This PR adds multiple data to the dataset overview drawer provided by the config endpoint and formats them accordingly. The appearance of this new data is contingent on `dataPortalProps.corpora_schema_version === "1.0.0"`
For QA launch cellxgene with a remixed dataset and click on the button in the upper left-hand corner or the updated button in the info menu.
~~Review opening is blocked by merge of #1805~~
---
Closes#1319
* 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
* 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 }
```
* Undo selection appends diffExp genes to user gene list
Fixes https://github.com/chanzuckerberg/cellxgene/issues/1171
Need: When a user performs a differential expression from within
a sub-selection (world) of the data and then resets the selection to all
cells (universe), the differential expression results are no longer
valid.
Approach:
* When the selection is reset, move the top (maxUserDefinedGenes
- len(userDefinedGenes) from the differential expression results to the
list of user defined genes
* Raise maxUserDefinedGenes to 25 to give users more room and
accommodate the extra genes transferred in from differential expression
Other commits:
* Choose different button icons
* Add diff exp genes to user defined genes on subset too
* Respond to feedback from @liaprins-czi and @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
* freeze objects
* component rendering perf work
* use PureComponent where safe
* remove obsolete WorldUtil code
* make brushable histogram a pure component
* menubar 1
* zoom switching
* centering, pixel perfect canvas
* remove dead args and code
* clipping
* remove log
* if
* connect props
* lint
* undo
* logo left, componetize
* graph back to full height
* shadow to top
* do not prematurely call event handlers during render
* change test to deal with async histogram creation
* left section padding
* lint
* adjust graph to account for top bar,
* lasso tests
* refine histogram tests
* remove testing (onlys)
* enforce column name uniqueness for obs and var
* parameterize the column name containing obs and var user-readable names
* use the new annotation index value from schema
* update f/e unit tests
* PR review suggestions
* lint
* immutable crossfilter
* first cut at reducer refactor with cascade model
* add initial redo/undo implementation
* small optimization
* integrate expression with history
* add tests for new reducers and fix a couple of small initialization bugs
* treat tiny lasso selections as a clear
* better function name for clarity
* fix undo for differential expression
* remove logging
* fix regression due to bad merge
* cleanup and comments for clarity
* improve undoable configuration for flexibility
* fix stale comments
* remove debugging code from production build
* rename categoricalSelectionState
* rename file
* improve comments
* initial dataframe commit
* initial dataframe port of core app
* rename variables for clarity
* remove unused import
* comment out unused code
* fix array handling bug in crossfilter dimension creation
* allow creation of empty dataframes
* handle non-existent columns
* handle non-existent columns
* revise tests for new dataframe
* comments for clarity
* comments for clarity
* generate bulk add placeholder with real gene names
* fix bug in gene name adding
* more dataframe unit tests
* fix bug - subset from current world, not universe
* put cut and pasted code into a single function
* improve caching of crossfilter
* remove cascading update bug from graph
* more performance work
* improve state handling for scatterplot
* performance optimization of critical path
* add column summarization
* dataframe utils
* add callOnceLazy
* fix tests
* minor updates found during review
* fix misspelling
* remove RESTv02 from function names
* comment cleanup
* cut/icut col parameter defaults to null
* break up large test
* improve tests and comments on dataframe at/has functions
* add Dataframe withCol/dropCol
* expression varData now stored in a dataframe
* dead code cleanup
* use dataframe.summarize()
* test cases for Dataframe.col.summarize
* update test cases for new dataframe summarize
* improve naming
* use new hasCol API
* add comments
* add more Dataframe.withCol tests
* add ability to specify row index in cut operation
* retire subsetVarData function
* correctly handle expression subsetting
* lint and improve comments
* rename cut to subset
* create helper file for controls reducer
* initial dataframe commit
* initial dataframe port of core app
* rename variables for clarity
* remove unused import
* comment out unused code
* fix array handling bug in crossfilter dimension creation
* allow creation of empty dataframes
* handle non-existent columns
* handle non-existent columns
* revise tests for new dataframe
* comments for clarity
* comments for clarity
* generate bulk add placeholder with real gene names
* fix bug in gene name adding
* more dataframe unit tests
* fix bug - subset from current world, not universe
* put cut and pasted code into a single function
* improve caching of crossfilter
* remove cascading update bug from graph
* more performance work
* improve state handling for scatterplot
* performance optimization of critical path
* add column summarization
* dataframe utils
* add callOnceLazy
* fix tests
* minor updates found during review
* fix misspelling
* remove RESTv02 from function names
* comment cleanup
* cut/icut col parameter defaults to null
* break up large test
* improve tests and comments on dataframe at/has functions
* add Dataframe withCol/dropCol
* expression varData now stored in a dataframe
* dead code cleanup
* use dataframe.summarize()
* test cases for Dataframe.col.summarize
* update test cases for new dataframe summarize
* improve naming
* use new hasCol API
* add comments
* add more Dataframe.withCol tests
* add ability to specify row index in cut operation
* retire subsetVarData function
* correctly handle expression subsetting
* lint and improve comments
* rename cut to subset
* changes based on PR review
* initial dataframe commit
* initial dataframe port of core app
* rename variables for clarity
* remove unused import
* comment out unused code
* fix array handling bug in crossfilter dimension creation
* allow creation of empty dataframes
* handle non-existent columns
* handle non-existent columns
* revise tests for new dataframe
* comments for clarity
* comments for clarity
* generate bulk add placeholder with real gene names
* fix bug in gene name adding
* more dataframe unit tests
* fix bug - subset from current world, not universe
* put cut and pasted code into a single function
* improve caching of crossfilter
* remove cascading update bug from graph
* more performance work
* improve state handling for scatterplot
* performance optimization of critical path
* add column summarization
* dataframe utils
* add callOnceLazy
* fix tests
* minor updates found during review
* fix misspelling
* remove RESTv02 from function names
* comment cleanup
* cut/icut col parameter defaults to null
* break up large test
* improve tests and comments on dataframe at/has functions
* lasso working
* break out invert into own function
* action
* add spatial dimension to crossfilter, in support of polygon lasso
* improve comments on new dimension API
* lasso vs zoom
* toast test
* modify webpack build to allow for global CSS; use CSS modules to scope component styling
* remove heatmap
* add label to index resets
* swapping out buttons for blueprint
* adding constants to globals
* swapping out blueprint buttons
* title position, sidebar improvements
* sidebar styles
* adding toasts for validation errors
* zebra section trial
* integrating blueprint, switching buttons over, breaking out scatter
* clean up console
* mocks for redux refactor - for discussion
* more API design on redux refactor
* add new reuqired dependencies for build
* change babel target to use modern browser
* remove dead code
* remove dead code - joy plots
* checkpoint on redux refactoring
* checkpoint on redux refactoring
* fix mistaken rebase conflict resolution
* dead code removal; add name to dataframe backmap
* rename dataframe to universe
* update eslint config to more closely match prettier
* lint
* more eslint updates to match prettier
* additional config to make eslint match prettier
* add expression data to Universe/World
* remove obsolete reducers
* lint fixes
* more eslint cleanup
* lint
* lint
* fix but in countAllOnes when dimensions gt 1
* lint; do not display name metadata field
* lint; colors refactor
* lint; colors refactor
* update comments
* first cut at regraph and reset
* enable object-curly-braces consistent mode
* lint, handle regraph with no selection
* fix expression scatterplot bugs
* fix regression legend display
* add expression data cache
* remove console logging
* reset cell color on regraph/reset
* remove obsolete server URLs
* rename UniverseV01 to Universe_REST_API_v01
* add additional comments on the varDataCache
* merge universe reducer into controls reducer; simplify initialization-related actions
* use spread operator
* fix erroneous comment
* convert universe and world state to plain objects, and functionalize supporting code (remove ES6 classes)
* use spread operator
* lint
* improve variable names
* rename obsCrossfilter to crossfilter and obsDimensionMap to dimensionMap
* rename controls2 to controls
Fixes the build error in the old version.
Reverted the API version since we changed directions from updating the API to refactoring the server structure instead.
Severiano Badajoz
