fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-10-10 05:20:56 +08:00
Code Issues Packages Projects Releases Wiki Activity
1,209 Commits 22 Branches 50 Tags
13246cb6d1f9798f5641bc7c4f61ba9331bff4e3
Commit Graph
100 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Bruce Martin 13246cb6d1 add more datasets (#1618) 
* add more datasets

* add more about links
 2020-07-10 14:55:55 -07:00
Bruce Martin dcbee43b88 add kampmann datasets (#1617) 
* add kampmann datasets

* build for production
 2020-07-10 05:12:21 -07:00
Bruce Martin 8898a9817c protect against non-integer array indexing (#1595) 
* do not assume non-iteger array bracket access will return undefined

* revert to spec
 2020-06-29 09:37:59 -07:00
Bruce Martin bc7a712048 refactor categorical controls state (#1549) 
* 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

* changes in response to PR review

* lint

* more PR comment changes

* more PR comment fixes

* lint

* more PR comment resolutions
 2020-06-10 12:56:38 -07:00
Bruce Martin 2ba4944f5c initial bug fixes and test improvements for the matrix refactor (#1503) 
* initial bug fixes and test improvements for the matrix refactor

* lint
 2020-06-02 09:47:40 -07:00
Bruce Martin 2992d17c1d add more detasets to hosted site (#1481) 
* add more detasets to hosted site

* fix build
 2020-05-19 14:24:27 -07:00
Bruce MartinandMatt Weiden c1bf491a96 Hooks for sentry integration (#1460) 
* add sentry webpack plugin

* allow override of webpack config

* work around cheerio inability to parse jinga templates

* webpack can not minify jinja templates

* allow script injection to specify other attributes

* allow script injection to specify other attributes

* Adjustments to make plugin systems work

* Add sourcemaps for javascript in prod webpack

* Update .gitignore

* Fix spelling errors

Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
 2020-05-08 15:59:56 -07:00
Bruce Martin f42f5151a6 Refactor build and CSP headers for Safari compat (#1442) 
* add unsafe-inline directive to style-src

* debugging - turn on csp reporting

* revert reporting only csp

* do not inline JS and CSS in build

* enable HTTPs only when in production mode

* remove debug printf

* fix clean target

* revert force_https removal
 2020-05-04 12:47:35 -07:00
Bruce MartinandColin Megill 05fcdaf93c Revised terms and privacy consent dialog, analytics hooks (#1426) 
* revised terms and privacy consent

* reorg code

* fix conditional

* Overlay reflects un-dissmissable state

* add inline scripts, and consent callback

* add csp_directive config hook

* revert config.yaml

* fix logic error

Co-authored-by: Colin Megill <colinmegill@gmail.com>
 2020-04-28 14:21:53 -07:00
Bruce Martin 3c191c3f93 add dsuid 25 (#1429) 2020-04-26 07:53:49 -07:00
Bruce Martin d31b7dc797 clamp brush selection range to data range (#1423) 2020-04-24 09:24:01 -07:00
Bruce Martin 735eb11eb7 refinments to csp (#1422) 2020-04-23 09:54:09 -07:00
Bruce Martin 9b12b729c9 more data (#1419) 2020-04-21 18:22:52 -07:00
Bruce Martin 8742f9094e cleanup (#1411) 2020-04-20 09:56:26 -07:00
Bruce Martin cbcd3f4f8f ensure crossfilter index dimensions match data (#1409) 2020-04-19 08:44:46 -07:00
Bruce Martin 5dc40158c4 disable eslint in github workflow (#1412) 2020-04-18 09:06:05 -07:00
Bruce Martin 55ef1448e8 CSP content hashes (#1406) 
* remove duplicate content-type header

* plumbing to compute CSP content hashes

* add logging of missing CSP hashes

* convert sub-class init protocol to static

* factor function

* lint
 2020-04-17 11:42:09 -07:00
Bruce Martin d22300e3db fix typo in cxgtool bool handler (#1404) 2020-04-17 11:11:14 -07:00
Bruce Martin a3df1a9f4a performance and correctness fixes to brushable histogram (#1390) 2020-04-13 20:03:46 -07:00
Bruce Martin 136093d583 add GET routes for expression data (#1387) 
* add GET routes for expression data

* fix comment typo
 2020-04-13 11:28:35 -07:00
Bruce Martin bff5745139 disable SSL cert verification (#1374) 2020-04-10 12:58:51 -07:00
Bruce Martin cfacdb15a8 fix typo (#1379) 2020-04-10 12:58:30 -07:00
Bruce Martin 2d2a7c2108 bump cache control max_age to one week (#1380) 2020-04-10 12:58:09 -07:00
Bruce Martin 61b330b9b0 fix non-finite condition in mean/var calculation (#1381) 2020-04-10 12:52:02 -07:00
Bruce Martin 0398249a20 CXG performance improvements (#1371) 
* initial kv cache

* add per-key locks

* comments

* memoize schema

* add missing initialization

* fix sever timing

* fetch only what is requested

* fix tests to not require strict ordering of columns

* clean up annotation request

* remove debugging print
 2020-04-09 10:19:26 -07:00
Bruce MartinandColin Megill e2a12ba9bb diffexp limit UI and configuration (#1336) 
* warning on maxCount for diffexp

* cleanup logging

* clarification

* make the limits configurable

* make diff exp limit work

* danger!

* remove debugging code

* fix merge with master

* fix unit tests

Co-authored-by: Colin Megill <colinmegill@gmail.com>
 2020-04-09 07:13:41 -07:00
Bruce Martin b466d952f9 add config and init for server timings (#1368) 
* add config and init for server timings

* add missing config error check
 2020-04-07 15:08:57 -07:00
Bruce Martin bcacb75296 load embeddings in parallel (#1352) 
* load embeddings in parallel

* correctly capture unclipped

* test

* another test

* add convenient copy assets target

* cleanup
 2020-04-07 09:48:07 -07:00
Bruce Martin 3b341a7191 add hcl dataset (#1366) 2020-04-07 07:51:32 -07:00
Bruce Martin 6193ae4997 Cleanup front-end build and python module contents (#1350) 
* cleanup build and module contents

* lint

* update chalk

* more cleanup

* fix unit test
 2020-04-06 19:04:06 -07:00
Bruce Martin ffa95b5a55 update s3fs requirements (#1348) 2020-04-05 09:22:32 -07:00
Bruce Martin 0d9f24115c cziscience landing page (#1347) 
* fix dead link in launch page

* first cut at landing page

* wording changes

* add additional refinements

* fixes from PR review
 2020-04-03 16:30:02 -07:00
Bruce Martin de8033e551 correctly handle categoricals that are not strings (#1346) 2020-04-03 15:50:02 -07:00
Bruce Martin 7c56041b11 categorical type handling fix (#1342) 
* fix numeric category conversion bug

* correctly compute categorical summaries

* lint

* remove debugging print
 2020-04-02 14:44:07 -07:00
Bruce Martin fa0164fdf6 use no-store cache control (#1337) 2020-04-02 09:20:35 -07:00
Bruce Martin c2a24ae0c6 add cache control headers (#1333) 
* add cache control headers

* add config param check
 2020-04-01 15:43:43 -07:00
Bruce Martin 33ce95ba09 work-around for column name encoding bug (#1324) 
* add attribute cleanup

* fix typo

* handle mappings

* logging

* fix regex

* remove debugging printfs

* update masked characters

* fix typo

* add missing incr
 2020-04-01 15:06:21 -07:00
Bruce Martin 708a5af039 Add fetch concurrency limit on obs annotation loading (#1318) 
* add fetch concurrency limit

* add tests for PromiseLimit
 2020-03-30 16:23:09 -07:00
Bruce Martin d4ec976aaa update locust routes to match new server URL structure (#1321) 2020-03-30 15:09:45 -07:00
Bruce MartinandColin Megill c8f98917c5 tos prompt (#1313) 
* tos toast

* finish ToS prompt

Co-authored-by: Colin Megill <colinmegill@gmail.com>
 2020-03-28 22:31:19 -07:00
Bruce Martin 8fac40b6ae various fixes for s3fs use (#1312) 
* various fixes for s3fs use

* lint
 2020-03-28 22:26:03 -07:00
Bruce Martin a398f85ccc turn off auto-reload in debug mode (#1301) 2020-03-26 13:34:56 -07:00
Bruce Martin 57938b487b remove static route redirects / bump static to top level (#1299) 
* add another favicon rule

* catch only top-level dataset names

* add config flag to disable redirects

* remove static redirect, point all links to top-level /static

* remove extraneous argument

* remove httpd redirect
 2020-03-26 10:45:10 -07:00
Bruce Martin 26605049a4 Various hardening to REST routes (#1293) 
* URL reweriting for static

* request size limits

* improve quotas, make tests work

* remove debugging code

* pass limits to front-end

* fix renaming boggle
 2020-03-25 16:14:52 -07:00
Bruce Martin 674f14f9bd harden dataset name handling (#1297) 2020-03-25 15:37:06 -07:00
Bruce Martin 752b9e4ab3 CORS and CSP headers (#1286) 
* do in-app compression only for CLI

* CORS and CSP headers

* lint

* add --debug to targets

* lint

* fix botched merge with master
 2020-03-24 08:05:37 -07:00
Bruce Martin d196cbc8f6 do in-app compression only for CLI (#1285) 2020-03-24 06:36:40 -07:00
Bruce Martin 96b092f0eb fix health root exception (#1283) 
* fix health root exception

* remove extraneous lambda
 2020-03-23 15:13:32 -07:00
Bruce MartinandMatt Weiden d99b84ba09 prepare - work around anndata bug (#1260) 
* work around anndata bug 344

* fix accidental cut and paste error

* Use modified make_index_unique function

Temporarily copy code from https://github.com/theislab/anndata/pull/345
until the issue is resolved and released.

* Add notes and test for make_index_unique

* Lint fix

* Format python

Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
 2020-03-22 12:27:59 -07:00
Bruce Martin db7a485796 tighten up error reporting (#1269) 
* black reformat

* tighten up error reporting

* lint

* fine tuning

* additional improvements in exception handling

* lint

* include exception and traceback in log

* fix typo
 2020-03-22 09:55:47 -07:00
Bruce Martin 1351c8f724 restrict methods on all endpoints (#1271) 
* restrict methods on all endpoints

* lint
 2020-03-22 08:23:28 -07:00
Bruce Martin de006f8f91 initial implementation of a health check route (#1262) 
* initial implementation of a health check route

* remove debugging code

* lint
 2020-03-20 14:21:32 -07:00
Bruce Martin 040dbd3a95 refine load test (#1257) 2020-03-20 14:09:12 -07:00
Bruce Martin 8f09a4b1bc JS package fixes (#1248) 
* Remove accidental package install from build

* remove accidental package install
 2020-03-18 19:00:28 -07:00
Bruce Martin 38c4ecac8c locust load test script (#1244) 
* initial version of a locustfile driver

* README
 2020-03-18 11:27:07 -07:00
Bruce Martin 1e8d89f8f2 refinements for 0.15 (#1226) 2020-03-13 16:30:47 -07:00
Bruce Martin 9bc83fdd02 update contributor process recommendations (#1213) 
* update contrib process recommendations

* fix typos

* clarification

* fix build instructions

* updates suggested by Matt

* fix dead link
 2020-03-13 11:41:30 -07:00
Bruce Martin f28bd52d79 fix performance regression caused by excessive rendering (#1219) 2020-03-12 15:05:08 -07:00
Bruce Martin 63f1f38f7c use AnchorButton so the tooltip dismisses (#1217) 2020-03-12 08:36:36 -07:00
Bruce Martin 8beeb57c96 Use DataLocator consistently on backend (#1208) 
* allow DataLocator to accept another locator as init param

* migrate to DataLocator

* migrate to DataLocator

* lint

* migrate to DataLocator

* add check for erroroneous use of remote path and annotations

* lint

* revert default data location - now back go CWD

* remove unused import
 2020-03-10 19:12:49 -07:00
Bruce Martin 28ddb60b2f update JS deps (#1203) 2020-03-10 10:59:12 -07:00
Bruce Martin ffdcc24a40 remove pinned tables dependency (#1202) 2020-03-10 07:47:54 -07:00
Bruce Martin 144b19c449 experimental re-embedding (#1186) 
* first cut at re-embedding route and back-end support

* update and expand config route tests

* add scanpy_umap

* add reembedding to config route parameters

* front-end support for reembedding fetch and UI

* remove unused imports

* add loading state

* save reembedding in reducer state

* improve withColsFrom

* transmit reembed schema to client; pick unique embedding names

* display embeddings

* format

* lint

* spaces, tab size 2

* lint

* test hack for smoke-test race

* back out hack sleep

* add check for backed mode

* add unit test for reembedding

* lint

* hide re-embedding CLI param from help
 2020-03-09 16:53:30 -07:00
Bruce Martin bf7d7342d5 Improve label picking (#1179) 
* 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
 2020-02-28 15:46:40 -07:00
Bruce Martin 7bc58bba2b undo/redo cleanup (#1165) 
* fix refactoring error which disabled annotation file clearing

* fix undo behavior on add category label

* fix various undo/redo bugs

* remove logging

* further refinement of annotation undo/redo and actions

* address PR comment
 2020-02-24 18:51:26 -07:00
Bruce Martin fb1f0c6469 fix latent crossfilter bug (#1162) 2020-02-21 14:14:41 -07:00
Bruce Martin d2bae0c4f6 CXG creator and dataset parameters (#1163) 
* remove redundant call to make_response (lint)

* initial commit of H5AD to CXG converter

* lint

* PR review suggested comments

* cxg adaptor now understands group metadata

* lint
 2020-02-21 12:49:45 -07:00
Bruce Martin 349c413d8b anndata X indexing & version compatibility improvements (#1157) 
* revert MatrixProxy; replace with correct use of adata slicing

* work around 0.6 adata slicing bug

* fix incorrect var slice

* simplify slicing of X

* add warning about performance impact of anndata<=0.7

* lint and remove unused code

* improve comment

* lint

* correctly parse versions

* temp files should preserve file suffix if possible - anndata 0.7 compat

* update anndata dependency to 0.6.20

* resolve PR review comments
 2020-02-19 09:57:51 -07:00
Bruce Martin e770db1e2c load annotations incrementally (#1107) 
* 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
 2020-02-10 11:22:27 -08:00
Bruce Martin 1c9b9f6a08 js package dep update (#1145) 
* js package dep update

* roll back start-server-and-test
 2020-02-05 13:11:05 -08:00
Bruce Martin 3afc03b95b fix state prop bug with camera transform (#1138) 2020-01-31 12:13:35 -08:00
Bruce Martin 69c639b14d pin anndata to 0.6.22post1 (#1122) 2020-01-22 13:23:05 -08:00
Bruce Martin 431c8bdabc disable magic nan parsing in read_csv (#1115) 2020-01-17 09:26:15 -08:00
Bruce Martin 8b329630f8 fix for issue 1112 - all user annotation category names must be unique across all obs annotatoins (#1114) 2020-01-16 09:28:29 -08:00
Bruce Martin 30f3ce49e4 update JS dependencies (#1106) 2020-01-15 17:11:51 -08:00
Bruce Martin 677433bbf5 Fix label sorting bugs (#1102) 
* move category label sort to utils

* refactor cat label sort

* fix category label sort and color assignment

* convert whitespace from tabs to spaces
 2020-01-09 13:34:25 -08:00
Bruce Martin 2d39cb3b30 sort the embedding names for the UI (#1098) 2020-01-09 06:33:14 -08:00
Bruce Martin 18177b108f fix 1090 - add unassigned label to the new category, not the source category (#1094) 2020-01-09 06:32:38 -08:00
Bruce Martin dfaf0d0603 allow hyphen in annotation file name (#1074) 
* remove old detritus

* allow hyphen in label file name
 2020-01-02 15:44:40 -08:00
Bruce Martin 6370025caf update all JS package deps (#1076) 
* update dependencies - minor revisions

* update min node_js version to 10

* major npm package dep updates

* a few more updates
 2020-01-02 09:14:09 -08:00
Bruce Martin c9b6044c4f release 0.13.0 (#1064) 2019-11-26 15:45:13 -08:00
Bruce Martin fa89a5a375 create annotations output dir if it does not exist (#1062) 
* create annotations output dir if it doees not exist

* lint
 2019-11-26 13:35:20 -08:00
Bruce Martin f8cef71eed help text changes (#1061) 
* requested CLI help changes for launch sub-command

* update file name prose

* more wording changes

* more PR requests
 2019-11-26 13:35:01 -08:00
Bruce Martin d2171b9a2f fix perf regression introduced by user anno changes (#1060) 2019-11-25 18:16:49 -08:00
Bruce Martin a593e95ab3 annotations CLI and file UX rework (#1049) 
* rename config param label-file

* annotations rework - CLI params, file naming and backups

* lint

* improve cli option error checks

* enable session cookies

* enable session cookies

* add session id

* name annotations file in multi-dataset and multi-user safe manner

* pass data user hash to front-end

* add annotation collection name support to front-end

* add constant for annotation data collection name

* parameterize annotation collection name; make it sticky in the session

* clarify comments

* hard wire a temporary data collection name for testing

* prettier

* test comment

* package command

* set annotations  filename dialog

* name  and hash are visible

* wire up data collection capture
 2019-11-25 15:28:28 -08:00
Bruce Martin 5713aa8792 category and label name validation updates (#1056) 
* update label validation with new schema

* add new error messages for new label errors; general cleanup
 2019-11-22 10:32:00 -08:00
Bruce Martin ee62dd355f [WIP] JS lint and dead code removal (#1053) 
* lint and dead code removal

* fix regressions
 2019-11-21 14:10:02 -08:00
bkmartinjr 0415c30f0b add security notice to readme 2019-11-20 10:42:27 -08:00
bkmartinjr 79e534e397 additional caveats/warnings for hosting 2019-11-20 10:40:00 -08:00
bkmartinjr f4919340e9 merge 2019-11-20 10:33:17 -08:00
bkmartinjr 976f9d9ff8 add hosting notes 2019-11-20 10:28:40 -08:00
Bruce Martin 9a540a4f0a fix erroneous state clearing (#1052) 2019-11-19 11:11:19 -08:00
Bruce Martin 2d0b646956 js dependency update (#1045) 2019-11-18 11:22:13 -08:00
Bruce Martin b284e6f820 Improve CLI help (#1025) 
* launch option changes

* more CLI help improvements

* change plot help

* additional changes requested

* change metavars for options and subcommand
 2019-11-14 13:02:40 -08:00
Bruce Martin 5ea9ac8a9e Add provenance header to labels CSV file (#1041) 
* add last mod time lookup to data locator

* store data locator in Driver

* save metadata header in labels csv

* lint

* fix tests

* change datetime format to second precision
 2019-11-14 12:33:48 -08:00
Bruce Martin a52e86a69b improve category and label name validation (#1034) 2019-11-13 09:40:37 -08:00
Bruce Martin 04c83993d2 clear color-by mode when current category is deleted (#1033) 2019-11-12 15:31:06 -08:00
bkmartinjr 54d144bb75 add build dependencies for igraph and louvain 2019-11-12 07:56:03 -08:00
bkmartinjr bf3bf58d6e improve launch docs 2019-11-09 13:03:47 -08:00
bkmartinjr 611c8b98b1 add --backed info to troubleshooting 2019-11-09 12:59:33 -08:00