def can_run(self):
"""Determines if task can actually run
This method first verifies the `MakeBlastDBTask` and
`DataImportTask` task have
`D3RTask.COMPLETE_STATUS` for status. The method then
verifies a `BlastNFilterTask` does not already exist.
If above is not true then self.set_error() is set
with information about the issue
:return: True if can run otherwise False
"""
self._can_run = False
self._error = None
# check blast
make_blastdb = MakeBlastDBTask(self._path, self._args)
make_blastdb.update_status_from_filesystem()
if make_blastdb.get_status() != D3RTask.COMPLETE_STATUS:
logger.info('Cannot run ' + self.get_name() + ' task ' +
'because ' + make_blastdb.get_name() + ' task' +
'has a status of ' + make_blastdb.get_status())
self.set_error(make_blastdb.get_name() + ' task has ' +
make_blastdb.get_status() + ' status')
return False
# check data import
data_import = DataImportTask(self._path, self._args)
data_import.update_status_from_filesystem()
if data_import.get_status() != D3RTask.COMPLETE_STATUS:
logger.info('Cannot run ' + self.get_name() + ' task ' +
'because ' + data_import.get_name() + ' task' +
'has a status of ' + data_import.get_status())
self.set_error(data_import.get_name() + ' task has ' +
data_import.get_status() + ' status')
return False
# check blast is not complete and does not exist
self.update_status_from_filesystem()
if self.get_status() == D3RTask.COMPLETE_STATUS:
logger.debug("No work needed for " + self.get_name() + " task")
return False
if self.get_status() != D3RTask.NOTFOUND_STATUS:
logger.warning(self.get_name() + " task was already " +
"attempted, but there was a problem")
self.set_error(self.get_dir_name() + ' already exists and ' +
'status is ' + self.get_status())
return False
self._can_run = True
return True
def test_constructor(self):
params = D3RParameters()
task = MakeBlastDBTask('/foo', params)
self.assertEqual(task.get_name(), 'makeblastdb')
self.assertEqual(task.get_stage(), 1)
self.assertEqual(task.get_status(), D3RTask.UNKNOWN_STATUS)
self.assertEqual(task.get_path(), '/foo')
self.assertEqual(task.get_dir_name(), 'stage.1.makeblastdb')
test_task.try_update_status_from_filesystem(self, task)