* unit tests for 64 bit conversion
* clean up type handling
* type inference tests
* more type inference fixes
* use schema to determine user intent for data typing
* stop using deprecated API
* fbs type encoding test
* add missing test
* add more tests
* correctly infer X type for CXG adaptor
* lint
* fix typo
* ts migration
* cleanup from PR review
* lint
* PR review changes
* __test: create geneset
* example dataset test geneset
* delete geneset test
* edit __test
* gene crud
* Update client/Makefile
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
* copy gene sets separately
* make fix
* ignore test files locally
* csv update
* updated csvs
* fix unit tests for gene set load routes
* add missing fix to czi_hosted unit test
* pin tiledb version, for czi_hosted backend, to <0.9
* Revert tiledb pin to be less than 0.9. Broken tests have been updated in main branch.
* newline, gitignore
* color by and subset
* diffexp sets equal
* add diff exp test class
* fix data class
* diffexp snapshot
* snapshot
* snap3
* snapshot parentInnerhtml
* remove snap
* updated anno snaps
* add test class to gene list div
* new snapshots
* kick off
* Revert "kick off"
This reverts commit 743f551d55.
* remove import
* eol
* revert changes to csv re: gene tests
* global name
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
Co-authored-by: Arathi Mani <arathi.mani@chanzuckerberg.com>
Co-authored-by: maniarathi <mani.arathi@gmail.com>
* feat: return two lists for diffexp (#2221)
* sp
* split out derive sort order, tests passing
* sp
* return diff exp results in two lists
* update
* copy implementation over to desktop
* add tests for two lists
* small fixes to complete backend implementation
* accept new diffexp response
* map diff exp response to genesets
* delete )
* name diffexp genesets with population names
* take constants out of state and allow width prop to override
* shorten mini-histo properly truncate and resize depending on expansion
* prepend new genesets
* rename data within diffexp action
* backend
* move diffexp ttest to common code module, update tests
* update for unit tests
* reference actual var
Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
Co-authored-by: Madison Dunitz <dunitzm@gmail.com>
* 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
* 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
This splits the backend into two parts: the local backend for desktop cellxgene and the AWS backend for hosted cellxgene. The local backend is in local_server while the hosted remains in server. The general idea is to copy everything from server to local_server, pull unneeded stuff out of local_server, and keep server as-is for this PR. Not touching server means all the infra and deployment code will continue working just as it did before so we can make those changes incrementally.
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
Bumps [ini](https://github.com/isaacs/ini) from 1.3.5 to 1.3.7.
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/npm/ini/commit/c74c8af35f32b801a7e82a8309eab792a95932f6"><code>c74c8af</code></a> 1.3.7</li>
<li><a href="https://github.com/npm/ini/commit/024b8b55ac1c980c6225607b007714c54eb501ba"><code>024b8b5</code></a> update deps, add linting</li>
<li><a href="https://github.com/npm/ini/commit/032fbaf5f0b98fce70c8cc380e0d05177a9c9073"><code>032fbaf</code></a> Use Object.create(null) to avoid default object property hazards</li>
<li><a href="https://github.com/npm/ini/commit/2da90391ef70db41d10f013e3a87f9a8c5d01a72"><code>2da9039</code></a> 1.3.6</li>
<li><a href="https://github.com/npm/ini/commit/cfea636f534b5ca7550d2c28b7d1a95d936d56c6"><code>cfea636</code></a> better git push script, before publish instead of after</li>
<li><a href="https://github.com/npm/ini/commit/56d2805e07ccd94e2ba0984ac9240ff02d44b6f1"><code>56d2805</code></a> do not allow invalid hazardous string as section name</li>
<li>See full diff in <a href="https://github.com/isaacs/ini/compare/v1.3.5...v1.3.7">compare view</a></li>
</ul>
</details>
<details>
<summary>Maintainer changes</summary>
<p>This version was pushed to npm by <a href="https://www.npmjs.com/~isaacs">isaacs</a>, a new releaser for ini since your current version.</p>
</details>
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* 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
Bruce Martin