Preparing for 0.3.0 release

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,67 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master ]
+  schedule:
+    - cron: '18 6 * * 6'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'javascript', 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more:
+        # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.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

Changelog.md

@@ -1,6 +1,14 @@
+# 0.3.0
+
+ * Added support for itemsource interface, allowing s3 hosting
+ * Removed support for http file uploads
+ * Only set wsgi.url_scheme when EXTERNAL_PROTOCOL is set (see issue #43) 
+ * Dropped flake8 due to conflicts with black
+ * Added code coverage metrics
+
 # 0.2.3
 
-* Added support for ProxyFix
+ * Added support for ProxyFix
 
 # 0.2.2
 

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

cellxgene_gateway/__init__.py

@@ -7,4 +7,4 @@
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
 
-__version__ = "0.2.3"
+__version__ = "0.3.0"

cellxgene_gateway/env.py

@@ -20,7 +20,7 @@ external_host = os.environ.get(
     os.environ.get("GATEWAY_HOST", f"localhost:{gateway_port}"),
 )
 external_protocol = os.environ.get(
-    "EXTERNAL_PROTOCOL", os.environ.get("GATEWAY_PROTOCOL", "http")
+    "EXTERNAL_PROTOCOL", os.environ.get("GATEWAY_PROTOCOL", None)
 )
 ip = os.environ.get("GATEWAY_IP")
 extra_scripts = os.environ.get("GATEWAY_EXTRA_SCRIPTS")

cellxgene_gateway/gateway.py

@@ -46,7 +46,8 @@ default_item_source = None
 
 def _force_https(app):
     def wrapper(environ, start_response):
-        environ["wsgi.url_scheme"] = env.external_protocol
+        if env.external_protocol is not None:
+            environ["wsgi.url_scheme"] = env.external_protocol
         return app(environ, start_response)
 
     return wrapper

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)