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45 Commits

Author SHA1 Message Date
Charlotte Weaver
39414503bd Revert "Format loaded dataset" 2018-08-14 10:40:21 -07:00
Charlotte Weaver
b884487789 Merge branch 'master' into csweaver/api-v2-init 2018-08-13 15:48:06 -07:00
Charlotte Weaver
ddaa7016a5 Quote formatting 
' => "
 2018-08-13 15:00:23 -07:00
Charlotte Weaver
d44d267bda Initial tests for the rest v2 refactor 
testing the annotations and the data format validation
 2018-08-10 16:57:41 -07:00
Charlotte Weaver
55fa9b892a Splitting the format validation and mandatory annotations 2018-08-10 16:38:07 -07:00
Charlotte Weaver
21a1f00a64 Set static folder to correct location 2018-08-09 14:25:11 -07:00
Charlotte Weaver
e96653b826 Serving favicon correctly 2018-08-09 14:14:45 -07:00
Charlotte Weaver
58000c1815 Format loaded dataset 
- create cell and gene ids
- recast numbers to float32/int32
 2018-08-09 11:23:43 -07:00
Charlotte Weaver
246f4e41f0 Merge pull request #156 from chanzuckerberg/csweaver/infer-metadata 
Infer schema if none exists
 2018-08-08 11:56:13 -07:00
Charlotte Weaver
af85792cce Don't forget unsigned ints! 2018-08-08 11:20:01 -07:00
Charlotte Weaver
f4780a9806 Moved add to parser out of try block. 2018-08-08 11:18:06 -07:00
Charlotte Weaver
2a11af2550 Formatting 2018-08-07 17:01:19 -07:00
Charlotte Weaver
e5c7c0c44a Warn instead if print when scanpy isn't available 2018-08-07 16:57:07 -07:00
Charlotte Weaver
bf19bb7dce Formatting 2018-08-07 16:38:25 -07:00
Charlotte Weaver
c2b3f331cf Add layout and diffexp calculations to cli options 2018-08-07 16:37:47 -07:00
Charlotte Weaver
499b9551f1 moved scanpy parser to scanpy class 2018-08-07 16:37:02 -07:00
Charlotte Weaver
ccee3e0a38 api host 0.0.0.0 -> 127.0.0.1 2018-08-07 15:43:13 -07:00
Charlotte Weaver
a2b699b05d Infer schema if none exists 2018-08-06 16:39:18 -07:00
Charlotte Weaver
e682028b8e Use flask's current_app 2018-08-03 10:54:43 -07:00
Charlotte Weaver
8dbb131afd Move data to a property of the app object 2018-08-02 16:18:17 -07:00
Charlotte Weaver
e11b905836 Cleaning up import statements 2018-08-02 11:34:00 -07:00
Charlotte Weaver
116cef551c Switch to default timeout for cache 2018-08-02 11:28:44 -07:00
Charlotte Weaver
0a36fac142 10 day cache (down from 1000) 
I can expect a scientist to leave this running over the weekend on their laptop and still expect fast results. If someone leaves it running for a few years the data can probably be safely recalculated.
 2018-08-01 15:48:56 -07:00
Charlotte Weaver
69fca7ea8b Using flask_caching instead 
More recent module, same API
 2018-08-01 15:46:04 -07:00
Charlotte Weaver
7642251d44 Add simple cache to backend 2018-08-01 13:32:04 -07:00
Charlotte Weaver
de5e0f4ea7 Address PR review issues 2018-07-20 11:43:31 -07:00
Charlotte Weaver
2c7a11ab80 Added cli command for run 2018-07-19 17:21:28 -07:00
Charlotte Weaver
45f61d87d7 Initial CLI 
added basic cli for running
 2018-07-18 21:45:07 -07:00
Charlotte Weaver
895cfcebe0 Added initial travis config file 2018-07-18 10:21:24 -07:00
Charlotte Weaver
28d341cf1c Fix default path for dataset 2018-07-17 16:03:06 -07:00
Charlotte Weaver
a5423a6911 Adding minor tests to scanpy calculation code 2018-07-16 11:48:53 -07:00
Charlotte Weaver
05b9a6833d Add tests for scanpy engine 2018-07-16 11:48:53 -07:00
Charlotte Weaver
02799cea8e No relative imports "up" 2018-07-12 12:59:34 -07:00
Charlotte Weaver
ba9e5f1e41 flake8/lint cleanup 2018-07-12 11:52:24 -07:00
Charlotte Weaver
f466ef6553 Added entry point to run cellxgene from console 2018-07-10 12:56:42 -07:00
Charlotte Weaver
0639759a90 Initial packaging working 
pip install works if client files are built and moved manually
 2018-07-06 15:44:22 -07:00
Charlotte Weaver
cd1b67fd09 Rename diffexpression 2018-07-06 15:41:08 -07:00
Charlotte Weaver
5b9ddfa1a6 Added documentation to filter 2018-07-06 15:40:21 -07:00
Charlotte Weaver
354eacc3c8 Remove cell ids from engine 
Previously I just removed them from the driver
 2018-07-06 15:38:42 -07:00
Charlotte Weaver
e3bf06ca61 Config file no longer necessary 
Config is solely from environment variables instead.
 2018-07-06 10:13:24 -07:00
Charlotte Weaver
85506db971 Updating to latest cellxgene client code 
Fixes the build error in the old version. 

Reverted the API version since we changed directions from updating the API to refactoring the server structure instead.
 2018-07-05 13:37:26 -07:00
Charlotte Weaver
2da62720dd Better documentation for driver/engines 
Removed the REST v2.0 documentation in favor of getting v1.0 working with driver/engine model
 2018-06-29 17:17:14 -07:00
Charlotte Weaver
56c932a443 Fixed categorical filter not being converted to type, added tests 2018-06-29 17:16:00 -07:00
Charlotte Weaver
40f5b94075 Consistency with quotes 
' -> "
 2018-06-29 13:14:58 -07:00
Charlotte Weaver
dd5fa57259 renaming backend, cellxgene to server, client respectively 2018-06-26 11:41:32 -07:00