* update package lock
* allow falsey vals
* remove old diff exp handling
* save diff exp results as geneset
* delete test
* check for undefined or null
* use global geneset description for diffexp
* remove diffexp special code, no longer showing adjpval + logfoldchange
* remove differential map to state
* remove clear from FSM, since we no longer support those actions
* restore controlHelpers test with todo
* colorby histo
* color graph by mean expression
* move var index after returns
* add genesets as an argument
* varindex
* undo redo for mean expression
* destructure
* ternary
* Revert "destructure"
This reverts commit 2d9432c1c7.
* color by mean for diffexp
* Remove door icon from log in button
* Move log in and info buttons from the top bar to in line with the cellxgene icon and dataset name
* Hover over on login button should say "Log in to cellxgene"
* Show email
closes#1830
* Separate userinfo from the config endpoint
previously information about if the user was logged in and their username
was part of the config endpoint.
However, the config endpoint was previously static, and has a cache control.
Rather than not caching the config, a new endpoint called "userinfo"
is created to handle that information.
The config endpoint still has the non-changing part of the authentication:
config:
authentication:
requires_client_login: True/False
login: <uri to login endoint if requires_client_login is True>
logout: <uri to logout endoint if requires_client_login is True>
The userinfo endpoint returns this information:
userinfo:
is_authenticated: True/False
username: <string if is_authenticated>
if authentication is not enabled then the config does not have an authentication key,
and userinfo returns None.
Also in the PR are a few minor code improvements and bug fixes
Co-authored-by: Colin Megill <colinmegill@gmail.com>
* refactor categorical controls state
* lint
* fix race condition in tests
* fix typo
* add missing update on subset
* remove obsolete code
* update jest and puppeteer major version; update all minors
* update when label changes
* remove lint from tests; increase timeouts in e2e tests
* initial refactoring to new async annomatrix
* refine error handling
* fix bad merge
* add continuous legend
* lint
* fix memoization in color table creators
* partial implementation of user defined annotations
* add new annotations action creator file
* first pass at user annotations
* additional user annotation bug fixes
* user annotation auto-save
* unit test cleanup
* lint
* refactor into multiple files
* cleanup
* add column GC
* fix several bugs in user annotations
* remove debug code
* no anonymous functions
* undo redo cleanup
* file cleanup
* scatterplot
* performance
* cleanup
* remove old code
* render in parallel with load
* fix race condition
* simply graph rendering
* render throttle DRY
* fix category label order
* fix typo in e2e test setup
* re-fix the e2e test setup
* be more tolerant of races
* anno matrix unit tests
* temp disable reembedding
* pilot port continuous histo to react-async
* name change
* lint
* fix repaint bug
* typo fix
* update snap to match new ids
* world/universe name cleanup
* move annoMatrix to src dir
* use private underscore naming convention
* fix corner case in all selected
* name cleanup
* add layout control
* init edge case
* lint
* port scatterplot
* fix label indexing bug and improve tests
* port category to react-async
* fix user annotation labelling while subset
* select all of prev layout on layout switch
* fix race with crossfilter update
* prettier lint
* fix misleading comment
* fix url composition in loader
* first pass at crossfilter tests
* lint
* lint
* fix typo
* improved error handling for network errors
* fix memoization bug
* add memo
* refactor for performnce
* add missing single-value handling in select exact parser
* small bugs discovered by tests
* lint
* additional crossfilter unit tests
* remove extraneous comment
* add support for automatic category determination
* lint
* fix render bug in category
* take advantage of schema categories guarantee
* lint
* do not clear history when resetting
* enhanced annomatrix gc
* lint
* finish renaming to follow conventions; fix clone race bug
* lint
* add priority based loading to improve initial data load UX
* crossfilter cache perf
* perf tuning
* remove timers
* documentation
* PR review changes
* PR review changes
* more PR review edits
* improve clarity of comment
* more PR review fixes
* port centroidLabels to use react-async
* remove dead code
* pr review updates
* oops, remove logging
* 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>
* 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>
* 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
* 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'
* maybe truncate string
* add string formatting to test
* correct import
* destructuring
* add maxlength
* test
* Respond to feedback from @bkmartinjr
Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
* Remove unused variables and imports
* Simplify conditional
* Fix typo
* Do not overprune var data cache
There is a bug in how the universe and world gene sets are constructed
and passed to `ControlsHelpers.pruneVarDataCache` that causes the var
data cache to be over-pruned. This commit fixes the issue.
Consider the following example from the node console:
```
❯ node
Welcome to Node.js v13.5.0.
Type ".help" for more information.
> new Set([1], [2], [3])
Set(1) { 1 }
```
What we really want is the set `Set(3) { 1, 2, 3 }`, which can be
constructed as:
```
> new Set([].concat([1], [2], [3]))
Set(3) { 1, 2, 3 }
```
* Disable ColorBy button for truncated categories
Fixes https://github.com/chanzuckerberg/cellxgene/issues/1156
For categories that have more than 100 labels we truncate the labels in
the UI, but still allowed users to ColorBy these categories. Coloring by
these categories can cause browsers to get bogged down.
This commit disables ColorBy for truncated categories.
* Minor documentation spelling and typo fixes
* Respond to feedback from @liaprins-czi
* Respond to feedback from @colinmegill and @bkmartinjr
* add simple error message helper
* port all label name pickers to use the new LabelInput component
* use pure components where possible
* cleanup
* more cleanup
* lint
* change new label prompt
* 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
* load annotations individually
* fix type check to be more general
* update node CI version from 10 to 12
* node 11
* debug print node version
* travis node version to latest
* try nvm
* remove extraneous node_js statement
* remove node version debugging printf
* incrementally load all annotations and layout
* process annotations and layout as they are loaded
* fix tests
* sort categories incrementally
* incrementally build category view summary; add category loading spinner
* add spinner to continuous metadata
* configure undoable reducer
* incremental crossfilter creation
* improve busy layout
* more layout cleanup
* correctly reconcile categories in schema
* refine layout of lsb spinners
* more spinner layout work
* more spinner layout
* always load layout before obs annotations
* add sample ontologies file
* add ontologies reducer
* Move select category to own component
* Dialog and Input factored out
* refactoring categorical, partway
* validationn
* anno
* suggest populates input
* frontend for ontology working
* initial implementation of back-end support for ontologies
* edit is now dialog again
* autosuggest working on edit
* part way through create arbitrary label
* handle choice in function
* pass duplicate cat prop
* editing works
* update test to match new CLI params
* fix occupancy alignment
* edit category as dialogue
* secondary button
* remove stubbed out ontologies
* add label setting upon new label creation
* Update legal characters for labels (#1119)
* Allow any term in the ontology (bypass legal name check)
* Add hyphens and parens to legal characters in names
* improve performance for large ontologies
* correctly handle case where ontologies are disabled
* fix logic error in CLI
Co-authored-by: Bruce Martin <bruce@chanzuckerberg.com>
* PR cleanup 1
* lint
* validate user generated labels
* finish hooking up connected suggest component
* protect against undefined callbacks
* Fix illegal characters error message
* break out npm run commands
* fix error detection on label edit
Co-authored-by: Bruce Martin <bruce@chanzuckerberg.com>
Co-authored-by: Sidney Bell <sidneymbell@users.noreply.github.com>
Bruce Martin