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558b68d0d5c7beef0de5eb1680219f33abda5a2a
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459 Commits
Author SHA1 Message Date
Colin Megill 558b68d0d5 geneset dialogue stub 2020-08-31 13:59:40 -04:00
Colin Megill 5a8ebef0d0 menus and buttons 2020-08-26 21:02:33 -04:00
Colin Megill 8befeda444 Merge branch 'main' into colinmegill/geneset-prototype 2020-08-25 16:17:49 -04:00
Severiano Badajoz 0a10b3ec2a sort object keys to our specification before generating user colormap (#1792) 2020-08-25 12:25:55 -07:00
Colin Megill 9f03491094 color by geneset stub 2020-08-25 15:21:42 -04:00
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 DunitzMadison DunitzmaniarathiSeveriano Badajoz
 		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
bmccandlessandColin Megill 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 cc6416168b mock reducer 2020-08-17 16:36:12 -04:00
Colin Megill 4ad9f5875a xx, yy (#1754) 2020-08-17 11:55:49 -04:00
Colin Megill bef631396c Merge branch 'main' into colinmegill/geneset-prototype 2020-08-17 10:49:57 -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 BadajozAmbrose J CarrTimmy Huang
 		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 Megillandbkmartinjr 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
Colin Megill adb0b65058 Merge branch 'main' into colinmegill/geneset-prototype 2020-07-20 12:15:11 -04:00
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
Bruce Martin b6412b5b8a ensure there is always an unassigned label in user created category (#1644) 2020-07-17 13:22:26 -07:00
Bruce Martin 7b99d1a1b8 update JS deps (#1642) 2020-07-17 12:38:54 -07:00
Bruce Martin 18d0fd78cf fix view stack bug (#1640) 2020-07-16 16:14:52 -07:00
bmccandless f223d7504e Small fix for handling display versions (#1625) 
* Small fix for handling display versions

Making a distinction between __version__ and the version we display in the info panel (displayr_version).
The hosted cellxgene can overwrite the display_version using a plugin.

Improve version handling in the customized assets
 2020-07-16 15:11:37 -07:00
Severiano Badajoz ed23d5dd9d fix truncation edge cases (#1637) 2020-07-16 14:00:57 -07:00
Bruce Martin c592ff35f6 improve graph loading UI (#1636) 2020-07-16 11:07:06 -07:00
Bruce Martin 2265bfc921 render perf refinements (#1632) 
* render performance improvements

* improve render perf

* remove logging

* lint

* improve memoziation
 2020-07-16 09:53:46 -07:00
Bruce Martin 17c1145ee4 protect against reference detach (#1634) 2020-07-16 09:53:15 -07:00
Bruce Martin 68cc0ae16c simply state management (#1628) 
* simply viewport size state management

* lint
 2020-07-15 10:31:42 -07:00