* 1510-smoke-test
* config default
* update tests
* update test config
* fix linter errors
* more comments
* address comments
* use npm install in push_tests.yml
* use environment.default.json
* adding docs
* Take care of @mweiden's nits
* Save screenshots in the __tests__/screenshots/ directory
* typo
* docs
* Add chart tests (#1580)
* merge tests
* check if bin creation returned null before rendering charts (#1576)
* check if bin creation returned null before rendering charts
* refactor chart rendering into functions (#1577)
* little fixes from PR
* reintroduce fix to check for null values
* change getAllByClass to return element
* slice instead
* new stackedbar test
* feedback-1573-test (#1579)
* feedback-1573-test
* enable whole test set
* revert tests
Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
* tweak test to actually render chart
* include snapshot
* remove async
* fix getAllHistograms
* properly grab id
Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
* 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>
* hosted, update order to look for config file.
The app now uses a local config.yaml file bundled with the artifact
(if present), if it exists, then looks in the CXG_CONFIG_FILE
environment variable. This is the reverse of previous behavior.
The purpose of this change is to move away from using the
config file on s3, since that could lead to problem where an older
version of the app uses a newer version of the config.
Also in this PR:
1. Changed documentation around dataroot, to describe the posibility of using lustre.
2. Added a few improvements around the secret manager region name. If we use lustre for dataroot and a local config file, then we will no longer be able to
auto determine the region for the secret manager. I plan to start using the
environment variable option for hosted cellxgene.
* small edit to README
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
* 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
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.
Andrew Tolopko