From bd765b0b24c8285b500cbf95a5eedaaacbeb3a4a Mon Sep 17 00:00:00 2001 From: Sergey Golitsynskiy Date: Wed, 20 Oct 2021 18:51:46 -0400 Subject: [PATCH] Replace all remaining instances of TSR.metadata --- .../datatypes/custom_datatype_manager.py | 2 +- lib/galaxy/tool_shed/galaxy_install/install_manager.py | 6 +++--- .../galaxy_install/installed_repository_manager.py | 10 +++++----- .../metadata/installed_repository_metadata_manager.py | 4 ++-- .../repository_dependency_manager.py | 4 ++-- .../tool_shed/galaxy_install/tool_migration_manager.py | 2 +- .../tool_shed/galaxy_install/tools/data_manager.py | 2 +- .../galaxy_install/tools/tool_panel_manager.py | 6 +++--- .../galaxy_install/update_repository_manager.py | 2 +- lib/galaxy/tool_shed/metadata/metadata_generator.py | 2 +- lib/galaxy/tool_shed/util/repository_util.py | 4 ++-- lib/galaxy/tools/cache.py | 2 +- .../webapps/galaxy/controllers/admin_toolshed.py | 6 +++--- test/unit/app/tools/test_toolbox.py | 2 +- 14 files changed, 27 insertions(+), 27 deletions(-) diff --git a/lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py b/lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py index 35f037e9944..a1350c3dedf 100644 --- a/lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py +++ b/lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py @@ -154,7 +154,7 @@ class CustomDatatypeLoader: Load proprietary datatypes and return information needed for loading custom datatypes converters and display applications later. """ - metadata = repository.metadata + metadata = repository.metadata_ repository_dict = None datatypes_config = get_config_from_disk(DATATYPES_CONFIG_FILENAME, relative_install_dir) if datatypes_config: diff --git a/lib/galaxy/tool_shed/galaxy_install/install_manager.py b/lib/galaxy/tool_shed/galaxy_install/install_manager.py index 73bf0067af8..66388d53f68 100644 --- a/lib/galaxy/tool_shed/galaxy_install/install_manager.py +++ b/lib/galaxy/tool_shed/galaxy_install/install_manager.py @@ -515,7 +515,7 @@ class InstallRepositoryManager: persist=True) irmm.generate_metadata_for_changeset_revision() irmm_metadata_dict = irmm.get_metadata_dict() - tool_shed_repository.metadata = irmm_metadata_dict + tool_shed_repository.metadata_ = irmm_metadata_dict # Update the tool_shed_repository.tool_shed_status column in the database. tool_shed_status_dict = repository_util.get_tool_shed_status_for_installed_repository(self.app, tool_shed_repository) if tool_shed_status_dict: @@ -934,7 +934,7 @@ class InstallRepositoryManager: shed_tool_conf=shed_tool_conf, reinstalling=reinstalling, tool_panel_section_mapping=tool_panel_section_mapping) - metadata = tool_shed_repository.metadata + metadata = tool_shed_repository.metadata_ if 'tools' in metadata and install_resolver_dependencies: self.update_tool_shed_repository_status(tool_shed_repository, self.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES) @@ -964,7 +964,7 @@ class InstallRepositoryManager: def update_tool_shed_repository(self, repository, tool_shed_url, latest_ctx_rev, latest_changeset_revision, install_new_dependencies=True, install_options=None): install_options = install_options or {} - original_metadata_dict = repository.metadata + original_metadata_dict = repository.metadata_ original_repository_dependencies_dict = original_metadata_dict.get('repository_dependencies', {}) original_repository_dependencies = original_repository_dependencies_dict.get('repository_dependencies', []) original_tool_dependencies_dict = original_metadata_dict.get('tool_dependencies', {}) diff --git a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py index 26b379d2573..d3e594d325e 100644 --- a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py @@ -87,10 +87,10 @@ class InstalledRepositoryManager: tpm=tpm, repository=repository, changeset_revision=repository.changeset_revision, - metadata_dict=repository.metadata) + metadata_dict=repository.metadata_) repository_tools_tups = irmm.get_repository_tools_tups() # Reload tools into the appropriate tool panel section. - tool_panel_dict = repository.metadata['tool_panel_section'] + tool_panel_dict = repository.metadata_['tool_panel_section'] tpm.add_to_tool_panel(repository.name, repository_clone_url, repository.installed_changeset_revision, @@ -105,7 +105,7 @@ class InstalledRepositoryManager: data_manager_relative_install_dir = os.path.join(data_manager_relative_install_dir, repository.name) dmh = data_manager.DataManagerHandler(self.app) dmh.install_data_managers(self.app.config.shed_data_manager_config_file, - repository.metadata, + repository.metadata_, repository.get_shed_config_dict(self.app), data_manager_relative_install_dir, repository, @@ -204,7 +204,7 @@ class InstalledRepositoryManager: name, repository_owner, changeset_revision) - if not updating and repository and repository.metadata: + if not updating and repository and repository.metadata_: installed_rd, missing_rd = self.get_installed_and_missing_repository_dependencies(repository) else: installed_rd, missing_rd = \ @@ -286,7 +286,7 @@ class InstalledRepositoryManager: if has_repository_dependencies: # The repository dependencies container will include only the immediate repository # dependencies of this repository, so the container will be only a single level in depth. - metadata = repository.metadata + metadata = repository.metadata_ installed_rd_tups = [] missing_rd_tups = [] for tsr in repository.repository_dependencies: diff --git a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py index 6619ef98773..b1a33244e91 100644 --- a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py +++ b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -87,10 +87,10 @@ class InstalledRepositoryMetadataManager(MetadataGenerator): def reset_all_metadata_on_installed_repository(self): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" if self.relative_install_dir: - original_metadata_dict = self.repository.metadata + original_metadata_dict = self.repository.metadata_ self.generate_metadata_for_changeset_revision() if self.metadata_dict != original_metadata_dict: - self.repository.metadata = self.metadata_dict + self.repository.metadata_ = self.metadata_dict self.update_in_shed_tool_config() self.app.install_model.context.add(self.repository) self.app.install_model.context.flush() diff --git a/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py b/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py index 97dd25cd1e5..3e552c203a3 100644 --- a/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py +++ b/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py @@ -233,10 +233,10 @@ class RepositoryDependencyInstallManager: # The database record for the tool shed repository currently being processed can be updated. # Get the repository metadata to see where it was previously located in the tool panel. tpm = tool_panel_manager.ToolPanelManager(self.app) - if repository_db_record and repository_db_record.metadata: + if repository_db_record and repository_db_record.metadata_: _, tool_panel_section_key = \ tpm.handle_tool_panel_selection(toolbox=self.app.toolbox, - metadata=repository_db_record.metadata, + metadata=repository_db_record.metadata_, no_changes_checked=no_changes_checked, tool_panel_section_id=tool_panel_section_id, new_tool_panel_section_label=new_tool_panel_section_label) diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py b/lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py index f7e49548d50..f0ed910e509 100644 --- a/lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py @@ -442,7 +442,7 @@ class ToolMigrationManager: persist=True) irmm.generate_metadata_for_changeset_revision() irmm_metadata_dict = irmm.get_metadata_dict() - tool_shed_repository.metadata = irmm_metadata_dict + tool_shed_repository.metadata_ = irmm_metadata_dict self.app.install_model.context.add(tool_shed_repository) self.app.install_model.context.flush() has_tool_dependencies = self.__has_tool_dependencies(irmm_metadata_dict) diff --git a/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py b/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py index 343b2fb081d..eff5a432122 100644 --- a/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py +++ b/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py @@ -149,7 +149,7 @@ class DataManagerHandler: return rval def remove_from_data_manager(self, repository): - metadata_dict = repository.metadata + metadata_dict = repository.metadata_ if metadata_dict and 'data_manager' in metadata_dict: shed_data_manager_conf_filename = self.app.config.shed_data_manager_config_file tree, error_message = parse_xml(shed_data_manager_conf_filename) diff --git a/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py b/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py index ba50383aa64..e97052a1709 100644 --- a/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py +++ b/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py @@ -212,7 +212,7 @@ class ToolPanelManager: tool_panel_dict = {} shed_tool_conf, tool_path, relative_install_dir = \ get_tool_panel_config_tool_path_install_dir(self.app, repository) - metadata = repository.metadata + metadata = repository.metadata_ # Create a dictionary of tool guid and tool config file name for each tool in the repository. guids_and_configs = {} if 'tools' in metadata: @@ -467,7 +467,7 @@ class ToolPanelManager: # information so the tools can be displayed in the same way when the repository is # activated or reinstalled. tool_panel_dict = self.generate_tool_panel_dict_from_shed_tool_conf_entries(repository) - repository.metadata['tool_panel_section'] = tool_panel_dict + repository.metadata_['tool_panel_section'] = tool_panel_dict self.app.install_model.context.add(repository) self.app.install_model.context.flush() # Create a list of guids for all tools that will be removed from the in-memory tool panel @@ -481,7 +481,7 @@ class ToolPanelManager: shed_tool_conf_dict = self.get_shed_tool_conf_dict(shed_tool_conf) if uninstall: # Remove from the shed_tool_conf file on disk. - self.remove_from_shed_tool_config(shed_tool_conf_dict, repository.metadata) + self.remove_from_shed_tool_config(shed_tool_conf_dict, repository.metadata_) def update_tool_panel_dict(self, tool_panel_dict, tool_panel_section_mapping, repository_tools_tups): for tool_guid in tool_panel_dict: diff --git a/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py index d780853de85..392628b51d2 100644 --- a/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py +++ b/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py @@ -109,7 +109,7 @@ class UpdateRepositoryManager: Update a tool_shed_repository database record with new information retrieved from the Tool Shed. This happens when updating an installed repository to a new changeset revision. """ - repository.metadata = updated_metadata_dict + repository.metadata_ = updated_metadata_dict tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, repository.tool_shed) clean_dependency_relationships(self.app, updated_metadata_dict, repository, tool_shed_url) # Update the repository.changeset_revision column in the database. diff --git a/lib/galaxy/tool_shed/metadata/metadata_generator.py b/lib/galaxy/tool_shed/metadata/metadata_generator.py index 98e18c10971..906799c2ce0 100644 --- a/lib/galaxy/tool_shed/metadata/metadata_generator.py +++ b/lib/galaxy/tool_shed/metadata/metadata_generator.py @@ -317,7 +317,7 @@ class MetadataGenerator: if self.updating_installed_repository: # Keep the original tool shed repository metadata if setting metadata on a repository # installed into a local Galaxy instance for which we have pulled updates. - original_repository_metadata = self.repository.metadata + original_repository_metadata = self.repository.metadata_ else: original_repository_metadata = None readme_file_names = _get_readme_file_names(str(self.repository.name)) diff --git a/lib/galaxy/tool_shed/util/repository_util.py b/lib/galaxy/tool_shed/util/repository_util.py index dcad79e1ce0..a32b8f227c7 100644 --- a/lib/galaxy/tool_shed/util/repository_util.py +++ b/lib/galaxy/tool_shed/util/repository_util.py @@ -112,7 +112,7 @@ def create_or_update_tool_shed_repository(app, name, description, installed_chan tool_shed_repository.description = description tool_shed_repository.changeset_revision = current_changeset_revision tool_shed_repository.ctx_rev = ctx_rev - tool_shed_repository.metadata = metadata_dict + tool_shed_repository.metadata_ = metadata_dict tool_shed_repository.includes_datatypes = includes_datatypes tool_shed_repository.deleted = deleted tool_shed_repository.uninstalled = uninstalled @@ -127,7 +127,7 @@ def create_or_update_tool_shed_repository(app, name, description, installed_chan installed_changeset_revision=installed_changeset_revision, changeset_revision=current_changeset_revision, ctx_rev=ctx_rev, - metadata=metadata_dict, + metadata_=metadata_dict, includes_datatypes=includes_datatypes, dist_to_shed=dist_to_shed, deleted=deleted, diff --git a/lib/galaxy/tools/cache.py b/lib/galaxy/tools/cache.py index 25a551d7f4b..199e5e2688a 100644 --- a/lib/galaxy/tools/cache.py +++ b/lib/galaxy/tools/cache.py @@ -301,7 +301,7 @@ class ToolShedRepositoryCache: def rebuild(self): self.repositories = self.session.query(ToolShedRepository).options( - defer(ToolShedRepository.metadata), joinedload('tool_dependencies') + defer(ToolShedRepository.metadata_), joinedload('tool_dependencies') ).all() repos_by_tuple = defaultdict(list) for repository in self.repositories + self.local_repositories: diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py index 7e92798353c..de0d6831c5d 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -177,7 +177,7 @@ class AdminToolshed(AdminGalaxy): message = escape(kwd.get('message', '')) status = kwd.get('status', 'done') repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id) - repository_metadata = repository.metadata + repository_metadata = repository.metadata_ shed_config_dict = repository.get_shed_config_dict(trans.app) tool_metadata = {} tool_lineage = [] @@ -863,7 +863,7 @@ class AdminToolshed(AdminGalaxy): new_tool_panel_section_label = kwd.get('new_tool_panel_section_label', '') tool_panel_section_key = None tool_panel_section_keys = [] - metadata = tool_shed_repository.metadata + metadata = tool_shed_repository.metadata_ # Keep track of tool dependencies defined for the current repository or those defined for any of # its repository dependencies. includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies @@ -1024,7 +1024,7 @@ class AdminToolshed(AdminGalaxy): latest_ctx_rev = kwd.get('latest_ctx_rev', None) tool_shed_repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id) repository_clone_url = common_util.generate_clone_url_for_installed_repository(trans.app, tool_shed_repository) - metadata = tool_shed_repository.metadata + metadata = tool_shed_repository.metadata_ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(tool_shed_repository.tool_shed)) tool_path = tool_shed_repository.get_tool_relative_path(trans.app)[0] if latest_changeset_revision and latest_ctx_rev: diff --git a/test/unit/app/tools/test_toolbox.py b/test/unit/app/tools/test_toolbox.py index e99349b2504..f1d767a4490 100644 --- a/test/unit/app/tools/test_toolbox.py +++ b/test/unit/app/tools/test_toolbox.py @@ -111,7 +111,7 @@ class BaseToolBoxTestCase(unittest.TestCase, UsesTools): } if config_filename: metadata['shed_config_filename'] = config_filename - repository = tool_shed_install.ToolShedRepository(metadata=metadata) + repository = tool_shed_install.ToolShedRepository(metadata_=metadata) repository.tool_shed = DEFAULT_TEST_REPO.tool_shed repository.owner = DEFAULT_TEST_REPO.owner repository.name = DEFAULT_TEST_REPO.name