Commit Graph
1484 Commits
Author SHA1 Message Date
Seve Badajoz 743f551d55 kick off 2021-07-01 14:17:50 -07:00
Seve Badajoz 159d3ef9b1 new snapshots 2021-07-01 14:17:50 -07:00
Seve Badajoz 1d8553824f add test class to gene list div 2021-07-01 14:17:50 -07:00
Severiano Badajoz 0b1826b3f3 Merge branch 'main' into colinmegill/#2042-geneset-tests 2021-07-01 14:17:21 -07:00
Colin Megill a20d99cde0 updated anno snaps 2021-07-01 11:37:10 -07:00
Colin Megill d3376b3163 remove snap 2021-07-01 11:29:38 -07:00
Severiano Badajoz b8b1d0dd9e fix: reset gene set colorScale on gene set deletion (#2264) 2021-06-30 16:46:44 -07:00
Madison Dunitz 5007d307a2 Dunitz/czi hosted test server (#2254)
update hosted unit tests to use wsgi server instead of cellxgene packages
2021-06-30 15:07:54 -07:00
Colin Megill e54d0e3412 snapshot parentInnerhtml 2021-06-30 12:53:42 -07:00
Colin Megill 1e2b27db80 snap3 2021-06-29 18:42:59 -07:00
Colin Megill 4e227ddb36 snapshot 2021-06-29 17:50:13 -07:00
Colin Megill 08d2080e06 diffexp snapshot 2021-06-29 16:50:59 -07:00
Seve Badajoz 8289e0ce0a fix data class 2021-06-28 13:55:23 -07:00
Seve Badajoz cd754b6ed3 add diff exp test class 2021-06-28 12:33:59 -07:00
Colin Megill 036cdd7880 diffexp sets equal 2021-06-24 18:34:42 -07:00
Colin Megill 1acf6f627a color by and subset 2021-06-24 13:06:28 -07:00
Colin Megill 168c8c6469 Merge branch 'main' into colinmegill/#2042-geneset-tests 2021-06-23 13:03:22 -07:00
Severiano Badajoz 82de4178d9 feat: add quick gene lookup functionality (#2250)
* add/remove gene functionality back with geneset style gene

* styling and expansion

* memo gene list to prevent re render
2021-06-23 13:59:10 -04:00
Colin Megill 6a773acef7 Merge remote-tracking branch 'origin/colinmegill/#2042-geneset-tests' into colinmegill/#2042-geneset-tests 2021-06-21 12:20:21 -07:00
Colin Megill 165c38de0e newline, gitignore 2021-06-21 12:20:14 -07:00
maniarathi d27dce1498 Merge branch 'main' into colinmegill/#2042-geneset-tests 2021-06-20 21:08:57 -07:00
Arathi Mani 4a9e53aa97 Revert tiledb pin to be less than 0.9. Broken tests have been updated in main branch. 2021-06-20 21:08:31 -07:00
maniarathi 023ae10822 Update unit tests for CXG conversion to check for actual content rather than file names alone which have changed with the recent 0.9 release of tiledb's python package. (#2249)
* Update unit tests for CXG conversion to check for actual content rather than file names alone which have changed with the recent 0.9 release of tiledb's python package.

* Some cleanup

* Undo a bad line
2021-06-19 09:37:05 -07:00
bkmartinjr d82b69d0ac pin tiledb version, for czi_hosted backend, to <0.9 2021-06-17 09:13:04 -07:00
bkmartinjr 40291b9bba add missing fix to czi_hosted unit test 2021-06-17 08:34:29 -07:00
bkmartinjr 2261d5e82c fix unit tests for gene set load routes 2021-06-17 08:06:42 -07:00
Colin Megill acc7436106 updated csvs 2021-06-16 20:48:24 -07:00
Colin Megill 4449b8cff2 csv update 2021-06-15 14:05:06 -07:00
Colin Megill f5bbe8a669 ignore test files locally 2021-06-14 16:21:32 -07:00
Colin Megill fd28c176db make fix 2021-06-14 13:39:06 -07:00
Colin Megill f320f7fd31 copy gene sets separately 2021-06-10 17:28:51 -07:00
Colin MegillandSeveriano Badajoz e075c487e2 Update client/Makefile
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
2021-06-09 17:43:40 -07:00
Colin Megill 0716cb1d3f Merge branch 'main' into colinmegill/#2042-geneset-tests 2021-06-08 17:05:27 -07:00
Colin Megill c78c367c34 gene crud 2021-06-08 17:03:40 -07:00
28b526b3fc feat: diffexp returns two genesets (#2230)
* 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>
2021-06-08 21:02:19 +00:00
Colin Megill 022ffc22e6 edit __test 2021-06-08 13:15:15 -07:00
Colin Megill 8b9a7b4283 delete geneset test 2021-06-07 15:41:55 -07:00
Colin Megill 10506059d3 example dataset test geneset 2021-06-07 10:27:08 -07:00
Colin Megill 68a5b632d1 __test: create geneset 2021-06-04 02:10:36 -07:00
Severiano Badajoz 7ed53c0f5b fix: add placeholder test so suite doesn't fail (#2233)
* comment out test suite

* actually just put in placeholdertest
2021-05-26 12:41:16 -07:00
Severiano Badajoz a4050f10e1 feat(geneset): save diff exp result as geneset (#2216)
* 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
2021-05-25 10:51:31 -07:00
Madison Dunitz 6f6634a4d9 add action to deploy on on push to canary branch (#2196)
* add action to deploy on on push to canary branch
2021-05-17 16:15:48 -07:00
Severiano Badajoz 265ccf3682 fix: use env specific secret (#2204) 2021-05-13 14:28:16 -07:00
maniarathi 59ec3afbb9 Pin versions of flatbuffer and Flask to be less than 2.0 (#2199) 2021-05-12 15:13:10 -07:00
Madison Dunitz 4666f1f044 add rule for static assest without dataset id (#2194) 2021-05-07 21:17:31 -07:00
Colin Megillandbkmartinjr d04dba225f Filename dialogue includes gene sets (#2185)
* change filenames

* gene-sets to anno dialogue

* logging, lambda

* celllabels

* cell dash labels

* space

* fix 2182 - annotation file name change on the backend

Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
2021-05-07 17:32:11 -04:00
Colin Megill 096d8ff1d2 Geneset remove toggle (#2184)
* no toggle, histo at top

* set mean expression, truncation

* gene set
2021-05-05 19:51:05 -04:00
Colin Megill 25b308c532 conditional colon (#2181) 2021-05-04 13:43:02 -04:00
Bruce Martin f2e9aecebe hosted gene sets routes, plus a few bug fixes (#2155)
* 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
2021-04-27 13:58:58 -07:00
maniarathi ebeb1c8818 Fix command to EB to use the artifact.zip file during deployment instead of the source code in the directory. (#2174) 2021-04-23 11:07:57 -07:00