Merge pull request #9465 from mvdbeek/fix_InstalledRepositoryManager_init

[20.01] Drop manage_dependency_relationships option

doc/source/admin/galaxy_options.rst

@@ -697,19 +697,6 @@
 :Type: int
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``manage_dependency_relationships``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    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.
-:Default: ``false``
-:Type: bool
-
-
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``tool_data_table_config_path``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

lib/galaxy/app.py

@@ -91,9 +91,7 @@ class UniverseApplication(config.ConfiguresGalaxyMixin):
         check_migrate_tools = self.config.check_migrate_tools
         self._configure_models(check_migrate_databases=self.config.check_migrate_databases, check_migrate_tools=check_migrate_tools, config_file=config_file)
 
-        # Manage installed tool shed repositories.
         self.installed_repository_manager = InstalledRepositoryManager(self)
-
         self._configure_datatypes_registry(self.installed_repository_manager)
         galaxy.model.set_datatypes_registry(self.datatypes_registry)
 

lib/galaxy/config/sample/galaxy.yml.sample

@@ -447,12 +447,6 @@ galaxy:
   # between 1 and 24.
   #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: false
-
   # XML config file that contains data table entries for the
   # ToolDataTableManager.  This file is manually # maintained by the
   # Galaxy administrator (.sample used if default does not exist).

lib/galaxy/tool_shed/galaxy_install/install_manager.py

@@ -215,10 +215,6 @@ class InstallToolDependencyManager(object):
                         if tool_dependency and tool_dependency.status in [self.install_model.ToolDependency.installation_status.INSTALLED,
                                                                           self.install_model.ToolDependency.installation_status.ERROR]:
                             installed_packages.append(tool_dependency)
-                            if self.app.config.manage_dependency_relationships:
-                                # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager.
-                                self.app.installed_repository_manager.handle_tool_dependency_install(tool_shed_repository,
-                                                                                                     tool_dependency)
         return installed_packages
 
     def install_via_fabric(self, tool_shed_repository, tool_dependency, install_dir, package_name=None, custom_fabfile_path=None,
@@ -946,10 +942,6 @@ class InstallRepositoryManager(object):
                 basic_util.remove_dir(work_dir)
             self.update_tool_shed_repository_status(tool_shed_repository,
                                                     self.install_model.ToolShedRepository.installation_status.INSTALLED)
-            if self.app.config.manage_dependency_relationships:
-                # Add the installed repository and any tool dependencies to the in-memory dictionaries
-                # in the installed_repository_manager.
-                self.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.
             repository_util.set_repository_attributes(self.app,

lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py

@@ -79,9 +79,6 @@ class InstalledRepositoryManager(object):
         # 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 = {}
-        if app.config.manage_dependency_relationships:
-            # Load defined dependency relationships for installed tool shed repositories and their contents.
-            self.load_dependency_relationships()
 
     def activate_repository(self, repository):
         """Activate an installed tool shed repository that has been marked as deactivated."""
@@ -651,90 +648,6 @@ class InstalledRepositoryManager(object):
                     deleted_tool_dependency_names.append(original_dependency_val_dict['name'])
         return updated_tool_dependency_names, deleted_tool_dependency_names
 
-    def handle_repository_install(self, repository):
-        """Load the dependency relationships for a repository that was just installed or reinstalled."""
-        # Populate self.repository_dependencies_of_installed_repositories.
-        self.add_entry_to_repository_dependencies_of_installed_repositories(repository)
-        # Populate self.installed_repository_dependencies_of_installed_repositories.
-        self.add_entry_to_installed_repository_dependencies_of_installed_repositories(repository)
-        # Populate self.tool_dependencies_of_installed_repositories.
-        self.add_entry_to_tool_dependencies_of_installed_repositories(repository)
-        # Populate self.installed_tool_dependencies_of_installed_repositories.
-        self.add_entry_to_installed_tool_dependencies_of_installed_repositories(repository)
-        for tool_dependency in repository.tool_dependencies:
-            # Populate self.runtime_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-            # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-
-    def handle_repository_uninstall(self, repository):
-        """Remove the dependency relationships for a repository that was just uninstalled."""
-        for tool_dependency in repository.tool_dependencies:
-            tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
-            # Remove this tool_dependency from all values in
-            # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies
-            altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {}
-            for (td_tup, installed_runtime_dependent_tool_dependency_tups) in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.items():
-                if tool_dependency_tup in installed_runtime_dependent_tool_dependency_tups:
-                    # Remove the tool_dependency from the list.
-                    installed_runtime_dependent_tool_dependency_tups.remove(tool_dependency_tup)
-                # Add the possibly altered list to the altered dictionary.
-                altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[td_tup] = \
-                    installed_runtime_dependent_tool_dependency_tups
-            self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = \
-                altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies
-            # Remove the entry for this tool_dependency from self.runtime_tool_dependencies_of_installed_tool_dependencies.
-            self.remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-            # Remove the entry for this tool_dependency from
-            # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
-            self.remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-        # Remove this repository's entry from self.installed_tool_dependencies_of_installed_repositories.
-        self.remove_entry_from_installed_tool_dependencies_of_installed_repositories(repository)
-        # Remove this repository's entry from self.tool_dependencies_of_installed_repositories
-        self.remove_entry_from_tool_dependencies_of_installed_repositories(repository)
-        # Remove this repository's entry from self.installed_repository_dependencies_of_installed_repositories.
-        self.remove_entry_from_installed_repository_dependencies_of_installed_repositories(repository)
-        # Remove this repository's entry from self.repository_dependencies_of_installed_repositories.
-        self.remove_entry_from_repository_dependencies_of_installed_repositories(repository)
-
-    def handle_tool_dependency_install(self, repository, tool_dependency):
-        """Load the dependency relationships for a tool dependency that was just installed independently of its containing repository."""
-        # The received repository must have a status of 'Installed'.  The value of tool_dependency.status will either be
-        # 'Installed' or 'Error', but we only need to change the in-memory dictionaries if it is 'Installed'.
-        if tool_dependency.is_installed:
-            # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-            # Populate self.installed_tool_dependencies_of_installed_repositories.
-            repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
-            tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
-            if repository_tup in self.installed_tool_dependencies_of_installed_repositories:
-                self.installed_tool_dependencies_of_installed_repositories[repository_tup].append(tool_dependency_tup)
-            else:
-                self.installed_tool_dependencies_of_installed_repositories[repository_tup] = [tool_dependency_tup]
-
-    def load_dependency_relationships(self):
-        """Load relationships for all installed repositories and tool dependencies into in-memnory dictionaries."""
-        # Get the list of installed tool shed repositories.
-        for repository in self.context.query(self.app.install_model.ToolShedRepository) \
-                                      .filter(self.app.install_model.ToolShedRepository.table.c.status ==
-                                              self.app.install_model.ToolShedRepository.installation_status.INSTALLED):
-            # Populate self.repository_dependencies_of_installed_repositories.
-            self.add_entry_to_repository_dependencies_of_installed_repositories(repository)
-            # Populate self.installed_repository_dependencies_of_installed_repositories.
-            self.add_entry_to_installed_repository_dependencies_of_installed_repositories(repository)
-            # Populate self.tool_dependencies_of_installed_repositories.
-            self.add_entry_to_tool_dependencies_of_installed_repositories(repository)
-            # Populate self.installed_tool_dependencies_of_installed_repositories.
-            self.add_entry_to_installed_tool_dependencies_of_installed_repositories(repository)
-        # Get the list of installed tool dependencies.
-        for tool_dependency in self.context.query(self.app.install_model.ToolDependency) \
-                                           .filter(self.app.install_model.ToolDependency.table.c.status ==
-                                                   self.app.install_model.ToolDependency.installation_status.INSTALLED):
-            # Populate self.runtime_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-            # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-
     def load_proprietary_datatypes(self):
         cdl = custom_datatype_manager.CustomDatatypeLoader(self.app)
         for tool_shed_repository in self.context.query(self.install_model.ToolShedRepository) \
@@ -814,10 +727,6 @@ class InstalledRepositoryManager(object):
         if remove_from_disk:
             repository.status = self.app.install_model.ToolShedRepository.installation_status.UNINSTALLED
             repository.error_message = None
-            if self.app.config.manage_dependency_relationships:
-                # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the
-                # installed_repository_manager.
-                self.handle_repository_uninstall(repository)
         else:
             repository.status = self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED
         self.app.install_model.context.current.add(repository)

lib/galaxy/webapps/galaxy/config_schema.yml

@@ -528,15 +528,6 @@ mapping:
           server process should be able to check for repository updates.  The
           setting for hours_between_check should be an integer between 1 and 24.
 
-      manage_dependency_relationships:
-        type: bool
-        default: false
-        required: false
-        desc: |
-          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.
-
       tool_data_table_config_path:
         type: str
         default: config/tool_data_table_conf.xml