* 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.
* add sentry webpack plugin
* allow override of webpack config
* work around cheerio inability to parse jinga templates
* webpack can not minify jinja templates
* allow script injection to specify other attributes
* allow script injection to specify other attributes
* Adjustments to make plugin systems work
* Add sourcemaps for javascript in prod webpack
* Update .gitignore
* Fix spelling errors
Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
* 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'
* Improve diffexp for tiledb
- The rows from the A and B sets are gathered and processed at the same time. In this
way the matrix is only accessed once instead of twice for each tile.
- There is now a single thread queue that gets shared between all callers of the diffexp.
This will slow down work if diffexp gets too busy.
- There is a target_workunit amount of work given to each thread. Previously the
workunit was (rows selected * width of tile), which could be small. Now multiple
column tiles can be combined into one workunit. If the target is too small then
thread and other overheads may reduce performance. If target_workunit is too large
then the size of the gathered sub matrix may take up too much memory.
- add configuration parameters (max_workers, cpu_multiplier, and target_workunit)
* Specialize diffexp for tiledb
This patch adds a new diffexp algorithm which is tuned for tiledb.
This algorithm was written by Bruce and is adapted here to plug into the
current framework. The anndata_adaptor still calls the original
algotithm (which was move from diffexp.py to diffexp_generic.py).
The cxg_adaptor now calls the new diffexp_tiledb version. Some
code is shared between the two.
This is part 1 of the diffexp for tiledb. Further tuning and
global throttles are still needed.
A script to run and time diffexp with various options is also
added: test/run_diffexp.py.
* s3 region should have a single config param
The s3 region can also now be automatically determined to further
reduce errors.
This patch also fixes a bug with order of handling the config params.
The tiledb config needs to be fixed before attempting to load
(need to handle_adaptor before handle_single_dataset)
* warning on maxCount for diffexp
* cleanup logging
* clarification
* make the limits configurable
* make diff exp limit work
* danger!
* remove debugging code
* fix merge with master
* fix unit tests
Co-authored-by: Colin Megill <colinmegill@gmail.com>
* Improvements to the matrix cache
- Add a timelimit for the matrix in the cache.
Once the timelimit is reached, the matrix can be removed.
- If a DatasetAccessError occurs, then remove the dataset
from the matrix cache.
Fixes#1322
* Added a config hook for secret key into the app.
the server first looks in an environment variable,
then looks in a config file.
For the cellxgene launch app, a default key is used if none is provided.
For the eb app, a secret key must be provided.
* Improved fix for matrix cache handling.
During the MatrixDataCacheItem acquire function there was a
time when the write lock was released and the read lock was taken.
During that time, the dataset could have been deleted, later
result in the MatrixDataCacheManageri data adaptor returning None.
The solution is to demote the writer lock to a reader lock instead
of unlocking and relocking.
Also, when a the cache needs to delete an entry, the delete
is done outside the MatrixDataCacheManager lock. This operation
only requires the write lock for the MatrixDataCacheItem.
Fixes#1255
* 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.
