updated tests, formatting

.github/workflows/pr-checks.yaml

@@ -22,7 +22,7 @@ jobs:
           pip install black
       - name: Run black
         run: |
-          black -l 79 . --check
+          black . --check
   # This job is copied over from `deploy.yaml`
   run-tests:
     runs-on: ubuntu-18.04

cellxgene_gateway/items/s3/s3item_source.py

@@ -29,8 +29,10 @@ class S3ItemSource(ItemSource):
     ):
         self._name = name
         self.s3 = s3fs.S3FileSystem()
-        if bucket.startswith('s3://'):
-            raise Exception(f"Bucket name should not include s3:// prefix, got {bucket}")
+        if bucket.startswith("s3://"):
+            raise Exception(
+                f"Bucket name should not include s3:// prefix, got {bucket}"
+            )
         self.bucket = bucket
         self.h5ad_suffix = h5ad_suffix
         self.annotation_dir_suffix = annotation_dir_suffix
@@ -69,7 +71,7 @@ class S3ItemSource(ItemSource):
             raise Exception(f"S3 url '{url}' does not exist.")
 
         s3key_map = dict(
-            (filepath[len(self.bucket) :].lstrip('/'), "s3://" + filepath)
+            (filepath[len(self.bucket) :].lstrip("/"), "s3://" + filepath)
             for filepath in sorted(self.s3.ls(url))
         )
 

tests/items/file/test_fileitem_source.py

@@ -5,7 +5,9 @@ from cellxgene_gateway.items.file.fileitem_source import FileItemSource
 
 
 class TestFileItemSource(unittest.TestCase):
-    def test_make_fileitem_from_path_GIVEN_annotation_file_THEN_name_lacks_csv(self):
+    def test_make_fileitem_from_path_GIVEN_annotation_file_THEN_name_lacks_csv(
+        self,
+    ):
         source = FileItemSource(tempfile.gettempdir(), "local")
         item = source.make_fileitem_from_path(
             "customanno.csv", "someh5ad_annotations", True

tests/test_cache_entry.py

@@ -2,6 +2,7 @@ import unittest
 
 from flask import Flask
 
+from cellxgene_gateway import flask_util
 from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
 from cellxgene_gateway.cache_key import CacheKey
 from cellxgene_gateway.gateway import app
@@ -27,13 +28,31 @@ class TestRenderEntry(unittest.TestCase):
         self.assertEqual(entry.status, CacheEntryStatus.loading)
 
     def test_GIVEN_absolute_static_url_THEN_include_path(self):
+        flask_util.include_source_in_url = False
         actual = CacheEntry.for_key(key, 8000).rewrite_text_content(
             "src:url(/static/assets/"
         )
-        expected = "src:url(/source/local/view/czi/pbmc3k.h5ad/static/assets/"
+        expected = "src:url(/view/czi/pbmc3k.h5ad/static/assets/"
         self.assertEqual(actual, expected)
 
     def test_GIVEN_absolute_src_THEN_include_path(self):
+        flask_util.include_source_in_url = False
+        actual = CacheEntry.for_key(key, 8000).rewrite_text_content(
+            '<link rel="shortcut icon" href="/static/assets/favicon.ico">'
+        )
+        expected = '<link rel="shortcut icon" href="/view/czi/pbmc3k.h5ad/static/assets/favicon.ico">'
+        self.assertEqual(actual, expected)
+
+    def test_GIVEN_absolute_static_url_include_source_THEN_include_path(self):
+        flask_util.include_source_in_url = True
+        actual = CacheEntry.for_key(key, 8000).rewrite_text_content(
+            "src:url(/static/assets/"
+        )
+        expected = "src:url(/source/local/view/czi/pbmc3k.h5ad/static/assets/"
+        self.assertEqual(actual, expected)
+
+    def test_GIVEN_absolute_src_include_source_THEN_include_path(self):
+        flask_util.include_source_in_url = True
         actual = CacheEntry.for_key(key, 8000).rewrite_text_content(
             '<link rel="shortcut icon" href="/static/assets/favicon.ico">'
         )