* Convert float annotations if possible.
The client converts all arrays to floats.
If a category contains integer labels, and that category is copied, it will contains floats (e.g 1.0 instead of 1).
When that category is put back to the server, it fails in the tiledb code, which does not accept floats.
The solution is to convert a float category to integer, if possible.
#1984
* updates
Previously if the user remove all annotations, the code would still generate a tiledb uri
in the write_labels call, and add that to the database. A tiledb array would not be written in this case.
When the read_labels was then called, it would find the entry in the database, attempt to open
the tiledb array, then fail.
The patch here will set the tiledb_uri to the empty string if all categories are removed.
When read_labels is called, it will see the empty uri and return None.
Furthermore, if the database does have a tiledb_uri that does not exist, or cannot be read,
then the code will now log a warning, and return None (instead of throwing an exception,
which results in a server error).
#1932
* add long title
* add organism to Dataset Metadata and create headers
* begin HTMLTable for metadata
* switch out truncating for scrolling
* add optional chaining to redux state mapping
Co-authored-by: maniarathi <mani.arathi@gmail.com>
Add the `cellxgene schema apply` and `cellxgene schema validate` subcommands.
The first takes an h5ad file and a yaml with config information and produces a new h5ad that follows the cellxgene data integration schema.
The second takes an h5ad and checks if it follows the schema version written into its metadata.
Both are currently marked as "experimental" as the primary intended users are still at CZI.
* Updates due dependency version changes.
h5py recently changes and now values once returned as str are now returned as bytes.
This would have caused a much larger change, so instead the version is restricted to <3.0.0.
This caused the bulk of the testing failues.
A few other changes were needed to make a few other tests pass.
#1959
* Revert "Remove Continuous vars with 1 value from histogram, add to info drawer (#1927)"
This reverts commit 242546371b.
* remove conditional rendering cases
* ignore pointer events
Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
* Fix bug in oauth.
The error checking was too specific, and missed a case.
Make the error checking catch all exceptions.
#1947
* Add logging when the cookie cannot be processed
* add tests
* run black
* run black and add disclaimer that tweaked errors on server
* lint
* change to get so it will return None
* tweak existing token instead of new one
* Trigger
* token is dict
* jsonify dict before encoding
* json dump instead of jsonify
* encode into bytes object
* use correct id token
* decode byte to string
* Update readme for eb server.
Update the README with new way of handling secrets.
Update portions that were out of date.
Add a section for Authentication and a placeholder for User Annotations.
Also remove an obsolete function that processes the AWS secrets.
#1522
Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
* remove single val continous metadata from histogram, add to info drawer
* refactor to save singleContinuous values in state
* fix edge case, single continuous values reappeard in rsb when clipped
This PR adds a few helpful additions regarding authentication.
Changes:
* e2e tests are now run on test_oauth via a passed config.yaml
* node dev server correctly handles `/login` and `/logout` endpoints to make developing for auth easier
* Introduced auth e2e tests to check that buttons display and work
* 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
* remove auth buttons and dataset info from info menu
* add auth buttons to menubar
* remove auth from top left
* new auth buttons
* move infomenu to lsb dir
* styling fixes
* feedback
* more feedback
Co-authored-by: Timmy Huang <thuang@chanzuckerberg.com>
* make testing plan
* create annotaions sets for different num categories/dataset size
* annotation creation testing
* create scale and perf tests for annotations
* create make commands for tests
* get cell count if not set in test_datasets dict
This PR does the following:
1. Add `login` and `logout` helper functions in `client/__tests__/e2e/cellxgeneActions.js`
2. Add conditional AuthN integration test in `client/__tests__/e2e/e2e.test.js`. The test will only run if env variable `TEST_AUTH_INTEGRATION` is `"true"`, which is only set in `single-cell-infra`'s Github Action flow. Corresponding PR [here](https://github.com/chanzuckerberg/single-cell-infra/pull/198)
* Remove door icon from log in button
* Move log in and info buttons from the top bar to in line with the cellxgene icon and dataset name
* Hover over on login button should say "Log in to cellxgene"
* Show email
closes#1830
bmccandless
