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
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
977c50ce8c
#66 switched from mocks to test request context
2022-06-07 07:22:30 -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
87a8dbfa78
#57 Reverted incorrect change to unit test
2021-12-21 13:59:30 -05:00
Alok Saldanha
9dc4409f1a
#57 added failing unit test
2021-12-21 12:03:39 -05:00
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
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
e74f6d01d1
added unit tests for dir_util
2021-04-23 07:14:09 -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
f16bd5e2b9
added test for SubprocessBackend.launch
2021-04-04 19:48:13 -04:00
Alok Saldanha
d2d22cecaa
updated tests, formatting
2021-04-02 11:52:49 -04:00
Alok Saldanha
76c1d9e80c
removed .csv suffix from annotation name
2021-03-29 07:28:16 -04:00
Alok Saldanha
76f3939fdd
rebased "Introduction of ItemSource interface" patch
2021-03-28 22:05:08 -04:00
Alok Saldanha
893092f199
fixed unit tests
2021-02-13 17:30:21 -05:00
Alok Saldanha
ce3eb0eedf
Merge branch 'gmerge' into gmaster
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# 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
61c7c43da7
blackened code
2020-08-16 17:07:23 -04:00
Alok Saldanha
8cdd23a57b
#24 switched to absolute paths
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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
Alok Saldanha
bfa80f7ef8
#22 blackened code
2020-08-10 17:56:32 -04:00
Alok Saldanha
63cdfe1953
#22 fixed failing tests
2020-08-10 17:56:24 -04:00
Alok Saldanha
6656de6214
#5 added failing test for path combination in render_entry
2019-09-19 13:01:08 -04:00
Alok Saldanha
f6d10946c6
#4 added failing test for cache pruning
2019-09-19 12:02:24 -04:00
Alok Saldanha
1e1de19878
added unit test
2019-09-16 10:58:02 -04:00
george-hall-ucl