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tool_shed.test.base package¶
Submodules¶
tool_shed.test.base.common module¶
tool_shed.test.base.test_db_util module¶
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tool_shed.test.base.test_db_util.
get_galaxy_repository_by_name_owner_changeset_revision
(repository_name, owner, changeset_revision)[source]¶
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tool_shed.test.base.test_db_util.
get_installed_repository_by_name_owner
(repository_name, owner, return_multiple=False)[source]¶
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tool_shed.test.base.test_db_util.
get_repository_reviews
(repository_id, reviewer_user_id=None, changeset_revision=None)[source]¶
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tool_shed.test.base.test_db_util.
get_reviews_ordered_by_changeset_revision
(repository_id, changelog_tuples, reviewer_user_id=None)[source]¶
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tool_shed.test.base.test_db_util.
get_repository_metadata_for_changeset_revision
(repository_id, changeset_revision)[source]¶
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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¶
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class
tool_shed.test.base.twilltestcase.
ShedTwillTestCase
(methodName='runTest')[source]¶ Bases:
galaxy_test.driver.testcase.DrivenFunctionalTestCase
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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
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create
(cntrller='user', email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='')[source]¶
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login
(email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='', logout_first=True)[source]¶
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submit_form
(form_no=0, button='runtool_btn', form=None, **kwd)[source]¶ Populates and submits a form from the keyword arguments.
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check_exported_repository_dependency
(dependency_filename, repository_name, repository_owner)[source]¶
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check_installed_repository_tool_dependencies
(installed_repository, strings_displayed=None, strings_not_displayed=None, dependencies_installed=False)[source]¶
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check_repository_dependency
(repository, depends_on_repository, depends_on_changeset_revision=None, changeset_revision=None)[source]¶
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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.
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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.
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check_string_count_in_page
(pattern, min_count, max_count=None)[source]¶ Checks the number of ‘pattern’ occurrences in the current browser page
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create_repository_dependency
(repository=None, repository_tuples=[], filepath=None, prior_installation_required=False, complex=False, package=None, version=None, strings_displayed=None, strings_not_displayed=None)[source]¶
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create_repository_review
(repository, review_contents_dict, changeset_revision=None, copy_from=None)[source]¶
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create_user_in_galaxy
(cntrller='user', email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='')[source]¶
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deactivate_repository
(installed_repository, strings_displayed=None, strings_not_displayed=None)[source]¶
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delete_files_from_repository
(repository, filenames=[], strings_displayed=['were deleted from the repository'], strings_not_displayed=None)[source]¶
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display_galaxy_browse_repositories_page
(strings_displayed=None, strings_not_displayed=None)[source]¶
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display_installed_jobs_list_page
(installed_repository, data_manager_names=None, strings_displayed=None, strings_not_displayed=None)[source]¶
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display_installed_repository_manage_page
(installed_repository, strings_displayed=None, strings_not_displayed=None)[source]¶
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display_manage_repository_page
(repository, changeset_revision=None, strings_displayed=None, strings_not_displayed=None)[source]¶
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display_repository_clone_page
(owner_name, repository_name, strings_displayed=None, strings_not_displayed=None)[source]¶
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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.
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display_reviewed_repositories_owned_by_user
(strings_displayed=None, strings_not_displayed=None)[source]¶
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display_repository_reviews_by_user
(user, strings_displayed=None, strings_not_displayed=None)[source]¶
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edit_repository_categories
(repository, categories_to_add=[], categories_to_remove=[], restore_original=True)[source]¶
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galaxy_login
(email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='', logout_first=True)[source]¶
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generate_simple_dependency_xml
(repository_tuples, filename, filepath, dependency_description='', complex=False, package=None, version=None, prior_installation_required=False)[source]¶
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get_env_sh_path
(tool_dependency_name, tool_dependency_version, repository)[source]¶ Return the absolute path to an installed repository’s env.sh file.
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get_repositories_category_api
(categories, strings_displayed=None, strings_not_displayed=None)[source]¶
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get_tool_dependency_path
(tool_dependency_name, tool_dependency_version, repository)[source]¶ Return the absolute path for an installed tool dependency.
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get_or_create_repository
(owner=None, strings_displayed=None, strings_not_displayed=None, **kwd)[source]¶
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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.
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get_tools_from_repository_metadata
(repository, include_invalid=False)[source]¶ Get a list of valid and (optionally) invalid tool dicts from the repository metadata.
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grant_write_access
(repository, usernames=[], strings_displayed=None, strings_not_displayed=None, post_submit_strings_displayed=None, post_submit_strings_not_displayed=None)[source]¶
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initiate_installation_process
(install_tool_dependencies=False, install_repository_dependencies=True, no_changes=True, new_tool_panel_section_label=None)[source]¶
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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]¶
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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=[], strings_not_displayed_in_iframe=[])[source]¶
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load_changeset_in_tool_shed
(repository_id, changeset_revision, strings_displayed=None, strings_not_displayed=None)[source]¶
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load_display_tool_page
(repository, tool_xml_path, changeset_revision, strings_displayed=None, strings_not_displayed=None)[source]¶
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load_invalid_tool_page
(repository, tool_xml, changeset_revision, strings_displayed=None, strings_not_displayed=None)[source]¶
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load_page_for_installed_tool
(tool_guid, strings_displayed=None, strings_not_displayed=None)[source]¶
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preview_repository_in_tool_shed
(name, owner, changeset_revision=None, strings_displayed=None, strings_not_displayed=None)[source]¶
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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]¶
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search_for_valid_tools
(search_fields={}, exact_matches=False, strings_displayed=None, strings_not_displayed=None, from_galaxy=False)[source]¶
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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]¶
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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.
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set_repository_deprecated
(repository, set_deprecated=True, strings_displayed=None, strings_not_displayed=None)[source]¶
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set_repository_malicious
(repository, set_malicious=True, strings_displayed=None, strings_not_displayed=None)[source]¶
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uninstall_repository
(installed_repository, strings_displayed=None, strings_not_displayed=None)[source]¶
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update_installed_repository
(installed_repository, strings_displayed=None, strings_not_displayed=None)[source]¶
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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]¶
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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]¶
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verify_installed_repository_no_tool_panel_section
(repository)[source]¶ Verify that there is no ‘tool_panel_section’ entry in the repository metadata.
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verify_repository_reviews
(repository, reviewer=None, strings_displayed=None, strings_not_displayed=None)[source]¶
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