Fix .metadata_ in tool_shed dir

lib/tool_shed/galaxy_install/dependency_display.py

@@ -441,7 +441,7 @@ def populate_containers_dict_from_repository_metadata(self, tool_shed_url, tool_
         when displaying repository dependencies for installed repositories and when displaying
         them for uninstalled repositories that are being reinstalled.
         """
-        metadata = repository.metadata
+        metadata = repository.metadata_
         if metadata:
             # Handle proprietary datatypes.
             datatypes = metadata.get('datatypes', None)
@@ -464,7 +464,7 @@ def populate_containers_dict_from_repository_metadata(self, tool_shed_url, tool_
                     readme_files_dict = readme_util.build_readme_files_dict(self.app,
                                                                             repository,
                                                                             repository.changeset_revision,
-                                                                            repository.metadata, tool_path)
+                                                                            repository.metadata_, tool_path)
             else:
                 readme_files_dict = None
             # Handle repository dependencies.

lib/tool_shed/test/base/twilltestcase.py

@@ -321,7 +321,7 @@ def check_galaxy_repository_db_status(self, repository_name, owner, expected_sta
             (installed_repository.status, expected_status)
 
     def check_galaxy_repository_tool_panel_section(self, repository, expected_tool_panel_section):
-        metadata = repository.metadata
+        metadata = repository.metadata_
         assert 'tools' in metadata, f'Tools not found in repository metadata: {metadata}'
         # If integrated_tool_panel.xml is to be tested, this test method will need to be enhanced to handle tools
         # from the same repository in different tool panel sections. Getting the first tool guid is ok, because
@@ -571,7 +571,7 @@ def display_galaxy_browse_repositories_page(self, strings_displayed=None, string
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def display_installed_jobs_list_page(self, installed_repository, data_manager_names=None, strings_displayed=None, strings_not_displayed=None):
-        data_managers = installed_repository.metadata.get('data_manager', {}).get('data_managers', {})
+        data_managers = installed_repository.metadata_.get('data_manager', {}).get('data_managers', {})
         if data_manager_names:
             if not isinstance(data_manager_names, list):
                 data_manager_names = [data_manager_names]
@@ -1500,14 +1500,14 @@ def verify_installed_repositories(self, installed_repositories=None, uninstalled
 
     def verify_installed_repository_metadata_unchanged(self, name, owner):
         installed_repository = test_db_util.get_installed_repository_by_name_owner(name, owner)
-        metadata = installed_repository.metadata
-        self.reset_installed_repository_metadata(installed_repository)
-        new_metadata = installed_repository.metadata
+        metadata = installed_repository.metadata_
+        self.reset_installed_repository_metadata_(installed_repository)
+        new_metadata = installed_repository.metadata_
         assert metadata == new_metadata, f'Metadata for installed repository {name} differs after metadata reset.'
 
     def verify_installed_repository_no_tool_panel_section(self, repository):
         '''Verify that there is no 'tool_panel_section' entry in the repository metadata.'''
-        metadata = repository.metadata
+        metadata = repository.metadata_
         assert 'tool_panel_section' not in metadata, f'Tool panel section incorrectly found in metadata: {metadata}'
 
     def verify_installed_repository_data_table_entries(self, required_data_table_entries):
@@ -1582,7 +1582,7 @@ def verify_tool_metadata_for_installed_repository(self, installed_repository, st
         if strings_not_displayed is None:
             strings_not_displayed = []
         repository_id = self.security.encode_id(installed_repository.id)
-        for tool in installed_repository.metadata['tools']:
+        for tool in installed_repository.metadata_['tools']:
             strings = list(strings_displayed)
             strings.extend([tool['id'], tool['description'], tool['version'], tool['guid'], tool['name']])
             params = dict(repository_id=repository_id, tool_id=tool['id'])

lib/tool_shed/test/functional/test_1070_invalid_tool.py

@@ -84,5 +84,5 @@ def test_0015_install_freebayes_repository(self):
                                                       strings_not_displayed=['bisulfite mapper'])
         self.verify_tool_metadata_for_installed_repository(installed_repository)
         self.update_installed_repository(installed_repository, strings_displayed=["there are no updates available"])
-        assert 'invalid_tools' in installed_repository.metadata, 'No invalid tools were defined in %s.' % \
+        assert 'invalid_tools' in installed_repository.metadata_, 'No invalid tools were defined in %s.' % \
             installed_repository.name

lib/tool_shed/test/functional/test_1300_reset_all_metadata.py

@@ -441,7 +441,7 @@ def test_9905_reset_metadata_on_all_repositories(self):
         repository_metadata = dict()
         repositories = self.test_db_util.get_all_installed_repositories(actually_installed=True)
         for repository in repositories:
-            repository_metadata[self.security.encode_id(repository.id)] = repository.metadata
+            repository_metadata[self.security.encode_id(repository.id)] = repository.metadata_
         self.reset_metadata_on_selected_installed_repositories(list(repository_metadata.keys()))
         for repository in repositories:
             self.test_db_util.ga_refresh(repository)
@@ -452,7 +452,7 @@ def test_9905_reset_metadata_on_all_repositories(self):
             # is normal and expected behavior, the functional tests assume that repository metadata will not change
             # in any way after a reset. A workaround is to remove the tool panel section from the stored repository
             # metadata dict, in order to eliminate the misleading detection of changed metadata.
-            if 'tool_panel_section' in old_metadata and 'tool_panel_section' not in repository.metadata:
+            if 'tool_panel_section' in old_metadata and 'tool_panel_section' not in repository.metadata_:
                 del old_metadata['tool_panel_section']
-            assert repository.metadata == old_metadata, 'Metadata for %s repository %s changed after reset. \nOld: %s\nNew: %s' % \
-                (repository.status, repository.name, old_metadata, repository.metadata)
+            assert repository.metadata_ == old_metadata, 'Metadata for %s repository %s changed after reset. \nOld: %s\nNew: %s' % \
+                (repository.status, repository.name, old_metadata, repository.metadata_)

lib/tool_shed/util/shed_util_common.py

@@ -175,7 +175,7 @@ def get_requirements_from_repository(repository):
     if not repository.includes_tools:
         return {}
     else:
-        return get_requirements_from_tools(repository.metadata.get('tools', []))
+        return get_requirements_from_tools(repository.metadata_.get('tools', []))
 
 
 def get_repository_categories(app, id):