* Enhance the AppConfig with external config sources.
The external config sources are currently environment variables
and AWS secrets manager.
The config file can be augmented with a section describing how
environmen variables and secrets can update config parameters.
benefits:
- it will enable the config to draw from more than one secret. This is useful
for shared secrets between cellxgene and data portal, as well as auth0 secrets.
- it will make it very straightforward to check the config before a deployment.
Part of #1859
* split out config
* add tests for base and app config, refactor client config out of app config
* refactor default config retrieval
* create config test class and helper functions
* move default_config into server to fix import issue
* separate backend base url from frontend
This is needed for auth, and to support a different location for the backend api server,
than the frontend.
part of chanzuckerberg/cellxgene#1778
new server config parameters: app__api_base_url, app__web_base_url
Also changed api_base_url in the oauth config section to "oauth_api_base_url" to
be less confusing with the app's api_base_url
Other minor changes:
changed how the jwt decode options are handled.
Previously they needed to be set in a test case, and there was some extra logic to handle that.
Now they are handled through comfig parameters, which makes it more general.
Also, add a feature to set the CORS support credentials, which seems
to be necessary for the backend/frontend separation, at least when run
locally. This part is sort of experimental, and may be removed or changed later.
* save tiledb array to s3, dont cache user annotations
* Add option to disable annotation filename prompt (#1787)
Co-authored-by: Madison Dunitz <dunitzm@gmail.com>
* set tiledb default context in cxg_adaptor
Co-authored-by: maniarathi <arathi.mani@chanzuckerberg.com>
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
* Add basic authentication in the server
A pattern for creating authentication methods is introduced, with three
authentication types defined:
none - no authentication
session - like the current session based auth used for user annotations
test - used to test the login/logout process end to end
The config endpoint now returns informations about the authentication, like if
the user is authenticated and their username. The redirect uri's for login and
logout are also returned if the authentication type requires login
This is the first a several PRs for authentication.
*. Update server tests to avoid hardcoded ports
test_api and test_nan_rest now use a common function for starting a test server,
than will initially choose a random port.
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.
Many of our matrices are log normalized, which tends to eliminate
the number of non zero values (if there were any). This prevents
the matrix from being stored as a sparse matrix. The solution here
is to use a simple transformation to make it sparse again. The most
common value from each column is subtracted from that column. These
values that were subtracted are saved in an array called X_col_shift.
The cellxgene code needs to understand how to undo the transformation when
operating over the X matrix.
- added script to create a synthetic dataset for testing
- added a script to convert an existing CXG dataset to a sparse CXG dataset
* Add server plugin system
Plugins are optional modules loaded at runtime. Specification:
* Plugins are loaded from the server.plugins module (directory
server/plugins)
* The import_plugins method is run as part of the initialization of the
server module in __init__.py
* Add plugins to the EB build process
* Remove bit of dead code
* Respond to feedback from @bmccandless
* Add user-defined category-label colors
Fixes https://github.com/chanzuckerberg/cellxgene/issues/1152
As described in https://github.com/chanzuckerberg/cellxgene/issues/1307
* Respond to feedback from @bkmartinjr in nodejs
* Respond to feedback from @bkmartinjr in python
* Add tests to the server module
* Autoformat python, run linter
* Make colors_get error handling specific
* Respond to feedback from @bkmartinjr
* Respond to feedback from @bkmartinjr
* Fix whitespace
* Fix python lint errrors
* Update documentation
* Add --disable-user-colors option to launch and cxgtool.py
* Fix python formatting
* Rename '--disable-user-colors' to '--disable-custom-colors'
* 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.
* Add user-generated annotations tests to the server
Partially completes https://github.com/chanzuckerberg/cellxgene/issues/969
* Auto-format python code
* @skip_if: passing lambdas > than property strings
* Respond to feedback from @bkmartinjr
