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https://github.com/Novartis/cellxgene-gateway.git
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78 lines
3.2 KiB
Python
78 lines
3.2 KiB
Python
import unittest
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from unittest.mock import MagicMock, patch
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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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@patch("subprocess.Popen")
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def test_launch_GIVEN_annotations_enabled_THEN_set_flags(self, popen):
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subprocess = MagicMock()
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subprocess.stdout.readline().decode.return_value = (
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"[cellxgene] Type CTRL-C at any time to exit.\n"
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)
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subprocess.stderr.read().decode.return_value = ""
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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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FileItem(
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"/czi/pbmc3k_annotations/", name="foo.csv", type=ItemType.annotation
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),
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)
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entry = CacheEntry.for_key(key, 8000)
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import cellxgene_gateway.subprocess_backend
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cellxgene_gateway.subprocess_backend.enable_annotations = True
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try:
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backend = cellxgene_gateway.subprocess_backend.SubprocessBackend()
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cellxgene_loc = "/some/cellxgene"
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backend.launch(cellxgene_loc, [], entry)
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finally:
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cellxgene_gateway.subprocess_backend.enable_annotations = False
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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 --annotations-file /tmp/czi/pbmc3k_annotations/foo.csv --gene-sets-file /tmp/czi/pbmc3k_annotations/foo_gene_sets.csv"
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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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