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Source code for galaxy.tool_util.verify.script

#!/usr/bin/env python

import argparse
import concurrent.futures.thread
import datetime as dt
import json
import logging
import os
import sys
import tempfile
from concurrent.futures import (
    thread,
    ThreadPoolExecutor,
)
from typing import (
    Any,
    Callable,
    Dict,
    List,
    NamedTuple,
    Optional,
)

import yaml

from galaxy.tool_util.verify.interactor import (
    DictClientTestConfig,
    GalaxyInteractorApi,
    verify_tool,
)

DESCRIPTION = """Script to quickly run a tool test against a running Galaxy instance."""
DEFAULT_SUITE_NAME = "Galaxy Tool Tests"
ALL_TESTS = -1
ALL_TOOLS = "*"
ALL_VERSION = "*"
LATEST_VERSION = None


[docs]class TestReference(NamedTuple): tool_id: str tool_version: Optional[str] test_index: int
[docs]class TestException(NamedTuple): tool_id: str exception: Exception was_recorded: bool
[docs]class Results: test_exceptions: List[TestException]
[docs] def __init__( self, default_suitename: str, test_json: str, append: bool = False, galaxy_url: Optional[str] = None ) -> None: self.test_json = test_json or "-" self.galaxy_url = galaxy_url test_results = [] suitename = default_suitename if append: assert test_json != "-" with open(test_json) as f: previous_results = json.load(f) test_results = previous_results["tests"] if "suitename" in previous_results: suitename = previous_results["suitename"] self.test_results = test_results self.test_exceptions = [] self.suitename = suitename
[docs] def register_result(self, result: Dict[str, Any]) -> None: self.test_results.append(result)
[docs] def register_exception(self, test_exception: TestException) -> None: self.test_exceptions.append(test_exception)
[docs] def already_successful(self, test_reference: TestReference) -> bool: test_data = self._previous_test_data(test_reference) if test_data: if "status" in test_data and test_data["status"] == "success": return True return False
[docs] def already_executed(self, test_reference: TestReference) -> bool: test_data = self._previous_test_data(test_reference) if test_data: if "status" in test_data and test_data["status"] != "skipped": return True return False
def _previous_test_data(self, test_reference: TestReference) -> Optional[Dict[str, Any]]: test_id = _test_id_for_reference(test_reference) for test_result in self.test_results: if test_result.get("id") != test_id: continue has_data = test_result.get("has_data", False) if has_data: test_data = test_result.get("data", {}) return test_data return None
[docs] def write(self) -> None: tests = sorted(self.test_results, key=lambda el: el["id"]) n_passed, n_failures, n_skips = 0, 0, 0 n_errors = len([e for e in self.test_exceptions if not e.was_recorded]) for test in tests: has_data = test.get("has_data", False) if has_data: test_data = test.get("data", {}) if "status" not in test_data: raise Exception(f"Test result data {test_data} doesn't contain a status key.") status = test_data["status"] if status == "success": n_passed += 1 elif status == "error": n_errors += 1 elif status == "skip": n_skips += 1 elif status == "failure": n_failures += 1 report_obj = { "version": "0.1", "suitename": self.suitename, "results": { "total": n_passed + n_failures + n_skips + n_errors, "errors": n_errors, "failures": n_failures, "skips": n_skips, }, "tests": tests, } if self.galaxy_url: report_obj["galaxy_url"] = self.galaxy_url if self.test_json == "-": print(json.dumps(report_obj)) else: with open(self.test_json, "w") as f: json.dump(report_obj, f)
[docs] def info_message(self) -> str: messages = [] passed_tests = self._tests_with_status("success") messages.append("Passed tool tests ({}): {}".format(len(passed_tests), [t["id"] for t in passed_tests])) failed_tests = self._tests_with_status("failure") messages.append("Failed tool tests ({}): {}".format(len(failed_tests), [t["id"] for t in failed_tests])) skipped_tests = self._tests_with_status("skip") messages.append("Skipped tool tests ({}): {}".format(len(skipped_tests), [t["id"] for t in skipped_tests])) errored_tests = self._tests_with_status("error") messages.append("Errored tool tests ({}): {}".format(len(errored_tests), [t["id"] for t in errored_tests])) return "\n".join(messages)
def _tests_with_status(self, status: str) -> List[Dict[str, Any]]: return [t for t in self.test_results if t.get("data", {}).get("status") == status]
[docs]def test_tools( galaxy_interactor: GalaxyInteractorApi, test_references: List[TestReference], results: Results, log: Optional[logging.Logger] = None, parallel_tests: int = 1, history_per_test_case: bool = False, history_name: Optional[str] = None, no_history_reuse: bool = False, no_history_cleanup: bool = False, publish_history: bool = False, retries: int = 0, verify_kwds: Optional[Dict[str, Any]] = None, ) -> None: """Run through tool tests and write report.""" verify_kwds = (verify_kwds or {}).copy() tool_test_start = dt.datetime.now() history_created = False test_history = None if not history_per_test_case: if not history_name: history_name = f"History for {results.suitename}" if log: log.info(f"History name is '{history_name}'") if not no_history_reuse: history = galaxy_interactor.get_history(history_name=history_name) if history: test_history = history["id"] if log: log.info(f"Using existing history with id '{test_history}', last updated: {history['update_time']}") if not test_history: history_created = True test_history = galaxy_interactor.new_history(history_name=history_name, publish_history=publish_history) if log: log.info(f"History created with id '{test_history}'") verify_kwds.update( { "no_history_cleanup": no_history_cleanup, "test_history": test_history, } ) with ThreadPoolExecutor(max_workers=parallel_tests) as executor: try: for test_reference in test_references: _test_tool( executor=executor, test_reference=test_reference, results=results, galaxy_interactor=galaxy_interactor, log=log, retries=retries, verify_kwds=verify_kwds, publish_history=publish_history, ) finally: # Always write report, even if test was cancelled. try: executor.shutdown(wait=True) except KeyboardInterrupt: executor._threads.clear() # type: ignore[attr-defined] thread._threads_queues.clear() # type: ignore[attr-defined] results.write() if log: if results.test_json == "-": destination = "standard output" else: destination = os.path.abspath(results.test_json) log.info(f"Report written to '{destination}'") log.info(results.info_message()) log.info(f"Total tool test time: {dt.datetime.now() - tool_test_start}") if history_created and not no_history_cleanup: galaxy_interactor.delete_history(test_history)
def _test_id_for_reference(test_reference: "TestReference") -> str: tool_id = test_reference.tool_id tool_version = test_reference.tool_version test_index = test_reference.test_index if tool_version and tool_id.endswith(f"/{tool_version}"): tool_id = tool_id[: -len(f"/{tool_version}")] label_base = tool_id if tool_version: label_base += f"/{str(tool_version)}" test_id = f"{label_base}-{str(test_index)}" return test_id def _test_tool( executor: concurrent.futures.thread.ThreadPoolExecutor, test_reference: "TestReference", results: Results, galaxy_interactor: GalaxyInteractorApi, log: Optional[logging.Logger], retries: int, publish_history: bool, verify_kwds: Dict[str, Any], ) -> None: tool_id = test_reference.tool_id tool_version = test_reference.tool_version test_index = test_reference.test_index # If given a tool_id with a version suffix, strip it off so we can treat tool_version # correctly at least in client_test_config. if tool_version and tool_id.endswith(f"/{tool_version}"): tool_id = tool_id[: -len(f"/{tool_version}")] test_id = _test_id_for_reference(test_reference) def run_test() -> None: run_retries = retries job_data = None job_exception = None def register(job_data_): nonlocal job_data job_data = job_data_ try: while run_retries >= 0: job_exception = None try: if log: log.info("Executing test '%s'", test_id) verify_tool( tool_id, galaxy_interactor, test_index=test_index, tool_version=tool_version, register_job_data=register, publish_history=publish_history, **verify_kwds, ) if log: log.info("Test '%s' passed", test_id) break except Exception as e: if log: log.warning("Test '%s' failed", test_id, exc_info=True) job_exception = e run_retries -= 1 finally: if job_data is not None: results.register_result( { "id": test_id, "has_data": True, "data": job_data, } ) if job_exception is not None: was_recorded = job_data is not None test_exception = TestException(tool_id, job_exception, was_recorded) results.register_exception(test_exception) executor.submit(run_test)
[docs]def build_case_references( galaxy_interactor: GalaxyInteractorApi, tool_id: str = ALL_TOOLS, tool_version: Optional[str] = LATEST_VERSION, test_index: int = ALL_TESTS, page_size: int = 0, page_number: int = 0, test_filters: Optional[List[Callable[[TestReference], bool]]] = None, log: Optional[logging.Logger] = None, ) -> List[TestReference]: test_references: List[TestReference] = [] if tool_id == ALL_TOOLS: tests_summary = galaxy_interactor.get_tests_summary() for tool_id, tool_versions_dict in tests_summary.items(): for tool_version, summary in tool_versions_dict.items(): for test_index in range(summary["count"]): test_reference = TestReference(tool_id, tool_version, test_index) test_references.append(test_reference) else: tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version) for i, tool_test_dict in enumerate(tool_test_dicts): this_tool_version = tool_test_dict.get("tool_version", tool_version) this_test_index = i if test_index == ALL_TESTS or i == test_index: test_reference = TestReference(tool_id, this_tool_version, this_test_index) test_references.append(test_reference) if test_filters is not None and len(test_filters) > 0: filtered_test_references: List[TestReference] = [] for test_reference in test_references: skip_test = False for test_filter in test_filters: if test_filter(test_reference): if log is not None: log.debug(f"Filtering test for {test_reference}, skipping") skip_test = True if not skip_test: filtered_test_references.append(test_reference) if log is not None: log.info( f"Skipping {len(test_references)-len(filtered_test_references)} out of {len(test_references)} tests." ) test_references = filtered_test_references if page_size > 0: slice_start = page_size * page_number slice_end = page_size * (page_number + 1) test_references = test_references[slice_start:slice_end] return test_references
[docs]def main(argv=None) -> None: if argv is None: argv = sys.argv[1:] args = arg_parser().parse_args(argv) try: run_tests(args) except Exception as exc: print(f"ERROR: {exc}", file=sys.stderr) sys.exit(1)
[docs]def run_tests( args: argparse.Namespace, test_filters: Optional[List[Callable[[TestReference], bool]]] = None, log: Optional[logging.Logger] = None, ) -> None: # Split out argument parsing so we can quickly build other scripts - such as a script # to run all tool tests for a workflow by just passing in a custom test_filters. test_filters = test_filters or [] log = log or setup_global_logger(__name__, verbose=args.verbose) client_test_config_path = args.client_test_config if client_test_config_path is not None: log.debug(f"Reading client config path {client_test_config_path}") with open(client_test_config_path) as f: client_test_config = yaml.full_load(f) else: client_test_config = {} def get_option(key): arg_val = getattr(args, key, None) if arg_val is None and key in client_test_config: val = client_test_config.get(key) else: val = arg_val return val output_json_path = get_option("output_json") galaxy_url = get_option("galaxy_url") galaxy_interactor_kwds = { "galaxy_url": galaxy_url, "master_api_key": get_option("admin_key"), "api_key": get_option("key"), "keep_outputs_dir": args.output, "download_attempts": get_option("download_attempts"), "download_sleep": get_option("download_sleep"), "test_data": get_option("test_data"), } tool_id = args.tool_id tool_version = args.tool_version tools_client_test_config = DictClientTestConfig(client_test_config.get("tools")) verbose = args.verbose galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds) results = Results(args.suite_name, output_json_path, append=args.append, galaxy_url=galaxy_url) skip = args.skip if skip == "executed": test_filters.append(results.already_executed) elif skip == "successful": test_filters.append(results.already_successful) test_references = build_case_references( galaxy_interactor, tool_id=tool_id, tool_version=tool_version, test_index=args.test_index, page_size=args.page_size, page_number=args.page_number, test_filters=test_filters, log=log, ) log.debug(f"Built {len(test_references)} test references to executed.") verify_kwds = dict( client_test_config=tools_client_test_config, force_path_paste=args.force_path_paste, skip_with_reference_data=not args.with_reference_data, quiet=not verbose, ) test_tools( galaxy_interactor, test_references, results, log=log, parallel_tests=args.parallel_tests, history_per_test_case=args.history_per_test_case, history_name=args.history_name, no_history_reuse=args.no_history_reuse, no_history_cleanup=args.no_history_cleanup, publish_history=get_option("publish_history"), verify_kwds=verify_kwds, ) exceptions = results.test_exceptions if exceptions: exception = exceptions[0] raise exception.exception
[docs]def setup_global_logger(name: str, log_file: Optional[str] = None, verbose: bool = False) -> logging.Logger: formatter = logging.Formatter("%(asctime)s %(levelname)-5s - %(message)s") console = logging.StreamHandler() console.setFormatter(formatter) logger = logging.getLogger(name) logger.setLevel(logging.DEBUG if verbose else logging.INFO) logger.addHandler(console) if not log_file: # delete = false is chosen here because it is always nice to have a log file # ready if you need to debug. Not having the "if only I had set a log file" # moment after the fact. temp = tempfile.NamedTemporaryFile(prefix="ephemeris_", delete=False) log_file = temp.name file_handler = logging.FileHandler(log_file) logger.addHandler(file_handler) logger.info(f"Storing log file in: {log_file}") return logger
[docs]def arg_parser() -> argparse.ArgumentParser: parser = argparse.ArgumentParser(description=DESCRIPTION) parser.add_argument("-u", "--galaxy-url", default="http://localhost:8080", help="Galaxy URL") parser.add_argument("-k", "--key", default=None, help="Galaxy User API Key") parser.add_argument("-a", "--admin-key", default=None, help="Galaxy Admin API Key") parser.add_argument( "--force_path_paste", default=False, action="store_true", help='This requires Galaxy-side config option "allow_path_paste" enabled. Allows for fetching test data locally. Only for admins.', ) parser.add_argument("-t", "--tool-id", default=ALL_TOOLS, help="Tool ID") parser.add_argument( "--tool-version", default=None, help="Tool Version (if tool id supplied). Defaults to just latest version, use * to test all versions", ) parser.add_argument( "-i", "--test-index", default=ALL_TESTS, type=int, help="Tool Test Index (starting at 0) - by default all tests will run.", ) parser.add_argument("-o", "--output", default=None, help="directory to dump outputs to") parser.add_argument( "--append", default=False, action="store_true", help="Extend a test record json (created with --output-json) with additional tests.", ) skip_group = parser.add_mutually_exclusive_group() skip_group.add_argument( "--skip-previously-executed", dest="skip", default="no", action="store_const", const="executed", help="When used with --append, skip any test previously executed.", ) skip_group.add_argument( "--skip-previously-successful", dest="skip", default="no", action="store_const", const="successful", help="When used with --append, skip any test previously executed successfully.", ) parser.add_argument("-j", "--output-json", default=None, help="output metadata json") parser.add_argument("--verbose", default=False, action="store_true", help="Verbose logging.") parser.add_argument("-c", "--client-test-config", default=None, help="Test config YAML to help with client testing") parser.add_argument("--suite-name", default=DEFAULT_SUITE_NAME, help="Suite name for tool test output") parser.add_argument("--with-reference-data", dest="with_reference_data", default=False, action="store_true") parser.add_argument( "--skip-with-reference-data", dest="with_reference_data", action="store_false", help="Skip tests the Galaxy server believes use data tables or loc files.", ) history_per_group = parser.add_mutually_exclusive_group() history_per_group.add_argument( "--history-per-suite", dest="history_per_test_case", default=False, action="store_false", help="Create new history per test suite (all tests in same history).", ) history_per_group.add_argument( "--history-per-test-case", dest="history_per_test_case", action="store_true", help="Create new history per test case.", ) history_per_group.add_argument("--history-name", default=None, help="Override default history name") parser.add_argument( "--no-history-reuse", default=False, action="store_true", help="Do not reuse histories if a matching one already exists.", ) parser.add_argument( "--no-history-cleanup", default=False, action="store_true", help="Perserve histories created for testing." ) parser.add_argument( "--publish-history", default=False, action="store_true", help="Publish test history. Useful for CI testing." ) parser.add_argument("--parallel-tests", default=1, type=int, help="Parallel tests.") parser.add_argument("--retries", default=0, type=int, help="Retry failed tests.") parser.add_argument( "--page-size", default=0, type=int, help="If positive, use pagination and just run one 'page' to tool tests." ) parser.add_argument( "--page-number", default=0, type=int, help="If page size is used, run this 'page' of tests - starts with 0." ) parser.add_argument( "--download-attempts", default=1, type=int, help="Galaxy may return a transient 500 status code for download if test results are written but not yet accessible.", ) parser.add_argument( "--download-sleep", default=1, type=int, help="If download attempts is greater than 1, the amount to sleep between download attempts.", ) parser.add_argument("--test-data", action="append", help="Add local test data path to search for missing test data") return parser
if __name__ == "__main__": main()