added token and path to codecov upload

.github/workflows/pr-checks.yaml

@@ -51,10 +51,17 @@ jobs:
         run: |
           eval "$(conda shell.bash hook)"
           conda activate cellxgene-gateway
-          coverage report --fail-under 41
+          coverage report --fail-under 47
           coverage xml -i
 
       - name: "Upload coverage to Codecov"
         uses: codecov/codecov-action@v1
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
           fail_ci_if_error: true
+          path_to_write_report: ./codecov_report.txt
+          verbose: true

README.md

@@ -2,6 +2,8 @@
 
 Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets. It displays an index of available h5ad (anndata) files. When a user clicks on a file name, it launches a Cellxgene Server instance that loads that particular data file and once it is available  proxies requests to that server.
 
+[![codecov](https://codecov.io/gh/Novartis/cellxgene-gateway/branch/master/graph/badge.svg?token=ndEFSzRKJn)](https://codecov.io/gh/Novartis/cellxgene-gateway)
+
 # Running locally
 
 ## Prequisites

tests/test_subprocess_backend.py

@@ -0,0 +1,42 @@
+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
+from cellxgene_gateway.items.file.fileitem_source import FileItemSource
+from cellxgene_gateway.items.item import ItemType
+from cellxgene_gateway.process_exception import ProcessException
+
+
+class TestSubprocessBackend(unittest.TestCase):
+    @patch("subprocess.Popen")
+    def test_launch_GIVEN_no_stdout_THEN_throw_ProcessException(self, popen):
+        subprocess = MagicMock()
+        subprocess.stdout.readline().decode.return_value = ""
+        subprocess.stderr.read().decode.return_value = "An unexpected error"
+        popen.return_value = subprocess
+
+        key = CacheKey(
+            FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
+            FileItemSource("/tmp", "local"),
+        )
+        entry = CacheEntry.for_key(key, 8000)
+        from cellxgene_gateway.subprocess_backend import SubprocessBackend
+
+        backend = SubprocessBackend()
+        cellxgene_loc = "/some/cellxgene"
+        scripts = ["http://example.com/script.js", "http://example.com/script2.js"]
+
+        with self.assertRaises(ProcessException) as context:
+            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"
+            ],
+            shell=True,
+            stderr=-1,
+            stdout=-1,
+        )
+        self.assertEqual("An unexpected error", context.exception.stderr)