Fix config schema packaging

lib/galaxy/config/__init__.py

@@ -63,9 +63,9 @@ from galaxy.web_stack import get_stack_facts
 from ..version import VERSION_MAJOR, VERSION_MINOR
 
 try:
-    from importlib.resources import files
+    from importlib.resources import files  # type: ignore[attr-defined]
 except ImportError:
-    from importlib_resources import files
+    from importlib_resources import files  # type: ignore[no-redef]
 
 if TYPE_CHECKING:
     from galaxy.jobs import JobConfiguration
@@ -77,7 +77,9 @@ if TYPE_CHECKING:
 log = logging.getLogger(__name__)
 
 GALAXY_APP_NAME = 'galaxy'
-GALAXY_CONFIG_SCHEMA_PATH = files('galaxy.webapps.galaxy') / 'config_schema.yml'
+GALAXY_SCHEMAS_PATH = files('galaxy.config') / 'schemas'
+GALAXY_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / 'config_schema.yml'
+UWSGI_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / 'uwsgi_schema.yml'
 LOGGING_CONFIG_DEFAULT: Dict[str, Any] = {
     'disable_existing_loggers': False,
     'version': 1,
@@ -628,7 +630,6 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         self._process_config(kwargs)
 
     def _load_schema(self):
-        # Schemas are symlinked to the root of the galaxy-app package
         return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
 
     def _override_tempdir(self, kwargs):

lib/galaxy/config/config_manage.py

@@ -22,7 +22,10 @@ if __name__ == '__main__':
     sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir)))
 
 
-from galaxy.config import GALAXY_CONFIG_SCHEMA_PATH
+from galaxy.config import (
+    GALAXY_CONFIG_SCHEMA_PATH,
+    UWSGI_SCHEMA_PATH,
+)
 from galaxy.config.schema import (
     AppSchema,
     OPTION_DEFAULTS,
@@ -48,7 +51,6 @@ UNHANDLED_FILTER_TYPE_MESSAGE = "Unhandled filter type encountered [%s] for sect
 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)
 RST_DESCRIPTION_WRAPPER = TextWrapper(initial_indent="    ", subsequent_indent="    ", break_long_words=False, break_on_hyphens=False)
-UWSGI_SCHEMA_PATH = "lib/galaxy/webapps/uwsgi_schema.yml"
 
 UWSGI_OPTIONS = dict([
     ('http', {
@@ -346,7 +348,7 @@ GALAXY_APP = App(
     "8080",
     ["galaxy.web.buildapp:app_factory"],  # TODO: Galaxy could call factory a few different things and they'd all be fine.
     "config/galaxy.yml",
-    GALAXY_CONFIG_SCHEMA_PATH,
+    str(GALAXY_CONFIG_SCHEMA_PATH),
     'galaxy.webapps.galaxy.buildapp:uwsgi_app()',
 )
 SHED_APP = App(
@@ -465,9 +467,8 @@ def _build_uwsgi_schema(args, app_desc):
         "desc": "uwsgi definition, see https://uwsgi-docs.readthedocs.io/en/latest/Options.html",
         "mapping": options
     }
-    path = os.path.join(args.galaxy_root, UWSGI_SCHEMA_PATH)
     contents = ordered_dump(schema)
-    _write_to_file(args, contents, path)
+    _write_to_file(args, contents, UWSGI_SCHEMA_PATH)
 
 
 def _find_config(args, app_desc):

lib/galaxy/config/schemas/uwsgi_schema.yml

@@ -0,0 +1 @@
+../../../../lib/galaxy/webapps/uwsgi_schema.yml

lib/galaxy/webapps/base/webapp.py

@@ -42,9 +42,9 @@ from galaxy.web.framework import (
 from galaxy.web_stack import get_app_kwds
 
 try:
-    from importlib.resources import files
+    from importlib.resources import files  # type: ignore[attr-defined]
 except ImportError:
-    from importlib_resources import files
+    from importlib_resources import files  # type: ignore[no-redef]
 
 log = logging.getLogger(__name__)
 

lib/galaxy/webapps/galaxy/uwsgi_schema.yml

@@ -1 +0,0 @@
-../uwsgi_schema.yml

packages/app/MANIFEST.in

@@ -1,5 +1,5 @@
 include *.rst *.txt LICENSE
-include galaxy/*.yml
+include galaxy/config/*.yml
 include galaxy/config/sample/*.sample*
 include galaxy/jobs/runners/util/job_script/*.sh
 include galaxy/tools/*tsv

packages/app/galaxy/config_schema.yml

@@ -1 +0,0 @@
-../../../lib/galaxy/webapps/galaxy/config_schema.yml

packages/app/galaxy/job_config_schema.yml

@@ -1 +0,0 @@
-../../../lib/galaxy/webapps/galaxy/job_config_schema.yml

packages/app/galaxy/uwsgi_schema.yml

@@ -1 +0,0 @@
-../../../lib/galaxy/webapps/galaxy/uwsgi_schema.yml

packages/app/setup.py

@@ -101,9 +101,9 @@ ENTRY_POINTS = '''
 PACKAGE_DATA = {
     # Be sure to update MANIFEST.in for source dist.
     'galaxy': [
-        'config_schema.yml',
-        'job_config_schema.yml',
-        'uwsgi_schema.yml',
+        'config/schemas/config_schema.yml',
+        'config/schemas/job_config_schema.yml',
+        'config/schemas/uwsgi_schema.yml',
         'config/sample/*',
     ],
     'tool_shed': [

pyproject.toml

@@ -40,6 +40,7 @@ future = "*"
 galaxy_sequence_utils = "*"
 gxformat2 = "*"
 h5py = "*"
+importlib_resources = "*"
 isa-rwval = "*"
 kombu = "*"
 lagom = "*"

test/unit/app/jobs/test_job_configuration.py

@@ -7,6 +7,7 @@ from unittest import mock
 
 from pykwalify.core import Core
 
+from galaxy.config import GALAXY_SCHEMAS_PATH
 from galaxy.job_metrics import JobMetrics
 from galaxy.jobs import JobConfiguration
 from galaxy.util import galaxy_directory, galaxy_samples_directory
@@ -422,7 +423,7 @@ class AdvancedJobConfYamlParserTestCase(AdvancedJobConfXmlParserTestCase):
 
 
 def test_yaml_advanced_validation():
-    schema = os.path.join(galaxy_directory(), "lib", "galaxy", "webapps", "galaxy", "job_config_schema.yml")
+    schema = GALAXY_SCHEMAS_PATH / 'job_config_schema.yml'
     integration_tests_dir = os.path.join(galaxy_directory(), "test", "integration")
     valid_files = [
         ADVANCED_JOB_CONF_YAML,
@@ -435,6 +436,6 @@ def test_yaml_advanced_validation():
     for valid_file in valid_files:
         c = Core(
             source_file=valid_file,
-            schema_files=[schema],
+            schema_files=[str(schema)],
         )
         c.validate()