Merge pull request galaxyproject#22286 from mvdbeek/fix-toolshed-imagine-url-encoding

[26.0] Fix toolshed static image url encoding

Author: jmchilton

lib/galaxy/tool_shed/util/shed_util_common.py

@@ -1,5 +1,6 @@
 import logging
 import re
+from urllib.parse import quote
 
 from galaxy import util
 from galaxy.tool_shed.util import repository_util
@@ -149,7 +150,10 @@ def set_image_paths(app, text, encoded_repository_id=None, tool_shed_repository=
             # We're in the tool shed.
             route_to_images = f"/repository/static/images/{encoded_repository_id}"
         elif tool_shed_repository and tool_id and tool_version:
-            route_to_images = f"shed_tool_static/{tool_shed_repository.tool_shed}/{tool_shed_repository.owner}/{tool_shed_repository.name}/{tool_id}/{tool_version}"
+            route_to_images = quote(
+                f"shed_tool_static/{tool_shed_repository.tool_shed}/{tool_shed_repository.owner}/{tool_shed_repository.name}/{tool_id}/{tool_version}",
+                safe="/",
+            )
         else:
             raise Exception(
                 "encoded_repository_id or tool_shed_repository and tool_id and tool_version must be provided"

lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py

@@ -2,7 +2,10 @@
 import os
 
 from galaxy import web
-from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.exceptions import (
+    ObjectNotFound,
+    RequestParameterInvalidException,
+)
 from galaxy.util.path import (
     join,
     safe_contains,
@@ -34,6 +37,8 @@ def index(self, trans, shed, owner, repo, tool, version, image_file, **kwargs):
         """
         guid = "/".join((shed, "repos", owner, repo, tool, version))
         tool = trans.app.toolbox.get_tool(guid)
+        if tool is None:
+            raise ObjectNotFound(f"Could not find tool with guid '{guid}'.")
         repo_path = os.path.abspath(tool._repository_dir)
         found_path = None
 

test/unit/tool_shed/test_shed_util_common.py

@@ -0,0 +1,56 @@
+from types import SimpleNamespace
+
+from galaxy.tool_shed.util.shed_util_common import set_image_paths
+
+
+def test_set_image_paths_encodes_special_characters_in_tool_id():
+    tool_shed_repository = SimpleNamespace(
+        tool_shed="toolshed.g2.bx.psu.edu",
+        owner="devteam",
+        name="emboss_5",
+    )
+    text = ".. image:: static/images/isochore.png"
+    result = set_image_paths(
+        app=None,
+        text=text,
+        tool_shed_repository=tool_shed_repository,
+        tool_id="EMBOSS: isochore47",
+        tool_version="5.0.0.1",
+    )
+    assert "EMBOSS%3A%20isochore47" in result
+    assert "EMBOSS: isochore47" not in result
+
+
+def test_set_image_paths_preserves_slashes_in_route():
+    tool_shed_repository = SimpleNamespace(
+        tool_shed="toolshed.g2.bx.psu.edu",
+        owner="devteam",
+        name="emboss_5",
+    )
+    text = ".. image:: isochore.png"
+    result = set_image_paths(
+        app=None,
+        text=text,
+        tool_shed_repository=tool_shed_repository,
+        tool_id="isochore",
+        tool_version="5.0.0",
+    )
+    assert "shed_tool_static/toolshed.g2.bx.psu.edu/devteam/emboss_5/isochore/5.0.0/" in result
+
+
+def test_set_image_paths_does_not_modify_http_urls():
+    tool_shed_repository = SimpleNamespace(
+        tool_shed="toolshed.g2.bx.psu.edu",
+        owner="devteam",
+        name="emboss_5",
+    )
+    text = ".. image:: https://example.com/image.png"
+    result = set_image_paths(
+        app=None,
+        text=text,
+        tool_shed_repository=tool_shed_repository,
+        tool_id="mytool",
+        tool_version="1.0",
+    )
+    assert ".. image:: https://example.com/image.png" in result
+    assert "shed_tool_static" not in result