#81 added unit test for gene sets

tests/test_subprocess_backend.py

@@ -1,7 +1,6 @@
 import unittest
 from unittest.mock import MagicMock, patch
 
-from cellxgene_gateway.backend_cache import BackendCache
 from cellxgene_gateway.cache_entry import CacheEntry
 from cellxgene_gateway.cache_key import CacheKey
 from cellxgene_gateway.items.file.fileitem import FileItem
@@ -40,3 +39,39 @@ class TestSubprocessBackend(unittest.TestCase):
             stdout=-1,
         )
         self.assertEqual("An unexpected error", context.exception.stderr)
+
+    @patch("subprocess.Popen")
+    def test_launch_GIVEN_annotations_enabled_THEN_set_flags(self, popen):
+        subprocess = MagicMock()
+        subprocess.stdout.readline().decode.return_value = (
+            "[cellxgene] Type CTRL-C at any time to exit.\n"
+        )
+        subprocess.stderr.read().decode.return_value = ""
+        popen.return_value = subprocess
+
+        key = CacheKey(
+            FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
+            FileItemSource("/tmp", "local"),
+            FileItem(
+                "/czi/pbmc3k_annotations/", name="foo.csv", type=ItemType.annotation
+            ),
+        )
+        entry = CacheEntry.for_key(key, 8000)
+        import cellxgene_gateway.subprocess_backend
+
+        cellxgene_gateway.subprocess_backend.enable_annotations = True
+        try:
+            backend = cellxgene_gateway.subprocess_backend.SubprocessBackend()
+            cellxgene_loc = "/some/cellxgene"
+
+            backend.launch(cellxgene_loc, [], entry)
+        finally:
+            cellxgene_gateway.subprocess_backend.enable_annotations = False
+        popen.assert_called_once_with(
+            [
+                "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"
+            ],
+            shell=True,
+            stderr=-1,
+            stdout=-1,
+        )