1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1d1084581b62/ Changeset: 1d1084581b62 User: Dave Bouvier Date: 2013-10-01 16:59:42 Summary: When installing repositories containing tools that have been migrated from the distribution to the tool shed, handle cases where the repository may have been successfully cloned, but is still in a New state. Affected #: 1 file
diff -r 7978a2884aa79c87650eb5aca1f934969f276fc0 -r 1d1084581b6219ee8ae7968c8109c8132e32a915 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -133,7 +133,7 @@ # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision> relative_clone_dir = os.path.join( self.tool_shed, 'repos', owner, name, changeset_revision ) clone_dir = os.path.join( self.tool_path, relative_clone_dir ) - if not self.__isinstalled( clone_dir ): + if not self.__iscloned( clone_dir ): repository_clone_url = os.path.join( self.tool_shed_url, 'repos', owner, name ) relative_install_dir = os.path.join( relative_clone_dir, name ) install_dir = os.path.join( clone_dir, name ) @@ -478,7 +478,15 @@ tool_shed_repository.name, tool_shed_repository.installed_changeset_revision ) clone_dir = os.path.join( self.tool_path, relative_clone_dir ) - if self.__isinstalled( clone_dir ): + cloned_ok = self.__iscloned( clone_dir ) + is_installed = False + # Any of the following states should count as installed in this context. + if tool_shed_repository.status in [ self.app.model.ToolShedRepository.installation_status.INSTALLED, + self.app.model.ToolShedRepository.installation_status.ERROR, + self.app.model.ToolShedRepository.installation_status.UNINSTALLED, + self.app.model.ToolShedRepository.installation_status.DEACTIVATED ]: + is_installed = True + if cloned_ok and is_installed: print "Skipping automatic install of repository '", tool_shed_repository.name, "' because it has already been installed in location ", clone_dir else: repository_clone_url = os.path.join( self.tool_shed_url, 'repos', tool_shed_repository.owner, tool_shed_repository.name ) @@ -489,9 +497,10 @@ tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) - suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) - cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) - if cloned_ok: + if not cloned_ok: + suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) + cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) + if cloned_ok and not is_installed: self.handle_repository_contents( tool_shed_repository=tool_shed_repository, repository_clone_url=repository_clone_url, relative_install_dir=relative_install_dir, @@ -592,7 +601,7 @@ return True return False
- def __isinstalled( self, clone_dir ): + def __iscloned( self, clone_dir ): full_path = os.path.abspath( clone_dir ) if os.path.exists( full_path ): for root, dirs, files in os.walk( full_path ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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