def test_can_run_with_complete_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
open(os.path.join(task.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
self.assertEquals(task.can_run(), False)
self.assertEquals(task.get_error(), None)
self.assertEquals(task._can_run, False)
finally:
shutil.rmtree(temp_dir)
def test_can_run_does_not_exist_or_error(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
# no make blast db
self.assertEquals(task.can_run(), False)
self.assertEquals(task.get_error(),
'makeblastdb task has notfound status')
self.assertEquals(task._can_run, False)
make_blast = MakeBlastDBTask(temp_dir, params)
make_blast.create_dir()
# make blast db failed
err_file = os.path.join(make_blast.get_dir(), D3RTask.ERROR_FILE)
open(err_file, 'a').close()
self.assertEquals(task.can_run(), False)
self.assertEquals(task.get_error(),
'makeblastdb task has error status')
self.assertEquals(task._can_run, False)
os.remove(err_file)
# make blast db success
open(os.path.join(make_blast.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
self.assertEquals(task.can_run(), True)
self.assertEquals(task.get_error(), None)
self.assertEquals(task._can_run, True)
task.create_dir()
open(os.path.join(task.get_dir(), D3RTask.ERROR_FILE), 'a').close()
self.assertEquals(task.can_run(), False)
self.assertEquals(task._can_run, False)
self.assertEquals(
task.get_error(),
task.get_dir_name() + ' already exists and ' + 'status is ' +
D3RTask.ERROR_STATUS)
finally:
shutil.rmtree(temp_dir)
def test_can_run(self):
tempDir = tempfile.mkdtemp()
try:
# try where makeblastdb is not complete
params = D3RParameters()
blastTask = BlastNFilterTask(tempDir, params)
self.assertEqual(blastTask.can_run(), False)
# try where makeblastdb failed
blastDb = MakeBlastDBTask(tempDir, params)
blastDb.create_dir()
errorFile = os.path.join(blastDb.get_path(),
blastDb.get_dir_name(),
D3RTask.ERROR_FILE)
open(errorFile, 'a').close()
self.assertEqual(blastTask.can_run(), False)
self.assertEqual(blastTask.get_error(),
'makeblastdb task has error status')
# try where data import is not complete
completeFile = os.path.join(blastDb.get_path(),
blastDb.get_dir_name(),
D3RTask.COMPLETE_FILE)
open(completeFile, 'a').close()
self.assertEqual(blastTask.can_run(), False)
self.assertEqual(blastTask.get_error(),
'dataimport task has ' + 'notfound status')
# try where data import failed
dataImport = DataImportTask(tempDir, params)
dataImport.create_dir()
errorFile = os.path.join(dataImport.get_path(),
dataImport.get_dir_name(),
D3RTask.ERROR_FILE)
open(errorFile, 'a').close()
self.assertEqual(blastTask.can_run(), False)
self.assertEqual(blastTask.get_error(),
'dataimport task has error status')
# try where blast can run
os.remove(errorFile)
completeFile = os.path.join(dataImport.get_dir(),
D3RTask.COMPLETE_FILE)
open(completeFile, 'a').close()
self.assertEqual(blastTask.can_run(), True)
self.assertEqual(blastTask.get_error(), None)
# try where blast exists
blastTask.create_dir()
self.assertEqual(blastTask.can_run(), False)
self.assertEqual(
blastTask.get_error(),
blastTask.get_dir_name() + ' already exists and' +
' status is unknown')
# try where blast is complete
completeFile = os.path.join(blastTask.get_path(),
blastTask.get_dir_name(),
D3RTask.COMPLETE_FILE)
open(completeFile, 'a').close()
self.assertEqual(blastTask.can_run(), False)
self.assertEqual(blastTask.get_error(), None)
finally:
shutil.rmtree(tempDir)
