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tool_shed package¶
Subpackages¶
- tool_shed.dependencies package
- Subpackages
- Submodules
- tool_shed.dependencies.attribute_handlers module
RepositoryDependencyAttributeHandler
RepositoryDependencyAttributeHandler.__init__()
RepositoryDependencyAttributeHandler.check_tag_attributes()
RepositoryDependencyAttributeHandler.handle_complex_dependency_elem()
RepositoryDependencyAttributeHandler.handle_elem()
RepositoryDependencyAttributeHandler.handle_sub_elem()
RepositoryDependencyAttributeHandler.handle_tag_attributes()
ToolDependencyAttributeHandler
- tool_shed.galaxy_install package
- tool_shed.grids package
- Submodules
- tool_shed.grids.admin_grids module
UserGrid
UserGrid.UserLoginColumn
UserGrid.UserNameColumn
UserGrid.GroupsColumn
UserGrid.RolesColumn
UserGrid.ExternalColumn
UserGrid.LastLoginColumn
UserGrid.StatusColumn
UserGrid.EmailColumn
UserGrid.title
UserGrid.model_class
UserGrid.default_sort_key
UserGrid.columns
UserGrid.global_actions
UserGrid.operations
UserGrid.standard_filters
UserGrid.use_paging
UserGrid.get_current_item()
RoleGrid
RoleGrid.NameColumn
RoleGrid.DescriptionColumn
RoleGrid.TypeColumn
RoleGrid.StatusColumn
RoleGrid.GroupsColumn
RoleGrid.RepositoriesColumn
RoleGrid.UsersColumn
RoleGrid.title
RoleGrid.model_class
RoleGrid.default_sort_key
RoleGrid.columns
RoleGrid.global_actions
RoleGrid.operations
RoleGrid.standard_filters
RoleGrid.use_paging
RoleGrid.apply_query_filter()
GroupGrid
ManageCategoryGrid
AdminRepositoryGrid
RepositoryMetadataGrid
RepositoryMetadataGrid.IdColumn
RepositoryMetadataGrid.NameColumn
RepositoryMetadataGrid.OwnerColumn
RepositoryMetadataGrid.RevisionColumn
RepositoryMetadataGrid.ToolsColumn
RepositoryMetadataGrid.DatatypesColumn
RepositoryMetadataGrid.WorkflowsColumn
RepositoryMetadataGrid.DeletedColumn
RepositoryMetadataGrid.DeprecatedColumn
RepositoryMetadataGrid.MaliciousColumn
RepositoryMetadataGrid.title
RepositoryMetadataGrid.model_class
RepositoryMetadataGrid.default_sort_key
RepositoryMetadataGrid.use_hide_message
RepositoryMetadataGrid.columns
RepositoryMetadataGrid.operations
RepositoryMetadataGrid.build_initial_query()
- tool_shed.grids.repository_grid_filter_manager module
- tool_shed.grids.repository_grids module
CategoryGrid
RepositoryGrid
RepositoryGrid.NameColumn
RepositoryGrid.TypeColumn
RepositoryGrid.HeadsColumn
RepositoryGrid.MetadataRevisionColumn
RepositoryGrid.LatestInstallableRevisionColumn
RepositoryGrid.TipRevisionColumn
RepositoryGrid.DescriptionColumn
RepositoryGrid.CategoryColumn
RepositoryGrid.RepositoryCategoryColumn
RepositoryGrid.UserColumn
RepositoryGrid.EmailColumn
RepositoryGrid.EmailAlertsColumn
RepositoryGrid.DeprecatedColumn
RepositoryGrid.title
RepositoryGrid.model_class
RepositoryGrid.default_sort_key
RepositoryGrid.use_hide_message
RepositoryGrid.columns
RepositoryGrid.default_filter
RepositoryGrid.num_rows_per_page
RepositoryGrid.use_paging
RepositoryGrid.allow_fetching_all_results
RepositoryGrid.build_initial_query()
DockerImageGrid
EmailAlertsRepositoryGrid
MatchedRepositoryGrid
MatchedRepositoryGrid.NameColumn
MatchedRepositoryGrid.DescriptionColumn
MatchedRepositoryGrid.RevisionColumn
MatchedRepositoryGrid.UserColumn
MatchedRepositoryGrid.title
MatchedRepositoryGrid.model_class
MatchedRepositoryGrid.default_sort_key
MatchedRepositoryGrid.use_hide_message
MatchedRepositoryGrid.columns
MatchedRepositoryGrid.operations
MatchedRepositoryGrid.num_rows_per_page
MatchedRepositoryGrid.use_paging
MatchedRepositoryGrid.build_initial_query()
InstallMatchedRepositoryGrid
MyWritableRepositoriesGrid
RepositoriesByUserGrid
RepositoriesInCategoryGrid
RepositoriesIOwnGrid
RepositoriesICanAdministerGrid
RepositoriesMissingToolTestComponentsGrid
MyWritableRepositoriesMissingToolTestComponentsGrid
DeprecatedRepositoriesIOwnGrid
RepositoriesWithInvalidToolsGrid
MyWritableRepositoriesWithInvalidToolsGrid
RepositoryMetadataGrid
RepositoryMetadataGrid.RepositoryNameColumn
RepositoryMetadataGrid.RepositoryTypeColumn
RepositoryMetadataGrid.RepositoryOwnerColumn
RepositoryMetadataGrid.ChangesetRevisionColumn
RepositoryMetadataGrid.MaliciousColumn
RepositoryMetadataGrid.DownloadableColumn
RepositoryMetadataGrid.HasRepositoryDependenciesColumn
RepositoryMetadataGrid.IncludesDatatypesColumn
RepositoryMetadataGrid.IncludesToolsColumn
RepositoryMetadataGrid.IncludesToolDependenciesColumn
RepositoryMetadataGrid.IncludesWorkflowsColumn
RepositoryMetadataGrid.title
RepositoryMetadataGrid.model_class
RepositoryMetadataGrid.default_sort_key
RepositoryMetadataGrid.columns
RepositoryMetadataGrid.default_filter
RepositoryMetadataGrid.num_rows_per_page
RepositoryMetadataGrid.use_paging
RepositoryMetadataGrid.allow_fetching_all_results
RepositoryMetadataGrid.build_initial_query()
RepositoryDependenciesGrid
DatatypesGrid
ToolDependenciesGrid
ToolsGrid
ValidCategoryGrid
ValidRepositoryGrid
- tool_shed.grids.repository_review_grids module
- tool_shed.grids.util module
build_changeset_revision_select_field()
filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components()
filter_by_latest_metadata_changeset_revision_that_has_invalid_tools()
get_latest_downloadable_repository_metadata()
get_latest_downloadable_repository_metadata_if_it_includes_tools()
get_latest_repository_metadata()
get_latest_repository_metadata_if_it_includes_invalid_tools()
- tool_shed.managers package
- tool_shed.metadata package
- Submodules
- tool_shed.metadata.metadata_generator module
MetadataGenerator
MetadataGenerator.__init__()
MetadataGenerator.generate_environment_dependency_metadata()
MetadataGenerator.generate_guid_for_object()
MetadataGenerator.generate_metadata_for_changeset_revision()
MetadataGenerator.generate_package_dependency_metadata()
MetadataGenerator.generate_repository_dependency_metadata()
MetadataGenerator.generate_tool_metadata()
MetadataGenerator.generate_tool_dependency_metadata()
MetadataGenerator.get_invalid_file_tups()
MetadataGenerator.get_metadata_dict()
MetadataGenerator.get_relative_path_to_repository_file()
MetadataGenerator.get_sample_files_from_disk()
MetadataGenerator.handle_repository_elem()
MetadataGenerator.set_changeset_revision()
MetadataGenerator.set_relative_install_dir()
MetadataGenerator.set_repository()
MetadataGenerator.set_repository_clone_url()
MetadataGenerator.set_repository_files_dir()
MetadataGenerator.update_repository_dependencies_metadata()
- tool_shed.metadata.repository_metadata_manager module
RepositoryMetadataManager
RepositoryMetadataManager.__init__()
RepositoryMetadataManager.add_tool_versions()
RepositoryMetadataManager.build_repository_ids_select_field()
RepositoryMetadataManager.clean_repository_metadata()
RepositoryMetadataManager.compare_changeset_revisions()
RepositoryMetadataManager.compare_data_manager()
RepositoryMetadataManager.compare_datatypes()
RepositoryMetadataManager.compare_readme_files()
RepositoryMetadataManager.compare_repository_dependencies()
RepositoryMetadataManager.compare_tool_dependencies()
RepositoryMetadataManager.compare_workflows()
RepositoryMetadataManager.create_or_update_repository_metadata()
RepositoryMetadataManager.different_revision_defines_tip_only_repository_dependency()
RepositoryMetadataManager.get_parent_id()
RepositoryMetadataManager.get_query_for_setting_metadata_on_repositories()
RepositoryMetadataManager.new_datatypes_metadata_required()
RepositoryMetadataManager.new_metadata_required_for_utilities()
RepositoryMetadataManager.new_readme_files_metadata_required()
RepositoryMetadataManager.new_repository_dependency_metadata_required()
RepositoryMetadataManager.new_tool_metadata_required()
RepositoryMetadataManager.new_tool_dependency_metadata_required()
RepositoryMetadataManager.new_workflow_metadata_required()
RepositoryMetadataManager.reset_all_metadata_on_repository_in_tool_shed()
RepositoryMetadataManager.reset_all_tool_versions()
RepositoryMetadataManager.reset_metadata_on_selected_repositories()
RepositoryMetadataManager.set_repository()
RepositoryMetadataManager.set_repository_metadata()
RepositoryMetadataManager.set_repository_metadata_due_to_new_tip()
- tool_shed.repository_types package
- Submodules
- tool_shed.repository_types.metadata module
- tool_shed.repository_types.registry module
- tool_shed.repository_types.repository_suite_definition module
- tool_shed.repository_types.tool_dependency_definition module
- tool_shed.repository_types.unrestricted module
- tool_shed.repository_types.util module
- tool_shed.test package
- Subpackages
- tool_shed.test.base package
- tool_shed.test.functional package
- Submodules
- tool_shed.test.functional.test_0000_basic_repository_features module
- tool_shed.test.functional.test_0010_repository_with_tool_dependencies module
- tool_shed.test.functional.test_0020_basic_repository_dependencies module
- tool_shed.test.functional.test_0030_repository_dependency_revisions module
- tool_shed.test.functional.test_0040_repository_circular_dependencies module
- tool_shed.test.functional.test_0050_circular_dependencies_4_levels module
- tool_shed.test.functional.test_0070_invalid_tool module
- tool_shed.test.functional.test_0080_advanced_circular_dependencies module
- tool_shed.test.functional.test_0090_tool_search module
- tool_shed.test.functional.test_0100_complex_repository_dependencies module
- tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies module
- tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners module
- tool_shed.test.functional.test_0130_datatype_converters module
- tool_shed.test.functional.test_0140_tool_help_images module
- tool_shed.test.functional.test_0150_prior_installation_required module
- tool_shed.test.functional.test_0160_circular_prior_installation_required module
- tool_shed.test.functional.test_0170_complex_prior_installation_required module
- tool_shed.test.functional.test_0300_reset_all_metadata module
- tool_shed.test.functional.test_0310_hg_api_features module
- tool_shed.test.functional.test_0400_repository_component_reviews module
- tool_shed.test.functional.test_0410_repository_component_review_access_control module
- tool_shed.test.functional.test_0420_citable_urls_for_repositories module
- tool_shed.test.functional.test_0430_browse_utilities module
- tool_shed.test.functional.test_0440_deleting_dependency_definitions module
- tool_shed.test.functional.test_0460_upload_to_repository module
- tool_shed.test.functional.test_0470_tool_dependency_repository_type module
- tool_shed.test.functional.test_0480_tool_dependency_xml_verification module
- tool_shed.test.functional.test_0530_repository_admin_feature module
- tool_shed.test.functional.test_0540_get_all_metadata_from_api module
- tool_shed.test.functional.test_0550_metadata_updated_dependencies module
- tool_shed.test.functional.test_1000_install_basic_repository module
- tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies module
- tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies module
- tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions module
- tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies module
- tool_shed.test.functional.test_1050_circular_dependencies_4_levels module
- tool_shed.test.functional.test_1070_invalid_tool module
- tool_shed.test.functional.test_1080_advanced_circular_dependency_installation module
- tool_shed.test.functional.test_1090_repository_dependency_handling module
- tool_shed.test.functional.test_1100_install_updated_repository_dependencies module
- tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies module
- tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency module
- tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners module
- tool_shed.test.functional.test_1150_datatype_converters module
- tool_shed.test.functional.test_1160_tool_help_images module
- tool_shed.test.functional.test_1170_prior_installation_required module
- tool_shed.test.functional.test_1180_circular_prior_installation_required module
- tool_shed.test.functional.test_1190_complex_prior_installation_required module
- tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository module
- tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies module
- tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies module
- tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions module
- tool_shed.test.functional.test_1300_reset_all_metadata module
- tool_shed.test.functional.test_1410_update_manager module
- tool_shed.test.functional.test_1430_repair_installed_repository module
- tool_shed.test.functional.test_1450_installing_datatypes_sniffers module
- tool_shed.test.functional.test_1460_data_managers module
- tool_shed.test.functional.test_1470_updating_installed_repositories module
- Submodules
- tool_shed.test.functional_tests module
- Subpackages
- tool_shed.tools package
- Submodules
- tool_shed.tools.data_table_manager module
ToolDataTableManager
ShedToolDataTableManager
ShedToolDataTableManager.__init__()
ShedToolDataTableManager.generate_repository_info_elem()
ShedToolDataTableManager.generate_repository_info_elem_from_repository()
ShedToolDataTableManager.get_tool_index_sample_files()
ShedToolDataTableManager.handle_missing_data_table_entry()
ShedToolDataTableManager.handle_sample_tool_data_table_conf_file()
ShedToolDataTableManager.get_target_install_dir()
ShedToolDataTableManager.install_tool_data_tables()
ShedToolDataTableManager.reset_tool_data_tables()
- tool_shed.tools.tool_validator module
ToolValidator
ToolValidator.can_use_tool_config_disk_file()
ToolValidator.concat_messages()
ToolValidator.copy_disk_sample_files_to_dir()
ToolValidator.get_latest_tool_config_revision_from_repository_manifest()
ToolValidator.get_list_of_copied_sample_files()
ToolValidator.handle_sample_files_and_load_tool_from_disk()
ToolValidator.handle_sample_files_and_load_tool_from_tmp_config()
ToolValidator.load_tool_from_changeset_revision()
ToolValidator.load_tool_from_tmp_config()
- tool_shed.tools.tool_version_manager module
- tool_shed.util package
- Submodules
- tool_shed.util.admin_util module
Admin
Admin.user_list_grid
Admin.role_list_grid
Admin.group_list_grid
Admin.delete_operation
Admin.undelete_operation
Admin.purge_operation
Admin.index()
Admin.center()
Admin.roles()
Admin.create_role()
Admin.rename_role()
Admin.manage_users_and_groups_for_role()
Admin.mark_role_deleted()
Admin.undelete_role()
Admin.purge_role()
Admin.groups()
Admin.rename_group()
Admin.manage_users_and_roles_for_group()
Admin.create_group()
Admin.mark_group_deleted()
Admin.undelete_group()
Admin.purge_group()
Admin.create_new_user()
Admin.reset_user_password()
Admin.mark_user_deleted()
Admin.undelete_user()
Admin.purge_user()
Admin.users()
Admin.name_autocomplete_data()
Admin.manage_roles_and_groups_for_user()
get_user()
get_role()
get_group()
- tool_shed.util.basic_util module
- tool_shed.util.commit_util module
- tool_shed.util.common_util module
accumulate_tool_dependencies()
check_tool_tag_set()
generate_clone_url_for_installed_repository()
generate_clone_url_for_repository_in_tool_shed()
generate_clone_url_from_repo_info_tup()
get_repository_dependencies()
get_protocol_from_tool_shed_url()
get_tool_shed_repository_ids()
get_tool_shed_url_from_tool_shed_registry()
get_tool_shed_repository_url()
get_user_by_username()
handle_galaxy_url()
handle_tool_shed_url_protocol()
parse_repository_dependency_tuple()
remove_port_from_tool_shed_url()
remove_protocol_and_port_from_tool_shed_url()
remove_protocol_and_user_from_clone_url()
remove_protocol_from_tool_shed_url()
- tool_shed.util.container_util module
- tool_shed.util.encoding_util module
- tool_shed.util.hg_util module
add_changeset()
archive_repository_revision()
clone_repository()
commit_changeset()
copy_file_from_manifest()
create_hgrc_file()
get_changectx_for_changeset()
get_config_from_disk()
get_ctx_file_path_from_manifest()
get_file_context_from_ctx()
get_named_tmpfile_from_ctx()
get_readable_ctx_date()
get_repository_heads()
get_reversed_changelog_changesets()
get_revision_label()
get_rev_label_changeset_revision_from_repository_metadata()
get_revision_label_from_ctx()
get_rev_label_from_changeset_revision()
pull_repository()
remove_path()
reversed_lower_upper_bounded_changelog()
reversed_upper_bounded_changelog()
update_repository()
init_repository()
changeset2rev()
- tool_shed.util.hgweb_config module
- tool_shed.util.metadata_util module
get_all_dependencies()
get_current_repository_metadata_for_changeset_revision()
get_dependencies_for_metadata_revision()
get_latest_changeset_revision()
get_latest_downloadable_changeset_revision()
get_latest_repository_metadata()
get_metadata_revisions()
get_next_downloadable_changeset_revision()
get_previous_metadata_changeset_revision()
get_repository_dependency_tups_from_repository_metadata()
get_repository_metadata_by_changeset_revision()
get_repository_metadata_by_id()
get_repository_metadata_by_repository_id_changeset_revision()
get_updated_changeset_revisions()
is_downloadable()
is_malicious()
- tool_shed.util.readme_util module
- tool_shed.util.repository_content_util module
- tool_shed.util.repository_util module
change_repository_name_in_hgrc_file()
create_or_update_tool_shed_repository()
create_repo_info_dict()
create_repository_admin_role()
create_repository()
extract_components_from_tuple()
generate_sharable_link_for_repository_in_tool_shed()
generate_tool_shed_repository_install_dir()
get_absolute_path_to_file_in_repository()
get_ids_of_tool_shed_repositories_being_installed()
get_installed_repository()
get_installed_tool_shed_repository()
get_prior_import_or_install_required_dict()
get_repo_info_dict()
get_repo_info_tuple_contents()
get_repositories_by_category()
get_repository_admin_role_name()
get_repository_and_repository_dependencies_from_repo_info_dict()
get_repository_by_id()
get_repository_by_name()
get_repository_by_name_and_owner()
get_repository_dependency_types()
get_repository_for_dependency_relationship()
get_repository_ids_requiring_prior_import_or_install()
get_repository_in_tool_shed()
get_repository_owner()
get_repository_owner_from_clone_url()
get_repository_query()
get_role_by_id()
get_tool_shed_from_clone_url()
get_tool_shed_repository_by_id()
get_tool_shed_status_for_installed_repository()
handle_role_associations()
is_tool_shed_client()
repository_was_previously_installed()
set_repository_attributes()
update_repository()
validate_repository_name()
- tool_shed.util.review_util module
- tool_shed.util.search_util module
- tool_shed.util.shed_index module
- tool_shed.util.shed_util_common module
can_eliminate_repository_dependency()
clean_dependency_relationships()
count_repositories_in_category()
generate_tool_guid()
get_categories()
get_category()
get_category_by_name()
get_requirements_from_tools()
get_requirements_from_repository()
get_tool_shed_repo_requirements()
get_ctx_rev()
get_next_prior_import_or_install_required_dict_entry()
get_repository_categories()
get_repository_file_contents()
get_repository_type_from_tool_shed()
get_tool_dependency_definition_metadata_from_tool_shed()
get_tool_panel_config_tool_path_install_dir()
get_tool_path_by_shed_tool_conf_filename()
get_user()
handle_email_alerts()
have_shed_tool_conf_for_install()
is_path_browsable()
is_path_within_dependency_dir()
is_path_within_repo()
open_repository_files_folder()
set_image_paths()
tool_shed_is_this_tool_shed()
- tool_shed.util.tool_dependency_util module
- tool_shed.util.tool_util module
- tool_shed.util.web_util module
- tool_shed.util.xml_util module
- tool_shed.utility_containers package
FailedTest
InvalidRepositoryDependency
InvalidToolDependency
MissingTestComponent
NotTested
PassedTest
RepositoryInstallationError
RepositorySuccessfulInstallation
ToolDependencyInstallationError
ToolDependencySuccessfulInstallation
ToolShedUtilityContainerManager
ToolShedUtilityContainerManager.__init__()
ToolShedUtilityContainerManager.build_invalid_repository_dependencies_root_folder()
ToolShedUtilityContainerManager.build_invalid_tool_dependencies_root_folder()
ToolShedUtilityContainerManager.build_repository_containers()
ToolShedUtilityContainerManager.generate_tool_dependencies_key()
- Submodules
- tool_shed.utility_containers.utility_container_manager module
- tool_shed.webapp package
url_for()
expose()
- Subpackages
- tool_shed.webapp.api package
BaseShedAPIController
- Submodules
- tool_shed.webapp.api.authenticate module
- tool_shed.webapp.api.categories module
- tool_shed.webapp.api.configuration module
- tool_shed.webapp.api.groups module
- tool_shed.webapp.api.repositories module
- tool_shed.webapp.api.repository_revisions module
- tool_shed.webapp.api.tools module
- tool_shed.webapp.api.users module
- tool_shed.webapp.controllers package
- Submodules
- tool_shed.webapp.controllers.admin module
- tool_shed.webapp.controllers.groups module
- tool_shed.webapp.controllers.hg module
- tool_shed.webapp.controllers.repository module
- tool_shed.webapp.controllers.repository_review module
- tool_shed.webapp.controllers.upload module
- tool_shed.webapp.controllers.user module
- tool_shed.webapp.framework package
- tool_shed.webapp.model package
now()
Base
APIKeys
User
PasswordResetToken
Group
Role
UserGroupAssociation
UserRoleAssociation
GroupRoleAssociation
RepositoryRoleAssociation
GalaxySession
Repository
ItemRatingAssociation
RepositoryRatingAssociation
Category
RepositoryCategoryAssociation
Tag
RepositoryMetadata
sort_by_attr()
- Subpackages
- Submodules
- tool_shed.webapp.model.mapping module
- tool_shed.webapp.search package
- tool_shed.webapp.security package
- tool_shed.webapp.util package
- tool_shed.webapp.api package
- Submodules
- tool_shed.webapp.app module
- tool_shed.webapp.buildapp module
- tool_shed.webapp.config module
- tool_shed.webapp.fast_app module
- tool_shed.webapp.fast_factory module