Alok Saldanha
05a95c2ca9
Prepare 0.4.0 release
2024-03-10 09:33:50 -04:00
Alok Saldanha
5d29153544
#87 remove version pins for markupsafe, flask and werkzeug
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also remove dependency on flask-api
2024-03-10 09:31:39 -04:00
Alok Saldanha
6a2bc409db
Prepare for 0.3.12 release
2024-03-03 07:45:47 -05:00
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
d32a31e855
#68 read process output until it exits
2022-06-20 21:46:19 -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
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
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
2f2541d2b1
#6 added info output of env
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improved logging config
2019-09-23 15:15:44 -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
a6c9456786
added support for gateway ttl and manual pruning
2019-09-16 17:12:29 -04:00
Eric Ma
952cb1e8e1
refactor to allow use with console entry points
2019-09-05 11:54:34 -04:00
Alok Saldanha