def test_run_fails_cause_evaluation_is_not_found(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.evaluation = '/bin/doesnotexist'
params.pdbdb = '/data/pdb'
docktask = D3RTask(temp_dir, params)
docktask.set_name('foo')
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
evaluation.run()
self.assertEqual(
evaluation.get_error(), 'Caught Exception trying to run ' +
'/bin/doesnotexist --pdbdb /data/pdb ' + '--dockdir ' +
docktask.get_dir() + ' --outdir ' + evaluation.get_dir() +
' : [Errno 2] No such file or directory')
# test files get created
errfile = os.path.join(evaluation.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
finally:
shutil.rmtree(temp_dir)
def test_run_succeeds_no_emailer(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.evaluation = 'true'
params.pdbdb = '/data/pdb'
docktask = D3RTask(temp_dir, params)
docktask.set_name('foo')
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
evaluation.run()
self.assertEqual(evaluation.get_error(), None)
# test files get created
errfile = os.path.join(evaluation.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), False)
compfile = os.path.join(evaluation.get_dir(),
D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(compfile), True)
stderr = os.path.join(evaluation.get_dir(), 'true.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(evaluation.get_dir(), 'true.stdout')
self.assertEqual(os.path.isfile(stdout), True)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_evaluation_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.evaluation = 'false'
params.pdbdb = '/data/pdb'
docktask = D3RTask(temp_dir, params)
docktask.set_name('foo')
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
evaluation.run()
self.assertEqual(
evaluation.get_error(),
'Non zero exit code: 1 received. Standard out: ' +
' Standard error: ')
# test file gets created
errfile = os.path.join(evaluation.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
stderr = os.path.join(evaluation.get_dir(), 'false.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(evaluation.get_dir(), 'false.stdout')
self.assertEqual(os.path.isfile(stdout), True)
finally:
shutil.rmtree(temp_dir)
def test_get_all_evaluation_tasks(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
# no evaluation tasks
task = PostEvaluationTask(temp_dir, params)
res = task.get_all_evaluation_tasks()
self.assertEqual(len(res), 0)
# directory in path that does NOT match suffix
task.create_dir()
os.makedirs(os.path.join(temp_dir, 'stage.x.1'), mode=0o755)
res = task.get_all_evaluation_tasks()
self.assertEqual(len(res), 0)
# one task, but is file (weird case)
weirdtaskfile = os.path.join(
temp_dir, 'stage.7.hi.' + EvaluationTaskFactory.SCORING_SUFFIX)
open(weirdtaskfile, 'a').close()
res = task.get_all_evaluation_tasks()
self.assertEqual(len(res), 0)
self.assertEqual(
task.get_email_log(),
'Just a note, found a task with valid name, but '
'it is not a directory ' + weirdtaskfile)
# one task
etask = EvaluationTask(temp_dir, 'foo.evaluation', None, params)
etask.create_dir()
res = task.get_all_evaluation_tasks()
self.assertEqual(len(res), 1)
self.assertTrue(res[0].get_dir_name(), etask.get_dir_name())
# three tasks two with non complete status
etask2 = EvaluationTask(temp_dir,
'bla_dock.extsubmission.evaluation', None,
params)
etask2.create_dir()
open(os.path.join(etask2.get_dir(), D3RTask.ERROR_FILE),
'a').close()
etask3 = EvaluationTask(temp_dir, '12_x.extsubmission.evaluation',
None, params)
etask3.create_dir()
open(os.path.join(etask3.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
res = task.get_all_evaluation_tasks()
self.assertEqual(len(res), 3)
d_name_list = []
for entry in res:
d_name_list.append(entry.get_dir_name())
self.assertTrue(etask.get_dir_name() in d_name_list)
self.assertTrue(etask2.get_dir_name() in d_name_list)
self.assertTrue(etask3.get_dir_name() in d_name_list)
finally:
shutil.rmtree(temp_dir)
def test_run_succeeds_with_emailer(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.evaluation = 'true'
params.pdbdb = '/data/pdb'
docktask = D3RTask(temp_dir, params)
docktask.set_name('12345' + EvaluationTask.EXT_SUBMISSION_SUFFIX)
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
evaluation = EvaluationTask(temp_dir, docktask.get_name(),
docktask, params)
plist = [
Participant('1name', '1d3rusername', '12345',
'[email protected],[email protected]')
]
smtpemailer = SmtpEmailer()
mockserver = D3RParameters()
mockserver.sendmail = Mock()
mockserver.quit = Mock()
smtpemailer.set_alternate_smtp_server(mockserver)
emailer = EvaluationEmailer(ParticipantDatabase(plist), None)
emailer.set_alternate_smtp_emailer(smtpemailer)
evaluation.set_evaluation_emailer(emailer)
evaluation.run()
self.assertEqual(evaluation.get_error(), None)
# test files get created
errfile = os.path.join(evaluation.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), False)
compfile = os.path.join(evaluation.get_dir(),
D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(compfile), True)
stderr = os.path.join(evaluation.get_dir(), 'true.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(evaluation.get_dir(), 'true.stdout')
self.assertEqual(os.path.isfile(stdout), True)
res = evaluation.get_email_log().endswith('\nSent evaluation '
'email to: [email protected],'
' [email protected]\n')
self.assertTrue(res)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_evaluation_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
docktask = D3RTask(temp_dir, params)
docktask.set_name('foo')
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
evaluation.run()
self.assertEqual(evaluation.get_error(), 'evaluation not set')
# test files get created
self.assertEqual(os.path.isdir(evaluation.get_dir()), True)
errfile = os.path.join(evaluation.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
finally:
shutil.rmtree(temp_dir)
def test_run_succeeds_one_evaluation_and_no_emailer(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.postevaluation = 'echo'
etask = EvaluationTask(
temp_dir, 'foo_dock.' + EvaluationTaskFactory.SCORING_SUFFIX,
None, params)
etask.create_dir()
task = PostEvaluationTask(temp_dir, params)
ctask = ChallengeDataTask(temp_dir, params)
task.run()
self.assertEqual(task.get_error(), None)
self.assertEqual(task.get_status(), D3RTask.COMPLETE_STATUS)
cfile = os.path.join(task.get_dir(), D3RTask.COMPLETE_FILE)
self.assertTrue(os.path.isfile(cfile))
stdout_file = os.path.join(task.get_dir(),
'echo' + D3RTask.STDOUT_SUFFIX)
self.assertTrue(os.path.isfile(stdout_file))
f = open(stdout_file, 'r')
data = f.read()
f.close()
ctaskdir = os.path.join(ctask.get_dir(),
ctask.get_celpp_challenge_data_dir_name())
self.assertTrue(' --evaluationdir ' + etask.get_dir() in data)
self.assertTrue(' --challengedir ' + ctaskdir in data)
self.assertTrue('--stageprefix stage.7. --evaluationsuffix ' +
'.extsubmission.evaluation$|.evaluation$' in data)
stderr_file = os.path.join(task.get_dir(),
'echo' + D3RTask.STDERR_SUFFIX)
self.assertTrue(os.path.isfile(stderr_file))
finally:
shutil.rmtree(temp_dir)
def test_get_evaluation_tasks_on_with_valid_completed_algo_dir(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
glidetask = GlideTask(temp_dir, params)
glidetask.create_dir()
open(os.path.join(glidetask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
etask = EvaluationTask(
temp_dir,
glidetask.get_name() + '.' +
EvaluationTaskFactory.SCORING_SUFFIX, glidetask, params)
etask.create_dir()
open(os.path.join(etask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
stf = EvaluationTaskFactory(temp_dir, params)
task_list = stf.get_evaluation_tasks()
self.assertEquals(len(task_list), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_evaluationdir_args(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
# no evaluation tasks
task = PostEvaluationTask(temp_dir, params)
res = task._get_evaluationdir_args()
self.assertEqual(res, '')
# one task
etask = EvaluationTask(temp_dir, 'foo.evaluation', None, params)
etask.create_dir()
res = task._get_evaluationdir_args()
self.assertEqual(
res, ' ' + PostEvaluationTask.EVALUATIONDIR_ARG + ' ' +
etask.get_dir())
# three tasks
etask2 = EvaluationTask(temp_dir,
'bla_dock.extsubmission.evaluation', None,
params)
etask2.create_dir()
open(os.path.join(etask2.get_dir(), D3RTask.ERROR_FILE),
'a').close()
etask3 = EvaluationTask(temp_dir, '12_x.extsubmission.evaluation',
None, params)
etask3.create_dir()
cfile = os.path.join(etask3.get_dir(), D3RTask.COMPLETE_FILE)
open(cfile, 'a').close()
res = task._get_evaluationdir_args()
self.assertTrue(' ' + PostEvaluationTask.EVALUATIONDIR_ARG + ' ' +
etask.get_dir() in res)
self.assertTrue(' ' + PostEvaluationTask.EVALUATIONDIR_ARG + ' ' +
etask2.get_dir() in res)
self.assertTrue(' ' + PostEvaluationTask.EVALUATIONDIR_ARG + ' ' +
etask3.get_dir() in res)
finally:
shutil.rmtree(temp_dir)
def test_run_succeeds_one_evaluation_with_emailer(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
foo_script = os.path.join(temp_dir, 'foo.py')
f = open(foo_script, 'w')
f.write('#! /usr/bin/env python\n')
f.write('import sys\nimport os\n')
f.write('outdir = sys.argv[1]\n')
f.write('sys.stdout.write(" ".join(sys.argv))\n')
f.write('f = open(os.path.join(outdir, "summary.txt"),"w")\n')
f.write('f.write("summary")\n')
f.write('f.flush()\nf.close()\n')
f.write('f = open(os.path.join(outdir, "yo.csv"), "a")\n')
f.write('f.write("hi")\nf.flush()\nf.close()\n')
f.write('sys.exit(0)\n')
f.flush()
f.close()
os.chmod(foo_script, stat.S_IRWXU)
params.postevaluation = foo_script
etask = EvaluationTask(
temp_dir, 'foo_dock.' + EvaluationTaskFactory.SCORING_SUFFIX,
None, params)
etask.create_dir()
task = PostEvaluationTask(temp_dir, params)
# setup emailer
smtpemailer = SmtpEmailer()
mockserver = D3RParameters()
mockserver.sendmail = Mock()
mockserver.quit = Mock()
smtpemailer.set_alternate_smtp_server(mockserver)
pee = PostEvaluationEmailer(['*****@*****.**'], smtpemailer)
task.set_evaluation_emailer(pee)
ctask = ChallengeDataTask(temp_dir, params)
task.run()
self.assertEqual(task.get_error(), None)
self.assertEqual(task.get_status(), D3RTask.COMPLETE_STATUS)
cfile = os.path.join(task.get_dir(), D3RTask.COMPLETE_FILE)
self.assertTrue(os.path.isfile(cfile))
stdout_file = os.path.join(task.get_dir(),
'foo.py' + D3RTask.STDOUT_SUFFIX)
self.assertTrue(os.path.isfile(stdout_file))
f = open(stdout_file, 'r')
data = f.read()
f.close()
ctaskdir = os.path.join(ctask.get_dir(),
ctask.get_celpp_challenge_data_dir_name())
self.assertTrue(' --evaluationdir ' + etask.get_dir() in data)
self.assertTrue(' --challengedir ' + ctaskdir in data)
self.assertTrue('--stageprefix stage.7. --evaluationsuffix ' +
'.extsubmission.evaluation$|.evaluation$' in data)
stderr_file = os.path.join(task.get_dir(),
'foo.py' + D3RTask.STDERR_SUFFIX)
f = open(stdout_file, 'r')
data = f.read()
f.close()
self.assertTrue(' --evaluationdir ' + etask.get_dir() in data)
self.assertTrue(os.path.isfile(stderr_file))
self.assertEqual(task.get_error(), None)
self.assertTrue('Sent post evaluation email to: '
'*****@*****.**' in task.get_email_log())
finally:
shutil.rmtree(temp_dir)
def test_get_uploadable_files(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = EvaluationTask(temp_dir, 'glide',
GlideTask(temp_dir, params), params)
# try with no dir
self.assertEqual(task.get_uploadable_files(), [])
# try with empty dir
task.create_dir()
self.assertEqual(task.get_uploadable_files(), [])
# try with final log
final_log = os.path.join(task.get_dir(), EvaluationTask.FINAL_LOG)
open(final_log, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 1)
flist.index(final_log)
# try with RMSD.txt
rmsd = os.path.join(task.get_dir(), EvaluationTask.RMSD_TXT)
open(rmsd, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 2)
flist.index(rmsd)
# try with empty pbdid dir
pbdid = os.path.join(task.get_dir(), '8www')
os.mkdir(pbdid)
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 2)
flist.index(rmsd)
# try with score/rot-LMCSS_doc_pv_complex1.pdb
score = os.path.join(pbdid, 'score')
os.mkdir(score)
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 2)
LMCSS = os.path.join(score, 'LMCSS-1fcz_1fcz_docked_complex.pdb')
open(LMCSS, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 3)
flist.index(LMCSS)
# try with score/rot-SMCSS_doc_pv_complex1.pdb
SMCSS = os.path.join(score, 'SMCSS-1fcz_2lbd_docked_complex.pdb')
open(SMCSS, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 4)
flist.index(SMCSS)
# try with score/rot-hiResApo_doc_pv_complex1.pdb
hiResApo = os.path.join(score,
'hiResHolo-1fcz_1fcy_docked_complex.pdb')
open(hiResApo, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 5)
flist.index(hiResApo)
# try with score/rot-hiResHolo_doc_pv_complex1.pdb
hiResHolo = os.path.join(
score, 'hiTanimoto-1fcz_1fcz_docked_complex.pdb')
open(hiResHolo, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 6)
flist.index(hiResHolo)
# try with score/crystal.pdb
crystal = os.path.join(score, 'crystal.pdb')
open(crystal, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 7)
flist.index(crystal)
# try with RMSD.pickle
rmsdpickle = os.path.join(task.get_dir(),
EvaluationTask.RMSD_PICKLE)
open(rmsdpickle, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 8)
flist.index(rmsdpickle)
# try with stderr/stdout files
errfile = os.path.join(task.get_dir(), 'evaluate.py.stderr')
open(errfile, 'a').close()
outfile = os.path.join(task.get_dir(), 'evaluate.py.stdout')
open(outfile, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 10)
flist.index(crystal)
flist.index(hiResHolo)
flist.index(hiResApo)
flist.index(SMCSS)
flist.index(LMCSS)
flist.index(errfile)
flist.index(outfile)
flist.index(final_log)
flist.index(rmsd)
flist.index(rmsdpickle)
finally:
shutil.rmtree(temp_dir)
def test_can_run(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
# no dock task found so it cannot run
docktask = D3RTask(temp_dir, params)
docktask.set_name('foo')
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
self.assertEqual(evaluation.can_run(), False)
self.assertEqual(evaluation.get_error(),
'foo task has notfound status')
# docktask running
docktask = D3RTask(temp_dir, params)
docktask.set_name('foo')
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.START_FILE),
'a').close()
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
self.assertEqual(evaluation.can_run(), False)
self.assertEqual(evaluation.get_error(),
'foo task has start status')
# docktask failed
error_file = os.path.join(docktask.get_dir(), D3RTask.ERROR_FILE)
open(error_file, 'a').close()
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
self.assertEqual(evaluation.can_run(), False)
self.assertEqual(evaluation.get_error(),
'foo task has error status')
# docktask success
os.remove(error_file)
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
self.assertEqual(evaluation.can_run(), True)
self.assertEqual(evaluation.get_error(), None)
# evaluation task exists already
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
evaluation.create_dir()
self.assertEqual(evaluation.can_run(), False)
self.assertEqual(
evaluation.get_error(),
evaluation.get_dir_name() +
' already exists and status is unknown')
# evaluation task already complete
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
open(os.path.join(evaluation.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
self.assertEqual(evaluation.can_run(), False)
self.assertEqual(evaluation.get_error(), None)
finally:
shutil.rmtree(temp_dir)