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#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`.
This commit is contained in:
george-hall-ucl
2023-07-06 07:59:12 -06:00
committed by Alok Saldanha
parent 390fe24ea4
commit 81c8ce4219
5 changed files with 35 additions and 4 deletions
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README.md
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@@ -76,6 +76,7 @@ Optional environment variables:
* `GATEWAY_EXPIRE_SECONDS` - time in seconds that a cellxgene process will remain idle before being terminated. Defaults to 3600 (one hour)
* `GATEWAY_EXTRA_SCRIPTS` - JSON array of script paths, will be embedded into each page and forwarded with `--scripts` to cellxgene server
* `GATEWAY_ENABLE_ANNOTATIONS` - Set to `true` or to `1` to enable cellxgene annotations.
* `GATEWAY_ENABLE_GENE_SETS` - Set to `true` or to `1` to enable cellxgene gene sets. Also enables `GATEWAY_ENABLE_ANNOTATIONS`.
* `GATEWAY_ENABLE_BACKED_MODE` - Set to `true` or to `1` to load AnnData in file-backed mode. This saves memory and speeds up launch time but may reduce overall performance.
* `GATEWAY_LOG_LEVEL` - default is `INFO`. set to `DEBUG` to increase logging and to `WARNING` to decrease logging.
* `S3_ENABLE_LISTINGS_CACHE` - Set to `true` or to `1` to cache listings of S3 folders for performance. If the cache becomes stale, set `filecrawl.html?refresh=true` query parameter to refresh the cache.