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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
2023-07-05 12:41:47 +01:00
committed by Alok Saldanha
parent 390fe24ea4
commit 81c8ce4219
5 changed files with 35 additions and 4 deletions
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2
tests/test_subprocess_backend.py
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@@ -33,7 +33,7 @@ class TestSubprocessBackend(unittest.TestCase):
backend.launch(cellxgene_loc, scripts, entry)
popen.assert_called_once_with(
[
"yes | /some/cellxgene launch /tmp/czi/pbmc3k.h5ad --port 8000 --host 127.0.0.1 --disable-annotations --scripts http://example.com/script.js --scripts http://example.com/script2.js"
"yes | /some/cellxgene launch /tmp/czi/pbmc3k.h5ad --port 8000 --host 127.0.0.1 --disable-annotations --disable-gene-sets-save --scripts http://example.com/script.js --scripts http://example.com/script2.js"
],
shell=True,
stderr=-1,