def _batch_job(batch_file, expected, job_type, argument=None):
file_instance = File.File(output.Output('test'))
scheduler = Scheduler.Scheduler()
job, columns = file_instance.parseBatchFile(batch_file)
result_id = scheduler.addJob('*****@*****.**',
job,
columns,
job_type,
argument=argument)
batch_job = BatchJob.query.filter_by(result_id=result_id).one()
left = batch_job.batch_queue_items.count()
assert left == len(expected)
scheduler.process()
left = batch_job.batch_queue_items.count()
assert left == 0
filename = 'batch-job-%s.txt' % result_id
result = io.open(os.path.join(settings.CACHE_DIR, filename),
encoding='utf-8')
next(result) # Header.
assert expected == [line.strip().split('\t') for line in result]
def test_invalid_zip_file():
"""
Random zip file input for batch job (invalid).
"""
path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data',
'image.zip')
batch_file = open(path, 'rb')
file_instance = File.File(output.Output('test'))
job, columns = file_instance.parseBatchFile(batch_file)
assert job is None
def batch_jobs_submit():
"""
Run batch jobs and render batch checker HTML form. The batch jobs are
added to the database by the scheduler and ran by the BatchChecker
daemon.
"""
job_type = request.form.get('job_type')
email = request.form.get('email')
# Note that this is always a seekable binary file object.
batch_file = request.files.get('file')
assemblies = Assembly.query \
.order_by(*Assembly.order_by_criteria) \
.all()
assembly_name_or_alias = request.form.get('assembly_name_or_alias',
settings.DEFAULT_ASSEMBLY)
errors = []
if not email:
email = '{}@website.mutalyzer'.format(request.remote_addr)
if job_type not in BATCH_JOB_TYPES:
errors.append('Invalid batch job type.')
if not file:
errors.append('Please select a local file for upload.')
if job_type == 'position-converter':
try:
Assembly.by_name_or_alias(assembly_name_or_alias)
except NoResultFound:
errors.append('Not a valid assembly.')
argument = assembly_name_or_alias
else:
argument = None
output = Output(__file__)
if not errors:
stats.increment_counter('batch-job/website')
scheduler = Scheduler.Scheduler()
file_instance = File.File(output)
job, columns = file_instance.parseBatchFile(batch_file)
if job is None:
errors.append('Could not parse input file, please check your '
'file format.')
else:
result_id = scheduler.addJob(email, job, columns, job_type,
argument=argument)
# Todo: We now assume that the job was not scheduled if there are
# messages, which is probably not correct.
if not output.getMessages():
return redirect(url_for('.batch_job_progress',
result_id=result_id))
for error in errors:
output.addMessage(__file__, 3, 'EBATCHJOB', error)
messages = map(util.message_info, output.getMessages())
return render_template('batch-jobs.html',
assemblies=assemblies,
assembly_name_or_alias=assembly_name_or_alias,
job_type=job_type,
max_file_size=settings.MAX_FILE_SIZE // 1048576,
messages=messages)