Alok Saldanha
0000a60eb0
#73 hide annotation links when disabled
2024-03-02 11:51:20 -05:00
Alok Saldanha
1e02e0abb8
Merge pull request #74 from Novartis/73_reorder_filecrawl
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#73 moved new annotation link to front
2024-03-02 11:44:49 -05:00
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
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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
2023-07-09 19:27:32 -04:00
Alok Saldanha
c7c156b4cf
Merge pull request #77 from aeisenbarth/filter-empty-folders
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Filter directories without h5ad files
2023-07-09 07:04:06 -06:00
Alok Saldanha
624d1f8567
#78 Revert "Rename argument "filter" to "subpath""
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This reverts commit fdd6cca297
2023-07-09 08:25:27 -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
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
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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
Andreas Eisenbarth
6607b15085
Exclude directories having no h5ad files
2022-10-12 17:31:22 +02:00
Andreas Eisenbarth
fdd6cca297
Rename argument "filter" to "subpath"
2022-10-12 13:40:39 +02:00
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
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
9a91cdf795
prepare for 0.3.9 release
2022-03-14 23:12:01 -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
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
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
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
fd0e7d9c31
preparing for 0.3.5 release
2021-07-18 09:43:45 -04:00
Alok Saldanha
82e43ff943
preparing for 0.3.4 release
2021-07-18 09:15:27 -04:00
Alok Saldanha
0375a717c9
#50 fixed bug in listing subdirs
2021-07-18 09:04:36 -04:00
Alok Saldanha
b7d14dba6a
preparing for 0.3.3 release
2021-07-12 20:03:14 -04:00
Alok Saldanha
264a324946
#48 fix bug in cache pruning
2021-07-12 19:19:29 -04:00
Alok Saldanha
7b799d0159
removed unused code
2021-04-23 07:00:53 -04:00
Alok Saldanha
a3a1a2d095
Preparing for 0.3.2 release
2021-04-22 19:01:07 -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
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
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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
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
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