#73 moved new annotation link to front

2026-09-16 05:17:55 +08:00 · 2022-08-21 08:15:09 -04:00
5 changed files with 67 additions and 50 deletions
--- a/cellxgene_gateway/filecrawl.py
+++ b/cellxgene_gateway/filecrawl.py
@@ -7,7 +7,7 @@
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.

-import os
+import html
 import urllib.parse

 from cellxgene_gateway import env, flask_util
@@ -19,19 +19,17 @@ def render_annotations(item, item_source):
    url = flask_util.view_url(
        item_source.get_annotations_subpath(item), item_source.name
    )
-    new_annotation = f"<a class='new' href='{url}'>new</a>"
+    new_annotation = [f"<a class='new' href='{url}'>new</a>"]
+
    annotations = (
-        ", ".join(
-            [
-                f"<a href='{CacheKey(item, item_source, a).view_url}/'>{a.name}</a>"
-                for a in item.annotations
-            ]
-        )
-        + ", "
+        [
+            f"<a href='{CacheKey(item, item_source, a).view_url}/'>{html.escape(a.name)}</a>"
+            for a in item.annotations
+        ]
        if item.annotations
-        else ""
+        else []
    )
-    return " | annotations: " + annotations + new_annotation
+    return "| annotations: " + ", ".join(new_annotation + annotations)


 def render_item(item, item_source):
--- a/examples/customized_docker_image/Dockerfile
+++ b/examples/customized_docker_image/Dockerfile
@@ -1,14 +0,0 @@
-FROM python:3.9
-
-RUN pip install cellxgene-gateway 'MarkupSafe<2.1'
-
-COPY customize_ui.sh customize_ui.sh
-RUN CELLXGENE_GATEWAY_DIR=/usr/local/lib/python3.9/site-packages/cellxgene_gateway . ./customize_ui.sh
-
-ENV CELLXGENE_DATA=/cellxgene-data
-ENV CELLXGENE_LOCATION=/usr/local/bin/cellxgene
-EXPOSE 5005
-
-RUN mkdir /cellxgene-data
-
-CMD ["cellxgene-gateway"]
--- a/examples/customized_docker_image/README.md
+++ b/examples/customized_docker_image/README.md
@@ -1,14 +0,0 @@
-# Purpose
-
-This is a simple example of how to make a small script to customize the UI of cellxgene-gateway. The script that does the customization is `customize_ui.sh`, it simply makes the main header green using CSS but you could do anything you want there (including adding more script tags, etc).
-
-# Usage
-
-```
-docker build -t cellxgene_custom .
-CELLXGENE_DATA=`pwd`/../../../cellxgene_data
-docker run -p 5005:5005 --mount src=$CELLXGENE_DATA,target=/cellxgene-data,type=bind cellxgene_custom
-```
-
-If you now open http://localhost:5005 you should see a green cellxgene gateway header.
-
--- a/examples/customized_docker_image/customize_ui.sh
+++ b/examples/customized_docker_image/customize_ui.sh
@@ -1,3 +0,0 @@
-# make the header bright green
-find "${CELLXGENE_GATEWAY_DIR}/templates" -name index.html -exec sed -i -e 's/<head>/<head>\
-> <style> header h3 {color: #0F0;} <\/style>/g' {} \;
--- a/tests/test_filecrawl.py
+++ b/tests/test_filecrawl.py
@@ -13,26 +13,76 @@ from cellxgene_gateway.items.item import ItemTree, ItemType
 source = FileItemSource("/tmp")


+def make_entry(subpath="somepath", annotations=None):
+    return FileItem(
+        subpath=subpath,
+        name="entry",
+        ext=".h5ad",
+        type=ItemType.h5ad,
+        annotations=annotations,
+    )
+
+
 class TestRenderEntry(unittest.TestCase):
    def test_GIVEN_path_both_slash_THEN_view_has_single_slash(self):
-        entry = FileItem(subpath="/somepath/", name="entry", type=ItemType.h5ad)
+        entry = make_entry(subpath="/somepath/")
        rendered = render_item(entry, source)
-        self.assertIn("view/somepath/entry/'", rendered)
+        self.assertIn("view/somepath/entry.h5ad/'", rendered)

    def test_GIVEN_path_starts_slash_THEN_view_has_single_slash(self):
-        entry = FileItem(subpath="/somepath", name="entry", type=ItemType.h5ad)
+        entry = make_entry(subpath="/somepath")
        rendered = render_item(entry, source)
-        self.assertIn("view/somepath/entry/'", rendered)
+        self.assertIn("view/somepath/entry.h5ad/'", rendered)

    def test_GIVEN_path_ends_slash_THEN_view_has_single_slash(self):
-        entry = FileItem(subpath="somepath/", name="entry", type=ItemType.h5ad)
+        entry = make_entry(subpath="somepath/")
        rendered = render_item(entry, source)
-        self.assertIn("view/somepath/entry/'", rendered)
+        self.assertIn("view/somepath/entry.h5ad/'", rendered)

    def test_GIVEN_path_no_slash_THEN_view_has_single_slash(self):
-        entry = FileItem(subpath="somepath", name="entry", type=ItemType.h5ad)
+        entry = make_entry(subpath="somepath")
        rendered = render_item(entry, source)
-        self.assertIn("view/somepath/entry/'", rendered)
+        self.assertIn("view/somepath/entry.h5ad/'", rendered)
+
+
+class TestRenderAnnotation(unittest.TestCase):
+    def test_GIVEN_no_annotation_THEN_new_alone(self):
+        entry = make_entry(annotations=None)
+        rendered = render_item(entry, source)
+        self.assertIn(
+            "> | annotations: <a class='new' href='/source/Files:/tmp/view/somepath/entry_annotations'>new</a></li>",
+            rendered,
+        )
+
+    def test_GIVEN_annotation_THEN_new_before(self):
+        annotation = FileItem(
+            subpath="somepath/entry_annotations",
+            name="annot",
+            ext=".csv",
+            type=ItemType.annotation,
+        )
+        entry = make_entry(annotations=[annotation])
+        rendered = render_item(entry, source)
+        self.assertIn(
+            "> | annotations: <a class='new' href='/source/Files:/tmp/view/somepath/entry_annotations'>new</a>,"
+            " <a href='/source/Files:/tmp/view/somepath/entry_annotations/annot.csv/'>annot</a></li>",
+            rendered,
+        )
+
+    def test_GIVEN_annotation_THEN_escaped(self):
+        annotation = FileItem(
+            subpath="somepath/entry_annotations",
+            name="hot&cold",
+            ext=".csv",
+            type=ItemType.annotation,
+        )
+        entry = make_entry(annotations=[annotation])
+        rendered = render_item(entry, source)
+        self.assertIn(
+            "> | annotations: <a class='new' href='/source/Files:/tmp/view/somepath/entry_annotations'>new</a>,"
+            " <a href='/source/Files:/tmp/view/somepath/entry_annotations/hot%26cold.csv/'>hot&amp;cold</a></li>",
+            rendered,
+        )


 class TestRenderItemSource(unittest.TestCase):