import abc import contextlib import logging import os import shutil import string import tarfile import tempfile import time from collections.abc import Iterator from json import loads from pathlib import Path from typing import ( Any, cast, Optional, TYPE_CHECKING, Union, ) from urllib.parse import ( quote_plus, urlencode, urlparse, ) import pytest import requests from mercurial import ( commands, hg, ui, ) from playwright.sync_api import Page from sqlalchemy import ( false, select, ) import galaxy.model.tool_shed_install as galaxy_model from galaxy.schema.schema import CheckForUpdatesResponse from galaxy.security import idencoding from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import ( InstalledRepositoryMetadataManager, ) from galaxy.tool_shed.unittest_utils import ( StandaloneInstallationTarget, ToolShedTarget, ) from galaxy.tool_shed.util.dependency_display import build_manage_repository_dict from galaxy.tool_shed.util.repository_util import check_for_updates from galaxy.util import ( DEFAULT_SOCKET_TIMEOUT, smart_str, ) from galaxy.util.compression_utils import CompressedFile from galaxy.util.resources import as_file from galaxy_test.base.api_asserts import assert_status_code_is_ok from galaxy_test.base.api_util import get_admin_api_key from galaxy_test.base.populators import wait_on_assertion from tool_shed.test.base.populators import TEST_DATA_REPO_FILES from tool_shed.util import ( hg_util, hgweb_config, xml_util, ) from tool_shed.webapp.model import Repository as DbRepository from tool_shed_client.schema import ( Category, CreateRepositoryRequest, Repository, RepositoryMetadata, UpdateRepositoryRequest, ) from . import ( common, test_db_util, ) from .api import ShedApiTestCase from .browser import ShedBrowser from .playwrightbrowser import PlaywrightShedBrowser from .populators import ToolShedPopulator if TYPE_CHECKING: from galaxy.model.scoped_session import install_model_scoped_session # Set a 10 minute timeout for repository installation. repository_installation_timeout = 600 log = logging.getLogger(__name__) class ToolShedInstallationClient(metaclass=abc.ABCMeta): @abc.abstractmethod def check_galaxy_repository_tool_panel_section( self, repository: galaxy_model.ToolShedRepository, expected_tool_panel_section: str ) -> None: """ """ @abc.abstractmethod def setup(self) -> None: """Setup client interaction.""" @abc.abstractmethod def deactivate_repository(self, installed_repository: galaxy_model.ToolShedRepository) -> None: """Deactivate the supplied repository.""" @abc.abstractmethod def display_installed_jobs_list_page( self, installed_repository: galaxy_model.ToolShedRepository, data_manager_names=None, strings_displayed=None ) -> None: """If available, check data manager jobs for supplied strings.""" @abc.abstractmethod def installed_repository_extended_info( self, installed_repository: galaxy_model.ToolShedRepository ) -> dict[str, Any]: """""" @abc.abstractmethod def install_repository( self, name: str, owner: str, changeset_revision: str, install_tool_dependencies: bool, install_repository_dependencies: bool, new_tool_panel_section_label: Optional[str], ) -> None: """""" @abc.abstractmethod def reactivate_repository(self, installed_repository: galaxy_model.ToolShedRepository) -> None: """""" @abc.abstractmethod def reset_metadata_on_installed_repositories(self, repositories: list[galaxy_model.ToolShedRepository]) -> None: """""" @abc.abstractmethod def reset_installed_repository_metadata(self, repository: galaxy_model.ToolShedRepository) -> None: """""" @abc.abstractmethod def uninstall_repository(self, installed_repository: galaxy_model.ToolShedRepository) -> None: """""" @abc.abstractmethod def update_installed_repository( self, installed_repository: galaxy_model.ToolShedRepository, verify_no_updates: bool = False ) -> dict[str, Any]: """""" @property @abc.abstractmethod def tool_data_path(self) -> str: """""" @property @abc.abstractmethod def shed_tool_data_table_conf(self) -> str: """""" @abc.abstractmethod def get_tool_names(self) -> list[str]: """""" @abc.abstractmethod def get_installed_repository_by_name_owner( self, repository_name: str, repository_owner: str ) -> galaxy_model.ToolShedRepository: """""" @abc.abstractmethod def get_installed_repositories_by_name_owner( self, repository_name: str, repository_owner: str ) -> list[galaxy_model.ToolShedRepository]: """""" @abc.abstractmethod def get_installed_repository_for( self, owner: Optional[str] = None, name: Optional[str] = None, changeset: Optional[str] = None ) -> Optional[dict[str, Any]]: """""" @abc.abstractmethod def get_all_installed_repositories(self) -> list[galaxy_model.ToolShedRepository]: """""" @abc.abstractmethod def refresh_tool_shed_repository(self, repo: galaxy_model.ToolShedRepository) -> None: """""" class GalaxyInteractorToolShedInstallationClient(ToolShedInstallationClient): """A Galaxy API + Database as a installation target for the tool shed.""" def __init__(self, testcase: "ShedTestCase"): self.testcase = testcase self._session = requests.Session() self._last_page_content = "" def setup(self): self._galaxy_login() def check_galaxy_repository_tool_panel_section( self, repository: galaxy_model.ToolShedRepository, expected_tool_panel_section: str ) -> None: metadata = repository.metadata_ assert "tools" in metadata, f"Tools not found in repository metadata: {metadata}" # If integrated_tool_panel.xml is to be tested, this test method will need to be enhanced to handle tools # from the same repository in different tool panel sections. Getting the first tool guid is ok, because # currently all tools contained in a single repository will be loaded into the same tool panel section. if repository.status in [ galaxy_model.ToolShedRepository.installation_status.UNINSTALLED, galaxy_model.ToolShedRepository.installation_status.DEACTIVATED, ]: tool_panel_section = _get_tool_panel_section_from_repository_metadata(metadata) else: tool_panel_section = self._get_tool_panel_section_from_api(metadata) assert ( tool_panel_section == expected_tool_panel_section ), f"Expected to find tool panel section *{expected_tool_panel_section}*, but instead found *{tool_panel_section}*\nMetadata: {metadata}\n" def deactivate_repository(self, installed_repository: galaxy_model.ToolShedRepository) -> None: encoded_id = self.testcase.security.encode_id(installed_repository.id) api_key = get_admin_api_key() response = requests.delete( f"{self.testcase.galaxy_url}/api/tool_shed_repositories/{encoded_id}", data={"remove_from_disk": False, "key": api_key}, timeout=DEFAULT_SOCKET_TIMEOUT, ) assert response.status_code != 403, response.content def display_installed_jobs_list_page( self, installed_repository: galaxy_model.ToolShedRepository, data_manager_names=None, strings_displayed=None ) -> None: data_managers = installed_repository.metadata_.get("data_manager", {}).get("data_managers", {}) if data_manager_names: if not isinstance(data_manager_names, list): data_manager_names = [data_manager_names] for data_manager_name in data_manager_names: assert ( data_manager_name in data_managers ), f"The requested Data Manager '{data_manager_name}' was not found in repository metadata." else: data_manager_name = list(data_managers.keys()) for data_manager_name in data_manager_names: params = {"id": data_managers[data_manager_name]["guid"]} self._visit_galaxy_url("/data_manager/jobs_list", params=params) content = self._last_page_content for expected in strings_displayed: if content.find(expected) == -1: raise AssertionError(f"Failed to find pattern {expected} in {content}") def installed_repository_extended_info( self, installed_repository: galaxy_model.ToolShedRepository ) -> dict[str, Any]: params = {"id": self.testcase.security.encode_id(installed_repository.id)} self._visit_galaxy_url("/admin_toolshed/manage_repository_json", params=params) json = self._last_page_content return loads(json) def install_repository( self, name: str, owner: str, changeset_revision: str, install_tool_dependencies: bool, install_repository_dependencies: bool, new_tool_panel_section_label: Optional[str], ): payload = { "tool_shed_url": self.testcase.url, "name": name, "owner": owner, "changeset_revision": changeset_revision, "install_tool_dependencies": install_tool_dependencies, "install_repository_dependencies": install_repository_dependencies, "install_resolver_dependencies": False, } if new_tool_panel_section_label: payload["new_tool_panel_section_label"] = new_tool_panel_section_label create_response = self.testcase.galaxy_interactor._post( "tool_shed_repositories/new/install_repository_revision", data=payload, admin=True ) assert_status_code_is_ok(create_response) create_response_object = create_response.json() if isinstance(create_response_object, dict): assert "status" in create_response_object assert "ok" == create_response_object["status"] # repo already installed... return assert isinstance(create_response_object, list) repository_ids = [repo["id"] for repo in create_response.json()] log.debug(f"Waiting for the installation of repository IDs: {repository_ids}") self._wait_for_repository_installation(repository_ids) def reactivate_repository(self, installed_repository: galaxy_model.ToolShedRepository) -> None: params = dict(id=self.testcase.security.encode_id(installed_repository.id)) url = "/admin_toolshed/restore_repository" self._visit_galaxy_url(url, params=params) def reset_metadata_on_installed_repositories(self, repositories: list[galaxy_model.ToolShedRepository]) -> None: repository_ids = [] for repository in repositories: repository_ids.append(self.testcase.security.encode_id(repository.id)) api_key = get_admin_api_key() response = requests.post( f"{self.testcase.galaxy_url}/api/tool_shed_repositories/reset_metadata_on_selected_installed_repositories", data={"repository_ids": repository_ids, "key": api_key}, timeout=DEFAULT_SOCKET_TIMEOUT, ) assert response.status_code != 403, response.content def uninstall_repository(self, installed_repository: galaxy_model.ToolShedRepository) -> None: encoded_id = self.testcase.security.encode_id(installed_repository.id) api_key = get_admin_api_key() response = requests.delete( f"{self.testcase.galaxy_url}/api/tool_shed_repositories/{encoded_id}", data={"remove_from_disk": True, "key": api_key}, timeout=DEFAULT_SOCKET_TIMEOUT, ) assert response.status_code != 403, response.content def update_installed_repository( self, installed_repository: galaxy_model.ToolShedRepository, verify_no_updates: bool = False ) -> dict[str, Any]: repository_id = self.testcase.security.encode_id(installed_repository.id) params = { "id": repository_id, } api_key = get_admin_api_key() response = requests.get( f"{self.testcase.galaxy_url}/api/tool_shed_repositories/check_for_updates?key={api_key}", params=params, timeout=DEFAULT_SOCKET_TIMEOUT, ) response.raise_for_status() response_dict = response.json() if verify_no_updates: assert "message" in response_dict message = response_dict["message"] assert "The status has not changed in the tool shed for repository" in message, str(response_dict) return response_dict def reset_installed_repository_metadata(self, repository: galaxy_model.ToolShedRepository) -> None: encoded_id = self.testcase.security.encode_id(repository.id) api_key = get_admin_api_key() response = requests.post( f"{self.testcase.galaxy_url}/api/tool_shed_repositories/reset_metadata_on_selected_installed_repositories", data={"repository_ids": [encoded_id], "key": api_key}, timeout=DEFAULT_SOCKET_TIMEOUT, ) assert response.status_code != 403, response.content @property def tool_data_path(self): return os.environ.get("GALAXY_TEST_TOOL_DATA_PATH") @property def shed_tool_data_table_conf(self): return os.environ.get("TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF") def get_tool_names(self) -> list[str]: response = self.testcase.galaxy_interactor._get("tools?in_panel=false") response.raise_for_status() tool_list = response.json() return [t["name"] for t in tool_list] def get_installed_repository_by_name_owner( self, repository_name: str, repository_owner: str ) -> galaxy_model.ToolShedRepository: return test_db_util.get_installed_repository_by_name_owner(repository_name, repository_owner) def get_installed_repositories_by_name_owner( self, repository_name: str, repository_owner: str ) -> list[galaxy_model.ToolShedRepository]: return test_db_util.get_installed_repository_by_name_owner( repository_name, repository_owner, return_multiple=True ) def get_installed_repository_for( self, owner: Optional[str] = None, name: Optional[str] = None, changeset: Optional[str] = None ) -> Optional[dict[str, Any]]: return self.testcase.get_installed_repository_for(owner=owner, name=name, changeset=changeset) def get_all_installed_repositories(self) -> list[galaxy_model.ToolShedRepository]: repositories = test_db_util.get_all_installed_repositories() for repository in repositories: test_db_util.ga_refresh(repository) return repositories def refresh_tool_shed_repository(self, repo: galaxy_model.ToolShedRepository) -> None: test_db_util.ga_refresh(repo) def _galaxy_login(self, email="test@bx.psu.edu", password="testuser", username="admin-user"): self._galaxy_logout() self._create_user_in_galaxy(email=email, password=password, username=username) params = {"login": email, "password": password, "session_csrf_token": self._galaxy_token()} self._visit_galaxy_url("/user/login", params=params) def _galaxy_logout(self): self._visit_galaxy_url("/user/logout", params=dict(session_csrf_token=self._galaxy_token())) def _create_user_in_galaxy(self, email="test@bx.psu.edu", password="testuser", username="admin-user"): params = { "username": username, "email": email, "password": password, "confirm": password, "session_csrf_token": self._galaxy_token(), } self._visit_galaxy_url("/user/create", params=params, allowed_codes=[200, 400]) def _galaxy_token(self): self._visit_galaxy_url("/") html = self._last_page_content token_def_index = html.find("session_csrf_token") token_sep_index = html.find("=", token_def_index) token_quote_start_index = html.find('"', token_sep_index) token_quote_end_index = html.find('"', token_quote_start_index + 1) token = html[(token_quote_start_index + 1) : token_quote_end_index] return token def _get_tool_panel_section_from_api(self, metadata): tool_metadata = metadata["tools"] tool_guid = quote_plus(tool_metadata[0]["guid"], safe="") api_url = f"/api/tools/{tool_guid}" self._visit_galaxy_url(api_url) tool_dict = loads(self._last_page_content) tool_panel_section = tool_dict["panel_section_name"] return tool_panel_section def _wait_for_repository_installation(self, repository_ids): # Wait until all repositories are in a final state before returning. This ensures that subsequent tests # are running against an installed repository, and not one that is still in the process of installing. if repository_ids: for repository_id in repository_ids: galaxy_repository = test_db_util.get_installed_repository_by_id( self.testcase.security.decode_id(repository_id) ) _wait_for_installation(galaxy_repository, test_db_util.ga_refresh) def _visit_galaxy_url(self, url, params=None, allowed_codes=None): if allowed_codes is None: allowed_codes = [200] url = f"{self.testcase.galaxy_url}{url}" url = self.testcase.join_url_and_params(url, params) response = self._session.get(url, timeout=DEFAULT_SOCKET_TIMEOUT) assert response.status_code in allowed_codes, "Invalid HTTP return code {}, allowed codes: {}".format( response.status_code, ", ".join(str(code) for code in allowed_codes), ) self._last_page_content = response.text return url class StandaloneToolShedInstallationClient(ToolShedInstallationClient): def __init__(self, testcase: "ShedTestCase"): self.testcase = testcase self.temp_directory = Path(tempfile.mkdtemp(prefix="toolshedtestinstalltarget")) tool_shed_target = ToolShedTarget( self.testcase.url, "Tool Shed for Testing", ) self._installation_target = StandaloneInstallationTarget(self.temp_directory, tool_shed_target=tool_shed_target) def setup(self) -> None: pass def check_galaxy_repository_tool_panel_section( self, repository: galaxy_model.ToolShedRepository, expected_tool_panel_section: str ) -> None: metadata = repository.metadata_ assert "tools" in metadata, f"Tools not found in repository metadata: {metadata}" # TODO: check actual toolbox if tool is already installed... tool_panel_section = _get_tool_panel_section_from_repository_metadata(metadata) assert ( tool_panel_section == expected_tool_panel_section ), f"Expected to find tool panel section *{expected_tool_panel_section}*, but instead found *{tool_panel_section}*\nMetadata: {metadata}\n" def deactivate_repository(self, installed_repository: galaxy_model.ToolShedRepository) -> None: irm = self._installation_target.installed_repository_manager errors = irm.uninstall_repository(repository=installed_repository, remove_from_disk=False) if errors: raise Exception( f"Attempting to uninstall tool dependencies for repository named {installed_repository.name} resulted in errors: {errors}" ) def display_installed_jobs_list_page( self, installed_repository: galaxy_model.ToolShedRepository, data_manager_names=None, strings_displayed=None ) -> None: raise NotImplementedError() def installed_repository_extended_info( self, installed_repository: galaxy_model.ToolShedRepository ) -> dict[str, Any]: self._installation_target.install_model.context.refresh(installed_repository) return build_manage_repository_dict(self._installation_target, "ok", installed_repository) def install_repository( self, name: str, owner: str, changeset_revision: str, install_tool_dependencies: bool, install_repository_dependencies: bool, new_tool_panel_section_label: Optional[str], ): tool_shed_url = self.testcase.url payload = { "tool_shed_url": tool_shed_url, "name": name, "owner": owner, "changeset_revision": changeset_revision, "install_tool_dependencies": install_tool_dependencies, "install_repository_dependencies": install_repository_dependencies, "install_resolver_dependencies": False, } if new_tool_panel_section_label: payload["new_tool_panel_section_label"] = new_tool_panel_section_label irm = InstallRepositoryManager(app=self._installation_target) installed_tool_shed_repositories = irm.install(str(tool_shed_url), name, owner, changeset_revision, payload) for installed_tool_shed_repository in installed_tool_shed_repositories or []: _wait_for_installation( installed_tool_shed_repository, self._installation_target.install_model.context.refresh ) def reactivate_repository(self, installed_repository: galaxy_model.ToolShedRepository) -> None: irm = self._installation_target.installed_repository_manager irm.activate_repository(installed_repository) def reset_metadata_on_installed_repositories(self, repositories: list[galaxy_model.ToolShedRepository]) -> None: for repository in repositories: irmm = InstalledRepositoryMetadataManager(self._installation_target) irmm.set_repository(repository) irmm.reset_all_metadata_on_installed_repository() def reset_installed_repository_metadata(self, repository: galaxy_model.ToolShedRepository) -> None: irmm = InstalledRepositoryMetadataManager(self._installation_target) irmm.set_repository(repository) irmm.reset_all_metadata_on_installed_repository() def uninstall_repository(self, installed_repository: galaxy_model.ToolShedRepository) -> None: irm = self._installation_target.installed_repository_manager errors = irm.uninstall_repository(repository=installed_repository, remove_from_disk=True) if errors: raise Exception( f"Attempting to uninstall tool dependencies for repository named {installed_repository.name} resulted in errors: {errors}" ) def update_installed_repository( self, installed_repository: galaxy_model.ToolShedRepository, verify_no_updates: bool = False ) -> dict[str, Any]: install_model_context = cast("install_model_scoped_session", self._installation_target.install_model.session) message, status = check_for_updates( self._installation_target.tool_shed_registry, install_model_context, installed_repository.id, ) response = CheckForUpdatesResponse(message=message, status=status) response_dict = response.dict() if verify_no_updates: assert "message" in response_dict message = response_dict["message"] assert "The status has not changed in the tool shed for repository" in message, str(response_dict) return response_dict def get_installed_repository_by_name_owner( self, repository_name: str, repository_owner: str ) -> galaxy_model.ToolShedRepository: return test_db_util.get_installed_repository_by_name_owner( repository_name, repository_owner, session=self._installation_target.install_model.context ) def get_installed_repositories_by_name_owner( self, repository_name: str, repository_owner: str ) -> list[galaxy_model.ToolShedRepository]: return test_db_util.get_installed_repository_by_name_owner( repository_name, repository_owner, return_multiple=True, session=self._installation_target.install_model.context, ) def get_installed_repository_for( self, owner: Optional[str] = None, name: Optional[str] = None, changeset: Optional[str] = None ) -> Optional[dict[str, Any]]: repository = get_installed_repository(self._installation_target.install_model.context, name, owner, changeset) if repository: return repository.to_dict() else: return None def get_all_installed_repositories(self) -> list[galaxy_model.ToolShedRepository]: repositories = test_db_util.get_all_installed_repositories( session=self._installation_target.install_model.context ) for repository in repositories: self._installation_target.install_model.context.refresh(repository) return repositories def refresh_tool_shed_repository(self, repo: galaxy_model.ToolShedRepository) -> None: self._installation_target.install_model.context.refresh(repo) @property def shed_tool_data_table_conf(self): return self._installation_target.config.shed_tool_data_table_config @property def tool_data_path(self): return self._installation_target.config.tool_data_path def get_tool_names(self) -> list[str]: tool_names = [] for _, tool in self._installation_target.toolbox.tools(): tool_names.append(tool.name) return tool_names @pytest.mark.usefixtures("shed_browser") class ShedTestCase(ShedApiTestCase): """Class of FunctionalTestCase geared toward HTML interactions using the Twill library.""" requires_galaxy: bool = False _installation_client: Optional[ToolShedInstallationClient] = None __browser: Optional[ShedBrowser] = None _logged_in_populator: Optional["ToolShedPopulator"] = None def setUp(self): super().setUp() # Security helper self.security = idencoding.IdEncodingHelper(id_secret="changethisinproductiontoo") self.history_id = None self.hgweb_config_dir = os.environ.get("TEST_HG_WEB_CONFIG_DIR") self.hgweb_config_manager = hgweb_config.hgweb_config_manager self.hgweb_config_manager.hgweb_config_dir = self.hgweb_config_dir self.tool_shed_test_tmp_dir: str = os.environ.get("TOOL_SHED_TEST_TMP_DIR", "") self.file_dir: str = os.environ.get("TOOL_SHED_TEST_FILE_DIR", "") self.shed_tool_conf = os.environ.get("GALAXY_TEST_SHED_TOOL_CONF") self.test_db_util = test_db_util if os.environ.get("TOOL_SHED_TEST_INSTALL_CLIENT") == "standalone": # TODO: once nose is out of the way - try to get away without # instantiating the unused Galaxy server here. installation_client_class: Union[ type[StandaloneToolShedInstallationClient], type[GalaxyInteractorToolShedInstallationClient] ] = StandaloneToolShedInstallationClient full_stack_galaxy = False else: installation_client_class = GalaxyInteractorToolShedInstallationClient full_stack_galaxy = True self.full_stack_galaxy = full_stack_galaxy if self.requires_galaxy and (self.__class__._installation_client is None): self.__class__._installation_client = installation_client_class(self) self.__class__._installation_client.setup() self._installation_client = self.__class__._installation_client @pytest.fixture(autouse=True) def inject_shed_browser(self, shed_browser: ShedBrowser): self.__browser = shed_browser @property def _browser(self) -> ShedBrowser: assert self.__browser return self.__browser def check_for_strings(self, strings_displayed=None, strings_not_displayed=None): strings_displayed = strings_displayed or [] strings_not_displayed = strings_not_displayed or [] if strings_displayed: for check_str in strings_displayed: self.check_page_for_string(check_str) if strings_not_displayed: for check_str in strings_not_displayed: self.check_string_not_in_page(check_str) def check_page_for_string(self, patt): """Looks for 'patt' in the current browser page""" self._browser.check_page_for_string(patt) def check_string_not_in_page(self, patt): """Checks to make sure 'patt' is NOT in the page.""" self._browser.check_string_not_in_page(patt) # Functions associated with user accounts def _submit_register_form(self, email: str, password: str, username: str, redirect: Optional[str] = None): self._browser.fill_form_value("registration", "email", email) if redirect is not None: self._browser.fill_form_value("registration", "redirect", redirect) self._browser.fill_form_value("registration", "password", password) self._browser.fill_form_value("registration", "confirm", password) self._browser.fill_form_value("registration", "username", username) self._browser.submit_form_with_name("registration", "create_user_button") @property def invalid_tools_labels(self) -> str: return "Invalid Tools" def create( self, cntrller: str = "user", email: str = "test@bx.psu.edu", password: str = "testuser", username: str = "admin-user", redirect: Optional[str] = None, ) -> tuple[bool, bool, bool]: return self._ensure_user_via_api(email, password, username) def _ensure_user_via_api(self, email: str, password: str, username: str) -> tuple[bool, bool, bool]: """Create user via admin API if not already present. Returns (previously_created, username_taken, invalid_username). """ admin = self.admin_api_interactor all_users = admin.get("users").json() if any(u["username"] == username for u in all_users): return (True, False, False) response = admin.post("users", json={"email": email, "username": username, "password": password}) if response.status_code != 200: # User creation failed (e.g. reserved username) return (False, False, True) return (False, False, False) def last_page(self): """ Return the last visited page (usually HTML, but can binary data as well). """ return self._browser.page_content() def user_api_interactor(self, email="test@bx.psu.edu", password="testuser"): return self._api_interactor_by_credentials(email, password) def user_populator(self, email="test@bx.psu.edu", password="testuser"): return self._get_populator(self.user_api_interactor(email=email, password=password)) def login( self, email: str = "test@bx.psu.edu", password: str = "testuser", username: str = "admin-user", redirect: Optional[str] = None, logout_first: bool = True, explicit_logout: bool = False, ): self.visit_url("/") if logout_first: self.logout(explicit=explicit_logout) # Ensure user exists via API previously_created, username_taken, invalid_username = self.create( email=email, password=password, username=username, redirect=redirect ) if invalid_username: return # Re-visit root after logout to get fresh session + CSRF token self.visit_url("/") cookies = self._page.context.cookies() csrf_token = "" for cookie in cookies: if cookie["name"] == "session_csrf_token": csrf_token = cookie["value"] break # Establish browser session via internal login API self._page.evaluate( """async ([login, password, csrfToken]) => { const response = await fetch('/api_internal/login', { method: 'PUT', headers: {'Content-Type': 'application/json'}, body: JSON.stringify({ login: login, password: password, session_csrf_token: csrfToken, }) }); if (!response.ok) { const text = await response.text(); throw new Error('Login failed: ' + response.status + ' ' + text); } return await response.json(); }""", [email, password, csrf_token], ) # Reload to pick up the new session self.visit_url("/") # Store a populator for the logged-in user so API calls use correct credentials # Use __class__ so it persists across test method instances self.__class__._logged_in_populator = self.user_populator(email=email, password=password) @property def _playwright_browser(self) -> PlaywrightShedBrowser: browser = self._browser assert isinstance(browser, PlaywrightShedBrowser) return browser @property def _page(self) -> Page: return self._playwright_browser._page def logout(self, explicit: bool = False): """logout of the current tool shed session. By default this is a logout if logged in action, however if explicit is True - ensure there is a session and be explicit in logging out to provide extract test structure. """ if explicit: self._playwright_browser.explicit_logout() else: self._playwright_browser.logout_if_logged_in() def submit_form(self, form_no=-1, button="runtool_btn", form=None, **kwd): """Populates and submits a form from the keyword arguments.""" # An HTMLForm contains a sequence of Controls. Supported control classes are: # TextControl, FileControl, ListControl, RadioControl, CheckboxControl, SelectControl, # SubmitControl, ImageControl self._browser.submit_form(form_no, button, form, **kwd) def join_url_and_params(self, url: str, params, query=None) -> str: if params is None: params = {} if query is None: query = urlparse(url).query if query: for query_parameter in query.split("&"): key, value = query_parameter.split("=") params[key] = value if params: url += f"?{urlencode(params)}" return url def visit_url(self, url: str, params=None, allowed_codes: Optional[list[int]] = None) -> str: parsed_url = urlparse(url) if len(parsed_url.netloc) == 0: url = f"http://{self.host}:{self.port}{parsed_url.path}" else: url = f"{parsed_url.scheme}://{parsed_url.netloc}{parsed_url.path}" url = self.join_url_and_params(url, params, query=parsed_url.query) if allowed_codes is None: allowed_codes = [200] return self._browser.visit_url(url, allowed_codes=allowed_codes) def write_temp_file(self, content, suffix=".html"): with tempfile.NamedTemporaryFile(suffix=suffix, prefix="testcase-", delete=False) as fh: fh.write(smart_str(content)) return fh.name def assign_admin_role(self, repository: Repository, user, as_email=None, as_password="testuser"): populator = self.user_populator(email=as_email, password=as_password) if as_email else self.populator populator.add_admin_user(repository, user.username) def browse_category(self, category: Category, strings_displayed=None, strings_not_displayed=None): self.visit_url(f"/repositories_by_category/{category.id}") self.check_for_strings(strings_displayed, strings_not_displayed) def browse_repository(self, repository: Repository, strings_displayed=None, strings_not_displayed=None): populator = self._logged_in_populator or self.populator detailed = populator.get_repository(repository) assert detailed.name == repository.name tip = self.get_repository_tip(repository) assert tip, f"Repository {repository.name} has no tip revision" def browse_tool_shed(self, url, strings_displayed=None, strings_not_displayed=None): url = "/repositories_by_category" self.visit_url(url) self.check_for_strings(strings_displayed, strings_not_displayed) def check_count_of_metadata_revisions_associated_with_repository(self, repository: Repository, metadata_count: int): metadata_revisions = self.get_repository_metadata(repository) assert ( len(metadata_revisions) == metadata_count ), f"Expected {metadata_count} metadata revisions, found {len(metadata_revisions)}" def check_for_valid_tools(self, repository, strings_displayed=None, strings_not_displayed=None): db_repository = self._db_repository(repository) tip = self.get_repository_tip(repository) repository_metadata = self.get_repository_metadata_by_changeset_revision(db_repository.id, tip) metadata = repository_metadata.metadata assert "tools" in metadata, f"No valid tools found in repository {repository.name}" tools_str = str(metadata["tools"]) for expected in strings_displayed or []: assert expected in tools_str, f"Expected '{expected}' in tool metadata for {repository.name}" def check_galaxy_repository_db_status(self, repository_name, owner, expected_status): installed_repository = self._get_installed_repository_by_name_owner(repository_name, owner) self._refresh_tool_shed_repository(installed_repository) assert ( installed_repository.status == expected_status ), f"Status in database is {installed_repository.status}, expected {expected_status}" def check_repository_dependency( self, repository: Repository, depends_on_repository: Repository, depends_on_changeset_revision=None, changeset_revision=None, ): # v2 doesn't display repository repository dependencies, they are deprecated pass def check_repository_metadata(self, repository: Repository, tip_only=True): if tip_only: assert ( self.tip_has_metadata(repository) and len(self.get_repository_metadata_revisions(repository)) == 1 ), "Repository tip is not a metadata revision: Repository tip - %s, metadata revisions - %s." else: assert ( len(self.get_repository_metadata_revisions(repository)) > 0 ), "Repository tip is not a metadata revision: Repository tip - {}, metadata revisions - {}.".format( self.get_repository_tip(repository), ", ".join(self.get_repository_metadata_revisions(repository)), ) def check_repository_tools_for_changeset_revision( self, repository: Repository, changeset_revision, tool_metadata_strings_displayed=None, tool_page_strings_displayed=None, ): """Check tool metadata for the given changeset revision contains expected strings.""" db_repository = self._db_repository(repository) test_db_util.refresh(db_repository) repository_metadata = self.get_repository_metadata_by_changeset_revision(db_repository.id, changeset_revision) metadata = repository_metadata.metadata if "tools" not in metadata: raise AssertionError(f"No tools in {repository.name} revision {changeset_revision}.") tools_str = str(metadata["tools"]) for expected in tool_metadata_strings_displayed or []: assert ( expected in tools_str ), f"Expected '{expected}' in tool metadata for {repository.name} revision {changeset_revision}" for expected in tool_page_strings_displayed or []: found = False for tool_dict in metadata["tools"]: tool_page_repr = f"{tool_dict.get('name', '')} (version {tool_dict.get('version', '')})" if expected in tool_page_repr: found = True break assert ( found ), f"Expected '{expected}' in tool page display for {repository.name} revision {changeset_revision}" def check_repository_invalid_tools_for_changeset_revision( self, repository: Repository, changeset_revision, strings_displayed=None, strings_not_displayed=None ): """Check that the changeset revision has invalid tools in its metadata.""" db_repository = self._db_repository(repository) repository_metadata = self.get_repository_metadata_by_changeset_revision(db_repository.id, changeset_revision) metadata = repository_metadata.metadata assert ( "invalid_tools" in metadata ), f"Metadata for changeset revision {changeset_revision} does not define invalid tools" assert len(metadata["invalid_tools"]) > 0, "invalid_tools list is empty" # Tool validation error messages (strings_displayed) were previously checked by loading # each tool via /repository/load_invalid_tool. That Mako route is being removed. # The metadata only stores which tool configs are invalid, not the error messages. def check_string_count_in_page(self, pattern, min_count: int, max_count: Optional[int] = None): """Checks the number of 'pattern' occurrences in the current browser page""" page = self.last_page() pattern_count = page.count(pattern) if max_count is None: max_count = min_count # The number of occurrences of pattern in the page should be between min_count # and max_count, so show error if pattern_count is less than min_count or greater # than max_count. if pattern_count < min_count or pattern_count > max_count: fname = self.write_temp_file(page) raise AssertionError( f"{pattern_count} occurrences of '{pattern}' found (min. {min_count}, max. {max_count}).\npage content written to '{fname}' " ) def check_galaxy_repository_tool_panel_section( self, repository: galaxy_model.ToolShedRepository, expected_tool_panel_section: str ) -> None: assert self._installation_client self._installation_client.check_galaxy_repository_tool_panel_section(repository, expected_tool_panel_section) def clone_repository(self, repository: Repository, destination_path: str) -> None: url = f"{self.url}/repos/{repository.owner}/{repository.name}" success, message = hg_util.clone_repository(url, destination_path, self.get_repository_tip(repository)) assert success is True, message def commit_and_push(self, repository, hgrepo, options, username, password): url = f"http://{username}:{password}@{self.host}:{self.port}/repos/{repository.user.username}/{repository.name}" commands.commit(ui.ui(), hgrepo, **options) # Try pushing multiple times as it transiently fails on Jenkins. # TODO: Figure out why that happens for _ in range(5): try: commands.push(ui.ui(), hgrepo, dest=url) except Exception as e: if str(e).find("Pushing to Tool Shed is disabled") != -1: return False else: return True raise def create_category(self, **kwd) -> Category: category_name = kwd["name"] try: category = self.populator.get_category_with_name(category_name) except ValueError: # not recreating this functionality in the UI I don't think? category = self.populator.new_category(category_name) return category return category def create_repository_dependency( self, repository: Repository, repository_tuples=None, filepath=None, prior_installation_required=False, complex=False, package=None, version=None, strings_displayed=None, strings_not_displayed=None, ): repository_tuples = repository_tuples or [] repository_names = [] if complex: filename = "tool_dependencies.xml" target = self.generate_complex_dependency_xml( filename=filename, filepath=filepath, repository_tuples=repository_tuples, package=package, version=version, ) else: for _, name, _, _ in repository_tuples: repository_names.append(name) dependency_description = f"{repository.name} depends on {', '.join(repository_names)}." filename = "repository_dependencies.xml" target = self.generate_simple_dependency_xml( repository_tuples=repository_tuples, filename=filename, filepath=filepath, dependency_description=dependency_description, prior_installation_required=prior_installation_required, ) self.add_file_to_repository(repository, target, filename, strings_displayed=strings_displayed) def deactivate_repository(self, installed_repository: galaxy_model.ToolShedRepository) -> None: assert self._installation_client self._installation_client.deactivate_repository(installed_repository) @contextlib.contextmanager def cloned_repo(self, repository: Repository) -> Iterator[str]: temp_directory = tempfile.mkdtemp(prefix="toolshedrepowithoutfiles") try: self.clone_repository(repository, temp_directory) shutil.rmtree(os.path.join(temp_directory, ".hg")) contents = os.listdir(temp_directory) if len(contents) == 1 and contents[0] == "repo": yield os.path.join(temp_directory, "repo") else: yield temp_directory finally: shutil.rmtree(temp_directory) def setup_freebayes_0010_repo(self, repository: Repository): strings_displayed = [ "Metadata may have been defined", "This file requires an entry", "tool_data_table_conf", ] self.add_file_to_repository(repository, "freebayes/freebayes.xml", strings_displayed=strings_displayed) strings_displayed = ["Upload a file named sam_fa_indices.loc.sample"] self.add_file_to_repository( repository, "freebayes/tool_data_table_conf.xml.sample", strings_displayed=strings_displayed ) self.add_file_to_repository(repository, "freebayes/sam_fa_indices.loc.sample") target = os.path.join("freebayes", "malformed_tool_dependencies", "tool_dependencies.xml") self.add_file_to_repository( repository, target, strings_displayed=["Exception attempting to parse", "invalid element name"] ) target = os.path.join("freebayes", "invalid_tool_dependencies", "tool_dependencies.xml") strings_displayed = [ "The settings for name, version and type from a contained tool configuration" ] # , strings_displayed=strings_displayed self.add_file_to_repository(repository, target) target = os.path.join("freebayes", "tool_dependencies.xml") self.add_file_to_repository(repository, target) def add_file_to_repository( self, repository: Repository, source: str, target: Optional[str] = None, strings_displayed=None, commit_message: Optional[str] = None, ): with self.cloned_repo(repository) as temp_directory: if target is None: target = os.path.basename(source) full_target = os.path.join(temp_directory, target) full_source = TEST_DATA_REPO_FILES.joinpath(source) with as_file(full_source) as full_source_path: shutil.copyfile(full_source_path, full_target) commit_message = commit_message or "Uploaded revision with added file." self._upload_dir_to_repository( repository, temp_directory, commit_message=commit_message, strings_displayed=strings_displayed ) def add_tar_to_repository(self, repository: Repository, source: str, strings_displayed=None): with self.cloned_repo(repository) as temp_directory: full_source = TEST_DATA_REPO_FILES.joinpath(source) with full_source.open("rb") as full_source_fileobj: with CompressedFile.open_tar(full_source_fileobj) as tar: tar.extractall(path=temp_directory) commit_message = "Uploaded revision with added files from tar." self._upload_dir_to_repository( repository, temp_directory, commit_message=commit_message, strings_displayed=strings_displayed ) def commit_tar_to_repository( self, repository: Repository, source: str, commit_message=None, strings_displayed=None ): full_source = TEST_DATA_REPO_FILES.joinpath(source) assert full_source.is_file(), f"Attempting to upload {full_source} as a tar which is not a file" populator = self.user_populator() if strings_displayed is None: # Just assume this is a valid upload... populator.upload_revision(repository, full_source, commit_message=commit_message) else: response = populator.upload_revision_raw(repository, full_source, commit_message=commit_message) try: text = response.json()["message"] except Exception: text = response.text for string_displayed in strings_displayed: if string_displayed not in text: raise AssertionError(f"Failed to find {string_displayed} in JSON response {text}") def delete_files_from_repository(self, repository: Repository, filenames: list[str]): with self.cloned_repo(repository) as temp_directory: for filename in filenames: to_delete = os.path.join(temp_directory, filename) os.remove(to_delete) commit_message = "Uploaded revision with deleted files." self._upload_dir_to_repository(repository, temp_directory, commit_message=commit_message) def _upload_dir_to_repository(self, repository: Repository, target, commit_message, strings_displayed=None): tf = tempfile.NamedTemporaryFile() with tarfile.open(tf.name, "w:gz") as tar: tar.add(target, arcname=".") target = os.path.abspath(tf.name) self.commit_tar_to_repository( repository, target, commit_message=commit_message, strings_displayed=strings_displayed ) def display_installed_jobs_list_page(self, installed_repository, data_manager_names=None, strings_displayed=None): assert self._installation_client self._installation_client.display_installed_jobs_list_page( installed_repository, data_manager_names, strings_displayed ) def display_installed_repository_manage_json(self, installed_repository): assert self._installation_client return self._installation_client.installed_repository_extended_info(installed_repository) def display_manage_repository_page( self, repository: Repository, changeset_revision=None, strings_displayed=None, strings_not_displayed=None ): params = {"id": repository.id} if changeset_revision: params["changeset_revision"] = changeset_revision url = f"/repositories/{repository.id}" self.visit_url(url, params=params) self.check_for_strings(strings_displayed, strings_not_displayed) def display_repository_clone_page( self, owner_name, repository_name, strings_displayed=None, strings_not_displayed=None ): url = f"/repos/{owner_name}/{repository_name}" self.visit_url(url) self.check_for_strings(strings_displayed, strings_not_displayed) def edit_repository_categories( self, repository: Repository, categories_to_add: list[str], categories_to_remove: list[str], restore_original=True, ) -> None: populator = self._logged_in_populator or self.populator all_categories = populator.get_categories() categories_by_name = {c.name: c for c in all_categories} db_repository = self._db_repository(repository) # Use encoded API IDs for current categories (raw DB IDs can't be decoded by the API) current_category_ids = {categories_by_name[rca.category.name].id for rca in db_repository.categories} add_ids = {categories_by_name[name].id for name in categories_to_add} remove_ids = {categories_by_name[name].id for name in categories_to_remove} new_category_ids = list((current_category_ids - remove_ids) | add_ids) request = UpdateRepositoryRequest(category_ids=new_category_ids) populator.update(repository, request) if restore_original: restore_request = UpdateRepositoryRequest(category_ids=list(current_category_ids)) populator.update(repository, restore_request) def edit_repository_information(self, repository: Repository, revert=True, **kwd): populator = self._logged_in_populator or self.populator db_repository = self._db_repository(repository) original_information = dict( repo_name=db_repository.name, description=db_repository.description, long_description=db_repository.long_description, ) # Map form field names to API field names request = UpdateRepositoryRequest( name=kwd.get("repo_name"), synopsis=kwd.get("description"), description=kwd.get("long_description"), type_=kwd.get("repository_type"), ) populator.update(repository, request) if revert: revert_request = UpdateRepositoryRequest( name=original_information["repo_name"], synopsis=original_information["description"], description=original_information["long_description"], ) populator.update(repository, revert_request) def escape_html(self, string, unescape=False): html_entities = [("&", "X"), ("'", "'"), ('"', """)] for character, replacement in html_entities: if unescape: string = string.replace(replacement, character) else: string = string.replace(character, replacement) return string def expect_repo_created_strings(self, name): return [ f"Repository {name}", f"Repository {name} has been created", ] def fetch_repository_metadata(self, repository: Repository, strings_displayed=None, strings_not_displayed=None): url = f"/api/repositories/{repository.id}/metadata" self.visit_url(url) self.check_for_strings(strings_displayed, strings_not_displayed) def generate_complex_dependency_xml(self, filename, filepath, repository_tuples, package, version): file_path = os.path.join(filepath, filename) dependency_entries = [] template = string.Template(common.new_repository_dependencies_line) for toolshed_url, name, owner, changeset_revision in repository_tuples: dependency_entries.append( template.safe_substitute( toolshed_url=toolshed_url, owner=owner, repository_name=name, changeset_revision=changeset_revision, prior_installation_required="", ) ) if not os.path.exists(filepath): os.makedirs(filepath) dependency_template = string.Template(common.complex_repository_dependency_template) repository_dependency_xml = dependency_template.safe_substitute( package=package, version=version, dependency_lines="\n".join(dependency_entries) ) # Save the generated xml to the specified location. open(file_path, "w").write(repository_dependency_xml) return file_path def generate_simple_dependency_xml( self, repository_tuples, filename, filepath, dependency_description="", complex=False, package=None, version=None, prior_installation_required=False, ): if not os.path.exists(filepath): os.makedirs(filepath) dependency_entries = [] if prior_installation_required: prior_installation_value = ' prior_installation_required="True"' else: prior_installation_value = "" for toolshed_url, name, owner, changeset_revision in repository_tuples: template = string.Template(common.new_repository_dependencies_line) dependency_entries.append( template.safe_substitute( toolshed_url=toolshed_url, owner=owner, repository_name=name, changeset_revision=changeset_revision, prior_installation_required=prior_installation_value, ) ) if dependency_description: description = f' description="{dependency_description}"' else: description = dependency_description template_parser = string.Template(common.new_repository_dependencies_xml) repository_dependency_xml = template_parser.safe_substitute( description=description, dependency_lines="\n".join(dependency_entries) ) # Save the generated xml to the specified location. full_path = os.path.join(filepath, filename) open(full_path, "w").write(repository_dependency_xml) return full_path def generate_temp_path(self, test_script_path, additional_paths=None): additional_paths = additional_paths or [] temp_path = os.path.join(self.tool_shed_test_tmp_dir, test_script_path, os.sep.join(additional_paths)) if not os.path.exists(temp_path): os.makedirs(temp_path) return temp_path def get_all_installed_repositories(self) -> list[galaxy_model.ToolShedRepository]: assert self._installation_client return self._installation_client.get_all_installed_repositories() def get_filename(self, filename, filepath=None): if filepath is not None: return os.path.abspath(os.path.join(filepath, filename)) else: return os.path.abspath(os.path.join(self.file_dir, filename)) def get_hg_repo(self, path): return hg.repository(ui.ui(), path.encode("utf-8")) def get_repositories_category_api( self, categories: list[Category], strings_displayed=None, strings_not_displayed=None ): for category in categories: url = f"/api/categories/{category.id}/repositories" self.visit_url(url) self.check_for_strings(strings_displayed, strings_not_displayed) def get_or_create_repository( self, category: Category, owner: str, name: str, strings_displayed=None, strings_not_displayed=None, **kwd ) -> Repository: repository = self.populator.get_repository_for(owner, name) if repository is None: category_id = category.id assert category_id # Use logged-in user's populator to create via API as the correct owner populator = self._logged_in_populator or self.populator request = CreateRepositoryRequest( name=name, synopsis=kwd.get("description", name), description=kwd.get("long_description", None), category_ids=category_id, ) repository = populator.create_repository(request) assert repository return repository def get_repo_path(self, repository: Repository) -> str: # An entry in the hgweb.config file looks something like: repos/test/mira_assembler = database/community_files/000/repo_123 lhs = f"repos/{repository.owner}/{repository.name}" try: return self.hgweb_config_manager.get_entry(lhs) except Exception: raise Exception( f"Entry for repository {lhs} missing in hgweb config file {self.hgweb_config_manager.hgweb_config}." ) def get_repository_changelog_tuples(self, repository): repo = self.get_hg_repo(self.get_repo_path(repository)) changelog_tuples = [] for changeset in repo.changelog: ctx = repo[changeset] changelog_tuples.append((ctx.rev(), ctx)) return changelog_tuples def _db_repository(self, repository: Repository) -> DbRepository: return self.test_db_util.get_repository_by_name_and_owner(repository.name, repository.owner) def get_repository_metadata(self, repository: Repository): return self.get_repository_metadata_for_db_object(self._db_repository(repository)) def get_repository_metadata_for_db_object(self, repository: DbRepository): return list(repository.metadata_revisions) def get_repository_metadata_by_changeset_revision(self, repository_id: int, changeset_revision): return test_db_util.get_repository_metadata_by_repository_id_changeset_revision( repository_id, changeset_revision ) or test_db_util.get_repository_metadata_by_repository_id_changeset_revision(repository_id, None) def get_repository_metadata_revisions(self, repository: Repository) -> list[str]: return [ str(repository_metadata.changeset_revision) for repository_metadata in self._db_repository(repository).metadata_revisions ] def _get_repository_by_name_and_owner(self, name: str, owner: str) -> Repository: repo = self.populator.get_repository_for(owner, name) if repo is None: repo = self.populator.get_repository_for(owner, name, deleted="true") assert repo return repo def get_repository_tip(self, repository: Repository) -> str: repo = self.get_hg_repo(self.get_repo_path(repository)) return str(repo[repo.changelog.tip()]) def get_repository_first_revision(self, repository: Repository) -> str: repo = self.get_hg_repo(self.get_repo_path(repository)) return str(repo[0]) def _get_metadata_revision_count(self, repository: Repository) -> int: repository_metadata: RepositoryMetadata = self.populator.get_metadata(repository, downloadable_only=False) return len(repository_metadata.root) def get_tools_from_repository_metadata(self, repository, include_invalid=False): """Get a list of valid and (optionally) invalid tool dicts from the repository metadata.""" valid_tools = [] invalid_tools = [] for repository_metadata in repository.metadata_revisions: if "tools" in repository_metadata.metadata: valid_tools.append( dict( tools=repository_metadata.metadata["tools"], changeset_revision=repository_metadata.changeset_revision, ) ) if include_invalid and "invalid_tools" in repository_metadata.metadata: invalid_tools.append( dict( tools=repository_metadata.metadata["invalid_tools"], changeset_revision=repository_metadata.changeset_revision, ) ) return valid_tools, invalid_tools def grant_write_access( self, repository: Repository, usernames=None, strings_displayed=None, strings_not_displayed=None, post_submit_strings_displayed=None, post_submit_strings_not_displayed=None, ): usernames = usernames or [] self.display_manage_repository_page(repository) self.check_for_strings(strings_displayed, strings_not_displayed) self._browser.grant_users_access(usernames) self.check_for_strings(post_submit_strings_displayed, post_submit_strings_not_displayed) def _install_repository( self, name: str, owner: str, category_name: str, install_tool_dependencies: bool = False, install_repository_dependencies: bool = True, changeset_revision: Optional[str] = None, preview_strings_displayed: Optional[list[str]] = None, new_tool_panel_section_label: Optional[str] = None, ) -> None: self.browse_tool_shed(url=self.url) category = self.populator.get_category_with_name(category_name) self.browse_category(category) self.preview_repository_in_tool_shed(name, owner, strings_displayed=preview_strings_displayed) repository = self._get_repository_by_name_and_owner(name, owner) assert repository # repository_id = repository.id if changeset_revision is None: changeset_revision = self.get_repository_tip(repository) assert self._installation_client self._installation_client.install_repository( name, owner, changeset_revision, install_tool_dependencies, install_repository_dependencies, new_tool_panel_section_label, ) def load_citable_url( self, 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, ): strings_displayed_in_iframe = strings_displayed_in_iframe or [] strings_not_displayed_in_iframe = strings_not_displayed_in_iframe or [] url = f"{self.url}/view/{username}" # If repository name is passed in, append that to the url. if repository_name: url += f"/{repository_name}" if changeset_revision: # Changeset revision should never be provided unless repository name also is. assert repository_name is not None, "Changeset revision is present, but repository name is not - aborting." url += f"/{changeset_revision}" # I think pagination broke this legacy test - so I added this url += "?rows_per_page=250" self.visit_url(url) self.check_for_strings(strings_displayed, strings_not_displayed) self.check_for_strings(strings_displayed_in_iframe, strings_not_displayed_in_iframe) def load_changeset_in_tool_shed( self, repository_id, changeset_revision, strings_displayed=None, strings_not_displayed=None ): # Verify changeset exists via HG repo directly populator = self._logged_in_populator or self.populator repository = populator.get_repository(repository_id) repo = self.get_hg_repo(self.get_repo_path(repository)) found = any(str(repo[cs]) == changeset_revision for cs in repo.changelog) assert found, f"Changeset {changeset_revision} not found" def load_checkable_revisions(self, strings_displayed=None, strings_not_displayed=None): params = { "do_not_test": "false", "downloadable": "true", "includes_tools": "true", "malicious": "false", "missing_test_components": "false", "skip_tool_test": "false", } self.visit_url("/api/repository_revisions", params=params) self.check_for_strings(strings_displayed, strings_not_displayed) def preview_repository_in_tool_shed( self, name: str, owner: str, changeset_revision: Optional[str] = None, strings_displayed=None, strings_not_displayed=None, ): repository = self._get_repository_by_name_and_owner(name, owner) assert repository if not changeset_revision: changeset_revision = self.get_repository_tip(repository) db_repository = self._db_repository(repository) repository_metadata = self.get_repository_metadata_by_changeset_revision(db_repository.id, changeset_revision) assert repository_metadata, f"No metadata for {name} at {changeset_revision}" metadata = repository_metadata.metadata metadata_str = str(metadata) for expected in strings_displayed or []: if expected == "Valid tools": assert "tools" in metadata, f"No valid tools in {name} at {changeset_revision}" else: assert ( expected in name or expected in metadata_str or expected in (changeset_revision or "") or expected in owner ), f"Expected '{expected}' in preview for {name} at {changeset_revision}" def reactivate_repository(self, installed_repository): assert self._installation_client self._installation_client.reactivate_repository(installed_repository) def reinstall_repository_api( self, installed_repository, install_repository_dependencies=True, install_tool_dependencies=False, new_tool_panel_section_label="", ): name = installed_repository.name owner = installed_repository.owner assert self._installation_client self._installation_client.install_repository( name, owner, installed_repository.installed_changeset_revision, install_tool_dependencies, install_repository_dependencies, new_tool_panel_section_label, ) def repository_is_new(self, repository: Repository) -> bool: repo = self.get_hg_repo(self.get_repo_path(repository)) tip_ctx = repo[repo.changelog.tip()] return tip_ctx.rev() < 0 def reset_metadata_on_selected_repositories(self, repository_ids): for repository_id in repository_ids: self.populator.reset_metadata(repository_id) def reset_metadata_on_installed_repositories(self, repositories): assert self._installation_client self._installation_client.reset_metadata_on_installed_repositories(repositories) def reset_repository_metadata(self, repository): populator = self._logged_in_populator or self.populator populator.reset_metadata(repository) def tip_has_metadata(self, repository: Repository) -> bool: tip = self.get_repository_tip(repository) db_repository = self._db_repository(repository) return test_db_util.get_repository_metadata_by_repository_id_changeset_revision(db_repository.id, tip) def _uninstall_repository(self, installed_repository: galaxy_model.ToolShedRepository) -> None: assert self._installation_client self._installation_client.uninstall_repository(installed_repository) def update_installed_repository( self, installed_repository: galaxy_model.ToolShedRepository, verify_no_updates: bool = False ) -> dict[str, Any]: assert self._installation_client return self._installation_client.update_installed_repository(installed_repository, verify_no_updates=False) def verify_installed_repositories(self, installed_repositories=None, uninstalled_repositories=None): installed_repositories = installed_repositories or [] uninstalled_repositories = uninstalled_repositories or [] for repository_name, repository_owner in installed_repositories: galaxy_repository = self._get_installed_repository_by_name_owner(repository_name, repository_owner) if galaxy_repository: assert ( galaxy_repository.status == "Installed" ), f"Repository {repository_name} should be installed, but is {galaxy_repository.status}" def verify_installed_repository_metadata_unchanged(self, name, owner): installed_repository = self._get_installed_repository_by_name_owner(name, owner) assert installed_repository metadata = installed_repository.metadata_ assert self._installation_client self._installation_client.reset_installed_repository_metadata(installed_repository) new_metadata = installed_repository.metadata_ assert metadata == new_metadata, f"Metadata for installed repository {name} differs after metadata reset." def verify_installed_repository_no_tool_panel_section(self, repository): """Verify that there is no 'tool_panel_section' entry in the repository metadata.""" metadata = repository.metadata_ assert "tool_panel_section" not in metadata, f"Tool panel section incorrectly found in metadata: {metadata}" @property def shed_tool_data_table_conf(self): assert self._installation_client return self._installation_client.shed_tool_data_table_conf @property def tool_data_path(self): assert self._installation_client return self._installation_client.tool_data_path def _refresh_tool_shed_repository(self, repo: galaxy_model.ToolShedRepository) -> None: assert self._installation_client self._installation_client.refresh_tool_shed_repository(repo) def verify_installed_repository_data_table_entries(self, required_data_table_entries): # The value of the received required_data_table_entries will be something like: [ 'sam_fa_indexes' ] shed_tool_data_table_conf = self.shed_tool_data_table_conf data_tables, error_message = xml_util.parse_xml(shed_tool_data_table_conf) with open(shed_tool_data_table_conf) as f: shed_tool_data_table_conf_contents = f.read() assert ( not error_message ), f"Failed to parse {shed_tool_data_table_conf} properly. File contents [{shed_tool_data_table_conf_contents}]" found = False # With the tool shed, the "path" attribute that is hard-coded into the tool_data_tble_conf.xml # file is ignored. This is because the tool shed requires the directory location to which this # path points to be empty except when a specific tool is loaded. The default location for this # directory configured for the tool shed is /shed-tool-data. When a tool is loaded # in the tool shed, all contained .loc.sample files are copied to this directory and the # ToolDataTableManager parses and loads the files in the same way that Galaxy does with a very # important exception. When the tool shed loads a tool and parses and loads the copied ,loc.sample # files, the ToolDataTableManager is already instantiated, and so its add_new_entries_from_config_file() # method is called and the tool_data_path parameter is used to over-ride the hard-coded "tool-data" # directory that Galaxy always uses. # # Tool data table xml structure: # # # line_type, value, path # #
# required_data_table_entry = None assert data_tables is not None for table_elem in data_tables.findall("table"): # The value of table_elem will be something like: for required_data_table_entry in required_data_table_entries: # The value of required_data_table_entry will be something like: 'sam_fa_indexes' if "name" in table_elem.attrib and table_elem.attrib["name"] == required_data_table_entry: found = True # We're processing something like: sam_fa_indexes file_elem = table_elem.find("file") # We have something like: # The "path" attribute of the "file" tag is the location that Galaxy always uses because the # Galaxy ToolDataTableManager was implemented in such a way that the hard-coded path is used # rather than allowing the location to be a configurable setting like the tool shed requires. file_path = file_elem.get("path", None) if file_elem is not None else None # The value of file_path will be something like: "tool-data/all_fasta.loc" assert ( file_path is not None ), f'The "path" attribute is missing for the {required_data_table_entry} entry.' # The following test is probably not necesary, but the tool-data directory should exist! galaxy_tool_data_dir, loc_file_name = os.path.split(file_path) assert ( galaxy_tool_data_dir is not None ), f"The hard-coded Galaxy tool-data directory is missing for the {required_data_table_entry} entry." assert os.path.exists(galaxy_tool_data_dir), "The Galaxy tool-data directory does not exist." # Make sure the loc_file_name was correctly copied into the configured directory location. configured_file_location = os.path.join(self.tool_data_path, loc_file_name) assert os.path.isfile( configured_file_location ), f'The expected copied file "{configured_file_location}" is missing.' # We've found the value of the required_data_table_entry in data_tables, which is the parsed # shed_tool_data_table_conf.xml, so all is well! break if found: break # We better have an entry like:
in our parsed data_tables # or we know that the repository was not correctly installed! if not found: if required_data_table_entry is None: raise AssertionError( f"No tables found in {shed_tool_data_table_conf}. File contents {shed_tool_data_table_conf_contents}" ) else: raise AssertionError( f"No entry for {required_data_table_entry} in {shed_tool_data_table_conf}. File contents {shed_tool_data_table_conf_contents}" ) def _get_installed_repository_by_name_owner( self, repository_name: str, repository_owner: str ) -> galaxy_model.ToolShedRepository: assert self._installation_client return self._installation_client.get_installed_repository_by_name_owner(repository_name, repository_owner) def _get_installed_repositories_by_name_owner( self, repository_name: str, repository_owner: str ) -> list[galaxy_model.ToolShedRepository]: assert self._installation_client return self._installation_client.get_installed_repositories_by_name_owner(repository_name, repository_owner) def _get_installed_repository_for( self, owner: Optional[str] = None, name: Optional[str] = None, changeset: Optional[str] = None ): assert self._installation_client return self._installation_client.get_installed_repository_for(owner=owner, name=name, changeset=changeset) def _assert_has_installed_repos_with_names(self, *names): for name in names: assert self._get_installed_repository_for(name=name) def _assert_has_no_installed_repos_with_names(self, *names): for name in names: assert not self._get_installed_repository_for(name=name) def _assert_has_missing_dependency( self, installed_repository: galaxy_model.ToolShedRepository, repository_name: str ) -> None: json = self.display_installed_repository_manage_json(installed_repository) assert ( "missing_repository_dependencies" in json ), f"Expecting missing dependency {repository_name} but no missing dependencies found." missing_repository_dependencies = json["missing_repository_dependencies"] folder = missing_repository_dependencies["folders"][0] assert "repository_dependencies" in folder rds = folder["repository_dependencies"] found_missing_repository_dependency = False missing_repos = set() for rd in rds: missing_repos.add(rd["repository_name"]) if rd["repository_name"] == repository_name: found_missing_repository_dependency = True assert ( found_missing_repository_dependency ), f"Expecting missing dependency {repository_name} but the missing repositories were {missing_repos}." def _assert_has_installed_repository_dependency( self, installed_repository: galaxy_model.ToolShedRepository, repository_name: str, changeset: Optional[str] = None, ) -> None: json = self.display_installed_repository_manage_json(installed_repository) if "repository_dependencies" not in json: name = installed_repository.name raise AssertionError(f"No repository dependencies were defined in {name}. manage json is {json}") repository_dependencies = json["repository_dependencies"] found = False for folder in repository_dependencies.get("folders"): for rd in folder["repository_dependencies"]: if rd["repository_name"] != repository_name: continue if changeset and rd["changeset_revision"] != changeset: continue found = True break assert found, f"Failed to find target repository dependency in {json}" def _assert_is_not_missing_dependency( self, installed_repository: galaxy_model.ToolShedRepository, repository_name: str ) -> None: json = self.display_installed_repository_manage_json(installed_repository) if "missing_repository_dependencies" not in json: return missing_repository_dependencies = json["missing_repository_dependencies"] folder = missing_repository_dependencies["folders"][0] assert "repository_dependencies" in folder rds = folder["repository_dependencies"] found_missing_repository_dependency = False for rd in rds: if rd["repository_name"] == repository_name: found_missing_repository_dependency = True assert not found_missing_repository_dependency def _assert_has_valid_tool_with_name(self, tool_name: str) -> None: def assert_has(): assert self._installation_client tool_names = self._installation_client.get_tool_names() assert tool_name in tool_names # May need to wait on toolbox reload. wait_on_assertion(assert_has, f"toolbox to contain {tool_name}", 10) def _assert_repo_has_tool_with_id( self, installed_repository: galaxy_model.ToolShedRepository, tool_id: str ) -> None: assert "tools" in installed_repository.metadata_, f"No valid tools were defined in {installed_repository.name}." tools = installed_repository.metadata_["tools"] found_it = False for tool in tools: # type: ignore[attr-defined] if "id" not in tool: continue if tool["id"] == tool_id: found_it = True break assert found_it, f"Did not find valid tool with name {tool_id} in {tools}" def _assert_repo_has_invalid_tool_in_file( self, installed_repository: galaxy_model.ToolShedRepository, name: str ) -> None: assert ( "invalid_tools" in installed_repository.metadata_ ), f"No invalid tools were defined in {installed_repository.name}." invalid_tools = installed_repository.metadata_["invalid_tools"] found_it = name in invalid_tools assert found_it, f"Did not find invalid tool file {name} in {invalid_tools}" def verify_unchanged_repository_metadata(self, repository: Repository): old_metadata = {} new_metadata = {} for metadata in self.get_repository_metadata(repository): old_metadata[metadata.changeset_revision] = metadata.metadata self.reset_repository_metadata(repository) for metadata in self.get_repository_metadata(repository): new_metadata[metadata.changeset_revision] = metadata.metadata # Python's dict comparison recursively compares sorted key => value pairs and returns true if any key or value differs, # or if the number of keys differs. assert old_metadata == new_metadata, f"Metadata changed after reset on repository {repository.name}." def _wait_for_installation(repository: galaxy_model.ToolShedRepository, refresh): final_states = [ galaxy_model.ToolShedRepository.installation_status.ERROR, galaxy_model.ToolShedRepository.installation_status.INSTALLED, ] # Wait until all repositories are in a final state before returning. This ensures that subsequent tests # are running against an installed repository, and not one that is still in the process of installing. timeout_counter = 0 while repository.status not in final_states: refresh(repository) timeout_counter = timeout_counter + 1 # This timeout currently defaults to 10 minutes. if timeout_counter > repository_installation_timeout: raise AssertionError( f"Repository installation timed out, {timeout_counter} seconds elapsed, repository state is {repository.status}." ) time.sleep(1) def _get_tool_panel_section_from_repository_metadata(metadata): tool_metadata = metadata["tools"] tool_guid = tool_metadata[0]["guid"] assert "tool_panel_section" in metadata, f"Tool panel section not found in metadata: {metadata}" tool_panel_section_metadata = metadata["tool_panel_section"] tool_panel_section = tool_panel_section_metadata[tool_guid][0]["name"] return tool_panel_section def get_installed_repository(session, name, owner, changeset): ToolShedRepository = galaxy_model.ToolShedRepository stmt = select(ToolShedRepository) if name is not None: stmt = stmt.where(ToolShedRepository.name == name) if owner is not None: stmt = stmt.where(ToolShedRepository.owner == owner) if changeset is not None: stmt = stmt.where(ToolShedRepository.changeset_revision == changeset) stmt = stmt.where(ToolShedRepository.deleted == false()) stmt = stmt.where(ToolShedRepository.uninstalled == false()) return session.scalars(stmt).one_or_none()