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
54b42607ae
Update the location of deployment assets for the eb server ( #1806 )
...
put deploy scripts in /static/cellxgene/deploy instead of /static/deploy
fixed chanzuckerberg/corpora-data-portal#558
2020-08-31 18:26:35 -07:00
maniarathi
ed865e9a57
Update the release process for community release to include release candidate versioning ( #1802 )
2020-08-31 16:16:21 -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
bmccandless
ab1b9368a0
fix pca call in reembeddings ( #1793 )
...
This had the wrong dim passed into n_comps,
and so failed when the number of genes was less than 50.
2020-08-25 17:21:39 -07:00
Severiano Badajoz
0a10b3ec2a
sort object keys to our specification before generating user colormap ( #1792 )
2020-08-25 12:25:55 -07:00
Prete
eb05d1cb5c
Update Dockerfile ( #1775 )
...
* Update Dockerfile
- Update Ubuntu Focal (20.04)
- Add `DEBIAN_FRONTEND=noninteractive` to prevent dialog boxes during installation
* Changed 'pip3 install --upgrade pip' to 'python3 -m pip install --upgrade pip' as described here https://github.com/pypa/pip/issues/5599
2020-08-25 09:37:38 -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
maniarathi
bc150a8469
Fixing bugs in cxg conversion tool ( #1782 )
2020-08-22 09:53:59 -07:00
maniarathi
a5c9ffa880
When reading annotations from tiledb, check if the values are byte literals and if so, decode them. Also pin s3f3 to 0.4.2. ( #1788 )
2020-08-22 09:42:11 -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>
#### 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
:-------------------------:|-------------------------|:-------------------------|:-------------------------|:-------------------------
 | **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 )
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[//]: # (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
bmccandless
924aaf9aef
Allow user_annotations in the eb app ( #1781 )
2020-08-18 17:13:57 -07:00
bmccandless
950be4426d
Handle the refresh token in oauth authentication ( #1766 )
...
* Handle the refresh token in oauth authentication
If the token has expired, then it can be refreshed to get a new token.
This is automatically handled by the server without the client being aware.
Also in the PR:
- refactor the auth_oauth.py file to more simply handle the save/restore of the token,
and the refresh token
- added an end2end test for oauth, which also tests refresh.
* adding python-jose and Authlib to requirements-dev.txt
They are needed in the auth_oauth test
2020-08-18 14:41:15 -07:00
maniarathi
053f39d49e
Cleaning up one script that makes use of the non-existent cxgtool. ( #1765 )
2020-08-17 18:40:26 -07:00
maniarathi
994c20c094
Move cxgtool into CLI and modularize conversion functions ( #1701 )
2020-08-17 17:28:29 -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
508889f74b
Refactoring cxg utility classes in preparation for CXG conversion tooling ( #1739 )
2020-08-14 16:51:13 -07:00
Madison Dunitz
b034055c35
update to get_secrets_key ( #1755 )
...
* raise exception when get_secrets fails, get db_uri and set as a default_dataset_config var
* log as info not an error
2020-08-14 18:17:21 -05:00
maniarathi
263e893b30
Revert "Patching ( #1744 )" ( #1748 )
...
This reverts commit 6848f7a8b2
2020-08-14 11:22:39 -07:00
Madison Dunitz
6a82030558
remove db_uri secret ( #1751 )
...
* remove db_uri secret
* add test to catch bug in future
2020-08-14 12:38:46 -05:00
Severiano Badajoz
018f653ec6
Sunset Heroku support ( #1740 )
...
* remove experimental heroku
* add aiohttp for dataset loading via url
* Add heroku deprecation section to docs
* remove Heroku related files from root
2020-08-14 10:22:29 -07:00
bmccandless
905308e09f
Move psycopg2==2.7.7 from requirements.txt to requirements-dev.txt ( #1747 )
2020-08-13 21:20:13 -07:00
bmccandless
3c04529523
Fix error message when datapath and dataroot are not provided ( #1746 )
...
* Fix error message when datapath and dataroot are not provided
Previously:
$ cellxgene launch
cellxgene] Starting the CLI...
AttributeError: 'NoneType' object has no attribute 'startswith'
With this fix:
$ cellxgene launch
[cellxgene] Starting the CLI...
Error: missing datapath
* lint
2020-08-13 21:10:02 -07:00
Madison Dunitz
2689d8d2c0
Create hosted user annotations [1685] ( #1726 )
...
* add function to retrieve latest annotation from db, db updates
* read and write tiledb arrays
* adding tests
2020-08-13 19:07:17 -05:00
Severiano Badajoz
1c4bb84f35
Properly generate hash and provide how-to ( #1745 )
...
* properly generate hash and provide how-to
* Add link to this PR
2020-08-13 16:50:54 -07:00
maniarathi
6848f7a8b2
Patching ( #1744 )
2020-08-13 14:36:42 -07:00
Timmy Huang
dda530a67c
add-GHActions-timeout-for-smoke-tests ( #1743 )
...
We need to explicitly set timeout for smoke tests, since GH Action's default is 360 mins (6 hours 😱 )
https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobsjob_idtimeout-minutes
Thank you!
2020-08-13 13:18:01 -07:00
Severiano Badajoz
a23aaa131d
regenerate hash and fix url ( #1742 )
...
The script hash had a typo in it and was incorrectly generated. The URL in the `img-src` directive also did not need to be encased in single-quotes.
Reviewers please double-check my hash generation against the inline-script here: https://github.com/chanzuckerberg/cellxgene/blob/main/client/configuration/webpack/obsoleteHTMLTemplate.html
2020-08-13 11:17:13 -07:00
Severiano Badajoz
53a268fb71
Surround script hash in single quotes ( #1735 )
...
* 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
* surround script has in single quotes
2020-08-12 11:31:12 -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
Madison Dunitz
80f6137528
retrieve latest annotation from db ( #1723 )
...
* add function to retrieve latest annotation from db, db updates
* dont create directory in s3
2020-08-11 15:48:12 -05:00
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
bmccandless
4291f6005d
fix logout for auth0 ( #1719 )
...
* fix logout for auth0
the redirect from logout needs to be registered, and therefore cannot
be an arbitrary path in the server. When the user logs out, they are
redirected to the index page
* no need to provide dataset to logout url
2020-08-06 11:52:19 -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
bmccandless
b5e5ee0168
Update hosted app to get the oauth client secret from the secret manager ( #1713 )
...
* Update the hosted app to get the oauth client secret from the secret manager
* fix to eb app, and set no cache on oauth endpoints
2020-08-05 12:00:35 -07:00
maniarathi
0d94c9e092
DRY-ing flatbuffer code ( #1716 )
2020-08-05 11:56:34 -07:00
maniarathi
cdae4f9f10
Reorganize the server testing directory ( #1705 )
2020-08-05 08:31:02 -07:00
Marcus Kinsella
550847f763
Add dataset 29 ( #1712 )
2020-08-04 16:03:44 -07:00
Marcus Kinsella
6bda27f554
Add datasets 45-47 ( #1706 )
2020-08-04 11:07:08 -07:00
Madison Dunitz
f632a8db91
Dunitz/db setup ( #1619 )
...
* initial database setup
2020-08-03 17:54:06 -05:00
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
