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 = server_config.single_dataset__datapath
else:
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)
# path_join returns a normalized path. Therefore it is
# sufficient to check that the datapath starts with the
# dataroot to determine that the datapath is under the dataroot.
if not datapath.startswith(dataroot):
raise DatasetAccessError(
f"Invalid dataset {url_dataroot}/{dataset}")
if datapath is 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(dataset_key, datapath, config)
def isvalid(url):
"""
Return True if this looks like a valid CXG, False if not. Just a quick/cheap
test, not to be fully trusted.
"""
if not tiledb.object_type(url, ctx=CxgAdaptor.tiledb_ctx) == "group":
return False
if not tiledb.object_type(path_join(url, "obs"), ctx=CxgAdaptor.tiledb_ctx) == "array":
return False
if not tiledb.object_type(path_join(url, "var"), ctx=CxgAdaptor.tiledb_ctx) == "array":
return False
if not tiledb.object_type(path_join(url, "X"), ctx=CxgAdaptor.tiledb_ctx) == "array":
return False
if not tiledb.object_type(path_join(url, "emb"), ctx=CxgAdaptor.tiledb_ctx) == "group":
return False
return True
def dataroot_test_index():
# the following index page is meant for testing/debugging purposes
data = '<!doctype html><html lang="en">'
data += "<head><title>Hosted Cellxgene</title></head>"
data += "<body><H1>Welcome to cellxgene</H1>"
config = current_app.app_config
server_config = config.server_config
auth = server_config.auth
if auth.is_valid_authentication_type():
if server_config.auth.is_user_authenticated():
data += f"<p>Logged in as {auth.get_user_id()} / {auth.get_user_name()} / {auth.get_user_email()}</p>"
if auth.requires_client_login():
if server_config.auth.is_user_authenticated():
data += f"<p><a href='{auth.get_logout_url(None)}'>Logout</a></p>"
else:
data += f"<p><a href='{auth.get_login_url(None)}'>Login</a></p>"
datasets = []
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:
MatrixDataLoader(location, app_config=config)
datasets.append((url_dataroot, fname))
except DatasetAccessError:
# skip over invalid datasets
pass
data += "<br/>Select one of these datasets...<br/>"
data += "<ul>"
datasets.sort()
for url_dataroot, dataset in datasets:
data += f"<li><a href={url_dataroot}/{dataset}>{dataset}</a></li>"
data += "</ul>"
data += "</body></html>"
return make_response(data)
def dataset_index(url_dataroot=None, dataset=None):
app_config = current_app.app_config
server_config = app_config.server_config
if dataset is None:
if app_config.is_multi_dataset():
return dataroot_index()
else:
location = server_config.single_dataset__datapath
else:
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)
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(url_dataroot, location,
app_config) as data_adaptor:
data_adaptor.set_uri_path(f"{url_dataroot}/{dataset}")
dataset_title = app_config.get_title(data_adaptor)
return render_template("index.html",
datasetTitle=dataset_title,
SCRIPTS=scripts,
INLINE_SCRIPTS=inline_scripts)
except DatasetAccessError as e:
return common_rest.abort_and_log(
e.status_code,
f"Invalid dataset {dataset}: {e.message}",
loglevel=logging.INFO,
include_exc_info=True)
def get_path(self, *urls):
return path_join(self.url, *urls)
def has_array(self, name):
a_type = tiledb.object_type(path_join(self.url, name), ctx=self.tiledb_ctx)
return a_type == "array"
