Commit Graph
1442 Commits
Author SHA1 Message Date
Colin Megill ac475d72d9 chevron after 2021-02-10 11:26:50 -08:00
Colin Megill e8f0a1d2cb icons, language consistency 2021-02-10 11:22:36 -08:00
Colin Megill fec1736820 prepopulate geneset with genes from modal 2021-01-28 15:07:31 -08:00
Colin Megill 84fcbb8652 handle delete gene from set 2021-01-28 13:54:32 -08:00
Colin Megill 9760277642 prototype: remove csv upload placeholder 2021-01-28 10:34:20 -08:00
Colin Megill 7c0569b9b6 add geneset, add gene, delete set 2021-01-27 13:05:48 -08:00
bkmartinjr b9479705ac rename data-dir cli param 2021-01-23 08:34:58 -08:00
bkmartinjr e0a0b77c5b add autosave 2021-01-22 14:07:34 -08:00
bkmartinjr 023976c992 client/src/actions/ 2021-01-22 14:06:43 -08:00
Colin Megill 996393f260 Merge remote-tracking branch 'origin/colinmegill/geneset-prototype' into colinmegill/geneset-prototype 2021-01-22 12:09:26 -08:00
Colin Megill c6ad970c41 add gene modals 2021-01-22 12:09:22 -08:00
bkmartinjr 0fd9579d00 fix typo 2021-01-22 10:32:54 -08:00
bkmartinjr 818bd9d80f fix sniffing bug 2021-01-21 15:37:43 -08:00
bkmartinjr 0001928317 wire e2e gene set loading prototype 2021-01-21 15:01:10 -08:00
bkmartinjr 7f1bb3e21e add geneset UI reducer 2021-01-19 15:00:49 -08:00
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 />


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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
bmccandless 7599af252d Update compatibility test (#2009)
Add comment in requirements about h5py and anndata.

  #1963
2020-12-21 14:38:07 -06:00
Trent Smith f07e174a06 Fix PR Template (#1999) 2020-12-17 16:29:23 -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
Trent Smith c428242878 pull request template (#1997) 2020-12-03 12:13:31 -08:00
Isaiah Norton 9be086b1e8 Use sparse=True for from_pandas (#1994) 2020-12-02 13:39:19 -08:00
maniarathi 9a34264f92 Pin tiledb version to exclude 0.7.2 (#1993) 2020-11-30 11:54:33 -05:00
maniarathi 66e55ba59a Replace outdated locustio package with locust package. (#1992) 2020-11-30 10:11:57 -05:00
maniarathi f700fb7757 Setup codeql scanning for security and code quality analysis (#1991) 2020-11-24 21:53:10 -05:00
maniarathi ae310097dd Fix typo (#1990) 2020-11-24 12:23:21 -05:00
maniarathi ea70a35a01 Fixing locust scale tests for cellxgene loading apis and adding a Github Actions workflow to run the tests every Sunday. (#1988) 2020-11-24 09:08:57 -08:00
maniarathi 16718f392f Sorry! Undo-ing commit to main 2020-11-24 10:22:24 -05:00
maniarathi ad6b1928e4 Upgrade anndata and h5py 2020-11-24 10:21:24 -05:00
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
Marcus Kinsella f77038ad58 Permit other keys in the cxguser cookie (#1982) 2020-11-18 17:58:33 -08:00
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
bmccandless 095db02439 Remove deprecated health endpoint (#1943)
NOTE:  do not push to main until the new path has been terraformed into all the environments.

 #1846
2020-11-13 10:49:11 -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
Isaiah Norton 34742b9a94 Add link to dev_docs in Contributing section (#1957) 2020-11-09 21:57:00 -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
bmccandless 23714bc9f8 Fix bug that occurs when all categories are removed. (#1974)
Previously if the user remove all annotations, the code would still generate a tiledb uri
in the write_labels call, and add that to the database.  A tiledb array would not be written in this case.
When the read_labels was then called, it would find the entry in the database, attempt to open
the tiledb array, then fail.

The patch here will set the tiledb_uri to the empty string if all categories are removed.
When read_labels is called, it will see the empty uri and return None.
Furthermore, if the database does have a tiledb_uri that does not exist, or cannot be read,
then the code will now log a warning, and return None (instead of throwing an exception,
which results in a server error).

 #1932
2020-11-06 18:04:14 -08:00
Marcus Kinsella e892e64685 Convert HGNC ids to their symbol (#1972)
There are entries in some var indexes like HGNC:18790. We'd like to convert that to its symbol, NSG1.
2020-11-06 09:27:49 -08:00
Marcus Kinsellaandmaniarathi 39a1124c35 Fix manifest to include schema definitions (#1965)
🤦

Co-authored-by: maniarathi <mani.arathi@gmail.com>
2020-11-05 09:41:05 -08:00
Bruce Martin b5856ff9bc fix accidental state error (#1966) 2020-11-04 18:46:04 -08:00