAULT_CONFIG.server__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.",
@@ -192,14 +192,14 @@ def server_args(func):
@click.option(
"--host",
metavar="<IP address>",
default=DEFAULT_CONFIG.server__host,
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.server__scripts,
default=DEFAULT_CONFIG.default_dataset_config.app__scripts,
multiple=True,
metavar="<text>",
help="Additional script files to include in HTML page. If not specified, "
@@ -220,7 +220,7 @@ def launch_args(func):
@server_args
@click.option(
"--dataroot",
default=DEFAULT_CONFIG.multi_dataset__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.",
@@ -232,7 +232,7 @@ def launch_args(func):
"-o",
"open_browser",
is_flag=True,
default=DEFAULT_CONFIG.server__open_browser,
default=DEFAULT_CONFIG.server_config.app__open_browser,
show_default=True,
help="Open web browser after launch.",
)
@@ -296,7 +296,7 @@ class CliLaunchServer(Server):
"application/octet-stream",
]
Compress(app)
if app_config.server__debug:
if app_config.server_config.app__debug:
CORS(app, supports_credentials=True)
@@ -362,6 +362,7 @@ def launch(
# app config
app_config = AppConfig()
server_config = app_config.server_config
try:
if config_file:
@@ -370,19 +371,22 @@ def launch(
# 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,
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,
@@ -394,13 +398,15 @@ def launch(
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)
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.
@@ -410,8 +416,8 @@ def launch(
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")
if not server_config.app__flask_secret_key:
app_config.update_server_config(app__flask_secret_key="SparkleAndShine")
app_config.complete_config(messagefn)
@@ -423,12 +429,12 @@ def launch(
# create the server
server = CliLaunchServer(app_config)
if not app_config.server__verbose:
if not server_config.app__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:
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:
@@ -436,16 +442,16 @@ def launch(
click.echo("[cellxgene] Type CTRL-C at any time to exit.")
if not app_config.server__verbose:
if not server_config.app__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,
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,
)
server/common/app_config.py
+511 -337
View File
@@ -38,170 +38,110 @@ class AppFeature(object):
class AppConfig(object):
"""AppConfig stores all the configuration for cellxgene. The configuration is divided into two main parts:
server attributes, and dataset attributes. The server_config contains attributes that refer to the server process
as a whole. The default_dataset_config referes to attributes that are associated with the features and
presentations of a dataset. The dataset config attributes can be overridden depending on the url by which the
dataset was accessed. These are stored in dataroot_config.
AppConfig has methods to initialize, modify, and access the configuration.
"""
def __init__(self):
# the default configuration (see default_config.py)
self.default_config = get_default_config()
self.attr_checked = {k: False for k in self.__mapping(self.default_config).keys()}
dc = self.default_config
try:
self.server__verbose = dc["server"]["verbose"]
self.server__debug = dc["server"]["debug"]
self.server__host = dc["server"]["host"]
self.server__port = dc["server"]["port"]
self.server__scripts = dc["server"]["scripts"]
self.server__inline_scripts = dc["server"]["inline_scripts"]
self.server__open_browser = dc["server"]["open_browser"]
self.server__about_legal_tos = dc["server"]["about_legal_tos"]
self.server__about_legal_privacy = dc["server"]["about_legal_privacy"]
self.server__force_https = dc["server"]["force_https"]
self.server__flask_secret_key = dc["server"]["flask_secret_key"]
self.server__generate_cache_control_headers = dc["server"]["generate_cache_control_headers"]
self.server__server_timing_headers = dc["server"]["server_timing_headers"]
self.server__csp_directives = dc["server"]["csp_directives"]
self.multi_dataset__dataroot = dc["multi_dataset"]["dataroot"]
self.multi_dataset__index = dc["multi_dataset"]["index"]
self.multi_dataset__allowed_matrix_types = dc["multi_dataset"]["allowed_matrix_types"]
self.multi_dataset__matrix_cache__max_datasets = dc["multi_dataset"]["matrix_cache"]["max_datasets"]
self.multi_dataset__matrix_cache__timelimit_s = dc["multi_dataset"]["matrix_cache"]["timelimit_s"]
self.single_dataset__datapath = dc["single_dataset"]["datapath"]
self.single_dataset__obs_names = dc["single_dataset"]["obs_names"]
self.single_dataset__var_names = dc["single_dataset"]["var_names"]
self.single_dataset__about = dc["single_dataset"]["about"]
self.single_dataset__title = dc["single_dataset"]["title"]
self.user_annotations__enable = dc["user_annotations"]["enable"]
self.user_annotations__type = dc["user_annotations"]["type"]
self.user_annotations__local_file_csv__directory = dc["user_annotations"]["local_file_csv"]["directory"]
self.user_annotations__local_file_csv__file = dc["user_annotations"]["local_file_csv"]["file"]
self.user_annotations__ontology__enable = dc["user_annotations"]["ontology"]["enable"]
self.user_annotations__ontology__obo_location = dc["user_annotations"]["ontology"]["obo_location"]
self.presentation__max_categories = dc["presentation"]["max_categories"]
self.presentation__custom_colors = dc["presentation"]["custom_colors"]
self.embeddings__names = dc["embeddings"]["names"]
self.embeddings__enable_reembedding = dc["embeddings"]["enable_reembedding"]
self.diffexp__enable = dc["diffexp"]["enable"]
self.diffexp__lfc_cutoff = dc["diffexp"]["lfc_cutoff"]
self.diffexp__top_n = dc["diffexp"]["top_n"]
self.diffexp__alg_cxg__max_workers = dc["diffexp"]["alg_cxg"]["max_workers"]
self.diffexp__alg_cxg__cpu_multiplier = dc["diffexp"]["alg_cxg"]["cpu_multiplier"]
self.diffexp__alg_cxg__target_workunit = dc["diffexp"]["alg_cxg"]["target_workunit"]
self.data_locator__s3__region_name = dc["data_locator"]["s3"]["region_name"]
self.adaptor__cxg_adaptor__tiledb_ctx = dc["adaptor"]["cxg_adaptor"]["tiledb_ctx"]
self.adaptor__anndata_adaptor__backed = dc["adaptor"]["anndata_adaptor"]["backed"]
self.limits__diffexp_cellcount_max = dc["limits"]["diffexp_cellcount_max"]
self.limits__column_request_max = dc["limits"]["column_request_max"]
except KeyError as e:
raise ConfigurationError(f"Unexpected config: {str(e)}")
# The annotation object is created during complete_config and stored here.
self.user_annotations = None
# The matrix data cache manager is created during the complete_config and stored here.
self.matrix_data_cache_manager = None
# the server configuration
self.server_config = ServerConfig(self, self.default_config["server"])
# the dataset config, unless overridden by an entry in dataroot_config
self.default_dataset_config = DatasetConfig(None, self, self.default_config["dataset"])
# a dictionary of keys to DatasetConfig objects. Each key must exist in the multi_dataset__dataroot
# attribute of the server_config.
self.dataroot_config = {}
# Set to true when config_completed is called
self.is_completed = False
def get_dataset_config(self, dataroot_key):
if self.server_config.single_dataset__datapath:
return self.default_dataset_config
else:
return self.dataroot_config.get(dataroot_key, self.default_dataset_config)
def check_config(self):
"""Verify all the attributes have been checked"""
if not self.is_completed:
raise ConfigurationError("The configuration has not been completed")
mapping = self.__mapping(self.default_config)
for key in mapping.keys():
if not self.attr_checked[key]:
raise ConfigurationError(f"The attr '{key}' has not been checked")
self.server_config.check_config()
self.default_dataset_config.check_config()
for dataset_config in self.dataroot_config.values():
dataset_config.check_config()
def __mapping(self, config):
"""Create a mapping from attribute names to (location in the config tree, value)"""
dc = copy.deepcopy(config)
mapping = {}
def update_server_config(self, **kw):
self.server_config.update(**kw)
self.is_complete = False
# special cases where the value could be a dict.
# If its value is not None, the entry is added to the mapping, and not included
# in the flattening below.
dictval_cases = [
("adaptor", "cxg_adaptor", "tiledb_ctx"),
("server", "csp_directives"),
("multi_dataset", "dataroot"),
]
for dictval_case in dictval_cases:
cur = dc
for part in dictval_case[:-1]:
cur = cur.get(part, {})
val = cur.get(dictval_case[-1])
if val is not None:
key = "__".join(dictval_case)
mapping[key] = (dictval_case, val)
del cur[dictval_case[-1]]
flat_config = flatten(dc)
for key, value in flat_config.items():
# name of the attribute
attr = "__".join(key)
mapping[attr] = (key, value)
return mapping
def update_default_dataset_config(self, **kw):
self.default_dataset_config.update(**kw)
# update all the other dataset configs, if any
for value in self.dataroot_config.values():
value.update(**kw)
self.is_complete = False
def update_from_config_file(self, config_file):
with open(config_file) as fyaml:
config = yaml.load(fyaml, Loader=yaml.FullLoader)
mapping = self.__mapping(config)
for attr, (key, value) in mapping.items():
if not hasattr(self, attr):
raise ConfigurationError(f"Unknown key from config file: {key}")
try:
setattr(self, attr, value)
except KeyError:
raise ConfigurationError(f"Unable to set config attribute: {key}")
self.server_config.update_from_config(config["server"], "server")
self.default_dataset_config.update_from_config(config["dataset"], "dataset")
self.attr_checked[attr] = False
per_dataset_config = config.get("per_dataset_config", {})
for key, dataroot_config in per_dataset_config.items():
self.add_dataroot_config(key, **dataroot_config)
self.is_completed = False
self.is_complete = False
def write_config(self, config_file):
"""output the config to a yaml file"""
mapping = self.__mapping(self.default_config)
for attrname in mapping.keys():
mapping[attrname] = getattr(self, attrname)
config = unflatten(mapping, splitter=lambda key: key.split("__"))
server = self.server_config.create_mapping(self.server_config.default_config)
dataset = self.default_dataset_config.create_mapping(self.default_dataset_config.default_config)
config = dict(server={}, dataset={})
for attrname in server.keys():
config["server__" + attrname] = getattr(self.server_config, attrname)
for attrname in dataset.keys():
config["dataset__" + attrname] = getattr(self.default_dataset_config, attrname)
if self.dataroot_config:
config["per_dataset_config"] = {}
for dataroot_tag, dataroot_config in self.dataroot_config.items():
dataset = dataroot_config.create_mapping(dataroot_config.default_config)
for attrname in dataset.keys():
config[f"per_dataset_config__{dataroot_tag}__" + attrname] = getattr(dataroot_config, attrname)
config = unflatten(config, splitter=lambda key: key.split("__"))
yaml.dump(config, open(config_file, "w"))
def update(self, **kw):
for key, value in kw.items():
if not hasattr(self, key):
raise ConfigurationError(f"unknown config parameter {key}.")
try:
if type(value) == tuple:
# convert tuple values to list values
value = list(value)
setattr(self, key, value)
except KeyError:
raise ConfigurationError(f"Unable to set config parameter {key}.")
self.attr_checked[key] = False
self.is_completed = False
def changes_from_default(self):
"""Return all the attribute that are different from the default"""
mapping = self.__mapping(self.default_config)
diff = []
for attrname, (key, defval) in mapping.items():
curval = getattr(self, attrname)
if curval != defval:
diff.append((attrname, curval, defval))
diff_server = self.server_config.changes_from_default()
diff_dataset = self.default_dataset_config.changes_from_default()
diff = dict(server=diff_server, dataset=diff_dataset)
return diff
def add_dataroot_config(self, dataroot_tag, **kw):
"""Create a new dataset config object based on the default dataset config, and kw parameters"""
if dataroot_tag in self.dataroot_config:
raise ConfigurationError(f"dataroot config already exists: {dataroot_tag}")
if type(self.server_config.multi_dataset__dataroot) != dict:
raise ConfigurationError("The server__multi_dataset__dataroot must be a dictionary")
if dataroot_tag not in self.server_config.multi_dataset__dataroot:
raise ConfigurationError(f"The dataroot_tag ({dataroot_tag}) not found in server__multi_dataset__dataroot")
self.is_completed = False
self.dataroot_config[dataroot_tag] = DatasetConfig(dataroot_tag, self, self.default_config["dataset"])
flat_config = self.default_dataset_config.create_mapping(self.default_dataset_config.default_config)
config = {key: value[1] for key, value in flat_config.items()}
self.dataroot_config[dataroot_tag].update(**config)
self.dataroot_config[dataroot_tag].update_from_config(kw, dataroot_tag)
def complete_config(self, messagefn=None):
"""The configure options are checked, and any additional setup based on the config
parameters is done"""
@@ -218,22 +158,149 @@ class AppConfig(object):
# messages we can give correct context for attributes with bad value.
context = dict(messagefn=messagefn)
self.handle_server(context)
self.handle_adaptor(context)
self.handle_data_locator(context)
self.handle_adaptor(context) # may depend on data_locator
self.handle_presentation(context)
self.handle_single_dataset(context) # may depend on adaptor
self.handle_multi_dataset(context) # may depend on adaptor
self.handle_user_annotations(context)
self.handle_embeddings(context)
self.handle_diffexp(context)
self.handle_limits(context)
self.server_config.complete_config(context)
self.default_dataset_config.complete_config(context)
for dataroot_config in self.dataroot_config.values():
dataroot_config.complete_config(context)
self.is_completed = True
self.check_config()
def __check_attr(self, attrname, vtype):
def get_matrix_data_cache_manager(self):
return self.server_config.matrix_data_cache_manager
def is_multi_dataset(self):
return self.server_config.multi_dataset__dataroot is not None
def get_title(self, data_adaptor):
return (
self.server_config.single_dataset__title
if self.server_config.single_dataset__title
else data_adaptor.get_title()
)
def get_about(self, data_adaptor):
return (
self.server_config.single_dataset__about
if self.server_config.single_dataset__about
else data_adaptor.get_about()
)
def get_client_config(self, data_adaptor):
"""
Return the configuration as required by the /config REST route
"""
server_config = self.server_config
dataset_config = data_adaptor.dataset_config
annotation = dataset_config.user_annotations
# FIXME The current set of config is not consistently presented:
# we have camalCase, hyphen-text, and underscore_text
# make sure the configuration has been checked.
self.check_config()
# features
features = [f.todict() for f in data_adaptor.get_features(annotation)]
# display_names
title = self.get_title(data_adaptor)
about = self.get_about(data_adaptor)
display_names = dict(engine=data_adaptor.get_name(), dataset=title)
# library_versions
library_versions = {}
library_versions.update(data_adaptor.get_library_versions())
library_versions["cellxgene"] = cellxgene_version
# links
links = {"about-dataset": about}
# parameters
parameters = {
"layout": dataset_config.embeddings__names,
"max-category-items": dataset_config.presentation__max_categories,
"obs_names": server_config.single_dataset__obs_names,
"var_names": server_config.single_dataset__var_names,
"diffexp_lfc_cutoff": dataset_config.diffexp__lfc_cutoff,
"backed": server_config.adaptor__anndata_adaptor__backed,
"disable-diffexp": not dataset_config.diffexp__enable,
"enable-reembedding": dataset_config.embeddings__enable_reembedding,
"annotations": False,
"annotations_file": None,
"annotations_dir": None,
"annotations_cell_ontology_enabled": False,
"annotations_cell_ontology_obopath": None,
"annotations_cell_ontology_terms": None,
"custom_colors": dataset_config.presentation__custom_colors,
"diffexp-may-be-slow": False,
"about_legal_tos": dataset_config.app__about_legal_tos,
"about_legal_privacy": dataset_config.app__about_legal_privacy,
}
data_adaptor.update_parameters(parameters)
if annotation:
annotation.update_parameters(parameters, data_adaptor)
# gather it all together
c = {}
config = c["config"] = {}
config["features"] = features
config["displayNames"] = display_names
config["library_versions"] = library_versions
config["links"] = links
config["parameters"] = parameters
config["limits"] = {
"column_request_max": server_config.limits__column_request_max,
"diffexp_cellcount_max": server_config.limits__diffexp_cellcount_max,
}
return c
class BaseConfig(object):
"""This class handles the mechanics of updating and checking attributes.
Derived classes are expected to store the actual attributes"""
def __init__(self, app_config, default_config, dictval_cases={}):
# reference back to the app_config
self.app_config = app_config
# the complete set of attribute and their default values (unflattened)
self.default_config = default_config
# attributes where the value may be a dict (and therefore are not flattened)
self.dictval_cases = dictval_cases
# used to make sure every attribute value is checked
self.attr_checked = {k: False for k in self.create_mapping(default_config).keys()}
def create_mapping(self, config):
"""Create a mapping from attribute names to (location in the config tree, value)"""
dc = copy.deepcopy(config)
mapping = {}
# special cases where the value could be a dict.
# If its value is not None, the entry is added to the mapping, and not included
# in the flattening below.
for dictval_case in self.dictval_cases:
cur = dc
for part in dictval_case[:-1]:
cur = cur.get(part, {})
val = cur.get(dictval_case[-1])
if val is not None:
key = "__".join(dictval_case)
mapping[key] = (dictval_case, val)
del cur[dictval_case[-1]]
flat_config = flatten(dc)
for key, value in flat_config.items():
# name of the attribute
attr = "__".join(key)
mapping[attr] = (key, value)
return mapping
def check_attr(self, attrname, vtype):
val = getattr(self, attrname)
if type(vtype) in (list, tuple):
if type(val) not in vtype:
@@ -250,48 +317,152 @@ class AppConfig(object):
self.attr_checked[attrname] = True
def handle_server(self, context):
self.__check_attr("server__verbose", bool)
self.__check_attr("server__debug", bool)
self.__check_attr("server__host", str)
self.__check_attr("server__port", (type(None), int))
self.__check_attr("server__scripts", list)
self.__check_attr("server__inline_scripts", list)
self.__check_attr("server__open_browser", bool)
self.__check_attr("server__force_https", bool)
self.__check_attr("server__flask_secret_key", (type(None), str))
self.__check_attr("server__generate_cache_control_headers", bool)
self.__check_attr("server__about_legal_tos", (type(None), str))
self.__check_attr("server__about_legal_privacy", (type(None), str))
self.__check_attr("server__server_timing_headers", bool)
self.__check_attr("server__csp_directives", (type(None), dict))
def check_config(self):
mapping = self.create_mapping(self.default_config)
for key in mapping.keys():
if not self.attr_checked[key]:
raise ConfigurationError(f"The attr '{key}' has not been checked")
if self.server__port:
if not is_port_available(self.server__host, self.server__port):
def update(self, **kw):
for key, value in kw.items():
if not hasattr(self, key):
raise ConfigurationError(f"unknown config parameter {key}.")
try:
if type(value) == tuple:
# convert tuple values to list values
value = list(value)
setattr(self, key, value)
except KeyError:
raise ConfigurationError(f"Unable to set config parameter {key}.")
self.attr_checked[key] = False
def update_from_config(self, config, prefix):
mapping = self.create_mapping(config)
for attr, (key, value) in mapping.items():
if not hasattr(self, attr):
raise ConfigurationError(f"Unknown key from config file: {prefix}__{attr}")
try:
setattr(self, attr, value)
except KeyError:
raise ConfigurationError(f"Unable to set config attribute: {prefix}__{attr}")
self.attr_checked[attr] = False
def changes_from_default(self):
"""Return all the attribute that are different from the default"""
mapping = self.create_mapping(self.default_config)
diff = []
for attrname, (key, defval) in mapping.items():
curval = getattr(self, attrname)
if curval != defval:
diff.append((attrname, curval, defval))
return diff
class ServerConfig(BaseConfig):
"""Manages the config attribute associated with the server."""
def __init__(self, app_config, default_config):
dictval_cases = [
("app", "csp_directives"),
("adaptor", "cxg_adaptor", "tiledb_ctx"),
("multi_dataset", "dataroot"),
]
super().__init__(app_config, default_config, dictval_cases)
dc = default_config
try:
self.app__verbose = dc["app"]["verbose"]
self.app__debug = dc["app"]["debug"]
self.app__host = dc["app"]["host"]
self.app__port = dc["app"]["port"]
self.app__open_browser = dc["app"]["open_browser"]
self.app__force_https = dc["app"]["force_https"]
self.app__flask_secret_key = dc["app"]["flask_secret_key"]
self.app__generate_cache_control_headers = dc["app"]["generate_cache_control_headers"]
self.app__server_timing_headers = dc["app"]["server_timing_headers"]
self.app__csp_directives = dc["app"]["csp_directives"]
self.multi_dataset__dataroot = dc["multi_dataset"]["dataroot"]
self.multi_dataset__index = dc["multi_dataset"]["index"]
self.multi_dataset__allowed_matrix_types = dc["multi_dataset"]["allowed_matrix_types"]
self.multi_dataset__matrix_cache__max_datasets = dc["multi_dataset"]["matrix_cache"]["max_datasets"]
self.multi_dataset__matrix_cache__timelimit_s = dc["multi_dataset"]["matrix_cache"]["timelimit_s"]
self.single_dataset__datapath = dc["single_dataset"]["datapath"]
self.single_dataset__obs_names = dc["single_dataset"]["obs_names"]
self.single_dataset__var_names = dc["single_dataset"]["var_names"]
self.single_dataset__about = dc["single_dataset"]["about"]
self.single_dataset__title = dc["single_dataset"]["title"]
self.diffexp__alg_cxg__max_workers = dc["diffexp"]["alg_cxg"]["max_workers"]
self.diffexp__alg_cxg__cpu_multiplier = dc["diffexp"]["alg_cxg"]["cpu_multiplier"]
self.diffexp__alg_cxg__target_workunit = dc["diffexp"]["alg_cxg"]["target_workunit"]
self.data_locator__s3__region_name = dc["data_locator"]["s3"]["region_name"]
self.adaptor__cxg_adaptor__tiledb_ctx = dc["adaptor"]["cxg_adaptor"]["tiledb_ctx"]
self.adaptor__anndata_adaptor__backed = dc["adaptor"]["anndata_adaptor"]["backed"]
self.limits__diffexp_cellcount_max = dc["limits"]["diffexp_cellcount_max"]
self.limits__column_request_max = dc["limits"]["column_request_max"]
except KeyError as e:
raise ConfigurationError(f"Unexpected config: {str(e)}")
# The matrix data cache manager is created during the complete_config and stored here.
self.matrix_data_cache_manager = None
def complete_config(self, context):
self.handle_app(context)
self.handle_data_locator(context)
self.handle_adaptor(context) # may depend on data_locator
self.handle_single_dataset(context) # may depend on adaptor
self.handle_multi_dataset(context) # may depend on adaptor
self.handle_diffexp(context)
self.handle_limits(context)
self.check_config()
def handle_app(self, context):
self.check_attr("app__verbose", bool)
self.check_attr("app__debug", bool)
self.check_attr("app__host", str)
self.check_attr("app__port", (type(None), int))
self.check_attr("app__open_browser", bool)
self.check_attr("app__force_https", bool)
self.check_attr("app__flask_secret_key", (type(None), str))
self.check_attr("app__generate_cache_control_headers", bool)
self.check_attr("app__server_timing_headers", bool)
self.check_attr("app__csp_directives", (type(None), dict))
if self.app__port:
if not is_port_available(self.app__host, self.app__port):
raise ConfigurationError(
f"The port selected {self.server__port} is in use, please configure an open port."
f"The port selected {self.app__port} is in use, please configure an open port."
)
else:
self.server__port = find_available_port(self.server__host, DEFAULT_SERVER_PORT)
self.app__port = find_available_port(self.app__host, DEFAULT_SERVER_PORT)
if self.server__debug:
if self.app__debug:
context["messagefn"]("in debug mode, setting verbose=True and open_browser=False")
self.server__verbose = True
self.server__open_browser = False
self.app__verbose = True
self.app__open_browser = False
else:
warnings.formatwarning = custom_format_warning
if not self.server__verbose:
if not self.app__verbose:
sys.tracebacklimit = 0
# secret key:
# first, from CXG_SECRET_KEY environment variable
# second, from config file
self.server__flask_secret_key = os.environ.get("CXG_SECRET_KEY", self.server__flask_secret_key)
self.app__flask_secret_key = os.environ.get("CXG_SECRET_KEY", self.app__flask_secret_key)
# CSP Directives are a dict of string: list(string) or string: string
if self.server__csp_directives is not None:
for k, v in self.server__csp_directives.items():
if self.app__csp_directives is not None:
for k, v in self.app__csp_directives.items():
if not isinstance(k, str):
raise ConfigurationError("CSP directive names must be a string.")
if isinstance(v, list):
@@ -301,26 +472,15 @@ class AppConfig(object):
elif not isinstance(v, str):
raise ConfigurationError("CSP directive value must be a string or list of strings.")
# scripts can be string (filename) or dict (attributes). Convert string to dict.
scripts = []
for s in self.server__scripts:
if isinstance(s, str):
scripts.append({"src": s})
elif isinstance(s, dict) and isinstance(s["src"], str):
scripts.append(s)
else:
raise ConfigurationError("Scripts must be string or dict")
self.server__scripts = scripts
def handle_data_locator(self, context):
self.__check_attr("data_locator__s3__region_name", (type(None), bool, str))
self.check_attr("data_locator__s3__region_name", (type(None), bool, str))
if self.data_locator__s3__region_name is True:
path = self.single_dataset__datapath or self.multi_dataset__dataroot
if type(path) == dict:
# if multi_dataset__dataroot is a dict, then use the first key
# that is in s3. NOTE: it is not supported to have dataroots
# in different regions.
paths = path.values()
paths = [val.get("dataroot") for val in path.values()]
for path in paths:
if path.startswith("s3://"):
break
@@ -332,16 +492,12 @@ class AppConfig(object):
region_name = None
self.data_locator__s3__region_name = region_name
def handle_presentation(self, context):
self.__check_attr("presentation__max_categories", int)
self.__check_attr("presentation__custom_colors", bool)
def handle_single_dataset(self, context):
self.__check_attr("single_dataset__datapath", (str, type(None)))
self.__check_attr("single_dataset__title", (str, type(None)))
self.__check_attr("single_dataset__about", (str, type(None)))
self.__check_attr("single_dataset__obs_names", (str, type(None)))
self.__check_attr("single_dataset__var_names", (str, type(None)))
self.check_attr("single_dataset__datapath", (str, type(None)))
self.check_attr("single_dataset__title", (str, type(None)))
self.check_attr("single_dataset__about", (str, type(None)))
self.check_attr("single_dataset__obs_names", (str, type(None)))
self.check_attr("single_dataset__var_names", (str, type(None)))
if self.single_dataset__datapath is None:
if self.multi_dataset__dataroot is None:
@@ -357,7 +513,7 @@ class AppConfig(object):
self.matrix_data_cache_manager = MatrixDataCacheManager(max_cached=1, timelimit_s=None)
# preload this data set
matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath, app_config=self)
matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath, app_config=self.app_config)
try:
matrix_data_loader.pre_load_validation()
except DatasetAccessError as e:
@@ -388,26 +544,46 @@ class AppConfig(object):
)
def handle_multi_dataset(self, context):
self.__check_attr("multi_dataset__dataroot", (type(None), dict, str))
self.__check_attr("multi_dataset__index", (type(None), bool, str))
self.__check_attr("multi_dataset__allowed_matrix_types", list)
self.__check_attr("multi_dataset__matrix_cache__max_datasets", int)
self.__check_attr("multi_dataset__matrix_cache__timelimit_s", (type(None), int, float))
self.check_attr("multi_dataset__dataroot", (type(None), dict, str))
self.check_attr("multi_dataset__index", (type(None), bool, str))
self.check_attr("multi_dataset__allowed_matrix_types", list)
self.check_attr("multi_dataset__matrix_cache__max_datasets", int)
self.check_attr("multi_dataset__matrix_cache__timelimit_s", (type(None), int, float))
if self.multi_dataset__dataroot is None:
return
if type(self.multi_dataset__dataroot) == str:
self.multi_dataset__dataroot = dict(d=self.multi_dataset__dataroot)
default_dict = dict(base_url="d", dataroot=self.multi_dataset__dataroot)
self.multi_dataset__dataroot = dict(d=default_dict)
for key in self.multi_dataset__dataroot.keys():
# sanity check for well formed keys
if type(key) != str:
raise ConfigurationError(f"error in multi_dataset__dataroot {key}")
if quote_plus(key) != key:
raise ConfigurationError(f"error in multi_dataset__dataroot {key}")
if os.path.split(os.path.normpath(key))[-1] != key:
raise ConfigurationError(f"error in multi_dataset__dataroot {key}")
for tag, dataroot_dict in self.multi_dataset__dataroot.items():
if "base_url" not in dataroot_dict:
raise ConfigurationError(f"error in multi_dataset__dataroot: missing base_url for tag {tag}")
if "dataroot" not in dataroot_dict:
raise ConfigurationError(f"error in multi_dataset__dataroot: missing dataroot, for tag {tag}")
base_url = dataroot_dict["base_url"]
# sanity check for well formed base urls
bad = False
if type(base_url) != str:
bad = True
elif os.path.normpath(base_url) != base_url:
bad = True
else:
base_url_parts = base_url.split("/")
if [quote_plus(part) for part in base_url_parts] != base_url_parts:
bad = True
if ".." in base_url_parts:
bad = True
if bad:
raise ConfigurationError(f"error in multi_dataset__dataroot base_url {base_url} for tag {tag}")
# verify all the base_urls are unique
base_urls = [d["base_url"] for d in self.multi_dataset__dataroot.values()]
if len(base_urls) > len(set(base_urls)):
raise ConfigurationError("error in multi_dataset__dataroot: base_urls must be unique")
# error checking
for mtype in self.multi_dataset__allowed_matrix_types:
@@ -423,13 +599,114 @@ class AppConfig(object):
timelimit_s=self.multi_dataset__matrix_cache__timelimit_s,
)
def handle_diffexp(self, context):
self.check_attr("diffexp__alg_cxg__max_workers", (str, int))
self.check_attr("diffexp__alg_cxg__cpu_multiplier", int)
self.check_attr("diffexp__alg_cxg__target_workunit", int)
max_workers = self.diffexp__alg_cxg__max_workers
cpu_multiplier = self.diffexp__alg_cxg__cpu_multiplier
cpu_count = os.cpu_count()
max_workers = min(max_workers, cpu_multiplier * cpu_count)
diffexp_tiledb.set_config(max_workers, self.diffexp__alg_cxg__target_workunit)
def handle_adaptor(self, context):
# cxg
self.check_attr("adaptor__cxg_adaptor__tiledb_ctx", dict)
regionkey = "vfs.s3.region"
if regionkey not in self.adaptor__cxg_adaptor__tiledb_ctx:
if type(self.data_locator__s3__region_name) == str:
self.adaptor__cxg_adaptor__tiledb_ctx[regionkey] = self.data_locator__s3__region_name
from server.data_cxg.cxg_adaptor import CxgAdaptor
CxgAdaptor.set_tiledb_context(self.adaptor__cxg_adaptor__tiledb_ctx)
# anndata
self.check_attr("adaptor__anndata_adaptor__backed", bool)
def handle_limits(self, context):
self.check_attr("limits__diffexp_cellcount_max", (type(None), int))
self.check_attr("limits__column_request_max", (type(None), int))
def exceeds_limit(self, limit_name, value):
limit_value = getattr(self, "limits__" + limit_name, None)
if limit_value is None: # disabled
return False
return value > limit_value
class DatasetConfig(BaseConfig):
"""Manages the config attribute associated with a dataset."""
def __init__(self, tag, app_config, default_config):
super().__init__(app_config, default_config)
self.tag = tag
dc = default_config
try:
self.app__scripts = dc["app"]["scripts"]
self.app__inline_scripts = dc["app"]["inline_scripts"]
self.app__about_legal_tos = dc["app"]["about_legal_tos"]
self.app__about_legal_privacy = dc["app"]["about_legal_privacy"]
self.presentation__max_categories = dc["presentation"]["max_categories"]
self.presentation__custom_colors = dc["presentation"]["custom_colors"]
self.user_annotations__enable = dc["user_annotations"]["enable"]
self.user_annotations__type = dc["user_annotations"]["type"]
self.user_annotations__local_file_csv__directory = dc["user_annotations"]["local_file_csv"]["directory"]
self.user_annotations__local_file_csv__file = dc["user_annotations"]["local_file_csv"]["file"]
self.user_annotations__ontology__enable = dc["user_annotations"]["ontology"]["enable"]
self.user_annotations__ontology__obo_location = dc["user_annotations"]["ontology"]["obo_location"]
self.embeddings__names = dc["embeddings"]["names"]
self.embeddings__enable_reembedding = dc["embeddings"]["enable_reembedding"]
self.diffexp__enable = dc["diffexp"]["enable"]
self.diffexp__lfc_cutoff = dc["diffexp"]["lfc_cutoff"]
self.diffexp__top_n = dc["diffexp"]["top_n"]
except KeyError as e:
raise ConfigurationError(f"Unexpected config: {str(e)}")
# The annotation object is created during complete_config and stored here.
self.user_annotations = None
def complete_config(self, context):
self.handle_app(context)
self.handle_presentation(context)
self.handle_user_annotations(context)
self.handle_embeddings(context)
self.handle_diffexp(context)
def handle_app(self, context):
self.check_attr("app__scripts", list)
self.check_attr("app__inline_scripts", list)
self.check_attr("app__about_legal_tos", (type(None), str))
self.check_attr("app__about_legal_privacy", (type(None), str))
# scripts can be string (filename) or dict (attributes). Convert string to dict.
scripts = []
for s in self.app__scripts:
if isinstance(s, str):
scripts.append({"src": s})
elif isinstance(s, dict) and isinstance(s["src"], str):
scripts.append(s)
else:
raise ConfigurationError("Scripts must be string or dict")
self.app__scripts = scripts
def handle_presentation(self, context):
self.check_attr("presentation__max_categories", int)
self.check_attr("presentation__custom_colors", bool)
def handle_user_annotations(self, context):
self.__check_attr("user_annotations__enable", bool)
self.__check_attr("user_annotations__type", str)
self.__check_attr("user_annotations__local_file_csv__directory", (type(None), str))
self.__check_attr("user_annotations__local_file_csv__file", (type(None), str))
self.__check_attr("user_annotations__ontology__enable", bool)
self.__check_attr("user_annotations__ontology__obo_location", (type(None), str))
self.check_attr("user_annotations__enable", bool)
self.check_attr("user_annotations__type", str)
self.check_attr("user_annotations__local_file_csv__directory", (type(None), str))
self.check_attr("user_annotations__local_file_csv__file", (type(None), str))
self.check_attr("user_annotations__ontology__enable", bool)
self.check_attr("user_annotations__ontology__obo_location", (type(None), str))
if self.user_annotations__enable:
# TODO, replace this with a factory pattern once we have more than one way
@@ -458,8 +735,11 @@ class AppConfig(object):
# if the user has specified a fixed label file, go ahead and validate it
# so that we can remove errors early in the process.
if self.single_dataset__datapath and self.user_annotations__local_file_csv__file:
with self.matrix_data_cache_manager.data_adaptor(self.single_dataset__datapath, self) as data_adaptor:
server_config = self.app_config.server_config
if server_config.single_dataset__datapath and self.user_annotations__local_file_csv__file:
with server_config.matrix_data_cache_manager.data_adaptor(
self.tag, server_config.single_dataset__datapath, self.app_config
) as data_adaptor:
data_adaptor.check_new_labels(self.user_annotations.read_labels(data_adaptor))
if self.user_annotations__ontology__enable or self.user_annotations__ontology__obo_location:
@@ -487,135 +767,29 @@ class AppConfig(object):
)
def handle_embeddings(self, context):
self.__check_attr("embeddings__names", list)
self.__check_attr("embeddings__enable_reembedding", bool)
self.check_attr("embeddings__names", list)
self.check_attr("embeddings__enable_reembedding", bool)
if self.single_dataset__datapath:
if self.app_config.server_config.single_dataset__datapath:
if self.embeddings__enable_reembedding:
matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath, app_config=self)
matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath, app_config=self.app_config)
if matrix_data_loader.matrix_data_type() != MatrixDataType.H5AD:
raise ConfigurationError("'enable-reembedding is only supported with H5AD files.")
if self.adaptor__anndata_adaptor__backed:
raise ConfigurationError("enable-reembedding is not supported when run in --backed mode.")
def handle_diffexp(self, context):
self.__check_attr("diffexp__enable", bool)
self.__check_attr("diffexp__lfc_cutoff", float)
self.__check_attr("diffexp__top_n", int)
self.__check_attr("diffexp__alg_cxg__max_workers", (str, int))
self.__check_attr("diffexp__alg_cxg__cpu_multiplier", int)
self.__check_attr("diffexp__alg_cxg__target_workunit", int)
self.check_attr("diffexp__enable", bool)
self.check_attr("diffexp__lfc_cutoff", float)
self.check_attr("diffexp__top_n", int)
if self.single_dataset__datapath:
with self.matrix_data_cache_manager.data_adaptor(self.single_dataset__datapath, self) as data_adaptor:
server_config = self.app_config.server_config
if server_config.single_dataset__datapath:
with server_config.matrix_data_cache_manager.data_adaptor(
self.tag, server_config.single_dataset__datapath, self.app_config
) as data_adaptor:
if self.diffexp__enable and data_adaptor.parameters.get("diffexp_may_be_slow", False):
context["messagefn"](
"CAUTION: due to the size of your dataset, "
"running differential expression may take longer or fail."
)
max_workers = self.diffexp__alg_cxg__max_workers
cpu_multiplier = self.diffexp__alg_cxg__cpu_multiplier
cpu_count = os.cpu_count()
max_workers = min(max_workers, cpu_multiplier * cpu_count)
diffexp_tiledb.set_config(max_workers, self.diffexp__alg_cxg__target_workunit)
def handle_adaptor(self, context):
# cxg
self.__check_attr("adaptor__cxg_adaptor__tiledb_ctx", dict)
regionkey = "vfs.s3.region"
if regionkey not in self.adaptor__cxg_adaptor__tiledb_ctx:
if type(self.data_locator__s3__region_name) == str:
self.adaptor__cxg_adaptor__tiledb_ctx[regionkey] = self.data_locator__s3__region_name
from server.data_cxg.cxg_adaptor import CxgAdaptor
CxgAdaptor.set_tiledb_context(self.adaptor__cxg_adaptor__tiledb_ctx)
# anndata
self.__check_attr("adaptor__anndata_adaptor__backed", bool)
def handle_limits(self, context):
self.__check_attr("limits__diffexp_cellcount_max", (type(None), int))
self.__check_attr("limits__column_request_max", (type(None), int))
def get_title(self, data_adaptor):
return self.single_dataset__title if self.single_dataset__title else data_adaptor.get_title()
def get_about(self, data_adaptor):
return self.single_dataset__about if self.single_dataset__about else data_adaptor.get_about()
def get_client_config(self, data_adaptor, annotation=None):
"""
Return the configuration as required by the /config REST route
"""
# FIXME The current set of config is not consistently presented:
# we have camalCase, hyphen-text, and underscore_text
# make sure the configuration has been checked.
self.check_config()
# features
features = [f.todict() for f in data_adaptor.get_features(annotation)]
# display_names
title = self.get_title(data_adaptor)
about = self.get_about(data_adaptor)
display_names = dict(engine=data_adaptor.get_name(), dataset=title)
# library_versions
library_versions = {}
library_versions.update(data_adaptor.get_library_versions())
library_versions["cellxgene"] = cellxgene_version
# links
links = {"about-dataset": about}
# parameters
parameters = {
"layout": self.embeddings__names,
"max-category-items": self.presentation__max_categories,
"obs_names": self.single_dataset__obs_names,
"var_names": self.single_dataset__var_names,
"diffexp_lfc_cutoff": self.diffexp__lfc_cutoff,
"backed": self.adaptor__anndata_adaptor__backed,
"disable-diffexp": not self.diffexp__enable,
"enable-reembedding": self.embeddings__enable_reembedding,
"annotations": False,
"annotations_file": None,
"annotations_dir": None,
"annotations_cell_ontology_enabled": False,
"annotations_cell_ontology_obopath": None,
"annotations_cell_ontology_terms": None,
"custom_colors": self.presentation__custom_colors,
"diffexp-may-be-slow": False,
"about_legal_tos": self.server__about_legal_tos,
"about_legal_privacy": self.server__about_legal_privacy,
}
data_adaptor.update_parameters(parameters)
if annotation:
annotation.update_parameters(parameters, data_adaptor)
# gather it all together
c = {}
config = c["config"] = {}
config["features"] = features
config["displayNames"] = display_names
config["library_versions"] = library_versions
config["links"] = links
config["parameters"] = parameters
config["limits"] = {
"column_request_max": self.limits__column_request_max,
"diffexp_cellcount_max": self.limits__diffexp_cellcount_max,
}
return c
def exceeds_limit(self, limit_name, value):
limit_value = getattr(self, "limits__" + limit_name, None)
if limit_value is None: # disabled
return False
return value > limit_value
server/common/default_config.py
+138 -108
View File
@@ -1,129 +1,159 @@
import yaml
default_config = """
# cellxgene configuration
server:
verbose: false
debug: false
host: "127.0.0.1"
port : null
app:
verbose: false
debug: false
host: "127.0.0.1"
port : null
open_browser: false
force_https: false
flask_secret_key: null
generate_cache_control_headers: false
server_timing_headers: false
csp_directives: null
# Scripts can be a list of either file names (string) or dicts containing keys src, integrity and crossorigin.
# these will be injected into the index template as script tags with these attributes set.
scripts: []
# Inline scripts are a list of file names, where the contents of the file will be injected into the index.
inline_scripts: []
multi_dataset:
# If dataroot is set, then cellxgene may serve multiple datasets. This parameter is not
# compatible with single_dataset/datapath.
# dataroot may be a string, representing the path to a directory or S3 prefix. In this
# case the datasets in that location are accessed from <server>/d/<datasetname>.
# example:
# dataroot: /path/to/datasets/
# or
# dataroot: s3://bucket/prefix/
#
# As an alternative, dataroot can be a dictionary, where a dataset key is associated with a base_url
# and a dataroot.
# example:
# dataroot:
# d1:
# base_url: set1
# dataroot: /path/to/set1_datasets/
# d2:
# base_url: set2/subdir
# dataroot: /path/to/set2_datasets/
#
# In this case, datasets can be accessed from <server>/set1/<datasetname> or
# <server>/set2/subdir/<datasetname>. It is possible to have different dataset configurations
# for datasets accessed through different dataroots. For example, in one dataroot, the
# user annotations could be enabled, and in another dataroot they could be disabled.
# To specify dataroot configurations, add a new top level dictionary to the config named
# per_dataset_config. Within per_dataset_config create a dictionary for each dataroot to specialize
# ("d1" or "d2" from the example). Each of these dictionaries has the exact same form as the "dataset"
# dictionary (see below).
# When this approach is used, the values for each configuration option are checked in
# this order: per_dataset_config/<key>, dataset, then the default values.
#
# example:
#
# per_dataset_config:
# d1:
# user_annotations:
# enable: false
# d2:
# user_annotations:
# enable: true
open_browser: false
about_legal_tos: null
about_legal_privacy: null
force_https: false
flask_secret_key: null
generate_cache_control_headers: false
server_timing_headers: false
csp_directives: null
dataroot: null
presentation:
max_categories: 1000
custom_colors: true
# The index page when in multi-dataset mode:
# false or null: this returns a 404 code
# true: loads a test index page, which links to the datasets that are available in the dataroot
# string/URL: redirect to this URL: flask.redirect(config.multi_dataset__index)
index: false
multi_dataset:
# If dataroot is set, then cellxgene may serve multiple datasets. This parameter is not
# compatable with single_dataset/datapath.
# dataroot may be a string, representing the path to a directory or S3 prefix. In this
# case the datasets in that location are accessed from <server>/d/<datasetname>.
# example:
# dataroot: /path/to/datasets/
# or
# dataroot: s3://bucket/prefix/
#
# As an alternative, dataroot can be a dictionary, mapping url prefixes to dataroot paths.
# example:
# dataroot:
# set1 : /path/to/set1_datasets/
# set2 : /path/to/set2_datasets/
# In this case, datasets can be accessed from <server>/set1/<datasetname> or
# <server>/set2/<datasetname>.
# A list of allowed matrix types. If an empty list, then all matrix types are allowed
allowed_matrix_types: []
dataroot: null
matrix_cache:
# The maximum number of datasets that may be opened at one time. The least recently used dataset
# is evicted from the cache first.
max_datasets: 5
# The index page when in multi-dataset mode:
# false or null: this returns a 404 code
# true: loads a test index page, which links to the datasets that are available in the dataroot
# string/URL: redirect to this URL: flask.redirect(config.multi_dataset__index)
index: false
# A matrix is automatically removed from the cache after timelimit_s number of seconds.
# If timelimit_s is set to None, then there is no time limit.
timelimit_s: 30
# A list of allowed matrix types. If an empty list, then all matrix types are allowed
allowed_matrix_types: []
single_dataset:
# If datapath is set, then cellxgene with serve a single dataset located at datapath. This parameter is not
# compatible with multi_dataset/dataroot.
datapath: null
obs_names: null
var_names: null
about: null
title: null
matrix_cache:
# The maximum number of datasets that may be opened at one time. The least recently used dataset
# is evicted from the cache first.
max_datasets: 5
diffexp:
alg_cxg:
# The number of threads to use is computed from: min(max_workers, cpu_multipler * cpu_count).
# Where cpu_count is determined at runtime.
max_workers: 64
cpu_multiplier: 4
# A matrix is automatically removed from the cache after timelimit_s number of seconds.
# If timelimit_s is set to None, then there is no time limit.
timelimit_s: 30
# The target number of matrix elements that are evaluated
# together in one thread.
target_workunit: 16_000_000
single_dataset:
datapath: null
obs_names: null
var_names: null
about: null
title: null
data_locator:
s3:
# s3 region name.
# if true, then the s3 location is automatically determined from the datapath or dataroot.
# if false/null, then do not set.
# if a string, then use that value (e.g. us-east-1).
region_name: true
user_annotations:
enable: true
type: local_file_csv
local_file_csv:
directory: null
file: null
ontology:
enable: false
obo_location: null
adaptor:
cxg_adaptor:
# The key/values under tiledb_ctx will be used to initialize the tiledb Context.
# If 'vfs.s3.region' is not set, then it will automatically use the setting from
# data_locator / s3 / region_name.
tiledb_ctx:
sm.tile_cache_size: 8589934592
sm.num_reader_threads: 32
embeddings:
names : []
enable_reembedding: false
diffexp:
enable: true
lfc_cutoff: 0.01
top_n: 10
alg_cxg:
# The number of threads to use is computed from: min(max_workers, cpu_multipler * cpu_count).
# Where cpu_count is determined at runtime.
max_workers: 64
cpu_multiplier: 4
# The target number of matrix elements that are evaluated
# together in one thread.
target_workunit: 16_000_000
data_locator:
s3:
# s3 region name.
# if true, then the s3 location is automatically determined from the datapath or dataroot.
# if false/null, then do not set.
# if a string, then use that value (e.g. us-east-1).
region_name: true
adaptor:
cxg_adaptor:
# The key/values under tiledb_ctx will be used to initialize the tiledb Context.
# If 'vfs.s3.region' is not set, then it will automatically use the setting from
# data_locator / s3 / region_name.
tiledb_ctx:
sm.tile_cache_size: 8589934592
sm.num_reader_threads: 32
anndata_adaptor:
anndata_adaptor:
backed: false
limits:
column_request_max: 32
diffexp_cellcount_max: null
limits:
column_request_max: 32
diffexp_cellcount_max: null
dataset:
app:
# Scripts can be a list of either file names (string) or dicts containing keys src, integrity and crossorigin.
# these will be injected into the index template as script tags with these attributes set.
scripts: []
# Inline scripts are a list of file names, where the contents of the file will be injected into the index.
inline_scripts: []
about_legal_tos: null
about_legal_privacy: null
presentation:
max_categories: 1000
custom_colors: true
user_annotations:
enable: true
type: local_file_csv
local_file_csv:
directory: null
file: null
ontology:
enable: false
obo_location: null
embeddings:
names : []
enable_reembedding: false
diffexp:
enable: true
lfc_cutoff: 0.01
top_n: 10
"""
server/common/health.py
+6 -4
View File
@@ -24,10 +24,12 @@ def health_check(config):
health = {"status": None, "version": "1", "releaseID": cellxgene_version}
checks = False
if config.single_dataset__datapath is not None:
checks = _is_accessible(config.single_dataset__datapath, config)
elif config.multi_dataset__dataroot is not None:
checks = all([_is_accessible(datapath, config) for datapath in config.multi_dataset__dataroot.values()])
server_config = config.server_config
if config.is_multi_dataset():
dataroots = [datapath_dict["dataroot"] for datapath_dict in server_config.multi_dataset__dataroot.values()]
checks = all([_is_accessible(dataroot, server_config) for dataroot in dataroots])
else:
checks = _is_accessible(server_config.single_dataset__datapath, server_config)
health["status"] = "pass" if checks else "fail"
code = HTTPStatus.OK if health["status"] == "pass" else HTTPStatus.BAD_REQUEST
server/common/rest.py
+21 -16
View File
@@ -97,12 +97,13 @@ def _query_parameter_to_filter(args):
return result
def schema_get_helper(data_adaptor, annotations):
def schema_get_helper(data_adaptor):
"""helper function to gather the schema from the data source and annotations"""
schema = data_adaptor.get_schema()
schema = copy.deepcopy(schema)
# add label obs annotations as needed
annotations = data_adaptor.dataset_config.user_annotations
if annotations is not None:
label_schema = annotations.get_schema(data_adaptor)
schema["annotations"]["obs"]["columns"].extend(label_schema)
@@ -110,20 +111,20 @@ def schema_get_helper(data_adaptor, annotations):
return schema
def schema_get(data_adaptor, annotations):
schema = schema_get_helper(data_adaptor, annotations)
def schema_get(data_adaptor):
schema = schema_get_helper(data_adaptor)
return make_response(jsonify({"schema": schema}), HTTPStatus.OK)
def config_get(app_config, data_adaptor, annotations):
config = app_config.get_client_config(data_adaptor, annotations)
def config_get(app_config, data_adaptor):
config = app_config.get_client_config(data_adaptor)
return make_response(jsonify(config), HTTPStatus.OK)
def annotations_obs_get(request, data_adaptor, annotations):
def annotations_obs_get(request, data_adaptor):
fields = request.args.getlist("annotation-name", None)
num_columns_requested = len(data_adaptor.get_obs_keys()) if len(fields) == 0 else len(fields)
if data_adaptor.config.exceeds_limit("column_request_max", num_columns_requested):
if data_adaptor.server_config.exceeds_limit("column_request_max", num_columns_requested):
return abort(HTTPStatus.BAD_REQUEST)
preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
if preferred_mimetype != "application/octet-stream":
@@ -131,6 +132,7 @@ def annotations_obs_get(request, data_adaptor, annotations):
try:
labels = None
annotations = data_adaptor.dataset_config.user_annotations
if annotations:
labels = annotations.read_labels(data_adaptor)
fbs = data_adaptor.annotation_to_fbs_matrix(Axis.OBS, fields, labels)
@@ -139,8 +141,9 @@ def annotations_obs_get(request, data_adaptor, annotations):
return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)
def annotations_put_fbs_helper(data_adaptor, annotations, fbs):
def annotations_put_fbs_helper(data_adaptor, fbs):
"""helper function to write annotations from fbs"""
annotations = data_adaptor.dataset_config.user_annotations
if annotations is None:
raise DisabledFeatureError("Writable annotations are not enabled")
@@ -150,7 +153,8 @@ def annotations_put_fbs_helper(data_adaptor, annotations, fbs):
annotations.write_labels(new_label_df, data_adaptor)
def annotations_obs_put(request, data_adaptor, annotations):
def annotations_obs_put(request, data_adaptor):
annotations = data_adaptor.dataset_config.user_annotations
if annotations is None:
return abort(HTTPStatus.NOT_IMPLEMENTED)
@@ -163,17 +167,17 @@ def annotations_obs_put(request, data_adaptor, annotations):
annotations.set_collection(anno_collection)
try:
annotations_put_fbs_helper(data_adaptor, annotations, fbs)
annotations_put_fbs_helper(data_adaptor, fbs)
res = json.dumps({"status": "OK"})
return make_response(res, HTTPStatus.OK, {"Content-Type": "application/json"})
except (ValueError, DisabledFeatureError, KeyError) as e:
return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)
def annotations_var_get(request, data_adaptor, annotations):
def annotations_var_get(request, data_adaptor):
fields = request.args.getlist("annotation-name", None)
num_columns_requested = len(data_adaptor.get_var_keys()) if len(fields) == 0 else len(fields)
if data_adaptor.config.exceeds_limit("column_request_max", num_columns_requested):
if data_adaptor.server_config.exceeds_limit("column_request_max", num_columns_requested):
return abort(HTTPStatus.BAD_REQUEST)
preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
if preferred_mimetype != "application/octet-stream":
@@ -181,6 +185,7 @@ def annotations_var_get(request, data_adaptor, annotations):
try:
labels = None
annotations = data_adaptor.dataset_config.user_annotations
if annotations is not None:
labels = annotations.read_labels(data_adaptor)
return make_response(
@@ -226,7 +231,7 @@ def data_var_get(request, data_adaptor):
def colors_get(data_adaptor):
if not data_adaptor.config.presentation__custom_colors:
if not data_adaptor.dataset_config.presentation__custom_colors:
return make_response(jsonify({}), HTTPStatus.OK)
try:
return make_response(jsonify(data_adaptor.get_colors()), HTTPStatus.OK)
@@ -235,7 +240,7 @@ def colors_get(data_adaptor):
def diffexp_obs_post(request, data_adaptor):
if not data_adaptor.config.diffexp__enable:
if not data_adaptor.dataset_config.diffexp__enable:
return abort(HTTPStatus.NOT_IMPLEMENTED)
args = request.get_json()
@@ -273,7 +278,7 @@ def diffexp_obs_post(request, data_adaptor):
def layout_obs_get(request, data_adaptor):
fields = request.args.getlist("layout-name", None)
num_columns_requested = len(data_adaptor.get_embedding_names()) if len(fields) == 0 else len(fields)
if data_adaptor.config.exceeds_limit("column_request_max", num_columns_requested):
if data_adaptor.server_config.exceeds_limit("column_request_max", num_columns_requested):
return abort(HTTPStatus.BAD_REQUEST)
preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
@@ -296,7 +301,7 @@ def layout_obs_get(request, data_adaptor):
def layout_obs_put(request, data_adaptor):
if not data_adaptor.config.embedding__enable_reembedding:
if not data_adaptor.dataset_config.embedding__enable_reembedding:
return abort(HTTPStatus.NOT_IMPLEMENTED)
preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
server/data_anndata/anndata_adaptor.py
+13 -20
View File
@@ -28,10 +28,9 @@ def anndata_version_is_pre_070():
class AnndataAdaptor(DataAdaptor):
def __init__(self, data_locator, config=None):
super().__init__(config)
def __init__(self, data_locator, app_config=None, dataset_config=None):
super().__init__(data_locator, app_config, dataset_config)
self.data = None
self.data_locator = data_locator
self._load_data(data_locator)
self._validate_and_initialize()
@@ -55,14 +54,8 @@ class AnndataAdaptor(DataAdaptor):
return data_locator.size() if data_locator.islocal() else 0
@staticmethod
def open(data_locator, config):
return AnndataAdaptor(data_locator, config)
def get_location(self):
return self.data_locator.uri_or_path
def get_data_locator(self):
return self.data_locator
def open(data_locator, app_config, dataset_config=None):
return AnndataAdaptor(data_locator, app_config, dataset_config)
def get_name(self):
return "cellxgene anndata adaptor version"
@@ -100,7 +93,7 @@ class AnndataAdaptor(DataAdaptor):
for (ax_name, var_name) in ((Axis.OBS, "obs"), (Axis.VAR, "var")):
config_name = f"single_dataset__{var_name}_names"
parameter_name = f"{var_name}_names"
name = getattr(self.config, config_name)
name = getattr(self.server_config, config_name)
df_axis = getattr(self.data, str(ax_name))
if name is None:
# Default: create unique names from index
@@ -161,7 +154,7 @@ class AnndataAdaptor(DataAdaptor):
with data_locator.local_handle() as lh:
# as of AnnData 0.6.19, backed mode performs initial load fast, but at the
# cost of significantly slower access to X data.
backed = "r" if self.config.adaptor__anndata_adaptor__backed else None
backed = "r" if self.server_config.adaptor__anndata_adaptor__backed else None
self.data = anndata.read_h5ad(lh, backed=backed)
except ValueError:
@@ -181,7 +174,7 @@ class AnndataAdaptor(DataAdaptor):
)
def _validate_and_initialize(self):
if anndata_version_is_pre_070() and self.config.adaptor__anndata_adaptor__backed:
if anndata_version_is_pre_070() and self.server_config.adaptor__anndata_adaptor__backed:
warnings.warn(
"Use of --backed mode with anndata versions older than 0.7 will have serious "
"performance issues. Please update to at least anndata 0.7 or later."
@@ -199,7 +192,7 @@ class AnndataAdaptor(DataAdaptor):
# heuristic
n_values = self.data.shape[0] * self.data.shape[1]
if (n_values > 1e8 and self.config.adaptor__anndata_adaptor__backed is True) or (n_values > 5e8):
if (n_values > 1e8 and self.server_config.adaptor__anndata_adaptor__backed is True) or (n_values > 5e8):
self.parameters.update({"diffexp_may_be_slow": True})
def _is_valid_layout(self, arr):
@@ -246,7 +239,7 @@ class AnndataAdaptor(DataAdaptor):
)
if isinstance(datatype, CategoricalDtype):
category_num = len(curr_axis[ann].dtype.categories)
if category_num > 500 and category_num > self.config.presentation__max_categories:
if category_num > 500 and category_num > self.dataset_config.presentation__max_categories:
warnings.warn(
f"{str(ax).title()} annotation '{ann}' has {category_num} categories, this may be "
f"cumbersome or slow to display. We recommend setting the "
@@ -277,7 +270,7 @@ class AnndataAdaptor(DataAdaptor):
c) cap total list of layouts at global const MAX_LAYOUTS
"""
# load default layouts from the data.
layouts = self.config.embeddings__names
layouts = self.dataset_config.embeddings__names
if layouts is None or len(layouts) == 0:
layouts = [key[2:] for key in self.data.obsm_keys() if type(key) == str and key.startswith("X_")]
@@ -329,9 +322,9 @@ class AnndataAdaptor(DataAdaptor):
def compute_diffexp_ttest(self, maskA, maskB, top_n=None, lfc_cutoff=None):
if top_n is None:
top_n = self.config.diffexp__top_n
top_n = self.dataset_config.diffexp__top_n
if lfc_cutoff is None:
lfc_cutoff = self.config.diffexp__lfc_cutoff
lfc_cutoff = self.dataset_config.diffexp__lfc_cutoff
return diffexp_generic.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff)
def get_colors(self):
@@ -355,7 +348,7 @@ class AnndataAdaptor(DataAdaptor):
return getattr(self.data.obs, term_name)
def get_obs_index(self):
name = self.config.single_dataset__obs_names
name = self.server_config.single_dataset__obs_names
if name is None:
return self.original_obs_index
else:
server/data_common/data_adaptor.py
+19 -17
View File
@@ -14,12 +14,17 @@ from server.common.app_config import AppFeature, AppConfig
class DataAdaptor(metaclass=ABCMeta):
"""Base class for loading and accessing matrix data"""
def __init__(self, config):
if type(config) != AppConfig:
def __init__(self, data_locator, app_config, dataset_config=None):
if type(app_config) != AppConfig:
raise TypeError("config expected to be of type AppConfig")
# location to the dataset
self.data_locator = data_locator
# config is the application configuration
self.config = config
self.app_config = app_config
self.server_config = self.app_config.server_config
self.dataset_config = dataset_config or app_config.default_dataset_config
# parameters set by this data adaptor based on the data.
self.parameters = {}
@@ -31,7 +36,7 @@ class DataAdaptor(metaclass=ABCMeta):
@staticmethod
@abstractmethod
def open(data_locator, config):
def open(data_locator, app_config, dataset_config):
pass
@staticmethod
@@ -109,13 +114,11 @@ class DataAdaptor(metaclass=ABCMeta):
def cleanup(self):
pass
@abstractmethod
def get_location(self):
pass
@abstractmethod
def get_data_locator(self):
pass
return self.data_locator
def get_location(self):
return self.data_locator.uri_or_path
def get_about(self):
return None
@@ -149,8 +152,8 @@ class DataAdaptor(metaclass=ABCMeta):
features = [
AppFeature("/cluster/", method="POST", available=False),
AppFeature("/layout/obs", method="GET", available=self.get_embedding_names() is not None),
AppFeature("/layout/obs", method="PUT", available=self.config.embeddings__enable_reembedding),
AppFeature("/diffexp/", method="POST", available=self.config.diffexp__enable),
AppFeature("/layout/obs", method="PUT", available=self.dataset_config.embeddings__enable_reembedding),
AppFeature("/diffexp/", method="POST", available=self.dataset_config.diffexp__enable),
AppFeature("/annotations/obs", method="PUT", available=annotations is not None),
]
return features
@@ -260,7 +263,6 @@ class DataAdaptor(metaclass=ABCMeta):
* currently only supports access on VAR axis
* currently only supports filtering on VAR axis
"""
if axis != Axis.VAR:
raise ValueError("Only VAR dimension access is supported")
@@ -273,7 +275,7 @@ class DataAdaptor(metaclass=ABCMeta):
raise FilterError("filtering on obs unsupported")
num_columns = self.get_shape()[1] if var_selector is None else np.count_nonzero(var_selector)
if self.config.exceeds_limit("column_request_max", num_columns):
if self.server_config.exceeds_limit("column_request_max", num_columns):
raise ExceedsLimitError("Requested dataframe columns exceed column request limit")
X = self.get_X_array(obs_selector, var_selector)
@@ -301,14 +303,14 @@ class DataAdaptor(metaclass=ABCMeta):
except (KeyError, IndexError):
raise FilterError("Error parsing filter")
if top_n is None:
top_n = self.config.diffexp__top_n
top_n = self.dataset_config.diffexp__top_n
if self.config.exceeds_limit(
if self.server_config.exceeds_limit(
"diffexp_cellcount_max", np.count_nonzero(obs_mask_A) + np.count_nonzero(obs_mask_B)
):
raise ExceedsLimitError("Diffexp request exceeds max cell count limit")
result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.config.diffexp__lfc_cutoff)
result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.dataset_config.diffexp__lfc_cutoff)
try:
return jsonify_numpy(result)
server/data_common/matrix_loader.py
+17 -15
View File
@@ -29,7 +29,7 @@ class MatrixDataCacheItem(object):
self.data_lock.r_release()
return None
def acquire_and_open(self, app_config):
def acquire_and_open(self, app_config, dataset_config=None):
"""returns the data_adaptor if cached. opens the data_adaptor if not.
In either case, the a reader lock is taken. Must call release when
the data_adaptor is no longer needed"""
@@ -43,7 +43,7 @@ class MatrixDataCacheItem(object):
if not self.data_adaptor:
try:
self.loader.pre_load_validation()
self.data_adaptor = self.loader.open(app_config)
self.data_adaptor = self.loader.open(app_config, dataset_config)
except Exception as e:
# necessary to hold the reader lock after an exception, since
# the release will occur when the context exits.
@@ -115,7 +115,7 @@ class MatrixDataCacheManager(object):
# will automatically be refreshed.
def __init__(self, max_cached, timelimit_s=None):
# key is location, value is a MatrixDataCacheInfo
# key is tuple(url_dataroot, location), value is a MatrixDataCacheInfo
self.datasets = {}
# lock to protect the datasets
@@ -131,20 +131,21 @@ class MatrixDataCacheManager(object):
self.timelimit_s = timelimit_s
@contextmanager
def data_adaptor(self, location, app_config):
def data_adaptor(self, url_dataroot, location, app_config):
# create a loader for to this location if it does not already exist
delete_adaptor = None
data_adaptor = None
cache_item = None
key = (url_dataroot, location)
with self.lock:
self.evict_old_datasets()
info = self.datasets.get(location)
info = self.datasets.get(key)
if info is not None:
info.last_access = time.time()
info.num_access += 1
self.datasets[location] = info
self.datasets[key] = info
data_adaptor = info.cache_item.acquire_existing()
cache_item = info.cache_item
@@ -165,19 +166,20 @@ class MatrixDataCacheManager(object):
loader = MatrixDataLoader(location, app_config=app_config)
cache_item = MatrixDataCacheItem(loader)
item = MatrixDataCacheInfo(cache_item, time.time())
self.datasets[location] = item
self.datasets[key] = item
try:
assert cache_item
if delete_adaptor:
delete_adaptor.delete()
if data_adaptor is None:
data_adaptor = cache_item.acquire_and_open(app_config)
dataset_config = app_config.get_dataset_config(url_dataroot)
data_adaptor = cache_item.acquire_and_open(app_config, dataset_config)
yield data_adaptor
except DatasetAccessError:
cache_item.release()
with self.lock:
del self.datasets[location]
del self.datasets[key]
cache_item.delete()
cache_item = None
raise
@@ -215,7 +217,7 @@ class MatrixDataType(Enum):
class MatrixDataLoader(object):
def __init__(self, location, matrix_data_type=None, app_config=None):
""" location can be a string or DataLocator """
region_name = None if app_config is None else app_config.data_locator__s3__region_name
region_name = None if app_config is None else app_config.server_config.data_locator__s3__region_name
self.location = DataLocator(location, region_name=region_name)
if not self.location.exists():
raise DatasetAccessError("Dataset does not exist.", HTTPStatus.NOT_FOUND)
@@ -254,12 +256,12 @@ class MatrixDataLoader(object):
if not app_config:
return True
if not app_config.multi_dataset__dataroot:
if not app_config.is_multi_dataset():
return True
if len(app_config.multi_dataset__allowed_matrix_types) == 0:
if len(app_config.server_config.multi_dataset__allowed_matrix_types) == 0:
return True
for val in app_config.multi_dataset__allowed_matrix_types:
for val in app_config.server_config.multi_dataset__allowed_matrix_types:
try:
if self.matrix_data_type == MatrixDataType(val):
return True
@@ -279,6 +281,6 @@ class MatrixDataLoader(object):
def file_size(self):
return self.matrix_type.file_size(self.location)
def open(self, app_config):
def open(self, app_config, dataset_config=None):
# create and return a DataAdaptor object
return self.matrix_type.open(self.location, app_config)
return self.matrix_type.open(self.location, app_config, dataset_config)
server/data_cxg/cxg_adaptor.py
+6 -13
View File
@@ -24,11 +24,10 @@ class CxgAdaptor(DataAdaptor):
{"sm.tile_cache_size": 8 * 1024 * 1024 * 1024, "sm.num_reader_threads": 32, "vfs.s3.region": "us-east-1"}
)
def __init__(self, data_locator, config=None):
super().__init__(config)
def __init__(self, data_locator, app_config=None, dataset_config=None):
super().__init__(data_locator, app_config, dataset_config)
self.lock = threading.Lock()
self.data_locator = data_locator
self.url = data_locator.uri_or_path
if self.url[-1] != "/":
self.url += "/"
@@ -66,8 +65,8 @@ class CxgAdaptor(DataAdaptor):
return 0
@staticmethod
def open(data_locator, args):
return CxgAdaptor(data_locator, args)
def open(data_locator, app_config, dataset_config=None):
return CxgAdaptor(data_locator, app_config, dataset_config)
def get_about(self):
return self.about if self.about else super().get_about()
@@ -75,12 +74,6 @@ class CxgAdaptor(DataAdaptor):
def get_title(self):
return self.title if self.title else super().get_title()
def get_location(self):
return self.url
def get_data_locator(self):
return self.data_locator
def get_name(self):
return "cellxgene cxg adaptor version"
@@ -196,9 +189,9 @@ class CxgAdaptor(DataAdaptor):
def compute_diffexp_ttest(self, maskA, maskB, top_n=None, lfc_cutoff=None):
if top_n is None:
top_n = self.config.diffexp__top_n
top_n = self.dataset_config.diffexp__top_n
if lfc_cutoff is None:
lfc_cutoff = self.config.diffexp__lfc_cutoff
lfc_cutoff = self.dataset_config.diffexp__lfc_cutoff
return diffexp_cxg.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff)
def get_colors(self):
server/eb/Makefile
+3 -1
View File
@@ -11,11 +11,13 @@ clean:
# Presumes that a top-level `make build-client` has been done to
# create the client static assets.
cwd := $(shell pwd)
.PHONY: build
build: clean
mkdir artifact.dir; \
(cd ../.. ; \
git ls-files server/ | cpio -pdm server/eb/artifact.dir ; ); \
git ls-files server/ | cpio -pdm $(cwd)/artifact.dir ; ); \
$(call copy_client_assets,../../client/build,artifact.dir/server) ; \
set -e ; \
cp app.py artifact.dir/application.py; \
server/eb/app.py
+25 -25
View File
@@ -58,6 +58,7 @@ class WSGIServer(Server):
@staticmethod
def _before_adding_routes(app, app_config):
script_hashes, style_hashes = WSGIServer.get_csp_hashes(app, app_config)
server_config = app_config.server_config
csp = {
"default-src": ["'self'"],
"connect-src": ["'self'"],
@@ -72,14 +73,14 @@ class WSGIServer(Server):
if not app.debug:
csp["upgrade-insecure-requests"] = ""
if app_config.server__csp_directives:
for k, v in app_config.server__csp_directives.items():
if server_config.app__csp_directives:
for k, v in server_config.app__csp_directives.items():
if not isinstance(v, list):
v = [v]
csp[k] = csp.get(k, []) + v
Talisman(
app, force_https=app_config.server__force_https, frame_options="DENY", content_security_policy=csp,
app, force_https=server_config.app__force_https, frame_options="DENY", content_security_policy=csp,
)
@staticmethod
@@ -102,16 +103,18 @@ class WSGIServer(Server):
@staticmethod
def compute_inline_scp_hashes(app, app_config):
inline_scripts = app_config.server__inline_scripts
dataset_configs = [app_config.default_dataset_config] + list(app_config.dataroot_config.values())
hashes = []
for script in inline_scripts:
with app.open_resource(f"../common/web/templates/{script}") as f:
content = f.read()
# we use jinja2 template include, which trims final newline if present.
if content[-1] == 0x0A:
content = content[0:-1]
hash = base64.b64encode(hashlib.sha256(content).digest())
hashes.append(f"'sha256-{hash.decode('utf-8')}'")
for dataset_config in dataset_configs:
inline_scripts = dataset_config.app__inline_scripts
for script in inline_scripts:
with app.open_resource(f"../common/web/templates/{script}") as f:
content = f.read()
# we use jinja2 template include, which trims final newline if present.
if content[-1] == 0x0A:
content = content[0:-1]
hash = base64.b64encode(hashlib.sha256(content).digest())
hashes.append(f"'sha256-{hash.decode('utf-8')}'")
return hashes
@staticmethod
@@ -156,7 +159,7 @@ try:
dataroot = os.getenv("CXG_DATAROOT")
if dataroot:
logging.info("Configuration from CXG_DATAROOT")
app_config.update(multi_dataset__dataroot=dataroot)
app_config.update_server_config(multi_dataset__dataroot=dataroot)
secret_name = os.getenv("CXG_AWS_SECRET_NAME")
if secret_name:
@@ -174,26 +177,23 @@ try:
sys.exit(1)
flask_secret_key = get_flask_secret_key(secret_region_name, secret_name)
app_config.update(server__flask_secret_key=flask_secret_key)
app_config.update_server_config(app__flask_secret_key=flask_secret_key)
# features are unsupported in the current hosted server
app_config.update(
user_annotations__enable=False,
embeddings__enable_reembedding=False,
multi_dataset__allowed_matrix_types=["cxg"],
app_config.update_default_dataset_config(
user_annotations__enable=False, embeddings__enable_reembedding=False,
)
app_config.update_server_config(multi_dataset__allowed_matrix_types=["cxg"],)
app_config.complete_config(logging.info)
if not app_config.server__flask_secret_key:
if not app_config.server_config.app__flask_secret_key:
logging.critical(
"flask_secret_key is not provided. Either set in config file, CXG_SECRET_KEY environment variable, "
"or in AWS Secret Manager"
)
sys.exit(1)
user_annotations = app_config.user_annotations
server = WSGIServer(app_config)
debug = False
@@ -203,10 +203,10 @@ except Exception:
logging.critical("Caught exception during initialization", exc_info=True)
sys.exit(1)
if app_config.multi_dataset__dataroot:
logging.info(f"starting server with multi_dataset__dataroot={app_config.multi_dataset__dataroot}")
elif app_config.single_dataset__datapath:
logging.info(f"starting server with single_dataset__datapath={app_config.single_dataset__datapath}")
if app_config.is_multi_dataset():
logging.info(f"starting server with multi_dataset__dataroot={app_config.server_config.multi_dataset__dataroot}")
else:
logging.info(f"starting server with single_dataset__datapath={app_config.server_config.single_dataset__datapath}")
if __name__ == "__main__":
try:
server/test/__init__.py
+20 -23
View File
@@ -27,21 +27,18 @@ def data_with_tmp_annotations(ext: MatrixDataType, annotations_fixture=False):
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.update_server_config(
single_dataset__obs_names=None, single_dataset__var_names=None, single_dataset__datapath=data_locator.path
)
config.update_default_dataset_config(
embeddings__names=["umap"], presentation__max_categories=100, diffexp__lfc_cutoff=0.01,
)
config.complete_config()
data = MatrixDataLoader(data_locator.abspath()).open(config)
annotations = AnnotationsLocalFile(None, annotations_file)
@@ -66,21 +63,21 @@ def skip_if(condition, reason: str):
return decorator
def app_config(data_locator, backed=False, extra={}):
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,
}
def app_config(data_locator, backed=False, extra_server_config={}, extra_dataset_config={}):
config = AppConfig()
config.update(**args)
config.update(**extra)
config.update_server_config(
single_dataset__obs_names=None,
single_dataset__var_names=None,
adaptor__anndata_adaptor__backed=backed,
single_dataset__datapath=data_locator,
limits__diffexp_cellcount_max=None,
limits__column_request_max=None,
)
config.update_default_dataset_config(
embeddings__names=["umap", "tsne", "pca"], presentation__max_categories=100, diffexp__lfc_cutoff=0.01
)
config.update_server_config(**extra_server_config)
config.update_default_dataset_config(**extra_dataset_config)
config.complete_config()
return config
server/test/run_diffexp.py
+2 -2
View File
@@ -32,8 +32,8 @@ def main():
args = parser.parse_args()
app_config = AppConfig()
app_config.single_dataset__datapath = args.dataset
app_config.server__verbose = True
app_config.update_server_config(single_dataset__datapath=args.dataset)
app_config.update_server_config(app__verbose=True)
app_config.complete_config()
loader = MatrixDataLoader(args.dataset)
server/test/test_anndata_adaptor.py
+2 -2
View File
@@ -107,9 +107,9 @@ class AdaptorTest(unittest.TestCase):
self.assertEqual(len(feature), 1)
check_feature("POST", "/cluster/", False)
check_feature("POST", "/diffexp/", self.data.config.diffexp__enable)
check_feature("POST", "/diffexp/", self.data.dataset_config.diffexp__enable)
check_feature("GET", "/layout/obs", True)
check_feature("PUT", "/layout/obs", self.data.config.embeddings__enable_reembedding)
check_feature("PUT", "/layout/obs", self.data.dataset_config.embeddings__enable_reembedding)
check_feature("PUT", "/annotations/obs", False)
def test_layout(self):
server/test/test_anndata_adaptor_data_load.py
+17 -16
View File
@@ -15,7 +15,7 @@ class DataLoadAdaptorTest(unittest.TestCase):
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.update_server_config(single_dataset__datapath=self.data_file.path)
config.complete_config()
self.data = AnndataAdaptor(self.data_file, config)
@@ -40,14 +40,18 @@ class DataLocatorAdaptorTest(unittest.TestCase):
Test various types of data locators we expect to consume
"""
def setUp(self):
self.args = {
"embeddings__names": ["umap"],
"presentation__max_categories": 100,
"single_dataset__obs_names": None,
"single_dataset__var_names": None,
"diffexp__lfc_cutoff": 0.01,
}
def get_basic_config(self):
config = AppConfig()
config.update_server_config(
single_dataset__obs_names=None,
single_dataset__var_names=None,
)
config.update_default_dataset_config(
embeddings__names=["umap"],
presentation__max_categories=100,
diffexp__lfc_cutoff=0.01,
)
return config
def stdAsserts(self, data):
""" run these each time we load the data """
@@ -57,9 +61,8 @@ class DataLocatorAdaptorTest(unittest.TestCase):
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 = self.get_basic_config()
config.update_server_config(single_dataset__datapath=locator.path)
config.complete_config()
data = AnndataAdaptor(locator, config)
self.stdAsserts(data)
@@ -67,15 +70,13 @@ class DataLocatorAdaptorTest(unittest.TestCase):
def test_url_https(self):
url = "https://raw.githubusercontent.com/chanzuckerberg/cellxgene/main/example-dataset/pbmc3k.h5ad"
locator = DataLocator(url)
config = AppConfig()
config.update(**self.args)
config = self.get_basic_config()
data = AnndataAdaptor(locator, config)
self.stdAsserts(data)
def test_url_http(self):
url = "http://raw.githubusercontent.com/chanzuckerberg/cellxgene/main/example-dataset/pbmc3k.h5ad"
locator = DataLocator(url)
config = AppConfig()
config.update(**self.args)
config = self.get_basic_config()
data = AnndataAdaptor(locator, config)
self.stdAsserts(data)
server/test/test_app_config.py
+50 -20
View File
@@ -11,60 +11,90 @@ import requests
class AppConfigTest(unittest.TestCase):
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)])
c.update_server_config(app__verbose=True, multi_dataset__dataroot="datadir")
v = c.server_config.changes_from_default()
self.assertCountEqual(v, [("app__verbose", True, False), ("multi_dataset__dataroot", "datadir", None)])
c = AppConfig()
c.update(server__scripts=(), server__inline_scripts=())
v = c.changes_from_default()
c.update_default_dataset_config(app__scripts=(), app__inline_scripts=())
v = c.server_config.changes_from_default()
self.assertCountEqual(v, [])
c = AppConfig()
c.update(server__scripts=[], server__inline_scripts=[])
v = c.changes_from_default()
c.update_default_dataset_config(app__scripts=[], app__inline_scripts=[])
v = c.default_dataset_config.changes_from_default()
self.assertCountEqual(v, [])
c = AppConfig()
c.update(server__scripts=("a", "b"), server__inline_scripts=["c", "d"])
v = c.changes_from_default()
self.assertCountEqual(v, [("server__scripts", ["a", "b"], []), ("server__inline_scripts", ["c", "d"], [])])
c.update_default_dataset_config(app__scripts=("a", "b"), app__inline_scripts=["c", "d"])
v = c.default_dataset_config.changes_from_default()
self.assertCountEqual(v, [("app__scripts", ["a", "b"], []), ("app__inline_scripts", ["c", "d"], [])])
def test_multi_dataset(self):
c = AppConfig()
# test for illegal url_dataroots
for illegal in ("a/b", "../b", "!$*", "\\n", "", "(bad)"):
c.update(multi_dataset__dataroot={illegal: f"{PROJECT_ROOT}/example-dataset"})
for illegal in ("../b", "!$*", "\\n", "", "(bad)"):
c.update_server_config(
multi_dataset__dataroot={"tag": {"base_url": illegal, "dataroot": "{PROJECT_ROOT}/example-dataset"}}
)
with self.assertRaises(ConfigurationError):
c.complete_config()
# test for legal url_dataroots
for legal in (
"d",
"this.is-okay_",
):
c.update(multi_dataset__dataroot={legal: f"{PROJECT_ROOT}/example-dataset"})
for legal in ("d", "this.is-okay_", "a/b"):
c.update_server_config(
multi_dataset__dataroot={"tag": {"base_url": legal, "dataroot": "{PROJECT_ROOT}/example-dataset"}}
)
c.complete_config()
# test that multi dataroots work end to end
c.update(
c.update_server_config(
multi_dataset__dataroot=dict(
set1=f"{PROJECT_ROOT}/example-dataset", set2=f"{PROJECT_ROOT}/server/test/test_datasets"
s1=dict(dataroot=f"{PROJECT_ROOT}/example-dataset", base_url="set1/1/2"),
s2=dict(dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", base_url="set2"),
s3=dict(dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", base_url="set3"),
)
)
# Change this default to test if the dataroot overrides below work.
c.update_default_dataset_config(app__about_legal_tos="tos_default.html")
# specialize the configs for set1
c.add_dataroot_config(
"s1", user_annotations__enable=False, diffexp__enable=True, app__about_legal_tos="tos_set1.html"
)
# specialize the configs for set2
c.add_dataroot_config(
"s2", user_annotations__enable=True, diffexp__enable=False, app__about_legal_tos="tos_set2.html"
)
# no specializations for set3 (they get the default dataset config)
c.complete_config()
with test_server(app_config=c) as server:
session = requests.Session()
r = session.get(f"{server}/set1/pbmc3k.h5ad/api/v0.2/config")
r = session.get(f"{server}/set1/1/2/pbmc3k.h5ad/api/v0.2/config")
data_config = r.json()
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
assert data_config["config"]["parameters"]["annotations"] is False
assert data_config["config"]["parameters"]["disable-diffexp"] is False
assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set1.html"
r = session.get(f"{server}/set2/pbmc3k.cxg/api/v0.2/config")
data_config = r.json()
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
assert data_config["config"]["parameters"]["annotations"] is True
assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set2.html"
r = session.get(f"{server}/set3/pbmc3k.cxg/api/v0.2/config")
data_config = r.json()
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
assert data_config["config"]["parameters"]["annotations"] is True
assert data_config["config"]["parameters"]["disable-diffexp"] is False
assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_default.html"
r = session.get(f"{server}/health")
assert r.json()["status"] == "pass"
server/test/test_diffexp.py
+4 -3
View File
@@ -15,8 +15,9 @@ class DiffExpTest(unittest.TestCase):
"""Tests the diffexp returns the expected results for one test case, using different
adaptor types and different algorithms."""
def load_dataset(self, path, extra={}):
config = app_config(path, extra=extra)
def load_dataset(self, path, extra_server_config={}, extra_dataset_config={}):
config = app_config(path, extra_server_config=extra_server_config,
extra_dataset_config=extra_dataset_config)
loader = MatrixDataLoader(path)
adaptor = loader.open(config)
return adaptor
@@ -100,7 +101,7 @@ class DiffExpTest(unittest.TestCase):
# create a sparse matrix
h5adfile = os.path.join(dirname, "sparse.h5ad")
create_test_h5ad(h5adfile, 2000, 2000, 10, apply_col_shift)
adaptor_anndata = self.load_dataset(h5adfile, extra=dict(embeddings__names=[]))
adaptor_anndata = self.load_dataset(h5adfile, extra_dataset_config=dict(embeddings__names=[]))
adata = adaptor_anndata.data
sparsename = os.path.join(dirname, "sparse.cxg")
server/test/test_eb.py
+54
View File
@@ -0,0 +1,54 @@
import unittest
import tempfile
import requests
import subprocess
from server.test import PROJECT_ROOT
from server.common.app_config import AppConfig
from contextlib import contextmanager
import time
@contextmanager
def run_eb_app(tempdirname):
ps = subprocess.Popen(["python", "artifact.dir/application.py"], cwd=tempdirname)
server = "http://localhost:5000"
for _ in range(10):
try:
requests.get(f"{server}/health")
break
except requests.exceptions.ConnectionError:
time.sleep(1)
try:
yield server
finally:
try:
ps.terminate()
except ProcessLookupError:
pass
class Elastic_Beanstalk_Test(unittest.TestCase):
def test_run(self):
tempdir = tempfile.TemporaryDirectory(dir=f"{PROJECT_ROOT}/server")
tempdirname = tempdir.name
c = AppConfig()
# test that eb works
c.update_server_config(
multi_dataset__dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", app__flask_secret_key="open sesame"
)
c.complete_config()
c.write_config(f"{tempdirname}/config.yaml")
subprocess.check_call(f"git ls-files . | cpio -pdm {tempdirname}", cwd=f"{PROJECT_ROOT}/server/eb", shell=True)
subprocess.check_call(["make", "build"], cwd=tempdirname)
with run_eb_app(tempdirname) as server:
session = requests.Session()
r = session.get(f"{server}/d/pbmc3k.cxg/api/v0.2/config")
data_config = r.json()
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
server/test/test_matrixcache.py
+3 -3
View File
@@ -21,13 +21,13 @@ class MatrixCacheTest(unittest.TestCase):
shutil.copytree(source, target)
def use_dataset(self, matrix_cache, dirname, app_config, dataset_index):
with matrix_cache.data_adaptor(os.path.join(dirname, str(dataset_index) + ".cxg"), app_config) as adaptor:
with matrix_cache.data_adaptor(None, os.path.join(dirname, str(dataset_index) + ".cxg"), app_config) as adaptor:
pass
return adaptor
def use_dataset_with_error(self, matrix_cache, dirname, app_config, dataset_index):
try:
with matrix_cache.data_adaptor(os.path.join(dirname, str(dataset_index) + ".cxg"), app_config):
with matrix_cache.data_adaptor(None, os.path.join(dirname, str(dataset_index) + ".cxg"), app_config):
raise DatasetAccessError("something bad happened")
except DatasetAccessError:
# the MatrixDataCacheManager rethrows the exception, so catch and ignore
@@ -38,7 +38,7 @@ class MatrixCacheTest(unittest.TestCase):
result = {}
for k, v in datasets.items():
# filter out the dirname and the .cxg from the name
newk = int(k[len(dirname) + 1 : -4])
newk = int(k[1][len(dirname) + 1 : -4])
result[newk] = v
return result
server/test/test_writable_annotation.py
+5 -4
View File
@@ -15,12 +15,13 @@ from server.data_common.matrix_loader import MatrixDataType
class WritableAnnotationTest(unittest.TestCase):
def setUp(self):
self.data, self.tmp_dir, self.annotations = data_with_tmp_annotations(MatrixDataType.H5AD)
self.data.dataset_config.user_annotations = self.annotations
def tearDown(self):
shutil.rmtree(self.tmp_dir)
def annotation_put_fbs(self, fbs):
annotations_put_fbs_helper(self.data, self.annotations, fbs)
annotations_put_fbs_helper(self.data, fbs)
res = json.dumps({"status": "OK"})
return res
@@ -112,7 +113,7 @@ class WritableAnnotationTest(unittest.TestCase):
# get
labels = self.annotations.read_labels(None)
fbsAll = self.data.annotation_to_fbs_matrix("obs", None, labels)
schema = schema_get_helper(self.data, self.annotations)
schema = schema_get_helper(self.data)
annotations = decode_fbs.decode_matrix_FBS(fbsAll)
obs_index_col_name = schema["annotations"]["obs"]["index"]
self.assertEqual(annotations["n_rows"], n_rows)
@@ -149,7 +150,7 @@ class WritableAnnotationTest(unittest.TestCase):
self.assertEqual(len(feature), 1)
check_feature("POST", "/cluster/", False)
check_feature("POST", "/diffexp/", self.data.config.diffexp__enable)
check_feature("POST", "/diffexp/", self.data.dataset_config.diffexp__enable)
check_feature("GET", "/layout/obs", True)
check_feature("PUT", "/layout/obs", self.data.config.embeddings__enable_reembedding)
check_feature("PUT", "/layout/obs", self.data.dataset_config.embeddings__enable_reembedding)
check_feature("PUT", "/annotations/obs", True)