mirror of
https://github.com/Novartis/cellxgene-gateway.git
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george-hall-ucl
81c8ce4219
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`.
43 lines
1.8 KiB
Python
43 lines
1.8 KiB
Python
import unittest
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from unittest.mock import MagicMock, patch
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from cellxgene_gateway.backend_cache import BackendCache
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from cellxgene_gateway.cache_entry import CacheEntry
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from cellxgene_gateway.cache_key import CacheKey
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from cellxgene_gateway.items.file.fileitem import FileItem
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from cellxgene_gateway.items.file.fileitem_source import FileItemSource
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from cellxgene_gateway.items.item import ItemType
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from cellxgene_gateway.process_exception import ProcessException
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class TestSubprocessBackend(unittest.TestCase):
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@patch("subprocess.Popen")
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def test_launch_GIVEN_no_stdout_THEN_throw_ProcessException(self, popen):
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subprocess = MagicMock()
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subprocess.stdout.readline().decode.return_value = ""
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subprocess.stderr.read().decode.return_value = "An unexpected error"
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popen.return_value = subprocess
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key = CacheKey(
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FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
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FileItemSource("/tmp", "local"),
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)
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entry = CacheEntry.for_key(key, 8000)
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from cellxgene_gateway.subprocess_backend import SubprocessBackend
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backend = SubprocessBackend()
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cellxgene_loc = "/some/cellxgene"
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scripts = ["http://example.com/script.js", "http://example.com/script2.js"]
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with self.assertRaises(ProcessException) as context:
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backend.launch(cellxgene_loc, scripts, entry)
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popen.assert_called_once_with(
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[
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"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"
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],
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shell=True,
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stderr=-1,
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stdout=-1,
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)
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self.assertEqual("An unexpected error", context.exception.stderr)
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