Fix startup when data_manager_config_file config option is set to…

… an empty value

by not resolving it to the `path_resolves_to` directory in such a case.

planemo (which we use in the converters tests) set this option to an
empty value when not testing data managers:

https://github.com/galaxyproject/planemo/blob/master/planemo/galaxy/config.py#L452

Resulting in this traceback:

```
Traceback (most recent call last):
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 68, in app_pair
    app = galaxy.app.UniverseApplication(global_conf=global_conf, is_webapp=True, **kwargs)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/app.py", line 777, in __init__
    self.data_managers = self._register_singleton(DataManagers)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/di.py", line 27, in _register_singleton
    instance = self[dep_type]
               ~~~~^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 381, in __getitem__
    return self.resolve(dep)
           ^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 265, in resolve
    return self._reflection_build_with_err_handling(dep_type, suppress_error)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 392, in _reflection_build_with_err_handling
    return self._reflection_build(dep_type)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 408, in _reflection_build
    return dep_type(**sub_deps)  # type: ignore
           ^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/tools/data_manager/manager.py", line 44, in __init__
    self.load_from_xml(filename)
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/tools/data_manager/manager.py", line 58, in load_from_xml
    tree = util.parse_xml(xml_filename)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/util/__init__.py", line 360, in parse_xml
    with source.open("rb") as f:
         ^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/pathlib.py", line 1013, in open
    return io.open(self, mode, buffering, encoding, errors, newline)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IsADirectoryError: [Errno 21] Is a directory: '/tmp/tmps2qq5htq'
```

Why this has become a problem
-----------------------------

Before commit 3282aa3 `util.parse_xml()`
would raise a `XMLSyntaxError` exception if passed a directory, but
now it raises `IsADirectoryError`, which is a subclass of `OSError` with
errno 21.
As a consequence when `load_from_xml()` in lib/galaxy/tools/data_manager/manager.py
calls `util.parse_xml()` passing a directory, the resulting exception
is now re-raised in the `except OSError as e:` branch instead of
just being logged, which is good since this is a misconfiguration.

N.B.: This will also need to be fixed in Planemo by not setting the
`data_manager_config_file` option when not needed.

lib/galaxy/config/__init__.py

@@ -511,10 +511,10 @@ def resolve(key):
             if not parent:  # base case: nothing else needs resolving
                 return path
             parent_path = resolve(parent)  # recursively resolve parent path
-            if path is not None:
+            if path:
                 path = os.path.join(parent_path, path)  # resolve path
             else:
-                path = parent_path  # or use parent path
+                log.warning("Trying to resolve path for the '%s' option but it's empty/None", key)
 
             setattr(self, key, path)  # update property
             _cache[key] = path  # cache it!
@@ -557,6 +557,8 @@ def get_path(current_path, initial_path):
             return current_path
 
         current_value = getattr(self, key)  # resolved path or list of resolved paths
+        if not current_value:
+            return
         if isinstance(current_value, list):
             initial_paths = listify(self._raw_config[key], do_strip=True)  # initial unresolved paths
             updated_paths = []

lib/galaxy/jobs/__init__.py

@@ -384,6 +384,8 @@ def __init__(self, app: MinimalManagerApp):
                             f" release of Galaxy. Please convert to YAML at {self.app.config.job_config_file} or"
                             f" explicitly set `job_config_file` to {job_config_file} to remove this message"
                         )
+                if not job_config_file:
+                    raise OSError()
                 if ".xml" in job_config_file:
                     tree = load(job_config_file)
                     job_config_dict = self.__parse_job_conf_xml(tree)

test/unit/config/test_path_graph.py

@@ -142,7 +142,7 @@ def test_resolves_to_invalid_type(monkeypatch):
 
 
 def test_resolves_with_empty_component(monkeypatch):
-    # A path can be None (root path is never None; may be asigned elsewhere)
+    # A path can be None (root path is never None; may be assigned elsewhere)
     mock_schema = {
         "path0": {
             "type": "str",
@@ -155,13 +155,13 @@ def test_resolves_with_empty_component(monkeypatch):
         "path2": {
             "type": "str",
             "default": "value2",
-            "path_resolves_to": "path1",
+            "path_resolves_to": "path0",
         },
     }
     monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(mock_schema))
     monkeypatch.setattr(BaseAppConfiguration, "_load_schema", lambda a: AppSchema(Path("no path"), "_"))
 
     config = BaseAppConfiguration()
     assert config.path0 == "value0"
-    assert config.path1 == "value0"
+    assert config.path1 is None
     assert config.path2 == "value0/value2"

test/unit/config/test_path_resolves_to.py

@@ -132,21 +132,21 @@ def test_kwargs_relative_path_old_prefix_for_other_option(mock_init):
 
 def test_kwargs_relative_path_old_prefix_empty_after_strip(mock_init):
     # Expect: use value from kwargs, strip old prefix, then resolve
-    new_path1 = "old-config"
+    new_path1 = "old-config/foo"
     config = BaseAppConfiguration(path1=new_path1)
 
-    assert config.path1 == "my-config/"  # stripped of old prefix, then resolved
+    assert config.path1 == "my-config/foo"  # stripped of old prefix, then resolved
     assert config.path2 == "my-data/my-data-files"  # stripped of old prefix, then resolved
     assert config.path3 == "my-other-files"  # no change
 
 
 def test_kwargs_set_to_null(mock_init):
-    # Expected: allow overriding with null, then resolve
+    # Expected: allow overriding with null
     # This is not a common scenario, but it does happen: one example is
     # `job_config` set to `None` when testing
     config = BaseAppConfiguration(path1=None)
 
-    assert config.path1 == "my-config"  # resolved
+    assert config.path1 is None
     assert config.path2 == "my-data/my-data-files"  # resolved
     assert config.path3 == "my-other-files"  # no change