Merge pull request #19341 from nsoranzo/misc_fixes_202412

Misc fixes 202412

.github/workflows/mulled.yaml

@@ -41,6 +41,8 @@ jobs:
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-mulled
       - name: Install Apptainer's singularity
         uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.3.6  # https://github.com/eWaterCycle/setup-apptainer/pull/68
       - name: Install tox
         run: pip install tox
       - name: Run tests

client/src/api/schema/schema.ts

@@ -28958,7 +28958,6 @@ export interface operations {
             };
             path: {
                 library_id: string;
-                /** @example F0123456789ABCDEF */
                 id: string;
             };
             cookie?: never;

doc/schema_template.md

@@ -21,6 +21,8 @@ number of tutorials on building Galaxy tools that would better serve that purpos
 $tag:tool://element[@name='tool']
 $tag:tool|description://element[@name='tool']//element[@name='description']
 $tag:tool|macros://complexType[@name='Macros']
+$tag:tool|entry_points://complexType[@name='EntryPoints']
+$tag:tool|entry_points|entry_point://complexType[@name='EntryPoint']
 $tag:tool|edam_topics://complexType[@name='EdamTopics']
 $tag:tool|edam_operations://complexType[@name='EdamOperations']
 $tag:tool|xrefs://complexType[@name='xrefs']

lib/galaxy/config/config_manage.py

@@ -57,7 +57,6 @@
 APP_DESCRIPTION = """Application to target for operation (i.e. galaxy, tool_shed, or reports))"""
 DRY_RUN_DESCRIPTION = """If this action modifies files, just print what would be the result and continue."""
 UNKNOWN_OPTION_MESSAGE = "Option [%s] not found in schema - either it is invalid or the Galaxy team hasn't documented it. If invalid, you should manually remove it. If the option is valid but undocumented, please file an issue with the Galaxy team."
-USING_SAMPLE_MESSAGE = "Config file not found, using sample."
 NO_APP_MAIN_MESSAGE = "No app:main section found, using application defaults throughout."
 YAML_COMMENT_WRAPPER = TextWrapper(
     initial_indent="# ", subsequent_indent="# ", break_long_words=False, break_on_hyphens=False
@@ -306,9 +305,11 @@ def _find_config(args: Namespace, app_desc: App) -> str:
             if os.path.exists(possible_ini_config):
                 path = possible_ini_config
 
-    if not path:
-        _warn(USING_SAMPLE_MESSAGE)
+    if path:
+        print(f"Found config file {path}")
+    else:
         path = os.path.join(args.galaxy_root, app_desc.sample_destination)
+        _warn(f"Config file not found, using sample {path}")
 
     return path
 
@@ -354,8 +355,8 @@ def _validate(args: Namespace, app_desc: App) -> None:
     path = _find_config(args, app_desc)
     # Allow empty mapping (not allowed by pykwalify)
     raw_config = _order_load_path(path)
-    if raw_config.get(app_desc.app_name) is None:
-        raw_config[app_desc.app_name] = {}
+    # Drop top-level keys (e.g. "gravity") except for app_desc.app_name
+    raw_config = {app_desc.app_name: raw_config.get(app_desc.app_name) or {}}
     # Rewrite the file any way to merge any duplicate keys
     with tempfile.NamedTemporaryFile("w", delete=False, suffix=".yml") as config_p:
         ordered_dump(raw_config, config_p)

lib/galaxy/config/schemas/config_schema.yml

@@ -1717,7 +1717,7 @@ mapping:
 
       helpsite_url:
         type: str
-        required: true
+        required: false
         default: https://help.galaxyproject.org/
         per_host: true
         desc: |

lib/galaxy/datatypes/interval.py

@@ -193,12 +193,7 @@ def set_meta(
     def displayable(self, dataset: DatasetProtocol) -> bool:
         try:
             return (
-                not dataset.deleted
-                and not dataset.dataset.purged
-                and dataset.has_data()
-                and dataset.state == dataset.states.OK
-                and dataset.metadata.columns > 0
-                and dataset.metadata.data_lines != 0
+                super().displayable(dataset)
                 and dataset.metadata.chromCol
                 and dataset.metadata.startCol
                 and dataset.metadata.endCol

lib/galaxy/tools/parameters/basic.py

@@ -258,13 +258,12 @@ def value_from_basic(self, value, app, ignore_errors=False):
         elif isinstance(value, MutableMapping) and value.get("__class__") == "UnvalidatedValue":
             return value["value"]
         # Delegate to the 'to_python' method
-        if ignore_errors:
-            try:
-                return self.to_python(value, app)
-            except Exception:
-                return value
-        else:
+        try:
             return self.to_python(value, app)
+        except Exception:
+            if not ignore_errors:
+                raise
+            return value
 
     def value_to_display_text(self, value) -> str:
         if is_runtime_value(value):

lib/galaxy/tools/parameters/grouping.py

@@ -161,9 +161,9 @@ def value_from_basic(self, value, app, ignore_errors=False):
                     else:
                         rval_dict[input.name] = input.value_from_basic(d[input.name], app, ignore_errors)
                 rval.append(rval_dict)
-        except Exception as e:
+        except Exception:
             if not ignore_errors:
-                raise e
+                raise
         return rval
 
     def get_initial_value(self, trans, context):
@@ -226,9 +226,9 @@ def value_from_basic(self, value, app, ignore_errors=False):
             for input in self.inputs.values():
                 if not ignore_errors or input.name in value:
                     rval[input.name] = input.value_from_basic(value[input.name], app, ignore_errors)
-        except Exception as e:
+        except Exception:
             if not ignore_errors:
-                raise e
+                raise
         return rval
 
     def get_initial_value(self, trans, context):
@@ -389,9 +389,9 @@ def value_from_basic(self, value, app, ignore_errors=False):
                     else:
                         rval_dict[input.name] = input.value_from_basic(d[input.name], app, ignore_errors)
                 rval.append(rval_dict)
-            except Exception as e:
+            except Exception:
                 if not ignore_errors:
-                    raise e
+                    raise
         return rval
 
     def get_file_count(self, trans, context):
@@ -794,9 +794,9 @@ def value_from_basic(self, value, app, ignore_errors=False):
                 # conditional's values dictionary.
                 if not ignore_errors or input.name in value:
                     rval[input.name] = input.value_from_basic(value[input.name], app, ignore_errors)
-        except Exception as e:
+        except Exception:
             if not ignore_errors:
-                raise e
+                raise
         return rval
 
     def get_initial_value(self, trans, context):

lib/galaxy/webapps/galaxy/services/library_contents.py

@@ -58,7 +58,7 @@
     str,
     Path(
         title="The encoded ID of a library folder or dataset.",
-        example="F0123456789ABCDEF",
+        examples=["F0123456789ABCDEF"],
         min_length=16,
         pattern="F?[0-9a-fA-F]+",
     ),

pytest.ini

@@ -1,5 +1,5 @@
 [pytest]
-addopts = --doctest-continue-on-failure --verbosity=1
+addopts = --doctest-continue-on-failure --verbosity=1 --showlocals
 asyncio_mode = auto
 log_level = DEBUG
 # Install pytest-memray and set memray to true here to enable memory profiling of tests

test/unit/tool_shed/test_shed_index.py

@@ -26,7 +26,9 @@ def whoosh_index_dir():
 @pytest.fixture(scope="module")
 def community_file_dir():
     extracted_archive_dir = tempfile.mkdtemp()
-    b = BytesIO(requests.get(URL).content)
+    response = requests.get(URL)
+    response.raise_for_status()
+    b = BytesIO(response.content)
     tarfile.open(fileobj=b, mode="r:gz").extractall(extracted_archive_dir)
     try:
         yield extracted_archive_dir

test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py

@@ -46,6 +46,6 @@ def test_singularity_container_test(tmp_path) -> None:
         "singularity",
         tmp_path,
     )
-    assert "samtools:1.0--1" in results["passed"]
-    assert "pybigwig:0.3.22--py36h54a71a5_0" in results["passed"]
-    assert "yasm:1.3.0--0" in results["notest"]
+    assert "samtools:1.0--1" in results["passed"], results
+    assert "pybigwig:0.3.22--py36h54a71a5_0" in results["passed"], results
+    assert "yasm:1.3.0--0" in results["notest"], results