Alok Saldanha
d747860118
made pruner a daemon thread
2025-11-08 18:40:33 -05:00
Alok Saldanha
55b268125f
blacken
2025-11-08 17:23:47 -05:00
Alok Saldanha
4df58f9ceb
fixe bug in status.json
2025-11-08 17:21:37 -05:00
Alok Saldanha
1d1d8b4e59
Address linter warnings
2025-11-08 10:57:50 -05:00
Alok Saldanha
f260180a76
set default_item_source and start pruner thread
2025-11-05 21:54:18 -05:00
Alok Saldanha
58ae41fe0c
Delay itemsource initialization until first request is served
2025-11-05 21:41:10 -05:00
Alok Saldanha
3e5accad65
fixed linting and tests
2025-11-04 06:57:43 -05:00
Andy
903d25763f
Fix AttributeError by storing ItemSource objects in default_item_source
...
Previously, default_item_source was set to a string ("s3" or "local"),
but matching_source() tried to access default_item_source.name, causing:
AttributeError: 'str' object has no attribute 'name'
This bug occurred when source_name=None (single data source configuration)
and has existed since the ItemSource interface was introduced in 2021.
Changes:
- Store the actual ItemSource object reference instead of string name
- Assign to intermediate variables (s3_source, file_source) for clarity
Fixes the error when viewing datasets with a single data source configured.
2025-10-29 14:08:56 -04:00
Andy
08c546f40a
Fix WSGI server initialization by extracting data source setup
...
Addresses the issue where Gunicorn/uWSGI servers import the gateway
module but never call main(), leaving item_sources empty and causing
the file crawler to fail.
Changes:
- Extract data source initialization into initialize_data_sources()
- Call initialization at module import time for WSGI compatibility
- Add _initialized flag to prevent double initialization
- Simplify main() to delegate to initialize_data_sources()
This ensures data sources are populated when running under WSGI servers
(Gunicorn, uWSGI) while maintaining backward compatibility with the
Flask development server.
Related to GitHub issues #33 and #92
2025-10-29 14:08:56 -04:00
Alok Saldanha
2754bc1ef1
#81 Combined GATEWAY_ENABLE_ANNOTATIONS and GATEWAY_ENABLE_GENE_SETS flags
2023-07-06 08:53:19 -06:00
Alok Saldanha
36c0a4d3d7
#68 add param to set log level
2022-06-20 21:29:19 -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
551cb46af8
#42 add support for is_authorized hook
2021-11-14 17:28:10 -05:00
Alok Saldanha
73a7920cc8
add back ip_address endpoint
2021-08-12 13:58:19 -04:00
Alok Saldanha
7b799d0159
removed unused code
2021-04-23 07:00:53 -04:00
Alok Saldanha
ccf1ba58a8
#45 add extra_scripts to cache_status page
2021-04-20 13:17:37 -04:00
Alok Saldanha
ae35d24d80
only set wsgi.url_scheme when EXTERNAL_PROTOCOL is set
2021-04-05 07:55:20 -04:00
Alok Saldanha
33331c9198
Template has correct relaunch_url.
2021-04-03 07:08:20 -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
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
f1f4b0c0ca
added environment variables for ProxyFix
2021-02-13 16:42:34 -05:00
Gregor Sturm
fbc18fb636
Add ProxyFix to gateway.py
2021-01-18 20:01:53 +01:00
Gregor Sturm
94062c2d64
apply proxy fix
2021-01-18 18:19:25 +01:00
Alok Saldanha
ce3eb0eedf
Merge branch 'gmerge' into gmaster
...
# Conflicts:
# cellxgene_gateway/backend_cache.py
# cellxgene_gateway/cache_entry.py
# cellxgene_gateway/env.py
# cellxgene_gateway/gateway.py
# cellxgene_gateway/subprocess_backend.py
# tests/test_cache_entry.py
# tests/test_dir_util.py
2020-08-30 13:47:22 -04:00
Alok Saldanha
9219336356
blackened code
2020-08-30 13:38:35 -04:00
Alok Saldanha
b689357f29
Applied "Formatting and new enumeration for Cellxgene-gateway" patch
2020-08-30 13:36:39 -04:00
Alok Saldanha
bfa80f7ef8
#22 blackened code
2020-08-10 17:56:32 -04:00
Alok Saldanha
578845b133
#22 Added /metadata/ip_address endpoint
2020-08-10 17:49:03 -04:00
Alok Saldanha
2b65c095a6
updated import to reflect change in werkzeug api
2020-03-23 03:49:20 -04:00
Alok Saldanha
9f1d217e50
#14 properly use the external protocol in 302 redirects
2020-01-08 03:32:06 -05:00
Alok Saldanha
6c611f55dd
#14 redirect prior to returning loading screen
2020-01-07 10:07:46 -05:00
Alok Saldanha
201f876341
#14 added custom method to create data dirs
2020-01-01 01:24:18 -05:00
Alok Saldanha
c03098af17
#14 enabled new annotations
...
Due to issue with opening annotation files with "-" in the name, this doesn't quite work.
2019-12-28 21:55:43 -05:00
Alok Saldanha
f41db75a24
#15 added intermediate index pages
2019-12-21 11:57:35 -05:00
Alok Saldanha
9532375eb0
#12 introduce GATEWAY_PORT, rename GATEWAY_HOST and GATEWAY_PROTOCOL to EXTERNAL_HOST and EXTERNAL_PROTOCOL
...
Keep GATEWAY_HOST and GATEWAY_PROTOCOL for backwards compatibility (for now)
2019-11-17 19:03:47 -05:00
Alok Saldanha
91c9607808
#9 fix race condition by grabbing lock before adding cache entry
2019-10-29 21:19:50 -04:00
Alok Saldanha
c937f90779
#8 added endpoint to return status json
2019-10-20 21:08:23 -04:00
Alok Saldanha
464ee87305
#7 added link to terminate loaded dataset
2019-10-20 20:53:38 -04:00
Alok Saldanha
2f2541d2b1
#6 added info output of env
...
improved logging config
2019-09-23 15:15:44 -04:00
Alok Saldanha
d3a290a3ab
#6 add GATEWAY_ENABLE_UPLOAD environment variable
...
routes that modify disk are not added unless the env variable is set.
2019-09-23 14:48:58 -04:00
Alok Saldanha
6cf953aaab
#5 added os.path.join to flask routes
...
Also added a subdir check for security.
2019-09-19 12:54:26 -04:00
Alok Saldanha
5c41dbb18d
#2 remove missing property
2019-09-17 11:35:25 -04:00
Alok Saldanha
820314adff
#2 blackened
2019-09-17 11:06:50 -04:00
Alok Saldanha
f7f49b3568
#2 added link to relaunch server on process error page
2019-09-17 11:05:22 -04:00
Alok Saldanha
2b259ab6b5
#2 added a way to relaunch a cellxgene server
2019-09-17 10:13:20 -04:00
Alok Saldanha
a6c9456786
added support for gateway ttl and manual pruning
2019-09-16 17:12:29 -04:00
Alok Saldanha
1b053092b4
added cache status
2019-09-16 13:40:50 -04:00
Alok Saldanha
1e1de19878
added unit test
2019-09-16 10:58:02 -04:00
Eric Ma
952cb1e8e1
refactor to allow use with console entry points
2019-09-05 11:54:34 -04:00
Alok Saldanha