Commit Graph
519 Commits
Author SHA1 Message Date
bkmartinjr 91e15e9026 gene set reducer 2021-01-19 14:59:46 -08:00
Colin Megill d1e117ebb9 Merge branch 'main' into colinmegill/geneset-prototype 2021-01-12 13:35:46 -08:00
dependabot[bot] db559467a2 Bump ini from 1.3.5 to 1.3.7 in /client (#2000)
Bumps [ini](https://github.com/isaacs/ini) from 1.3.5 to 1.3.7.
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/npm/ini/commit/c74c8af35f32b801a7e82a8309eab792a95932f6"><code>c74c8af</code></a> 1.3.7</li>
<li><a href="https://github.com/npm/ini/commit/024b8b55ac1c980c6225607b007714c54eb501ba"><code>024b8b5</code></a> update deps, add linting</li>
<li><a href="https://github.com/npm/ini/commit/032fbaf5f0b98fce70c8cc380e0d05177a9c9073"><code>032fbaf</code></a> Use Object.create(null) to avoid default object property hazards</li>
<li><a href="https://github.com/npm/ini/commit/2da90391ef70db41d10f013e3a87f9a8c5d01a72"><code>2da9039</code></a> 1.3.6</li>
<li><a href="https://github.com/npm/ini/commit/cfea636f534b5ca7550d2c28b7d1a95d936d56c6"><code>cfea636</code></a> better git push script, before publish instead of after</li>
<li><a href="https://github.com/npm/ini/commit/56d2805e07ccd94e2ba0984ac9240ff02d44b6f1"><code>56d2805</code></a> do not allow invalid hazardous string as section name</li>
<li>See full diff in <a href="https://github.com/isaacs/ini/compare/v1.3.5...v1.3.7">compare view</a></li>
</ul>
</details>
<details>
<summary>Maintainer changes</summary>
<p>This version was pushed to npm by <a href="https://www.npmjs.com/~isaacs">isaacs</a>, a new releaser for ini since your current version.</p>
</details>
<br />


[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=ini&package-manager=npm_and_yarn&previous-version=1.3.5&new-version=1.3.7)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---

<details>
<summary>Dependabot commands and options</summary>
<br />

You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language

You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/chanzuckerberg/cellxgene/network/alerts).

</details>
2021-01-04 17:14:45 -08:00
dependabot[bot] 96362b0b98 Bump urijs from 1.19.2 to 1.19.5 in /client (#2012)
Bumps [urijs](https://github.com/medialize/URI.js) from 1.19.2 to 1.19.5.
- [Release notes](https://github.com/medialize/URI.js/releases)
- [Changelog](https://github.com/medialize/URI.js/blob/gh-pages/CHANGELOG.md)
- [Commits](https://github.com/medialize/URI.js/compare/v1.19.2...v1.19.5)

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-01-04 16:45:23 -08:00
Marcus Kinsella 46d02b1987 Handle schema v1.1.0 (#2002)
Correctly display datasets that follow schema version 1.1.0
2020-12-14 15:20:29 -08:00
Colin Megill 8248fce412 Merge branch 'main' into colinmegill/geneset-prototype 2020-12-08 14:51:22 -08:00
Colin Megill 0a9a78bd85 merge main 2020-12-03 15:25:49 -08:00
Severiano Badajoz 0b91371ea8 check if viewport has changed and render accordingly (#1996) 2020-12-03 15:14:57 -08:00
bmccandless 2cc02a84cb Convert float annotations if possible. (#1987)
* Convert float annotations if possible.

The client converts all arrays to floats.
If a category contains integer labels, and that category is copied, it will contains floats (e.g 1.0 instead of 1).
When that category is put back to the server, it fails in the tiledb code, which does not accept floats.
The solution is to convert a float category to integer, if possible.

  #1984

* updates
2020-11-20 17:01:53 -06:00
Timmy Huang 2cf55ab819 thuang-compress-annotation (#1980)
* thuang-compress-annotation

* compress test

* use zlib.decompress directly
2020-11-17 14:05:07 -08:00
Colin Megill 36939d99fa geneset show mean expression 2020-11-17 12:55:17 -08:00
Colin Megill 0ee62a86a0 render diffexp as geneset 2020-11-17 12:42:16 -08:00
Colin Megill a9665df7e7 move create category to top 2020-11-17 12:13:02 -08:00
Colin Megill f1d53d6dc4 don't clear diffexp on subset 2020-11-17 12:04:23 -08:00
Colin Megill db4ac5e1e5 bump number of genes to 50 2020-11-17 11:23:13 -08:00
dependabot[bot]andSeveriano Badajoz 85fc000418 Bump dot-prop from 4.2.0 to 4.2.1 in /client (#1954)
Bumps [dot-prop](https://github.com/sindresorhus/dot-prop) from 4.2.0 to 4.2.1.
- [Release notes](https://github.com/sindresorhus/dot-prop/releases)
- [Commits](https://github.com/sindresorhus/dot-prop/compare/v4.2.0...v4.2.1)

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>
2020-11-09 22:05:34 -08:00
06b88cda20 do not update GPU buffers if data has not changed (#1967)
Co-authored-by: maniarathi <mani.arathi@gmail.com>
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
2020-11-09 10:41:39 -08:00
Bruce Martin b5856ff9bc fix accidental state error (#1966) 2020-11-04 18:46:04 -08:00
Severiano Badajoz d87551ce5e fix version check (#1968)
Inverted the schema version check so that we check that it IS 1.0.0.

![image](https://user-images.githubusercontent.com/8716829/98184898-5c897b00-1ec0-11eb-89f7-c293dfbe8439.png)
2020-11-04 17:43:41 -08:00
Severiano Badajozandmaniarathi a5c9ae2432 Data drawer final round of prod QA fixes (#1955)
* add long title

* add organism to Dataset Metadata and create headers

* begin HTMLTable for metadata

* switch out truncating for scrolling

* add optional chaining to redux state mapping

Co-authored-by: maniarathi <mani.arathi@gmail.com>
2020-11-04 09:43:43 -08:00
Severiano BadajozandMadison Dunitz 727af83152 remove conditional rendering cases from color legend (#1952)
* Revert "Remove Continuous vars with 1 value from histogram, add to info drawer (#1927)"

This reverts commit 242546371b.

* remove conditional rendering cases

* ignore pointer events

Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
2020-10-28 15:35:28 -07:00
Severiano Badajoz 924b518492 Revert "Remove Continuous vars with 1 value from histogram, add to info drawer (#1927)" (#1953)
This reverts commit 242546371b.
2020-10-27 17:12:13 -07:00
maniarathi 9793398737 Add in missing previous crossfilter which was causing the re-embedding feature to fail. (#1936) 2020-10-21 09:16:13 -07:00
Severiano Badajoz c9f9549118 Adopt JS standards once userinfo data is in frontend (#1930) 2020-10-16 11:59:28 -07:00
Madison Dunitz 242546371b Remove Continuous vars with 1 value from histogram, add to info drawer (#1927)
* remove single val continous metadata from histogram, add to info drawer

* refactor to save singleContinuous values in state

* fix edge case, single continuous values reappeard in rsb when clipped
2020-10-14 12:46:24 -05:00
maniarathi 798976e4c1 Fix custom color handling (#1929) 2020-10-13 15:47:56 -07:00
maniarathi 5325495123 Speed up dataset drawer rendering (#1926) 2020-10-12 11:20:58 -07:00
Severiano Badajozandczimergebot beb46bf3df add and check system arg to state auth type in e2e test(#1924)
* add and check system arg to state auth type

* add tolower

Co-authored-by: czimergebot <35308261+czimergebot@users.noreply.github.com>
2020-10-09 12:42:02 -06:00
maniarathi 86ff48ae36 Revert "Allow columns encoded in float64 to be rendered as part of continuous value histograms. (#1905)" (#1925)
This reverts commit b048fd8d9a.
2020-10-09 10:09:32 -07:00
Timmy Huang c01a2c72b6 thuang-1840-authn-prompt (#1911) 2020-10-08 16:57:53 -07:00
Severiano Badajoz 6677d0de56 disable profile picture (#1923) 2020-10-08 12:16:02 -06:00
Severiano Badajoz c4c48b9a57 create e2e test for auth buttons (#1907)
This PR adds a few helpful additions regarding authentication.

Changes:
* e2e tests are now run on test_oauth via a passed config.yaml 
* node dev server correctly handles `/login` and `/logout` endpoints to make developing for auth easier
* Introduced auth e2e tests to check that buttons display and work
2020-10-08 10:02:40 -07:00
Severiano BadajozandTimmy Huang 1c4c501c43 Auth UI tweaks (#1915)
* remove auth buttons and dataset info from info menu

* add auth buttons to menubar

* remove auth from top left

* new auth buttons

* move infomenu to lsb dir

* styling fixes

* feedback

* more feedback

Co-authored-by: Timmy Huang <thuang@chanzuckerberg.com>
2020-10-07 15:02:55 -07:00
Colin Megill 6f23f1e7e5 mini 2020-10-06 17:32:05 -07:00
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]andSeveriano Badajoz 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 Badajozandczimergebot 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
Colin Megill 86d369e63e toggleable 2020-09-29 11:17:40 -07:00
Colin Megill 77c44af0b1 expand button 2020-09-28 23:03:13 -07:00
Colin Megill 274298484c add isExpanded state to gene, and pass to histogram 2020-09-28 16:11:52 -07:00
Colin Megill 5b846e5dfa remove have fetched 2020-09-28 16:11:20 -07:00
Severiano Badajoz 21dfdb91a9 skip user annos when building dataset metadata (#1881) 2020-09-28 13:17:14 -07:00
Colin Megill 8f94736956 test data 2020-09-28 12:48:53 -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
Colin Megill 58e81ba020 re-add isuserdefined 2020-09-22 13:55:37 -07:00
Colin Megill c93c5a375c reenable add genes 2020-09-21 17:51:34 -07:00