fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-10-05 05:38:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

Introduce a config file to cellxgene (#1264)

Browse Source 
* Introduce a config file to cellxgene

The config file format is in yaml.  The default config is located
in server/common/default_config.py.  A user may create a yaml file
that contains a subset of these fields.  It can be used during cellxgene
launch, or for hosted cellxgene.

The code has also been refactored.  Much of the logic to check arguments
has moved from launch to app config.

It is now possible to set the tiledb context parameters using the config
file.  Other feature will soon be handled in a similar way.
This commit is contained in:
bmccandless
2020-03-22 09:34:11 -07:00
committed by GitHub
parent 1351c8f724
commit 8180be83b8
19 changed files with 691 additions and 348 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/app/app.py
+14 -14
View File
@@ -26,14 +26,14 @@ webbp = Blueprint("webapp", "server.common.web", template_folder="templates")
def dataset_index(dataset=None):
config = current_app.app_config
if dataset is None:
if config.datapath:
location = config.datapath
if config.single_dataset__datapath:
location = config.single_dataset__datapath
else:
return dataroot_index()
else:
location = path_join(config.dataroot, dataset)
location = path_join(config.multi_dataset__dataroot, dataset)
scripts = config.scripts
scripts = config.server__scripts
try:
cache_manager = current_app.matrix_data_cache_manager
@@ -59,13 +59,13 @@ def get_data_adaptor(dataset=None):
config = current_app.app_config
if dataset is None:
datapath = config.datapath
datapath = config.single_dataset__datapath
else:
datapath = path_join(config.dataroot, dataset)
datapath = path_join(config.multi_dataset__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(config.dataroot):
if not datapath.startswith(config.multi_dataset__dataroot):
raise DatasetAccessError("Invalid dataset {dataset}")
if datapath is None:
@@ -100,10 +100,10 @@ def dataroot_test_index():
try:
config = current_app.app_config
locator = DataLocator(config.dataroot)
locator = DataLocator(config.multi_dataset__dataroot)
datasets = []
for fname in locator.ls():
location = path_join(config.dataroot, fname)
location = path_join(config.multi_dataset__dataroot, fname)
try:
MatrixDataLoader(location, app_config=config)
datasets.append(fname)
@@ -118,7 +118,7 @@ def dataroot_test_index():
data += f"<li><a href={dataset}>{dataset}</a></li>"
data += "</ul>"
except Exception as e:
data += f"<br/>Unable to locate datasets from {config.dataroot}: {str(e)}"
data += f'<br/>Unable to locate datasets from {config.multi_dataset__dataroot}: {str(e)}'
data += "</body></html>"
return make_response(data)
@@ -127,12 +127,12 @@ 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.multi_dataset__index:
abort(404)
elif config.multi_dataset_index is True:
elif config.multi_dataset__index is True:
return dataroot_test_index()
else:
return redirect(config.dataroot_index)
return redirect(config.multi_dataset__index)
class SchemaAPI(Resource):
@@ -222,7 +222,7 @@ class Server:
self.app.register_blueprint(webbp)
api_version = "/api/v0.2"
if app_config.datapath:
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)