def setUp(self):
logging.info("Creating test sqlite database")
copy2(dirpath + "/test_pipeline.db.template",
dirpath + "/test_pipeline.db")
logging.info("Connecting to hive test sqlite database " + dirpath +
"/test_pipeline.db")
self.hive = HiveInstance("sqlite:///" + dirpath + "/test_pipeline.db")
def get_hive(process):
if process not in hives.keys():
if process not in process_lookup.keys():
raise ProcessNotFoundError("Process " + str(process) +
" not known")
hives[process] = HiveInstance(process_lookup[process]['hive_uri'])
return hives[process]
def get_hive(process):
if process not in hives:
if process not in process_lookup:
raise ProcessNotFoundError('Process %s not known' % process)
hives[process] = HiveInstance(process_lookup[process]['hive_uri'])
return hives[process]
from ensembl_prodinf.exceptions import HTTPRequestError
from ensembl_prodinf.config import load_config_json
app = Flask(__name__, instance_relative_config=True)
app.config.from_object('db_config')
app.analysis = app.config["HIVE_ANALYSIS"]
app.blacklisted_status_hosts = set(app.config['BLACKLISTED_STATUS_HOSTS'])
app.config['SWAGGER'] = {
'title': 'Database copy REST endpoints',
'uiversion': 2
}
swagger = Swagger(app)
app.hive = HiveInstance(app.config["HIVE_URI"])
app.logger.addHandler(app_logging.file_handler(__name__))
app.logger.addHandler(app_logging.default_handler())
app.logger.info(app.config)
app.servers = load_config_json(app.config['SERVER_URIS_FILE'])
def is_running(pid):
try:
os.kill(pid, 0)
except OSError as err:
return False
return True
class HiveTest(unittest.TestCase):
"""Create fresh database file"""
def setUp(self):
logging.info("Creating test sqlite database")
copy2(dirpath + "/test_pipeline.db.template",
dirpath + "/test_pipeline.db")
logging.info("Connecting to hive test sqlite database " + dirpath +
"/test_pipeline.db")
self.hive = HiveInstance("sqlite:///" + dirpath + "/test_pipeline.db")
"""Basic test case for creating a new job"""
def test_create_job(self):
job1 = self.hive.create_job('TestRunnable', {'x': 'y', 'a': 'b'})
logging.debug(job1)
job2 = self.hive.get_job_by_id(job1.job_id)
logging.debug(job2)
self.assertEquals(job1.job_id, job2.job_id)
self.assertEquals(job1.analysis.logic_name, job2.analysis.logic_name)
self.assertEquals(job1.input_id, job2.input_id)
"""Test case for checking on a finished semaphore"""
def test_check_semaphore_success(self):
semaphore_data = self.hive.get_semaphore_data(2)
logging.debug(semaphore_data)
status = self.hive.check_semaphores_for_job(semaphore_data)
logging.debug("Status for 2 is " + status)
self.assertEquals(status, 'complete',
"Checking expected status for completed semaphore")
"""Test case for checking on a failed semaphore"""
def test_check_semaphore_failure(self):
semaphore_data = self.hive.get_semaphore_data(8)
logging.debug(semaphore_data)
status = self.hive.check_semaphores_for_job(semaphore_data)
logging.debug("Status for 8 is " + status)
self.assertEquals(status, 'failed',
"Checking expected status for failed semaphore")
"""Test case for checking on a completed single job"""
def test_check_job_success(self):
job = self.hive.get_job_by_id(20)
logging.debug(job)
status = self.hive.get_job_tree_status(job)
self.assertEquals("complete", status,
"Checking status of completed single job")
"""Test case for checking on a failed single job"""
def test_check_job_failure(self):
job = self.hive.get_job_by_id(11)
logging.debug(job)
status = self.hive.get_job_tree_status(job)
self.assertEquals("failed", status,
"Checking status of failed single job")
"""Test case for checking on a completed job factory"""
def test_check_job_tree_success(self):
job = self.hive.get_job_by_id(1)
logging.debug(job)
status = self.hive.get_job_tree_status(job)
logging.debug(status)
self.assertEquals("complete", status,
"Checking status of completed job factory")
"""Test case for checking on a failed job factory"""
def test_check_job_tree_failure(self):
job = self.hive.get_job_by_id(7)
logging.debug(job)
status = self.hive.get_job_tree_status(job)
logging.debug(status)
self.assertEquals("failed", status,
"Checking status of failed job factory")
"""Test case for getting output on a completed job factory"""
def test_get_job_output_success(self):
output = self.hive.get_result_for_job_id(1)
logging.debug(output)
self.assertEquals('complete', output['status'],
"Checking status of successful job factory output")
self.assertTrue(output['output'] != None,
"Checking output of successful job factory output")
"""Test case for getting output a failed job factory"""
def test_get_job_output_failed(self):
output = self.hive.get_result_for_job_id(7)
logging.debug(output)
self.assertEquals(
'failed', output['status'],
"Checking status of unsuccessful job factory output")
self.assertTrue('output' not in output,
"Checking output of unsuccessful job factory output")
"""Test case for listing all jobs"""
def test_get_all_results(self):
jobs = self.hive.get_all_results('TestRunnable')
self.assertEquals(1, len(jobs), "Checking we got just one job")
"""Remove test database file"""
def tearDown(self):
logging.info("Removing test sqlite database")
def get_hive():
global hive
if hive is None:
hive = HiveInstance(app.config["HIVE_URI"])
return hive