* add case to removing labels
* add disabled state to centroid button
* fix centroid test button clicking order
* don't accidentally un-toggle first color
* run eslint --fix
* camelcase
* camelCase config part 1
* part 2
* part 3 - removing subscripts
* fix "class-methods-use-this"
* fix "class-methods-use-this"
* fix eslint ignores
* add eslint ignore for set state in update
* reformat comments to appease eslint
* add a11y features
* sort-comp fix
* a11y fix
* add ignore for set state in update
* add a11y htmlFor
* remove unused toast
* remove unnecessary bind
* add ignore for set state in update
* add rel="noopener noreferrer"
Using target="_blank" without rel="noopener noreferrer" is a security risk: see https://mathiasbynens.github.io/rel-noopener
* use arrow function to bind
* remove unused definitions/declarations
* prettier
* remove unused state
* add comments to empty catch blocks remove curly brackets
* escape '
* use eqeqeq
* switch from default export
* remove ignore log
* remove static
* fix import
* revert subscripting config
* clean-up
* remove unnecessary subscript
* fix new errors from master
* change category click handler to a class property
* fix camelcase changes that slipped by
* unused import
* Fix newly introduced ESLint errors from addGenes
6.7 does not have the `hidden` flag used in the code. Users building the
app with an older version of click within the current range specified by
requirements.txt may fail.
* 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>
* Refactor CSS layout and react logic for layout
Fixes https://github.com/chanzuckerberg/cellxgene/issues/1022
* Menubar should wrap inside middle pane instead of overlapping left
sidebar when window is scrunched
* cellxgene should have a minimum width of 1240px
1. Replace absolute positioning and dimension calculation with css grid
2. Use flexbox for wrapping menubar buttons
* Middle pane (graph) can calculate its own size
* Removing components calculating their size/position relative to
eachother increases modularity, decreases use of global variables
* Improved some scrollbar behavior
* Removed responsive reducer, propagating window size to components
triggers unnecessary events and encourages breaking modularity; doing
this made some components state agnostic
Reference: https://css-tricks.com/snippets/css/complete-guide-grid/
* Reposition the continuous legend
* Small fixes
* Respond to feedback from @colinmegill
* Respond to feedback from @colinmegill
Add more documentation on the renderGraph method.
* app_config, fix bug with list/tuple command line arguments.
There was a error caused by pyyaml using lists, and click using tuples.
Now tuples are automatically converted to lists when the config is
updated.
* Add server plugin system
Plugins are optional modules loaded at runtime. Specification:
* Plugins are loaded from the server.plugins module (directory
server/plugins)
* The import_plugins method is run as part of the initialization of the
server module in __init__.py
* Add plugins to the EB build process
* Remove bit of dead code
* Respond to feedback from @bmccandless
* 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 unsafe-inline directive to style-src
* debugging - turn on csp reporting
* revert reporting only csp
* do not inline JS and CSS in build
* enable HTTPs only when in production mode
* remove debug printf
* fix clean target
* revert force_https removal
* Return empty colors for .cxg v0.0 files
Fixes https://github.com/chanzuckerberg/cellxgene/issues/1440
The CxgAdaptor.get_colors method currently assumes that the .cxg file has
cxg_group_metadata. As a result, the /api/v0.2/colors endpoint always fails for
.cxg v0.0 files.
* Add test fixture
Fixes https://github.com/chanzuckerberg/cellxgene/issues/1433
When selection is deselected the world is reset to the universe the
crossfilter is reset to that in the resetCache, including the embeddings
in the layout_XY dim. However, the embedding selection stays the same.
If the embedding selected is not the default, the embedding shown to the
user will be different than the embedding layout_XY in the crossfilter,
causing lasso selections to be made against the wrong embedding
coordinates
* 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'
* hello world
* stuff
* successful build
* updates"
* maybe a basic example
* simplify
* reamde into dockerfile
* some more stuff
* Release procfile
* package.json at top levle
* don't release in procfile for now
* more package.json stuff
* copy assets
* merge master
* not in the relase phase
* revert not necessary
* pin gunicorn version
* reset common.mk
* Update package.json
Co-authored-by: Madison Dunitz <dunitzm@gmail.com>
* Cleanup the backend-dev convenience method
* Add the frontend_dev convenience method
frontend_dev is a soup-to-nuts convenience method for setting up the FE
development environment with node running a the client code on port 3000
with the a separate cellxgene package serving the API over port 5005 in
the background.
The script can be run from Finder.
* Update the developer scripts documentation
* Remove the 'test' make target in the client Makefile
Rationale:
* Given how long the smoke tests take to run, it is unlikely that
developers will want to run all tests together.
* It is unlikely that developers will have set up the backend server
properly for the tests to pass.
* Available commands should be safe-ish and not lend themselves to
confusing errors.
* You can still group tests by concatenating them in a make command, as
in `make unit-test smoke-test`.
* This target isn't used in any of our CI pipelines -- KISS.
* Some version of python3...
* Minor typos in docs
* Respond to feedback from @bkmartinjr
* Make adjustments so that DATASET path is predictable
* Simplify environment defaults a bit
Matt Weiden