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.get_galaxy_repository_by_name_owner_changeset_revision(repository_name, owner, changeset_revision)[source]¶
- tool_shed.test.base.test_db_util.get_installed_repository_by_name_owner(repository_name, owner, return_multiple=False)[source]¶
- tool_shed.test.base.test_db_util.get_repository_reviews(repository_id, reviewer_user_id=None, changeset_revision=None)[source]¶
- tool_shed.test.base.test_db_util.get_reviews_ordered_by_changeset_revision(repository_id, changelog_tuples, reviewer_user_id=None)[source]¶
- tool_shed.test.base.test_db_util.get_repository_metadata_for_changeset_revision(repository_id, changeset_revision)[source]¶
- tool_shed.test.base.test_db_util.get_repository_review_by_user_id_changeset_revision(user_id, repository_id, changeset_revision)[source]¶
tool_shed.test.base.twilltestcase module¶
- class tool_shed.test.base.twilltestcase.ShedTwillTestCase(methodName='runTest')[source]¶
Bases:
DrivenFunctionalTestCase
Class of FunctionalTestCase geared toward HTML interactions using the Twill library.
- check_page(strings_displayed, strings_displayed_count, strings_not_displayed)[source]¶
Checks a page for strings displayed, not displayed and number of occurrences of a string
- create(cntrller='user', email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='')[source]¶
- login(email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='', logout_first=True)[source]¶
- submit_form(form_no=- 1, button='runtool_btn', form=None, **kwd)[source]¶
Populates and submits a form from the keyword arguments.
- check_exported_repository_dependency(dependency_filename, repository_name, repository_owner)[source]¶
- check_repository_dependency(repository, depends_on_repository, depends_on_changeset_revision=None, changeset_revision=None)[source]¶
- check_repository_tools_for_changeset_revision(repository, changeset_revision, tool_metadata_strings_displayed=None, tool_page_strings_displayed=None)[source]¶
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, changeset_revision, strings_displayed=None, strings_not_displayed=None)[source]¶
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)[source]¶
Checks the number of ‘pattern’ occurrences in the current browser page
- create_repository_dependency(repository=None, repository_tuples=None, filepath=None, prior_installation_required=False, complex=False, package=None, version=None, strings_displayed=None, strings_not_displayed=None)[source]¶
- create_repository_review(repository, review_contents_dict, changeset_revision=None, copy_from=None)[source]¶
- create_user_in_galaxy(cntrller='user', email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='')[source]¶
- deactivate_repository(installed_repository, strings_displayed=None, strings_not_displayed=None)[source]¶
- delete_files_from_repository(repository, filenames=None, strings_displayed=None, strings_not_displayed=None)[source]¶
- display_galaxy_browse_repositories_page(strings_displayed=None, strings_not_displayed=None)[source]¶
- display_installed_jobs_list_page(installed_repository, data_manager_names=None, strings_displayed=None, strings_not_displayed=None)[source]¶
- display_installed_repository_manage_page(installed_repository, strings_displayed=None, strings_not_displayed=None)[source]¶
- display_manage_repository_page(repository, changeset_revision=None, strings_displayed=None, strings_not_displayed=None)[source]¶
- display_repository_clone_page(owner_name, repository_name, strings_displayed=None, strings_not_displayed=None)[source]¶
- display_repository_file_contents(repository, filename, filepath=None, strings_displayed=None, strings_not_displayed=None)[source]¶
Find a file in the repository and display the contents.
- display_reviewed_repositories_owned_by_user(strings_displayed=None, strings_not_displayed=None)[source]¶
- display_repository_reviews_by_user(user, strings_displayed=None, strings_not_displayed=None)[source]¶
- edit_repository_categories(repository, categories_to_add=None, categories_to_remove=None, restore_original=True)[source]¶
- galaxy_login(email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='', logout_first=True)[source]¶
- generate_simple_dependency_xml(repository_tuples, filename, filepath, dependency_description='', complex=False, package=None, version=None, prior_installation_required=False)[source]¶
- get_repositories_category_api(categories, strings_displayed=None, strings_not_displayed=None)[source]¶
- get_or_create_repository(owner=None, strings_displayed=None, strings_not_displayed=None, **kwd)[source]¶
- get_repository_file_list(repository, base_path, current_path=None)[source]¶
Recursively load repository folder contents and append them to a list. Similar to os.walk but via /repository/open_folder.
- get_tools_from_repository_metadata(repository, include_invalid=False)[source]¶
Get a list of valid and (optionally) invalid tool dicts from the repository metadata.
- grant_write_access(repository, usernames=None, strings_displayed=None, strings_not_displayed=None, post_submit_strings_displayed=None, post_submit_strings_not_displayed=None)[source]¶
- initiate_installation_process(install_tool_dependencies=False, install_repository_dependencies=True, no_changes=True, new_tool_panel_section_label=None)[source]¶
- install_repository(name, owner, category_name, install_resolver_dependencies=False, install_tool_dependencies=False, install_repository_dependencies=True, changeset_revision=None, strings_displayed=None, strings_not_displayed=None, preview_strings_displayed=None, post_submit_strings_displayed=None, new_tool_panel_section_label=None, includes_tools_for_display_in_tool_panel=True, **kwd)[source]¶
- 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)[source]¶
- load_changeset_in_tool_shed(repository_id, changeset_revision, strings_displayed=None, strings_not_displayed=None)[source]¶
- load_display_tool_page(repository, tool_xml_path, changeset_revision, strings_displayed=None, strings_not_displayed=None)[source]¶
- load_invalid_tool_page(repository, tool_xml, changeset_revision, strings_displayed=None, strings_not_displayed=None)[source]¶
- load_page_for_installed_tool(tool_guid, strings_displayed=None, strings_not_displayed=None)[source]¶
- preview_repository_in_tool_shed(name, owner, changeset_revision=None, strings_displayed=None, strings_not_displayed=None)[source]¶
- reinstall_repository(installed_repository, install_repository_dependencies=True, install_tool_dependencies=False, no_changes=True, new_tool_panel_section_label='', strings_displayed=None, strings_not_displayed=None)[source]¶
- search_for_valid_tools(search_fields=None, exact_matches=False, strings_displayed=None, strings_not_displayed=None, from_galaxy=False)[source]¶
- send_message_to_repository_owner(repository, message, strings_displayed=None, strings_not_displayed=None, post_submit_strings_displayed=None, post_submit_strings_not_displayed=None)[source]¶
- set_form_value(form, kwd, field_name, field_value)[source]¶
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, set_deprecated=True, strings_displayed=None, strings_not_displayed=None)[source]¶
- set_repository_malicious(repository, set_malicious=True, strings_displayed=None, strings_not_displayed=None)[source]¶
- uninstall_repository(installed_repository, strings_displayed=None, strings_not_displayed=None)[source]¶
- update_installed_repository(installed_repository, strings_displayed=None, strings_not_displayed=None)[source]¶
- upload_file(repository, filename, filepath, valid_tools_only, uncompress_file, remove_repo_files_not_in_tar, commit_message, strings_displayed=None, strings_not_displayed=None)[source]¶
- 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)[source]¶
- verify_installed_repository_no_tool_panel_section(repository)[source]¶
Verify that there is no ‘tool_panel_section’ entry in the repository metadata.
- verify_repository_reviews(repository, reviewer=None, strings_displayed=None, strings_not_displayed=None)[source]¶
- verify_tool_metadata_for_installed_repository(installed_repository, strings_displayed=None, strings_not_displayed=None)[source]¶
- test_data_resolver: TestDataResolver¶