fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-17 05:47:58 +08:00
Code Issues Packages Projects Releases Wiki Activity
1,336 Commits 22 Branches 50 Tags
eb108feb37fc4e244b717bb9bc8a1bf14ed55f17
Commit Graph

462 Commits

Author SHA1 Message Date
maniarathi
b048fd8d9a Allow columns encoded in float64 to be rendered as part of continuous value histograms. (#1905) 2020-10-06 12:59:07 -07:00
Timmy Huang
8bd4cbd1e5 1807-authN-smoke-test (#1898) 
This PR does the following:

1. Add `login` and `logout` helper functions in `client/__tests__/e2e/cellxgeneActions.js`
2. Add conditional AuthN integration test in `client/__tests__/e2e/e2e.test.js`. The test will only run if env variable `TEST_AUTH_INTEGRATION` is `"true"`, which is only set in `single-cell-infra`'s Github Action flow. Corresponding PR [here](https://github.com/chanzuckerberg/single-cell-infra/pull/198)
 2020-10-01 12:29:59 -07:00
dependabot[bot]
e6c996ca93 Bump bl from 4.0.2 to 4.0.3 in /client (#1810) 
Bumps [bl](https://github.com/rvagg/bl) from 4.0.2 to 4.0.3.
- [Release notes](https://github.com/rvagg/bl/releases)
- [Commits](https://github.com/rvagg/bl/compare/v4.0.2...v4.0.3)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
 2020-09-30 15:24:51 -07:00
Timmy Huang
99152dd5aa add-menu-test-id (#1895) 2020-09-30 12:53:51 -07:00
Colin Megill
04a3c3c6b6 Partial fix for 1830 (#1863) 
* 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
 2020-09-30 11:45:10 -07:00
maniarathi
4aabb8e092 Make sure there are more than 1 values in a category before rendering it (#1871) 2020-09-29 15:32:21 -07:00
Severiano Badajoz
7bee09cd16 Add blueprint eslint plugin (#1892) 
* add bp3 eslint plugin

* first eslint runthrough + manual changes

* small fixes

* update snapshots

* update h1 to h4

Co-authored-by: czimergebot <35308261+czimergebot@users.noreply.github.com>
 2020-09-29 15:00:56 -07:00
Severiano Badajoz
21dfdb91a9 skip user annos when building dataset metadata (#1881) 2020-09-28 13:17:14 -07:00
Severiano Badajoz
374bb11279 Handle case where new drag starts while existing lasso is not finished (#1864) 
* handle case where new drag starts while existing lasso is not finished

* flip variable
 2020-09-28 10:34:47 -07:00
Severiano Badajoz
210042814f Info Drawer format adjustments (#1853) 
This PR tweaks the look and feel of the info drawer in response to QA from @signechambers1
 2020-09-18 13:16:28 -07:00
Severiano Badajoz
3e9cb0265e Fix InfoFormat parameter checking (#1831) 
Went through and ensured that undefined/null values were caught and handled correctly in render functions.  Also documented some of the more complicated functions.

---
Closes #1825
 2020-09-15 12:03:59 -07:00
maniarathi
4b240920e2 Pass in the previous crossfilter when creating a new annomatrix for a switched embedding in order to retain the previous selection of cells. (#1832) 
* 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
 2020-09-12 10:32:00 -07:00
Severiano Badajoz
5583e91392 Pull config values into dataset overview drawer (#1814) 
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.


![image](https://user-images.githubusercontent.com/8716829/92670435-de966280-f2c8-11ea-87f1-8591c959a586.png)


~~Review opening is blocked by merge of #1805~~

---

Closes #1319
 2020-09-10 16:41:05 -07:00
Severiano Badajoz
89b68723cc Create dataset info drawer (#1805) 
* create infoDrawer

* create read/writes to redux store

* reimplement reducer that vanished

* remove aboutURL stuff from title

* add formatting and style

* s/length/size and make metadata items list items

* remove comment

* remove empty singletons

* refactor into async react component

* Clean up skeleton

* swap out for loop for map

* add comment

* replace placeholder

* switch ternary for `&&`

* event handling fixes and PR feedback

* add button and move click handler to button

* ditch empty categories

* move drawer button handling to redux

* remove categorical move note

* PR feedback from colin

* update snapshot

* remove hover state
 2020-09-09 17:55:43 -07:00
Severiano Badajoz
437fd5feda Correctly check if mini histograms shouldn't be rendered (#1809) 
* ensure that function returns a boolean value

* change function used to check if mini histogram should not render
 2020-09-01 16:45:50 -07:00
bmccandless
f8cdb12892 Fix frontend mishandling of null userinfo (#1795) 
* Fix frontend mishandling of null userinfo

If the authentication is disabled, the userinfo endpoint returns null.
This case needs to be handled.

 #1780

* Small fix for handling refesh tokens in auth
 2020-08-26 13:01:50 -07:00
Severiano Badajoz
0a10b3ec2a sort object keys to our specification before generating user colormap (#1792) 2020-08-25 12:25:55 -07:00
Timmy Huang
9a40b28172 thuang-fix-static-asset-font (#1791) 
This seems to fix the font URL path, at least locally for both `:3000` and `:5005`

<img width="1296" alt="Screen Shot 2020-08-24 at 4 01 07 PM" src="https://user-images.githubusercontent.com/6309723/91106044-8a338780-e626-11ea-885f-e5c268f3ecf0.png">

<img width="1377" alt="Screen Shot 2020-08-24 at 4 01 28 PM" src="https://user-images.githubusercontent.com/6309723/91106047-8dc70e80-e626-11ea-95b0-62e47cc6303f.png">
 2020-08-24 17:05:46 -07:00
Madison Dunitz
65ea1b673f Dunitz 1685 hosted annotations (#1789) 
* save tiledb array to s3, dont cache user annotations

* Add option to disable annotation filename prompt (#1787)

Co-authored-by: Madison Dunitz <dunitzm@gmail.com>

* set tiledb default context in cxg_adaptor

Co-authored-by: maniarathi <arathi.mani@chanzuckerberg.com>
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
 2020-08-24 18:26:08 -05:00
maniarathi
5dfe0043c3 Serves static assets from each dataset root URL and switch the publicPath to be a relative path. (#1786) 2020-08-22 10:04:40 -07:00
Snyk bot
fae9ac9382 Upgrade lodash from 4.17.15 to 4.17.20 (#1759) 
<h3>Snyk has created this PR to fix one or more vulnerable packages in the `npm` dependencies of this project.</h3>

![merge advice](https://app.snyk.io/badges/merge-advice/?package_manager=npm&package_name=lodash&from_version=4.17.15&to_version=4.17.20&pr_id=31842747-752f-42e7-b1f2-8fa3f51d0e21&visibility=true&has_feature_flag=false)



#### Changes included in this PR

- Changes to the following files to upgrade the vulnerable dependencies to a fixed version:
    - client/package.json
    - client/package-lock.json



#### Vulnerabilities that will be fixed
##### With an upgrade:
Severity                   | Priority Score (*)                   | Issue                   | Breaking Change                   | Exploit Maturity
:-------------------------:|-------------------------|:-------------------------|:-------------------------|:-------------------------
![high severity](https://res.cloudinary.com/snyk/image/upload/w_20,h_20/v1561977819/icon/h.png "high severity")  |  **776/1000**  <br/> **Why?** Recently disclosed, Has a fix available, CVSS 9.8  | Prototype Pollution <br/>[SNYK-JS-LODASH-590103](https://snyk.io/vuln/SNYK-JS-LODASH-590103) |  No  | No Known Exploit 

(*) Note that the real score may have changed since the PR was raised.











Check the changes in this PR to ensure they won't cause issues with your project.



------------



**Note:** *You are seeing this because you or someone else with access to this repository has authorized Snyk to open fix PRs.*

For more information:  <img src="https://api.segment.io/v1/pixel/track?data=eyJ3cml0ZUtleSI6InJyWmxZcEdHY2RyTHZsb0lYd0dUcVg4WkFRTnNCOUEwIiwiYW5vbnltb3VzSWQiOiIzMTg0Mjc0Ny03NTJmLTQyZTctYjFmMi04ZmEzZjUxZDBlMjEiLCJldmVudCI6IlBSIHZpZXdlZCIsInByb3BlcnRpZXMiOnsicHJJZCI6IjMxODQyNzQ3LTc1MmYtNDJlNy1iMWYyLThmYTNmNTFkMGUyMSJ9fQ==" width="0" height="0"/>
🧐 [View latest project report](https://app.snyk.io/org/cellxgene/project/9195ddb9-6feb-469e-ad47-f5dc24c811fe)

🛠 [Adjust project settings](https://app.snyk.io/org/cellxgene/project/9195ddb9-6feb-469e-ad47-f5dc24c811fe/settings)

📚 [Read more about Snyk's upgrade and patch logic](https://support.snyk.io/hc/en-us/articles/360003891078-Snyk-patches-to-fix-vulnerabilities)

[//]: # (snyk:metadata:{"prId":"31842747-752f-42e7-b1f2-8fa3f51d0e21","dependencies":[{"name":"lodash","from":"4.17.15","to":"4.17.20"}],"packageManager":"npm","projectPublicId":"9195ddb9-6feb-469e-ad47-f5dc24c811fe","projectUrl":"https://app.snyk.io/org/cellxgene/project/9195ddb9-6feb-469e-ad47-f5dc24c811fe?utm_source=github&utm_medium=fix-pr","type":"auto","patch":[],"vulns":["SNYK-JS-LODASH-590103"],"upgrade":["SNYK-JS-LODASH-590103"],"isBreakingChange":false,"env":"prod","prType":"fix","templateVariants":["updated-fix-title","priorityScore","merge-advice-badge-shown"],"priorityScoreList":[776]})
 2020-08-20 11:03:30 -07:00
Severiano Badajoz
1acb8e4a6f Remove support for non-chromium Edge (#1761) 
* bump browserlist Edge to 79+

* bump edge version on unsupported browser page
 2020-08-17 16:51:58 -07:00
bmccandless
298924fef5 Separate userinfo from the config endpoint (#1728) 
* Separate userinfo from the config endpoint

previously information about if the user was logged in and their username
was part of the config endpoint.
However, the config endpoint was previously static, and has a cache control.
Rather than not caching the config, a new endpoint called "userinfo"
is created to handle that information.

The config endpoint still has the non-changing part of the authentication:

  config:
    authentication:
        requires_client_login:  True/False
        login: <uri to login endoint if requires_client_login is True>
        logout: <uri to logout endoint if requires_client_login is True>

The userinfo endpoint returns this information:

  userinfo:
    is_authenticated:  True/False
    username: <string if is_authenticated>

if authentication is not enabled then the config does not have an authentication key,
and userinfo returns None.

Also in the PR are a few minor code improvements and bug fixes

Co-authored-by: Colin Megill <colinmegill@gmail.com>
 2020-08-17 13:41:03 -07:00
Colin Megill
4ad9f5875a xx, yy (#1754) 2020-08-17 11:55:49 -04:00
maniarathi
263e893b30 Revert "Patching (#1744)" (#1748) 
This reverts commit 6848f7a8b2.
 2020-08-14 11:22:39 -07:00
maniarathi
6848f7a8b2 Patching (#1744) 2020-08-13 14:36:42 -07:00
Severiano Badajoz
518768e8f8 change asset src's to S3 links (#1734) 
* add disclaimer about changing the script

* add hash for obsolete browser script

* add explicit domain img-src

* add single quotes

* add quotes to `data:`

* change order and remove single quotes

* lint, remove extra slash, and make hash an array

* add links to S3
 2020-08-12 10:38:49 -07:00
maniarathi
44c738e2f4 Bumping version of cellxgene for desktop release (#1733) 2020-08-12 09:58:52 -07:00
Severiano Badajoz
f221856ae1 add CSP sources for obsolete browser prompt (#1731) 
Adds script hash and explicit domain to `img-src` directive
 2020-08-11 16:50:46 -07:00
maniarathi
49b89ba7af Swap using href to using origin+pathname to avoid errors with including any query parameters from being passed in. (#1722) 2020-08-07 10:02:22 -07:00
Severiano Badajoz
018daacdbb create truncation edge case snapshot tests (#1695) 2020-08-07 09:54:01 -07:00
Colin Megill
c913935d90 Login / Logout button (#1718) 
* first pass auth button

* only pop anno dialogue if authenticated

* add config to ignore

* remove config
 2020-08-06 14:39:58 -04:00
Severiano Badajoz
8d96477fae Remove hash source from CSP style-src directive (#1717) 
* remove style csp hash generation + lint

* remove references to style_hashes
 2020-08-05 16:43:35 -07:00
Severiano Badajoz
b18f96da77 check for bins change for canvas draw (#1693) 
* check for bins change for canvas draw

* PR feedback
 2020-08-05 15:20:03 -07:00
maniarathi
cdae4f9f10 Reorganize the server testing directory (#1705) 2020-08-05 08:31:02 -07:00
Severiano Badajoz
8bbc183647 Explicit Browser Support (#1682) 
* add FastestSmallestTextEncoderDecoder polyfill

* remove nomodule from script import

* add browserslist

* add obsolete-webpack-plugin

* switch out modern-browser for preset-env

* add prompt on non target browser

* propagate prod changes to dev

* add core-js-3 and TextEncoder TextDecoder (#1671)

* add script to remove react, style html

* propagate changes to prod

* add script-ext-html-webpack-plugin for async

* more styling

* add eslint-plugin-compat

* extend compat plugin

* add existing polyfills

* add github fetch polyfill

* add AbortController polyfill

* change promptOnNonTargetBrowser to false

* propagate

* add browser links

* prettier

* add browser support to readme

* move polyfills to webpack

* remove CDN encoder polyfill

* Add no Explorer support

* fix incorrect package name

* propagate changes

* Update README.md

Co-authored-by: Ambrose J Carr <ambrosejcarr@users.noreply.github.com>

* add new deps

* create shared config

* swap out html-loader for filestream

* sanitize template

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
Co-authored-by: Ambrose J Carr <ambrosejcarr@users.noreply.github.com>
 2020-08-03 12:50:09 -07:00
dependabot[bot]
bb2326525e Bump elliptic from 6.5.2 to 6.5.3 in /client (#1697) 
Bumps [elliptic](https://github.com/indutny/elliptic) from 6.5.2 to 6.5.3.
- [Release notes](https://github.com/indutny/elliptic/releases)
- [Commits](https://github.com/indutny/elliptic/compare/v6.5.2...v6.5.3)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2020-07-31 13:54:56 -04:00
Bruce Martin
f2fbeff511 add support for corpora default_embedding field (#1696) 
* fix mispelling

* re-implement re-embedding

* always load base embedding to fetch counts

* format

* lint

* fix tests

* lint

* fix accept handling

* test log

* more debug

* more

* more

* more

* more

* remove logging

* logging

* jsonify

* remove debugging logs

* lint

* clean up errors a bit

* fix issue found in PR review

* add support for corpora default_embedding

* fix botched merge

* PR review

* PR review
 2020-07-31 07:36:48 -07:00
Severiano Badajoz
055511fe60 fix colorby popup settings (#1694) 2020-07-30 15:33:48 -07:00
Bruce Martin
75cb513dd9 re-implement re-embeddings (#1679) 
* fix mispelling

* re-implement re-embedding

* always load base embedding to fetch counts

* format

* lint

* fix tests

* lint

* fix accept handling

* test log

* more debug

* more

* more

* more

* more

* remove logging

* logging

* jsonify

* remove debugging logs

* lint

* clean up errors a bit

* fix issue found in PR review

* PR review changes
 2020-07-30 12:31:36 -07:00
Bruce Martin
bbef27b8c9 minor prose change on embedding chooser (#1678) 2020-07-27 19:34:04 -07:00
Bruce Martin
14cd1b9f0b work around blueprint restriction (#1677) 2020-07-27 12:52:22 -07:00
Bruce Martin
0a626537d5 subset embedding UI improvement (#1667) 
* add user flag feature to annomatrix

* add implicit subsetting for partial embeddings

* lint

* add embedding cell counts to embedding choice menu

* layout
 2020-07-27 09:58:14 -07:00
dependabot[bot]
ad1bda07e9 Bump codecov from 3.7.0 to 3.7.1 in /client (#1654) 
Bumps [codecov](https://github.com/codecov/codecov-node) from 3.7.0 to 3.7.1.
- [Release notes](https://github.com/codecov/codecov-node/releases)
- [Commits](https://github.com/codecov/codecov-node/compare/v3.7.0...v3.7.1)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2020-07-27 11:53:57 -04:00
Bruce Martin
83d572cde2 force categorical treatment of user annotations (#1663) 2020-07-22 17:02:19 -07:00
Colin Megill
03bad04436 Embedding button to lower left, cell selection (#1658) 
* embedding

* menu bottom left

* button

* change gutters to support lower toolbar

* fix scatterplot layout

* fix tests to match new layout

* fix smoke tests to match new layout

* better sentence, dataset.nObs to top

* scatterplot position

Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
 2020-07-22 18:48:21 -04:00
Bruce Martin
a44da11f3f correctly handle non-string categoricals (#1660) 2020-07-22 12:14:31 -07:00
Bruce Martin
009fa2ff02 clear selection state upon subset (#1655) 2020-07-21 12:51:39 -07:00
Bruce Martin
2715157793 categorical UI improvements (#1649) 
* return undefined for unknown fields

* memoize fetch response

* handle rename of user annotation

* performance and cleanup

* fix snapshots

* fix comment

* lint
 2020-07-20 08:52:41 -07:00
Bruce Martin
410566f5e1 fix label selection on trunctated category lists (#1646) 2020-07-17 17:16:15 -07:00