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 fda924af642..06558b4e497 100644 --- a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py @@ -56,24 +56,6 @@ class InstalledRepositoryManager: # and whose values are a list of tuples defining tool_shed_repository objects (whose status is 'Installed') that require # the key. self.installed_dependent_repositories_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') - # and whose values are a list of tuples defining its immediate tool_dependency objects (whose status can be anything). - # The value defines only the immediate tool dependencies of the repository and does not include any dependencies of the - # tool dependencies. - self.tool_dependencies_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') - # and whose values are a list of tuples defining its immediate tool_dependency objects (whose status is 'Installed'). - # The value defines only the immediate tool dependencies of the repository and does not include any dependencies of the - # tool dependencies. - self.installed_tool_dependencies_of_installed_repositories = {} - # Keep an in-memory dictionary whose keys are tuples defining tool_dependency objects (whose status is 'Installed') and - # whose values are a list of tuples defining tool_dependency objects (whose status can be anything) required by the - # installed tool dependency at runtime. The value defines the entire tool dependency tree. - self.runtime_tool_dependencies_of_installed_tool_dependencies = {} - # Keep an in-memory dictionary whose keys are tuples defining tool_dependency objects (whose status is 'Installed') and - # 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 = {} @property def tool_paths(self): @@ -176,35 +158,6 @@ class InstalledRepositoryManager: else: self.installed_dependent_repositories_of_installed_repositories[required_repository_tup] = [repository_tup] - def add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(self, tool_dependency): - """Add an entry to self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.""" - tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency) - if tool_dependency_tup not in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: - tool_shed_repository_id, name, version, type = tool_dependency_tup - debug_msg = f"Adding an entry for version {version} of {type} {name} " - debug_msg += "to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies." - log.debug(debug_msg) - status = self.install_model.ToolDependency.installation_status.INSTALLED - installed_runtime_dependent_tool_dependency_tups = self.get_runtime_dependent_tool_dependency_tuples(tool_dependency, - status=status) - self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[tool_dependency_tup] = \ - installed_runtime_dependent_tool_dependency_tups - - def add_entry_to_installed_tool_dependencies_of_installed_repositories(self, repository): - """Add an entry to self.installed_tool_dependencies_of_installed_repositories.""" - repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository) - if repository_tup not in self.installed_tool_dependencies_of_installed_repositories: - tool_shed, name, owner, installed_changeset_revision = repository_tup - debug_msg = f"Adding an entry for revision {installed_changeset_revision} of repository {name} owned by {owner} " - debug_msg += "to installed_tool_dependencies_of_installed_repositories." - log.debug(debug_msg) - installed_tool_dependency_tups = [] - for tool_dependency in repository.tool_dependencies: - if tool_dependency.status == self.app.install_model.ToolDependency.installation_status.INSTALLED: - tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency) - installed_tool_dependency_tups.append(tool_dependency_tup) - self.installed_tool_dependencies_of_installed_repositories[repository_tup] = installed_tool_dependency_tups - def add_entry_to_repository_dependencies_of_installed_repositories(self, repository): """Add an entry to self.repository_dependencies_of_installed_repositories.""" repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository) @@ -216,33 +169,6 @@ class InstalledRepositoryManager: repository_dependency_tups = self.get_repository_dependency_tups_for_installed_repository(repository, status=None) self.repository_dependencies_of_installed_repositories[repository_tup] = repository_dependency_tups - def add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(self, tool_dependency): - """Add an entry to self.runtime_tool_dependencies_of_installed_tool_dependencies.""" - tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency) - if tool_dependency_tup not in self.runtime_tool_dependencies_of_installed_tool_dependencies: - tool_shed_repository_id, name, version, type = tool_dependency_tup - debug_msg = f"Adding an entry for version {version} of {type} {name} " - debug_msg += "to runtime_tool_dependencies_of_installed_tool_dependencies." - log.debug(debug_msg) - runtime_dependent_tool_dependency_tups = self.get_runtime_dependent_tool_dependency_tuples(tool_dependency, - status=None) - self.runtime_tool_dependencies_of_installed_tool_dependencies[tool_dependency_tup] = \ - runtime_dependent_tool_dependency_tups - - def add_entry_to_tool_dependencies_of_installed_repositories(self, repository): - """Add an entry to self.tool_dependencies_of_installed_repositories.""" - repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository) - if repository_tup not in self.tool_dependencies_of_installed_repositories: - tool_shed, name, owner, installed_changeset_revision = repository_tup - debug_msg = f"Adding an entry for revision {installed_changeset_revision} of repository {name} owned by {owner} " - debug_msg += "to tool_dependencies_of_installed_repositories." - log.debug(debug_msg) - tool_dependency_tups = [] - for tool_dependency in repository.tool_dependencies: - tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency) - tool_dependency_tups.append(tool_dependency_tup) - self.tool_dependencies_of_installed_repositories[repository_tup] = tool_dependency_tups - def get_containing_repository_for_tool_dependency(self, tool_dependency_tup): tool_shed_repository_id, name, version, type = tool_dependency_tup return self.app.install_model.context.query(self.app.install_model.ToolShedRepository).get(tool_shed_repository_id) @@ -883,26 +809,6 @@ class InstalledRepositoryManager: log.debug(debug_msg) del self.installed_repository_dependencies_of_installed_repositories[repository_tup] - def remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(self, tool_dependency): - """Remove an entry from self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.""" - tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency) - if tool_dependency_tup in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: - tool_shed_repository_id, name, version, type = tool_dependency_tup - debug_msg = f"Removing entry for version {version} of {type} {name} " - debug_msg += "from installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies." - log.debug(debug_msg) - del self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[tool_dependency_tup] - - def remove_entry_from_installed_tool_dependencies_of_installed_repositories(self, repository): - """Remove an entry from self.installed_tool_dependencies_of_installed_repositories.""" - repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository) - if repository_tup in self.installed_tool_dependencies_of_installed_repositories: - tool_shed, name, owner, installed_changeset_revision = repository_tup - debug_msg = f"Removing entry for revision {installed_changeset_revision} of repository {name} owned by {owner} " - debug_msg += "from installed_tool_dependencies_of_installed_repositories." - log.debug(debug_msg) - del self.installed_tool_dependencies_of_installed_repositories[repository_tup] - def remove_entry_from_repository_dependencies_of_installed_repositories(self, repository): """Remove an entry from self.repository_dependencies_of_installed_repositories.""" repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository) @@ -913,26 +819,6 @@ class InstalledRepositoryManager: log.debug(debug_msg) del self.repository_dependencies_of_installed_repositories[repository_tup] - def remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies(self, tool_dependency): - """Remove an entry from self.runtime_tool_dependencies_of_installed_tool_dependencies.""" - tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency) - if tool_dependency_tup in self.runtime_tool_dependencies_of_installed_tool_dependencies: - tool_shed_repository_id, name, version, type = tool_dependency_tup - debug_msg = "Removing entry for version %s of %s %s from runtime_tool_dependencies_of_installed_tool_dependencies." % \ - (version, type, name) - log.debug(debug_msg) - del self.runtime_tool_dependencies_of_installed_tool_dependencies[tool_dependency_tup] - - def remove_entry_from_tool_dependencies_of_installed_repositories(self, repository): - """Remove an entry from self.tool_dependencies_of_installed_repositories.""" - repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository) - if repository_tup in self.tool_dependencies_of_installed_repositories: - tool_shed, name, owner, installed_changeset_revision = repository_tup - debug_msg = "Removing entry for revision %s of repository %s owned by %s from tool_dependencies_of_installed_repositories." % \ - (installed_changeset_revision, name, owner) - log.debug(debug_msg) - del self.tool_dependencies_of_installed_repositories[repository_tup] - def repository_dependency_needed_only_for_compiling_tool_dependency(self, repository, repository_dependency): for rd_tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td: tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup