* 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
There is a small chicken and egg problem.
The config file could be in s3, therefore when using the DataLocator to
download the config file, we don't yet have an app_config object.
Adding a check to handle this case.
Mostly this is just instructions for how to do this,
with a small addition to the makefile.
This enables support for serving the about_legal_tos and about_legal_privacy
from the cellxgene server.
* 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.
See sample of current behavior below:
```
venv❯ cellxgene prepare example-dataset/pbmc3k.h5ad
[cellxgene] Starting CLI...
Error: [cellxgene] cellxgene prepare has not been installed. Please run
`pip install cellxgene[prepare]` to install the necessary requirements.
~/workspace/cellxgene mweiden/446-custom-color-palette*
1 venv❯ pip install cellxgene[prepare]
zsh: no matches found: cellxgene[prepare]
```
Fix:
Wrap cellxgene[prepare] in single quotes.
* 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
* work around anndata bug 344
* fix accidental cut and paste error
* Use modified make_index_unique function
Temporarily copy code from https://github.com/theislab/anndata/pull/345
until the issue is resolved and released.
* Add notes and test for make_index_unique
* Lint fix
* Format python
Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
* 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
* Fix for favicon with --dataroot
* fix static assets in hosted cxg
The web proxy at aws eb was not finding the static assets.
The solution here is very simple: just copy the directory
containing the static assets to the top level of the artifact.zip.
This is not really the ideal solution. According to the AWS
docs you can make a mapping to the correct location in an
an ebextentions config file. I tried this and many combinations but
was not able to get this to work following that pattern.
Since we control the construction of the zip file, the solution
here isn't bad, but it could probably be made better.
* 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
* early, non-working eb config
* hosted cellxgene
In this PR, contains scripts and instructions for deploying cellxgene
for AWS elastic beanstalk. It supports the multi-dataset option.
The Makefile in the server/eb directory creates an artifact.zip
file, which can be deploy at AWS EB.
The server/eb directory contains:
app.py - flask app to run the server
Makefile - which creates an artifact.zip file which can be deployed.
README.md - instructions for setting up and deploying the eb app.
* hosted cellxgene (#38)
In this PR, contains scripts and instructions for deploying cellxgene
for AWS elastic beanstalk. It supports the multi-dataset option.
The Makefile in the server/eb directory creates an artifact.zip
file, which can be deploy at AWS EB.
The server/eb directory contains:
app.py - flask app to run the server
Makefile - which creates an artifact.zip file which can be deployed.
README.md - instructions for setting up and deploying the eb app.
* Update how artifact.zip is created
prune the server/test and server/eb directories
* Remove debugging print statements
* fixes from review comments
* fix lint
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
* Add undo/redo tests for annotations
Fixes https://github.com/chanzuckerberg/cellxgene/issues/969
... also refactor the tests for DRY.
* Add done()
* Make e2e annotations tests safer to concurrency
* Add data-testclass for save state.
* Simplify tests and make them dependent on save state
* Add codecov to Push Test workflow
* Empty commit
* Clear reports and tag each with flags
* Tag code reports by test
* Fix codecov tags
* One more fix
* 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.
* revert MatrixProxy; replace with correct use of adata slicing
* work around 0.6 adata slicing bug
* fix incorrect var slice
* simplify slicing of X
* add warning about performance impact of anndata<=0.7
* lint and remove unused code
* improve comment
* lint
* correctly parse versions
* temp files should preserve file suffix if possible - anndata 0.7 compat
* update anndata dependency to 0.6.20
* resolve PR review comments
* Add smoke test for annotations features
* Do not save during annotations tests
* Fix botched rebase in dev guidelines
* Revert "Do not save during annotations tests"
This reverts commit f0bd970bb2.
* Respond to feedback from @bkmartinjr
