* first cut at hosted gs routes
* lint
* update tests to match csv parser changes
* update tests to new API
* update gene set name validation rules to match requirements
* add path mapping from dataset to geneset
* add test cases for geneset GET route
* fix test assertion
* remove debugging code
* update gene set uri mapping function
* fix error message
* allow extra user-specified headers in gene set csv file
* clarify comment
* 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
* geneset description add
* edit geneset description
* default state for desc
* remove log
* naming, todo
* check for both dup name and desc
* fixes
* do not store gene set modal state in history stack
* Update createGenesetDialogue.js
* Update editGenesetNameDialogue.js
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
* first cut at GET /genesets route
* update existing tests to match code changes
* more GET /genesets and initial tests
* add missing test fixture
* geneset validation accepts OTA format
* genesets route: better error handling, more tests
* lint
* genesets reducer and initial load
* fix lint
* add autosave support for genesets
* remove debug logging
* fix typo
* fix another typo
* update smoke test config for genesets
* smoke test fixes
* more fiddling with smoke tests
The HistogramFooter needs to distinguish between an undefined
value and a value of 0. If the pvalAdj was 0, then the logFolChange
was previously not showing up.
#1888
* Convert float annotations if possible.
The client converts all arrays to floats.
If a category contains integer labels, and that category is copied, it will contains floats (e.g 1.0 instead of 1).
When that category is put back to the server, it fails in the tiledb code, which does not accept floats.
The solution is to convert a float category to integer, if possible.
#1984
* updates
* add long title
* add organism to Dataset Metadata and create headers
* begin HTMLTable for metadata
* switch out truncating for scrolling
* add optional chaining to redux state mapping
Co-authored-by: maniarathi <mani.arathi@gmail.com>
* Revert "Remove Continuous vars with 1 value from histogram, add to info drawer (#1927)"
This reverts commit 242546371b.
* remove conditional rendering cases
* ignore pointer events
Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
* remove single val continous metadata from histogram, add to info drawer
* refactor to save singleContinuous values in state
* fix edge case, single continuous values reappeard in rsb when clipped
This PR adds a few helpful additions regarding authentication.
Changes:
* e2e tests are now run on test_oauth via a passed config.yaml
* node dev server correctly handles `/login` and `/logout` endpoints to make developing for auth easier
* Introduced auth e2e tests to check that buttons display and work
* remove auth buttons and dataset info from info menu
* add auth buttons to menubar
* remove auth from top left
* new auth buttons
* move infomenu to lsb dir
* styling fixes
* feedback
* more feedback
Co-authored-by: Timmy Huang <thuang@chanzuckerberg.com>
* 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
Went through and ensured that undefined/null values were caught and handled correctly in render functions. Also documented some of the more complicated functions.
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Closes#1825
* Pass in the previous crossfilter when creating a new annomatrix for a switched embedding in order to retain the previous selection of cells.
* Address Bruce's PR comment
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~~
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Closes#1319
Bruce Martin
