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Author SHA1 Message Date
Alok Saldanha 4e63ff95a8 #87 blacken 2024-03-02 12:25:21 -05:00
Alok Saldanha c1111e2cb4 #87 patch enable annotations 2024-03-02 12:23:11 -05:00
Alok Saldanha c4b9084286 #87 Fix test 2024-03-02 12:08:57 -05:00
Alok Saldanha 35c8e8180c #87 temporarily pin versions 2024-03-02 11:55:07 -05:00
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 
#73 moved new annotation link to front
 2024-03-02 11:44:49 -05:00
Alok Saldanha 66cca86b51 Merge remote-tracking branch 'ghall/just_gene_sets' 2024-03-02 11:09:00 -05:00
Alok Saldanha f046e7c5d2 Merge pull request #88 from Mye-InfoBank/master 
Fix dockerfile installation problems
 2024-02-24 09:22:49 -05:00
Nico Trummer a8f6e45f34 Implement pip upgrade to Dockerfile 2024-02-21 09:47:46 +01:00
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 
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 v0.3.11 2023-07-09 19:27:32 -04:00
Alok Saldanha c7c156b4cf Merge pull request #77 from aeisenbarth/filter-empty-folders 
Filter directories without h5ad files
 2023-07-09 07:04:06 -06:00
Alok Saldanha 624d1f8567 #78 Revert "Rename argument "filter" to "subpath"" 
This reverts commit fdd6cca297.
 2023-07-09 08:25:27 -04:00
Alok Saldanha 79c3f588b6 Merge pull request #80 from Novartis/79_add_docker_example 
79 add docker example
 2023-07-09 06:05:50 -06:00
Alok Saldanha d8fd07572c Merge pull request #83 from Novartis/81_gene_set_support 
gene set support
 2023-07-09 06:03:33 -06:00
Alok Saldanha 64d636a1c5 #81 added unit test for gene sets 2023-07-09 07:46:01 -04:00
Alok Saldanha 7b314d4457 #81 switch to latest ubuntu 2023-07-06 17:15:00 -06:00
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 
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 f296efcc55 #79 added cellxgene-data directory so it actually works 2022-12-21 16:02:50 -05:00
Alok Saldanha facfb27d5c #79 add simple example to customize cellxgene-gateway ui 2022-12-21 15:42:13 -05:00
Andreas Eisenbarth 6607b15085 Exclude directories having no h5ad files 2022-10-12 17:31:22 +02:00
Andreas Eisenbarth 0e92b73347 Add test case for dirs without h5ad 2022-10-12 17:31:22 +02:00
Andreas Eisenbarth 88b9b815c0 Adjust test case for dirs with h5ad 2022-10-12 17:31:22 +02:00
Andreas Eisenbarth 6ef82b36f1 For running individual tests, make sure flask_util.view_url is callable 2022-10-12 16:36:46 +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 v0.3.10 2022-06-20 21:50:42 -04:00
Alok Saldanha 590565bea2 Merge pull request #69 from Novartis/68_read_from_subprocess 
68 read from subprocess
 2022-06-20 21:50:28 -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 eaa157079c Merge pull request #67 from Novartis/docker 
Remove version pins to upgrade Flask
 2022-06-07 12:06:49 -04:00
Alok Saldanha 977c50ce8c #66 switched from mocks to test request context 2022-06-07 07:22:30 -04:00
Alok Saldanha 833cad3bc2 #66 remove version pins 2022-06-07 06:17:11 -04:00
Alok Saldanha c5f3c68740 Merge pull request #66 from romanhaa/docker 
Dockerise cellxgene-gateway
 2022-06-07 06:04:13 -04:00
Roman Hillje d944a31d59 Dockerise cellxgene-gateway 2022-05-20 19:44:46 +02:00
Alok Saldanha 5814cb9943 clarified purpose of refresh query param 2022-03-14 23:17:57 -04:00
Alok Saldanha 9a91cdf795 prepare for 0.3.9 release v0.3.9 2022-03-14 23:12:01 -04:00
Alok Saldanha 25aff5c020 Merge pull request #60 from Novartis/59_s3_caching 
#59 add refresh query param to force refresh of S3 cache
 2022-03-14 23:08:45 -04:00
Alok Saldanha 6bcb594712 #59 add temporary workaround for jinja 2022-03-14 22:58:06 -04:00
Alok Saldanha f9ed4c4047 #59 document S3_ENABLE_LISTINGS_CACHE 2022-03-14 22:36:42 -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
Alok Saldanha 09db93b2b5 Merge pull request #62 from arogozhnikov/patch-1 
Force reload of s3 file structure on every request
 2022-03-14 20:45:20 -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