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Author SHA1 Message Date
Alok Saldanha 0c5adc9fef Merge pull request #99 from andynu/gunicorn-support 
Gunicorn support for now. Will revisit populating item sources on module load to improve reusability of module (specifically in tests for now).
 2025-11-05 06:55:39 -05:00
Alok Saldanha 3d0166904b Merge pull request #90 from Novartis/dependabot/pip/flask-2.2.5 
Bump flask from 2.2.2 to 2.2.5
 2024-03-03 07:31:42 -05:00
Alok Saldanha 1e02e0abb8 Merge pull request #74 from Novartis/73_reorder_filecrawl 
#73 moved new annotation link to front
 2024-03-02 11:44:49 -05:00
Alok Saldanha f046e7c5d2 Merge pull request #88 from Mye-InfoBank/master 
Fix dockerfile installation problems
 2024-02-24 09:22:49 -05:00
Alok Saldanha 9d10932b06 prepare for 0.3.11 release 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 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 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
Alok Saldanha a00403c60e #73 moved new annotation link to front 2022-08-21 08:15:09 -04:00
Alok Saldanha 390fe24ea4 prepare for 0.3.10 release 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
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 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
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 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 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 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 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 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 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 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
Alok Saldanha c29e5c0d92 #45 implemented test__list_items__pass_filter_into_scan_directory 2021-04-22 06:59:08 -04:00
Alok Saldanha a3e3b6cea8 #45 implemented test__scan_directory__properly_recurses_suburls 2021-04-21 08:21:46 -04:00
Alok Saldanha 687dc31b7a improved error message on invalid extra scripts 2021-04-21 06:21:26 -04:00
Alok Saldanha 68da42ae0e #45 implemented test_GIVEN_some_filter_THEN_includes_filterpart_in_heading 2021-04-20 13:32:28 -04:00
Alok Saldanha ccf1ba58a8 #45 add extra_scripts to cache_status page 2021-04-20 13:17:37 -04:00
Alok Saldanha d072034911 #45 pass filter into scan_directory 
also include filterpart in heading
 2021-04-20 06:03:16 -04:00
Alok Saldanha 1200629d74 #45 handle keys as full subpath rather than last path element 2021-04-20 05:57:48 -04:00
Alok Saldanha dba13ccacd lowering threshold due to including of itemsource modules 2021-04-05 08:10:55 -04:00
Alok Saldanha 3239aefad4 Preparing for v0.3.1 release 2021-04-05 08:06:25 -04:00
Alok Saldanha dd727a9469 added missing __init__.py 2021-04-05 08:04:48 -04:00
Alok Saldanha ae5cf09d04 Preparing for 0.3.0 release 2021-04-05 07:55:20 -04:00
Alok Saldanha ae35d24d80 only set wsgi.url_scheme when EXTERNAL_PROTOCOL is set 2021-04-05 07:55:20 -04:00
Alokito ad3517f002 Create codeql-analysis.yml 2021-04-05 07:08:34 -04:00
Alok Saldanha 2cefc6d741 added token and path to codecov upload 2021-04-05 06:53:44 -04:00
Alok Saldanha 1586c9a3e8 added code coverage badge 2021-04-04 20:03:02 -04:00
Alok Saldanha f16bd5e2b9 added test for SubprocessBackend.launch 2021-04-04 19:48:13 -04:00
Alok Saldanha 10105c43a8 added support for code coverage 2021-04-04 14:55:13 -04:00
Alokito 638923fb43 Merge pull request #44 from Novartis/itemsource 
Itemsource
 2021-04-03 07:15:35 -04:00
Alok Saldanha 169da934b1 updated annotation.js comment 2021-04-03 07:12:50 -04:00
Alok Saldanha 33331c9198 Template has correct relaunch_url. 2021-04-03 07:08:20 -04:00
Alok Saldanha d2d22cecaa updated tests, formatting 2021-04-02 11:52:49 -04:00
Alok Saldanha 5c488d8d5e only include source path element in url when multiple sources 2021-04-02 11:40:11 -04:00
Alok Saldanha b1ae9e8ce8 ensure s3 bucket does not include trailing slash 2021-04-02 11:37:11 -04:00
Alok Saldanha 76c1d9e80c removed .csv suffix from annotation name 2021-03-29 07:28:16 -04:00
Alok Saldanha 586dc6623a ensure annotation directory for new annotations 2021-03-29 07:03:05 -04:00
Alok Saldanha 76f3939fdd rebased "Introduction of ItemSource interface" patch 2021-03-28 22:05:08 -04:00
Alok Saldanha 5404a8b0f3 removed trailing slash from render_annotations 2021-03-28 21:59:03 -04:00
Alok Saldanha 6f2b372d32 Preparing for 0.2.3 release 2021-02-28 09:55:26 -05:00
Alokito 25755d3f69 Merge pull request #41 from Novartis/grst_master 
Grst master
 2021-02-22 08:59:05 -05:00
Alok Saldanha 942410bb44 added instructions on pre-commit installation to README.md 2020-12-31 17:12:11 -05:00
Alokito 0d084a405e Merge pull request #38 from Novartis/feature/action_push 
Feature/action push
 2020-12-31 16:33:30 -05:00
Alok Saldanha 49d679e779 try evaling the bash hook 
per https://github.com/conda/conda/issues/7980
 2020-12-31 13:23:25 -05:00
Alok Saldanha 5e6faa4b02 run pr checks on push 2020-12-31 13:06:56 -05:00
Alokito 9fe846c786 Merge pull request #37 from ericmjl/master 
Migrated PR checks to GitHub actions
 2020-12-28 11:38:26 -05:00
Alokito 21ff56ea8b Merge pull request #35 from dfeinzeig/fix/redirect 
add missing trailing slash in effort to avoid whatever is redirecting
 2020-10-28 07:39:06 -04:00
Alok Saldanha d5246d4b4b prepared for 0.2.2 release 2020-09-08 21:11:59 -04:00
Alok Saldanha 465373ca7e #30 black formatting 2020-09-08 21:11:59 -04:00
Alok Saldanha fc83523c84 #30 added missing js asset 2020-09-08 21:07:18 -04:00
Alok Saldanha 5349df36e8 prepared for 0.2.1 release 
updated docs
made GATEWAY_IP optional
 2020-08-18 20:02:24 -04:00
Alokito 13802b72b9 Merge pull request #26 from Novartis/feature/25 
#25 added CELLXGENE_ARGS environment variable
 2020-08-18 19:45:31 -04:00
Alok Saldanha 0f8092e07a #25 added CELLXGENE_ARGS environment variable 2020-08-16 17:08:06 -04:00
Alok Saldanha 61c7c43da7 blackened code 2020-08-16 17:07:23 -04:00
Alokito 0604a0ca9f Merge pull request #27 from Novartis/feature/24 
Feature/24
 2020-08-16 17:05:49 -04:00
Alok Saldanha 8cdd23a57b #24 switched to absolute paths 
relative paths won't necessarily work in css files
 2020-08-16 16:17:28 -04:00
Alok Saldanha 486206bd32 #24 make static paths relative 2020-08-16 16:06:34 -04:00