Merge branch 'release_26.0' into dev

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/tools/parameters/basic.py

@@ -2451,15 +2451,25 @@ class DataToolParameter(BaseDataToolParameter):
         # Route each to the correct options list by type so the client can
         # match them by id *and* src.
         for value in job_input_values:
-            if isinstance(value, (HistoryDatasetCollectionAssociation, HistoryDatasetAssociation)):
+            if isinstance(value, HistoryDatasetCollectionAssociation):
+                # HDCAs are handled by the dataset collections section below;
+                # only add here if not visible in the current history.
+                if value.deleted or not value.visible or value.history != history:
+                    if value.deleted:
+                        state = "deleted"
+                    elif not value.visible:
+                        state = "hidden"
+                    else:
+                        state = "not in current history"
+                    append(d["options"]["hdca"], value, f"({state}) {value.name}", "hdca", True)
+            elif isinstance(value, HistoryDatasetAssociation):
                 if value.deleted:
                     state = "deleted"
                 elif not value.visible:
                     state = "hidden"
                 else:
                     state = "not in current history"
-                src = "hdca" if isinstance(value, HistoryDatasetCollectionAssociation) else "hda"
-                append(d["options"][src], value, f"({state}) {value.name}", src, True)
+                append(d["options"]["hda"], value, f"({state}) {value.name}", "hda", True)
             elif isinstance(value, DatasetCollectionElement):
                 append_dce(value)
             elif isinstance(value, LibraryDatasetDatasetAssociation):

lib/galaxy/tools/parameters/dynamic_options.py

@@ -1079,10 +1079,10 @@ def _get_ref_data(other_values, ref_name):
         if is_runtime_value(ref):
             return []
         raise ValueError
-    if isinstance(ref, DatasetCollectionElement) and ref.hda:
-        ref = ref.hda
+    if isinstance(ref, DatasetCollectionElement):
+        return ref.dataset_instances
     if isinstance(ref, (DatasetFilenameWrapper, HistoryDatasetAssociation, LibraryDatasetDatasetAssociation)):
-        ref = [ref]
+        return [ref]
     elif isinstance(ref, HistoryDatasetCollectionAssociation):
-        ref = ref.to_hda_representative(multiple=True)
+        return ref.to_hda_representative(multiple=True)
     return ref

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

@@ -2,7 +2,10 @@ import logging
 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 @@ class ShedToolStatic(BaseUIController):
         """
         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
 

lib/galaxy_test/api/test_tools.py

@@ -286,6 +286,26 @@ class TestToolsApi(ApiTestCase, TestsTools):
             assert "hg18_value" in option_values
             assert "mm10_value" in option_values
 
+    @skip_without_tool("dbkey_filter_collection_input")
+    def test_run_dbkey_filter_nested_collection_dce(self):
+        with self.dataset_populator.test_history() as history_id:
+            list_list = self.dataset_collection_populator.create_list_of_list_in_history(history_id, wait=True).json()
+            # Set dbkey on the datasets in the inner list
+            for outer_element in list_list["elements"]:
+                for inner_element in outer_element["object"]["elements"]:
+                    hda_id = inner_element["object"]["id"]
+                    self.dataset_populator._put(
+                        f"histories/{history_id}/contents/{hda_id}", {"genome_build": "hg19"}, json=True
+                    )
+            # Get DCE ID of the inner list element - this is a DatasetCollectionElement
+            # wrapping a child collection (not an HDA)
+            dce_id = list_list["elements"][0]["id"]
+            inputs = {
+                "inputs": {"src": "dce", "id": dce_id},
+                "index": "hg19_value",
+            }
+            self._run("dbkey_filter_collection_input", history_id, inputs, assert_ok=True)
+
     @skip_without_tool("cheetah_problem_unbound_var_input")
     def test_legacy_biotools_xref_injection(self):
         url = self._api_url("tools/cheetah_problem_unbound_var_input")

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