fork/cellxgene-gateway
1
0
Fork 0
mirror of https://github.com/Novartis/cellxgene-gateway.git synced 2026-09-28 09:28:11 +08:00
Code Issues Packages Projects Releases Wiki Activity
214 Commits 17 Branches 22 Tags
19caa6cb8047ed8b2d18667a9bca9b68d2cadf5e
Commit Graph
214 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
george-hall-ucl 19caa6cb80 Sorry -- forgot to lint 2023-08-08 16:04:03 +01:00
george-hall-ucl 56bd079024 Save gene sets without cell annotations 
This fixes a bug whereby new gene_sets csv files created without
accompanying cell-level annotations could not be detected by the
filecrawler.
 2023-08-08 15:49:57 +01:00
Alok Saldanha 9d10932b06 prepare for 0.3.11 release v0.3.11 2023-07-09 19:27:32 -04:00
Alok Saldanha c7c156b4cf Merge pull request #77 from aeisenbarth/filter-empty-folders 
Filter directories without h5ad files
 2023-07-09 07:04:06 -06:00
Alok Saldanha 624d1f8567 #78 Revert "Rename argument "filter" to "subpath"" 
This reverts commit fdd6cca297.
 2023-07-09 08:25:27 -04:00
Alok Saldanha 79c3f588b6 Merge pull request #80 from Novartis/79_add_docker_example 
79 add docker example
 2023-07-09 06:05:50 -06:00
Alok Saldanha d8fd07572c Merge pull request #83 from Novartis/81_gene_set_support 
gene set support
 2023-07-09 06:03:33 -06:00
Alok Saldanha 64d636a1c5 #81 added unit test for gene sets 2023-07-09 07:46:01 -04:00
Alok Saldanha 7b314d4457 #81 switch to latest ubuntu 2023-07-06 17:15:00 -06:00
Alok Saldanha 2754bc1ef1 #81 Combined GATEWAY_ENABLE_ANNOTATIONS and GATEWAY_ENABLE_GENE_SETS flags 2023-07-06 08:53:19 -06:00
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 f296efcc55 #79 added cellxgene-data directory so it actually works 2022-12-21 16:02:50 -05:00
Alok Saldanha facfb27d5c #79 add simple example to customize cellxgene-gateway ui 2022-12-21 15:42:13 -05:00
Andreas Eisenbarth 6607b15085 Exclude directories having no h5ad files 2022-10-12 17:31:22 +02:00
Andreas Eisenbarth 0e92b73347 Add test case for dirs without h5ad 2022-10-12 17:31:22 +02:00
Andreas Eisenbarth 88b9b815c0 Adjust test case for dirs with h5ad 2022-10-12 17:31:22 +02:00
Andreas Eisenbarth 6ef82b36f1 For running individual tests, make sure flask_util.view_url is callable 2022-10-12 16:36:46 +02:00
Andreas Eisenbarth fdd6cca297 Rename argument "filter" to "subpath" 2022-10-12 13:40:39 +02:00
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