Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

tool_shed.test.base package

Submodules

tool_shed.test.base.common module

tool_shed.test.base.test_db_util module

tool_shed.test.base.test_db_util.sa_session()

tool_shed.test.base.test_db_util.install_session()

tool_shed.test.base.test_db_util.delete_obj(obj)

tool_shed.test.base.test_db_util.delete_user_roles(user)

tool_shed.test.base.test_db_util.flush(obj)

tool_shed.test.base.test_db_util.get_all_repositories()

tool_shed.test.base.test_db_util.get_all_installed_repositories(actually_installed=False)

tool_shed.test.base.test_db_util.get_galaxy_repository_by_name_owner_changeset_revision(repository_name, owner, changeset_revision)

tool_shed.test.base.test_db_util.get_installed_repository_by_id(repository_id)

tool_shed.test.base.test_db_util.get_installed_repository_by_name_owner(repository_name, owner, return_multiple=False)

tool_shed.test.base.test_db_util.get_role(user, role_name)

tool_shed.test.base.test_db_util.get_repository_role_association(repository_id, role_id)

tool_shed.test.base.test_db_util.get_repository_by_id(repository_id)

tool_shed.test.base.test_db_util.get_repository_downloadable_revisions(repository_id)

tool_shed.test.base.test_db_util.get_repository_metadata_for_changeset_revision(repository_id: int, changeset_revision: Optional[str]) → RepositoryMetadata

tool_shed.test.base.test_db_util.get_role_by_name(role_name)

tool_shed.test.base.test_db_util.get_user(email)

tool_shed.test.base.test_db_util.get_user_by_name(username)

tool_shed.test.base.test_db_util.mark_obj_deleted(obj)

tool_shed.test.base.test_db_util.refresh(obj)

tool_shed.test.base.test_db_util.ga_refresh(obj)

tool_shed.test.base.test_db_util.get_repository_by_name_and_owner(name, owner_username, return_multiple=False)

tool_shed.test.base.test_db_util.get_repository_metadata_by_repository_id_changeset_revision(repository_id, changeset_revision)

tool_shed.test.base.twilltestcase module

class tool_shed.test.base.twilltestcase.ShedTwillTestCase

Bases: ShedApiTestCase

Class of FunctionalTestCase geared toward HTML interactions using the Twill library.

setUp()

check_for_strings(strings_displayed=None, strings_not_displayed=None)

check_page(strings_displayed, strings_displayed_count, strings_not_displayed)

Checks a page for strings displayed, not displayed and number of occurrences of a string

check_page_for_string(patt)

Looks for ‘patt’ in the current browser page

check_string_not_in_page(patt)

Checks to make sure ‘patt’ is NOT in the page.

create(cntrller='user', email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='')

last_page()

Return the last visited page (usually HTML, but can binary data as well).

last_url()

login(email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='', logout_first=True)

logout()

showforms()

Shows form, helpful for debugging new tests

submit_form(form_no=-1, button='runtool_btn', form=None, **kwd)

Populates and submits a form from the keyword arguments.

visit_url(url, params=None, doseq=False, allowed_codes=None)

write_temp_file(content, suffix='.html')

assign_admin_role(repository: Repository, user)

browse_category(category: Category, strings_displayed=None, strings_not_displayed=None)

browse_repository(repository: Repository, strings_displayed=None, strings_not_displayed=None)

browse_repository_dependencies(strings_displayed=None, strings_not_displayed=None)

browse_tool_shed(url, strings_displayed=None, strings_not_displayed=None)

browse_tool_dependencies(strings_displayed=None, strings_not_displayed=None)

browse_tools(strings_displayed=None, strings_not_displayed=None)

check_count_of_metadata_revisions_associated_with_repository(repository: Repository, metadata_count)

check_exported_repository_dependency(dependency_filename, repository_name, repository_owner)

check_for_valid_tools(repository, strings_displayed=None, strings_not_displayed=None)

check_galaxy_repository_db_status(repository_name, owner, expected_status)

check_galaxy_repository_tool_panel_section(repository, expected_tool_panel_section)

check_repository_changelog(repository: Repository, strings_displayed=None, strings_not_displayed=None)

check_repository_dependency(repository: Repository, depends_on_repository, depends_on_changeset_revision=None, changeset_revision=None)

check_repository_metadata(repository: Repository, tip_only=True)

check_repository_tools_for_changeset_revision(repository: Repository, changeset_revision, tool_metadata_strings_displayed=None, tool_page_strings_displayed=None)

Loop through each tool dictionary in the repository metadata associated with the received changeset_revision. For each of these, check for a tools attribute, and load the tool metadata page if it exists, then display that tool’s page.

check_repository_invalid_tools_for_changeset_revision(repository: Repository, changeset_revision, strings_displayed=None, strings_not_displayed=None)

Load the invalid tool page for each invalid tool associated with this changeset revision and verify the received error messages.

check_string_count_in_page(pattern, min_count, max_count=None)

Checks the number of ‘pattern’ occurrences in the current browser page

clone_repository(repository: Repository, destination_path: str) → None

commit_and_push(repository, hgrepo, options, username, password)

create_category(**kwd) → Category

create_repository_dependency(repository: Optional[Repository] = None, repository_tuples=None, filepath=None, prior_installation_required=False, complex=False, package=None, version=None, strings_displayed=None, strings_not_displayed=None)

create_user_in_galaxy(cntrller='user', email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='')

deactivate_repository(installed_repository, strings_displayed=None, strings_not_displayed=None)

delete_files_from_repository(repository: Repository, filenames: List[str])

delete_repository(repository: Repository) → None

display_installed_jobs_list_page(installed_repository, data_manager_names=None, strings_displayed=None, strings_not_displayed=None)

display_installed_repository_manage_json(installed_repository)

display_manage_repository_page(repository: Repository, changeset_revision=None, strings_displayed=None, strings_not_displayed=None)

display_repository_clone_page(owner_name, repository_name, strings_displayed=None, strings_not_displayed=None)

display_repository_file_contents(repository: Repository, filename, filepath=None, strings_displayed=None, strings_not_displayed=None)

Find a file in the repository and display the contents.

edit_repository_categories(repository: Repository, categories_to_add=None, categories_to_remove=None, restore_original=True) → None

edit_repository_information(repository: Repository, revert=True, **kwd)

enable_email_alerts(repository: Repository, strings_displayed=None, strings_not_displayed=None) → None

escape_html(string, unescape=False)

expect_repo_created_strings(name)

fetch_repository_metadata(repository: Repository, strings_displayed=None, strings_not_displayed=None)

galaxy_token()

galaxy_login(email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='', logout_first=True)

galaxy_logout()

generate_complex_dependency_xml(filename, filepath, repository_tuples, package, version)

generate_simple_dependency_xml(repository_tuples, filename, filepath, dependency_description='', complex=False, package=None, version=None, prior_installation_required=False)

generate_temp_path(test_script_path, additional_paths=None)

get_datatypes_count()

get_filename(filename, filepath=None)

get_hg_repo(path)

get_repositories_category_api(categories: List[Category], strings_displayed=None, strings_not_displayed=None)

get_or_create_repository(category: Category, owner=None, strings_displayed=None, strings_not_displayed=None, **kwd) → Optional[Repository]

get_repo_path(repository: Repository) → str

get_repository_changelog_tuples(repository)

get_repository_file_list(repository: Repository, base_path: str, current_path=None) → List[str]

Recursively load repository folder contents and append them to a list. Similar to os.walk but via /repository/open_folder.

get_repository_metadata(repository: Repository)

get_repository_metadata_for_db_object(repository: Repository)

get_repository_metadata_by_changeset_revision(repository_id: int, changeset_revision)

get_repository_metadata_revisions(repository: Repository) → List[str]

get_repository_tip(repository: Repository) → str

get_tools_from_repository_metadata(repository, include_invalid=False)

Get a list of valid and (optionally) invalid tool dicts from the repository metadata.

get_tool_panel_section_from_api(metadata)

get_tool_panel_section_from_repository_metadata(metadata)

grant_role_to_user(user, role)

grant_write_access(repository: Repository, usernames=None, strings_displayed=None, strings_not_displayed=None, post_submit_strings_displayed=None, post_submit_strings_not_displayed=None)

load_citable_url(username, repository_name, changeset_revision, encoded_user_id, encoded_repository_id, strings_displayed=None, strings_not_displayed=None, strings_displayed_in_iframe=None, strings_not_displayed_in_iframe=None)

load_changeset_in_tool_shed(repository_id, changeset_revision, strings_displayed=None, strings_not_displayed=None)

load_checkable_revisions(strings_displayed=None, strings_not_displayed=None)

load_display_tool_page(repository: Repository, tool_xml_path, changeset_revision, strings_displayed=None, strings_not_displayed=None)

load_invalid_tool_page(repository: Repository, tool_xml, changeset_revision, strings_displayed=None, strings_not_displayed=None)

preview_repository_in_tool_shed(name: str, owner: str, changeset_revision: Optional[str] = None, strings_displayed=None, strings_not_displayed=None)

reactivate_repository(installed_repository)

reinstall_repository_api(installed_repository, install_repository_dependencies=True, install_tool_dependencies=False, new_tool_panel_section_label='')

repository_is_new(repository: Repository) → bool

reset_installed_repository_metadata(repository)

reset_metadata_on_selected_repositories(repository_ids)

reset_metadata_on_selected_installed_repositories(repository_ids)

reset_repository_metadata(repository)

revoke_write_access(repository, username)

search_for_valid_tools(search_fields=None, exact_matches=False, strings_displayed=None, strings_not_displayed=None, from_galaxy=False)

send_message_to_repository_owner(repository: Repository, message: str, strings_displayed=None, strings_not_displayed=None, post_submit_strings_displayed=None, post_submit_strings_not_displayed=None) → None

set_form_value(form, kwd, field_name, field_value)

Set the form field field_name to field_value if it exists, and return the provided dict containing that value. If the field does not exist in the provided form, return a dict without that index.

set_repository_deprecated(repository: Repository, set_deprecated=True, strings_displayed=None, strings_not_displayed=None)

set_repository_malicious(repository: Repository, set_malicious=True, strings_displayed=None, strings_not_displayed=None) → None

tip_has_metadata(repository: Repository) → bool

undelete_repository(repository: Repository) → None

uninstall_repository(installed_repository, strings_displayed=None, strings_not_displayed=None)

update_installed_repository_api(installed_repository, verify_no_updates=False)

update_tool_shed_status()

upload_file(repository: Repository, filename, filepath, valid_tools_only, uncompress_file, remove_repo_files_not_in_tar, commit_message, strings_displayed=None, strings_not_displayed=None)

upload_url(repository, url, filepath, valid_tools_only, uncompress_file, remove_repo_files_not_in_tar, commit_message, strings_displayed=None, strings_not_displayed=None)

verify_installed_repositories(installed_repositories=None, uninstalled_repositories=None)

verify_installed_repository_metadata_unchanged(name, owner)

verify_installed_repository_no_tool_panel_section(repository)

Verify that there is no ‘tool_panel_section’ entry in the repository metadata.

verify_installed_repository_data_table_entries(required_data_table_entries)

verify_unchanged_repository_metadata(repository: Repository)

visit_galaxy_url(url, params=None, doseq=False, allowed_codes=None)

wait_for_repository_installation(repository_ids)