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Author SHA1 Message Date
Alok Saldanha
5a650334df #81 moved gene set check into fileitem_source 2023-07-06 08:18:50 -06:00
george-hall-ucl
81c8ce4219 #81 Add support for gene sets 
This adds the flag `GATEWAY_ENABLE_GENE_SETS` to enable support for gene
sets.  To simplify implementation, activating this flag also activates
`GATEWAY_ENABLE_ANNOTATIONS`.  The gene sets are saved in a file that
has the same name as the annotations `csv` but with `_gene_sets`
appended to the file name (before the extension).  This file is hidden
in filecrawler, and the gene sets are loaded when the associated
annotations file is loaded.

If the annotations file is missing, then an Exception is raised.

I have updated one unit test to make it expect
`--disable-gene-sets-save` in the default case (i.e. if
`GATEWAY_ENABLE_ANNOTATIONS = 0`).  All units tests pass.

I have updated the README to document `GATEWAY_ENABLE_GENE_SETS`.
 2023-07-06 07:59:12 -06:00
Alok Saldanha
390fe24ea4 prepare for 0.3.10 release v0.3.10 2022-06-20 21:50:42 -04:00
Alok Saldanha
590565bea2 Merge pull request #69 from Novartis/68_read_from_subprocess 
68 read from subprocess
 2022-06-20 21:50:28 -04:00
Alok Saldanha
d32a31e855 #68 read process output until it exits 2022-06-20 21:46:19 -04:00
Alok Saldanha
0cd551382e #65 add environment variable to control how long cellxgene processes can remain idle 2022-06-20 21:46:19 -04:00
Alok Saldanha
36c0a4d3d7 #68 add param to set log level 2022-06-20 21:29:19 -04:00
Alok Saldanha
8d8a0a3483 #68 close responses 2022-06-20 21:29:19 -04:00
Alok Saldanha
eaa157079c Merge pull request #67 from Novartis/docker 
Remove version pins to upgrade Flask
 2022-06-07 12:06:49 -04:00
Alok Saldanha
977c50ce8c #66 switched from mocks to test request context 2022-06-07 07:22:30 -04:00
Alok Saldanha
833cad3bc2 #66 remove version pins 2022-06-07 06:17:11 -04:00
Alok Saldanha
c5f3c68740 Merge pull request #66 from romanhaa/docker 
Dockerise cellxgene-gateway
 2022-06-07 06:04:13 -04:00
Roman Hillje
d944a31d59 Dockerise cellxgene-gateway 2022-05-20 19:44:46 +02:00
Alok Saldanha
5814cb9943 clarified purpose of refresh query param 2022-03-14 23:17:57 -04:00
Alok Saldanha
9a91cdf795 prepare for 0.3.9 release v0.3.9 2022-03-14 23:12:01 -04:00
Alok Saldanha
25aff5c020 Merge pull request #60 from Novartis/59_s3_caching 
#59 add refresh query param to force refresh of S3 cache
 2022-03-14 23:08:45 -04:00
Alok Saldanha
6bcb594712 #59 add temporary workaround for jinja 2022-03-14 22:58:06 -04:00
Alok Saldanha
f9ed4c4047 #59 document S3_ENABLE_LISTINGS_CACHE 2022-03-14 22:36:42 -04:00
Alok Saldanha
a9753c4101 #59 change s3 cache variable from S3_DISABLE_LISTINGS_CACHE to S3_ENABLE_LISTINGS_CACHE 2022-03-14 22:36:42 -04:00
Alok Saldanha
fd48920c5b #59 add refresh query param to force refresh of S3 cache 2022-03-14 21:44:05 -04:00
Alok Saldanha
09db93b2b5 Merge pull request #62 from arogozhnikov/patch-1 
Force reload of s3 file structure on every request
 2022-03-14 20:45:20 -04:00
Alex Rogozhnikov
3e3bd22512 add environment variable S3_DISABLE_LISTINGS_CACHE per Alok's request 2022-03-14 09:59:55 -07:00
Alex Rogozhnikov
893b2f1af1 remove listing cache at the level of fs 2022-03-11 03:20:06 -08:00
Alex Rogozhnikov
757487b772 Force reload folder on every request 2022-03-11 02:43:29 -08:00
Alok Saldanha
87a8dbfa78 #57 Reverted incorrect change to unit test 2021-12-21 13:59:30 -05:00
Alok Saldanha
9c38e48c5c prepare for 0.3.8 release v0.3.8 2021-12-21 12:19:02 -05:00
Alok Saldanha
073f5f945c #57 changed logic to take last path element 2021-12-21 12:05:01 -05:00
Alok Saldanha
9dc4409f1a #57 added failing unit test 2021-12-21 12:03:39 -05:00
Alok Saldanha
551cb46af8 #42 add support for is_authorized hook 2021-11-14 17:28:10 -05:00
Alok Saldanha
620181ae4d prepare for 0.3.7 release v0.3.7 2021-08-12 14:02:26 -04:00
Alok Saldanha
73a7920cc8 add back ip_address endpoint 2021-08-12 13:58:19 -04:00
Alok Saldanha
ed3e999cd1 prepare for 0.3.6 release v0.3.6 2021-07-18 10:42:42 -04:00
Alok Saldanha
2ae2e53863 Pin version of workzeug 
This is required by earlier flask-api versions

  File "/home/alokito/code/cellxgene-gateway/cellxgene_gateway/gateway.py", line 25, in <module>
    from flask_api import status
  File "/home/alokito/miniconda3/envs/cellxgene-gateway/lib/python3.7/site-packages/flask_api/__init__.py", line 1, in <module>
    from flask_api.app import FlaskAPI
  File "/home/alokito/miniconda3/envs/cellxgene-gateway/lib/python3.7/site-packages/flask_api/app.py", line 6, in <module>
    from flask_api.request import APIRequest
  File "/home/alokito/miniconda3/envs/cellxgene-gateway/lib/python3.7/site-packages/flask_api/request.py", line 9, in <module>
    from werkzeug._compat import to_unicode
ModuleNotFoundError: No module named 'werkzeug._compat'
 2021-07-18 10:32:10 -04:00
Alok Saldanha
fd0e7d9c31 preparing for 0.3.5 release 0.3.5 2021-07-18 09:43:45 -04:00
Alok Saldanha
98ef6efd0c pinned version of flask, to match cellxgene 2021-07-18 09:39:52 -04:00
Alok Saldanha
82e43ff943 preparing for 0.3.4 release v0.3.4 2021-07-18 09:15:27 -04:00
Alok Saldanha
f8a77423eb Merge pull request #51 from Novartis/nested_subdirs 
Enable listing nested subdirs
 2021-07-18 09:14:16 -04:00
Alok Saldanha
0375a717c9 #50 fixed bug in listing subdirs 2021-07-18 09:04:36 -04:00
Alok Saldanha
4bf57832a0 #50 added failing test for listing subdirs 2021-07-18 08:51:37 -04:00
Alok Saldanha
b7d14dba6a preparing for 0.3.3 release 0.3.3 2021-07-12 20:03:14 -04:00
Alok Saldanha
26286f94b1 Merge pull request #49 from Novartis/fix_cache_pruning 
Fix cache pruning
 2021-07-12 19:26:53 -04:00
Alok Saldanha
264a324946 #48 fix bug in cache pruning 2021-07-12 19:19:29 -04:00
Alok Saldanha
520069a825 #48 added failing test for cache pruning 2021-07-12 19:12:52 -04:00
Alok Saldanha
3cb0e4d725 added test for is_port_in_use 2021-05-11 07:27:30 -04:00
Alok Saldanha
d2b508e371 Create SECURITY.md 2021-05-06 05:02:36 -04:00
Alok Saldanha
e74f6d01d1 added unit tests for dir_util 2021-04-23 07:14:09 -04:00
Alok Saldanha
7b799d0159 removed unused code 2021-04-23 07:00:53 -04:00
Alok Saldanha
1f0885afdd added pypi badges to Readme.md 2021-04-22 19:16:05 -04:00
Alok Saldanha
a3a1a2d095 Preparing for 0.3.2 release v0.3.2 2021-04-22 19:01:07 -04:00
Alok Saldanha
b4739b0cbb Merge pull request #46 from Novartis/nested_s3 
This PR should address https://github.com/Novartis/cellxgene-gateway/issues/45
 2021-04-22 07:06:17 -04:00