Source code for toil.test.utils.toilDebugTest

# Copyright (C) 2015-2021 Regents of the University of California
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.
import logging
import os
import subprocess
import tempfile

import pytest

from toil.lib.resources import glob
from toil.test import slow
from toil.version import python

logger = logging.getLogger(__name__)

[docs] def workflow_debug_jobstore() -> str: job_store_path = os.path.join(tempfile.mkdtemp(), "toilWorkflowRun") subprocess.check_call( [ python, os.path.abspath("src/toil/test/utils/ABCWorkflowDebug/"), job_store_path, ] ) return job_store_path
[docs] @slow def testJobStoreContents(): """ Test toilDebugFile.printContentsOfJobStore(). Runs a workflow that imports 'B.txt' and '' into the jobStore. 'A.txt', 'C.txt', 'ABC.txt' are then created. This checks to make sure these contents are found in the jobStore and printed. """ contents = ["A.txt", "B.txt", "C.txt", "ABC.txt", ""] subprocess.check_call( [ python, os.path.abspath("src/toil/utils/"), workflow_debug_jobstore(), "--logDebug", "--listFilesInJobStore=True", ] ) jobstoreFileContents = os.path.abspath("jobstore_files.txt") files = [] match = 0 with open(jobstoreFileContents) as f: for line in f: files.append(line.strip()) for xfile in files: for expected_file in contents: if xfile.endswith(expected_file): match = match + 1 logger.debug(files) logger.debug(contents) logger.debug(match) # C.txt will match twice (once with 'C.txt', and once with 'ABC.txt') assert match == 6 os.remove(jobstoreFileContents)
[docs] def fetchFiles(symLink: bool, jobStoreDir: str, outputDir: str): """ Fn for testFetchJobStoreFiles() and testFetchJobStoreFilesWSymlinks(). Runs a workflow that imports 'B.txt' and '' into the jobStore. 'A.txt', 'C.txt', 'ABC.txt' are then created. This test then attempts to get a list of these files and copy them over into our output diectory from the jobStore, confirm that they are present, and then delete them. """ contents = ["A.txt", "B.txt", "C.txt", "ABC.txt", ""] cmd = [ python, os.path.abspath("src/toil/utils/"), jobStoreDir, "--fetch", "*A.txt", "*B.txt", "*C.txt", "*ABC.txt", "*", f"--localFilePath={outputDir}", f"--useSymlinks={symLink}", ] print(cmd) subprocess.check_call(cmd) for xfile in contents: matchingFilesFound = glob(glob_pattern="*" + xfile, directoryname=outputDir) assert len(matchingFilesFound) >= 1 for fileFound in matchingFilesFound: assert fileFound.endswith(xfile) and os.path.exists(fileFound) if fileFound.endswith("-" + xfile): os.remove(fileFound)
# expected run time = 4s
[docs] def testFetchJobStoreFiles() -> None: """Test toilDebugFile.fetchJobStoreFiles() symlinks.""" job_store_dir = workflow_debug_jobstore() output_dir = os.path.join(os.path.dirname(job_store_dir), "testoutput") os.makedirs(output_dir, exist_ok=True) for symlink in (True, False): fetchFiles(symLink=symlink, jobStoreDir=job_store_dir, outputDir=output_dir)