Alok Saldanha
2754bc1ef1
#81 Combined GATEWAY_ENABLE_ANNOTATIONS and GATEWAY_ENABLE_GENE_SETS flags
2023-07-06 08:53:19 -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
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
ae35d24d80
only set wsgi.url_scheme when EXTERNAL_PROTOCOL is set
2021-04-05 07:55:20 -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
d3ee04b6e5
blacken
2021-02-13 17:02:55 -05:00
Alok Saldanha
f1f4b0c0ca
added environment variables for ProxyFix
2021-02-13 16:42:34 -05:00
Alok Saldanha
465373ca7e
#30 black formatting
2020-09-08 21:11:59 -04:00
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
5349df36e8
prepared for 0.2.1 release
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updated docs
made GATEWAY_IP optional
2020-08-18 20:02:24 -04:00
Alok Saldanha
0f8092e07a
#25 added CELLXGENE_ARGS environment variable
2020-08-16 17:08:06 -04:00
Alok Saldanha
bfa80f7ef8
#22 blackened code
2020-08-10 17:56:32 -04:00
Fidel Ramírez
9a130a8eb7
updated arguments for cellxgene v 0.15. Added option for backed mode.
2020-05-04 13:49:09 +02:00
Alok Saldanha
c03098af17
#14 enabled new annotations
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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
9532375eb0
#12 introduce GATEWAY_PORT, rename GATEWAY_HOST and GATEWAY_PROTOCOL to EXTERNAL_HOST and EXTERNAL_PROTOCOL
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Keep GATEWAY_HOST and GATEWAY_PROTOCOL for backwards compatibility (for now)
2019-11-17 19:03:47 -05:00
Alok Saldanha
2f2541d2b1
#6 added info output of env
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improved logging config
2019-09-23 15:15:44 -04:00
Alok Saldanha
d3a290a3ab
#6 add GATEWAY_ENABLE_UPLOAD environment variable
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routes that modify disk are not added unless the env variable is set.
2019-09-23 14:48:58 -04:00
Alok Saldanha
820314adff
#2 blackened
2019-09-17 11:06:50 -04:00
Alok Saldanha
a6c9456786
added support for gateway ttl and manual pruning
2019-09-16 17:12:29 -04:00
Alok Saldanha
1e1de19878
added unit test
2019-09-16 10:58:02 -04:00
Alok Saldanha
15998beb68
added support for GATEWAY_EXTRA_SCRIPTS
2019-09-16 10:32:35 -04:00
Eric Ma
7e9611e3b6
take out deployemnt_env
2019-09-06 13:59:52 -04:00
Eric Ma
952cb1e8e1
refactor to allow use with console entry points
2019-09-05 11:54:34 -04:00
Alok Saldanha