Went through and ensured that undefined/null values were caught and handled correctly in render functions. Also documented some of the more complicated functions.
---
Closes#1825
* app config bug fix:
When reading a config file that included per_dataset_config,
the dataroot specializations were applied, but not the default config.
This PR fixes that and also includes a test for this case.
* Fixes from frontend/backend url separation
This fixes the CORS and CSP headers.
Also, in thie commit, I removed the cors_supports_credentials config parameter,
which was recently introduced.
Instead, the logic determines the need to use CORS headers if the
web_page_url is set.
#1778
* Pass in the previous crossfilter when creating a new annomatrix for a switched embedding in order to retain the previous selection of cells.
* Address Bruce's PR comment
* 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.
When generating a config file, you can do this:
> cellxgene launch --dump-default-config > myconfig.yaml
And then modify the myconfig.yaml.
However, if an upgrade is available then you would get extra lines in the yaml
file, which are not yaml code:
There's a new version of cellxgene available (0.16.4)!
To upgrade, run the following: pip install --upgrade cellxgene
To solve this problem, the upgrade messages are sent to stderr instead,
so they will appear on the screen and not in the config file.
Alternatives:
One workaround is "cellxgene --no-upgrade-check launch --dump-default-config > myconfig.yaml"
But that's a bit verbose and not user friendly.
The way we've setup the upgrade check to be separate and before the launch sub command,
makes other code changes more involved.
#1826
This PR adds multiple data to the dataset overview drawer provided by the config endpoint and formats them accordingly. The appearance of this new data is contingent on `dataPortalProps.corpora_schema_version === "1.0.0"`
For QA launch cellxgene with a remixed dataset and click on the button in the upper left-hand corner or the updated button in the info menu.
~~Review opening is blocked by merge of #1805~~
---
Closes#1319
* Fix frontend mishandling of null userinfo
If the authentication is disabled, the userinfo endpoint returns null.
This case needs to be handled.
#1780
* Small fix for handling refesh tokens in auth
* 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>
* Handle the refresh token in oauth authentication
If the token has expired, then it can be refreshed to get a new token.
This is automatically handled by the server without the client being aware.
Also in the PR:
- refactor the auth_oauth.py file to more simply handle the save/restore of the token,
and the refresh token
- added an end2end test for oauth, which also tests refresh.
* adding python-jose and Authlib to requirements-dev.txt
They are needed in the auth_oauth test
Colin Megill
