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018f653ec6be6c3e1846ea847fbb7ce295ec892a
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Author SHA1 Message Date
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
0.16.0 		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
bmccandless
ce13a9c7ca oauth support, add the token in a configuration specified cookie (#1702) 
* oauth support, add the token in a configuration specified cookie

Previously, the id token was stored in the session token.
Now, it can be placed in a different cookie with different properties.
 2020-08-03 10:45:21 -07:00
bmccandless
2afa48cf11 add oauth authentication (#1681) 
* add oauth authentication

Add support for OAuth2.

Change the interface to AuthTypeBase
  - better handling of config parameters
  - add a complete_setup function for additional setup steps

Added a function wrapper to enforce authentication for the
routes that require authenticaiton.

* change fsspec requirement

fsspec 0.8.0 breaks our tests
it imports a module that is does not require.
 2020-07-31 18:16:57 -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
Madison Dunitz
d748b9f691 use czi-sci-single-cell-eng github user/access token (#1698) 2020-07-30 15:54:57 -05:00
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
bmccandless
bd147abb3f Fix eb logging. (#1692) 
It now logs the requests to the file

Fixes #1611
 2020-07-29 16:03:47 -07:00
bmccandless
5633d7c761 Fix server exception classes (#1683) 
str(e) and e.message will both show the error message.
refactored the error.py file to simplify our exception class definitions
 2020-07-29 13:05:59 -07:00
maniarathi
af3a76c354 Adding relative links support to jekyll (#1680) 2020-07-29 12:38:46 -07:00
Bruce Martin
59f989d26f initial support for corpora schema conventions (#1676) 
* initial support for corpora schema conventions

* remove debugging print

* add corpora util module

* tests

* lint

* PR review edits

* PR changes

* more PR changes

* more PR chnages

* PR fixes

* formatting

* PR updates

* lint

* PR review
 2020-07-28 17:32:27 -07:00
bmccandless
5285556415 Add basic authentication in the server (#1670) 
* Add basic authentication in the server

A pattern for creating authentication methods is introduced, with three
authentication types defined:
  none - no authentication
  session - like the current session based auth used for user annotations
  test - used to test the login/logout process end to end

The config endpoint now returns informations about the authentication, like if
the user is authenticated and their username.  The redirect uri's for login and
logout are also returned if the authentication type requires login

This is the first a several PRs for authentication.

*. Update server tests to avoid hardcoded ports

test_api and test_nan_rest now use a common function for starting a test server,
than will initially choose a random port.
 2020-07-28 13:28:30 -07:00
Bruce Martin
bbef27b8c9 minor prose change on embedding chooser (#1678) 2020-07-27 19:34:04 -07:00
maniarathi
38ce1f90fb Update issue templates 2020-07-27 12:57:59 -07:00
maniarathi
98c5cae9f4 Update issue templates 2020-07-27 12:55:44 -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
maniarathi
c25dd33d28 Removing duplicate index.html and regenerating files. (#1672) 2020-07-27 09:57:48 -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
Ambrose J Carr
27f75641cc update index links to include 'post' directory (#1666) 
* update index links to include 'post' directory

* rebuild github pages site

* document how to develop documentation

* build, not serve
 2020-07-23 21:49:57 -07:00
bmccandless
0344cfacce Fix the app config for reembedding and add a test (#1664) 
* Fix the app config for reembedding and add a test

* Add scanpy to requirements-dev
 2020-07-23 12:27:53 -07:00
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