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 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'
* 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.
* 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
* 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
* black reformat
* tighten up error reporting
* lint
* fine tuning
* additional improvements in exception handling
* lint
* include exception and traceback in log
* fix typo
* 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.
* Improve hosted cellxgene
- option to turn off the test index page, or supply a page for redirect.
For EB, The default is to return 404. For cli launch, the default is the test page.
- option to select which matrix types are allowed for multi dataset servers.
For EB, The default is CXG only. For cli launch, the default is any matrix type.
- Return early with an error response if diffexp is requested when not configured
- Verified that reembedings and user annotations also return with an error response
if used when not enabled.
TODO: The new options cannot currently be set by the user.
I plan to add a configuration file where these and all other settings can be set.
Fixes#1210Fixes#1228Fixes#1229
* allow DataLocator to accept another locator as init param
* migrate to DataLocator
* migrate to DataLocator
* lint
* migrate to DataLocator
* add check for erroroneous use of remote path and annotations
* lint
* revert default data location - now back go CWD
* remove unused import
* first cut at re-embedding route and back-end support
* update and expand config route tests
* add scanpy_umap
* add reembedding to config route parameters
* front-end support for reembedding fetch and UI
* remove unused imports
* add loading state
* save reembedding in reducer state
* improve withColsFrom
* transmit reembed schema to client; pick unique embedding names
* display embeddings
* format
* lint
* spaces, tab size 2
* lint
* test hack for smoke-test race
* back out hack sleep
* add check for backed mode
* add unit test for reembedding
* lint
* hide re-embedding CLI param from help
* 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
This PR contains a refactoring to make adding new features easier.
The new features include supporting the tiledb format, and the multi dataset application.
The refactoring includes
Simplifying the directory structure and files.
a class structure to handle annotations (currently one type: AnnotationsLocalFile).
a class to handle application configuration
a class structure to handle matrix data (currently AnndataAdaptor and CxgAdaptor). CxgAdaptor uses tiledb.
Algorithms that were previously dependent on the scanpy anndata object are now generalized to work with an abstract interface.
The multi dataset option is not fully supported yet, and so the option to use it is hidden.
Use "cli launch --dataroot ..."
To access this feature.
All combinations of app single dataset/ app multi dataset and AnndataAdaptor/CxgAdaptor work with all the features, such as annotations, ontologies, diffexp.
