1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4df1be355e4f/ Changeset: 4df1be355e4f User: greg Date: 2014-02-19 19:05:25 Summary: Make managing an in-memory registry of bi-directional installed repository dependency relationships a configurable option for Galaxy instances. Affected #: 6 files diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -95,6 +95,7 @@ self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) + self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', True ) ) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) self.hours_between_check = kwargs.get( 'hours_between_check', 12 ) try: diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -271,9 +271,10 @@ if remove_from_disk_checked: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED tool_shed_repository.error_message = None - # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the - # installed_repository_manager. - trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) + if trans.app.config.manage_dependency_relationships: + # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the + # installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) else: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED trans.install_model.context.add( tool_shed_repository ) diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -62,8 +62,9 @@ # whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key # at runtime. The value defines the entire tool dependency tree. self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} - # Load defined dependency relationships for installed tool shed repositories and their contents. - self.load_dependency_relationships() + if app.config.manage_dependency_relationships: + # Load defined dependency relationships for installed tool shed repositories and their contents. + self.load_dependency_relationships() def add_entry_to_installed_repository_dependencies_of_installed_repositories( self, repository ): """ diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -602,8 +602,9 @@ suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.install_model.ToolShedRepository.installation_status.INSTALLED ) - # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager. - trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository ) + if trans.app.config.manage_dependency_relationships: + # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository ) else: # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. set_repository_attributes( trans, diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -507,8 +507,9 @@ if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, app.install_model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + if app.config.manage_dependency_relationships: + # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. + app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) elif elem.tag == 'set_environment': # <set_environment version="1.0"> # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -152,6 +152,11 @@ #enable_tool_shed_check = False #hours_between_check = 12 +# Enable use of an in-memory registry with bi-directional relationships +# between repositories (i.e., in addition to lists of dependencies for a +# repository, keep an in-memory registry of dependent items for each repository. +#manage_dependency_relationships = True + # XML config file that contains data table entries for the ToolDataTableManager. This file is manually # maintained by the Galaxy administrator. #tool_data_table_config_path = tool_data_table_conf.xml Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.