def test_update_job_status(self):
"""
Tests that a job can update its status
"""
job_type = 'SIMILARITY'
params = {
'search_type': 'SIMILARITY',
'structure':
'[H]C1(CCCN1C(=N)N)CC1=NC(=NO1)C1C=CC(=CC=1)NC1=NC(=CS1)C1C=CC(Br)=CC=1',
'threshold': '70'
}
docker_image_url = 'some url'
with self.flask_app.app_context():
job_must_be = delayed_job_models.get_or_create(
job_type, params, docker_image_url)
job_id = job_must_be.id
new_data = {
'progress': 50,
'status_log': 'Loading database',
'status_description': '{"msg":"Smiles file loaded"}'
}
token = token_generator.generate_job_token(job_id)
headers = {'X-Job-Key': token}
client = self.client
response = client.patch(f'/status/{job_id}',
data=new_data,
headers=headers)
self.assertEqual(response.status_code,
200,
msg='The request should have not failed')
job_got = delayed_job_models.get_job_by_id(job_id)
# be sure to have a fresh version of the object
DB.session.rollback()
DB.session.expire(job_got)
DB.session.refresh(job_got)
progress_got = job_got.progress
self.assertEqual(progress_got,
new_data['progress'],
msg=f'The progress was not updated correctly!')
status_log_got = job_got.status_log
self.assertIsNotNone(status_log_got,
msg=f'The status log was not set correctly!')
self.assertNotEqual(
status_log_got,
new_data['status_log'],
msg=f'It seems that the status log was not saved'
f'correctly. It should be accumulative')
status_description_got = job_got.status_description
self.assertEqual(
status_description_got,
new_data['status_description'],
msg=f'The status description was not updated correctly!')
def test_job_token_is_generated(self):
"""
Test that the token for a job is generated
"""
with self.flask_app.app_context():
job_type = 'SIMILARITY'
params = {
'search_type': 'SIMILARITY',
'structure':
'[H]C1(CCCN1C(=N)N)CC1=NC(=NO1)C1C=CC(=CC=1)NC1=NC(=CS1)C1C=CC(Br)=CC=1',
'threshold': '70'
}
docker_image_url = 'some_url'
job_must_be = delayed_job_models.get_or_create(
job_type, params, docker_image_url)
token_got = token_generator.generate_job_token(job_must_be.id)
key = RUN_CONFIG.get('server_secret_key')
data_got = jwt.decode(token_got, key, algorithms=['HS256'])
self.assertEqual(data_got.get('job_id'),
job_must_be.id,
msg='The token was not generated correctly!')
def create_params_file(job, input_files_desc):
"""
Creates the parameters file for the job
:param job: job oject for which the parmeters file will be created
"""
job_token = token_generator.generate_job_token(job.id)
run_params = {
'job_id': job.id,
'job_token': job_token,
'inputs': prepare_job_inputs(job, input_files_desc),
'output_dir': get_job_output_dir_path(job),
'custom_job_config': get_custom_job_config_repo_params(job),
'status_update_endpoint': {
'url': f'http://{RUN_CONFIG.get("status_update_host")}'
f'{RUN_CONFIG.get("base_path", "")}/status/{job.id}',
'method': 'PATCH'
},
'custom_statistics_endpoint': {
'url':
f'http://{RUN_CONFIG.get("status_update_host")}'
f'{RUN_CONFIG.get("base_path", "")}'
f'/custom_statistics/submit_statistics/{job.type.lower()}_job/{job.id}',
'method':
'POST'
},
'job_params': json.loads(job.raw_params),
}
run_params_path = get_job_run_params_file_path(job)
# delete file if existed before, just in case
if os.path.exists(run_params_path):
os.remove(run_params_path)
with open(run_params_path, 'w') as out_file:
out_file.write(yaml.dump(run_params))
def test_a_job_cannot_update_another_jobs_statistics(self):
"""
Tests that a job cannot update the statistics of another job
"""
job_type = 'TEST'
params = {
'instruction':
'RUN_NORMALLY',
'seconds':
1,
'api_url':
'https://www.ebi.ac.uk/chembl/api/data/similarity/CN1C(=O)C=C(c2cccc(Cl)c2)c3cc(ccc13)C@@(c4ccc(Cl)cc4)c5cncn5C/80.json'
}
docker_image_url = 'some url'
with self.flask_app.app_context():
job_must_be = delayed_job_models.get_or_create(
job_type, params, docker_image_url)
job_id = job_must_be.id
statistics = {
'duration': 1,
}
token = token_generator.generate_job_token('another_id')
headers = {'X-JOB-KEY': token}
client = self.client
response = client.post(
f'/custom_statistics/submit_statistics/test_job/{job_id}',
data=statistics,
headers=headers)
self.assertEqual(
response.status_code,
401,
msg=
'I should not be authorised to upload statistics of another job'
)
def test_a_job_cannot_update_another_job_progress(self):
"""
Tests that a job can not use its token to update another job's status
"""
job_type = 'SIMILARITY'
params = {
'search_type': 'SIMILARITY',
'structure':
'[H]C1(CCCN1C(=N)N)CC1=NC(=NO1)C1C=CC(=CC=1)NC1=NC(=CS1)C1C=CC(Br)=CC=1',
'threshold': '70'
}
docker_image_url = 'some url'
with self.flask_app.app_context():
job_must_be = delayed_job_models.get_or_create(
job_type, params, docker_image_url)
job_id = job_must_be.id
new_data = {
'progress': 50,
'status_log': 'Loading database',
}
token = token_generator.generate_job_token('another_id')
headers = {'X-JOB-KEY': token}
client = self.client
response = client.patch(f'/status/{job_id}',
data=new_data,
headers=headers)
self.assertEqual(
response.status_code,
401,
msg=
'I should not be authorised to modify the status of another job'
)
def test_job_can_be_submitted(self):
"""
Test that a job can be submitted
"""
with self.flask_app.app_context():
job_type = 'TEST'
docker_image_url = 'some_url'
input_files_desc, input_files_hashes, params = self.prepare_mock_job_args(
)
print('TEST INPUT ')
print(input_files_desc)
submission_result = job_submission_service.submit_job(
job_type, input_files_desc, input_files_hashes,
docker_image_url, params)
job_id = submission_result.get('job_id')
job_data = delayed_job_models.get_job_by_id(job_id).public_dict()
# -----------------------------------------------
# Test Run Dir
# -----------------------------------------------
job_run_dir_must_be = os.path.join(
job_submission_service.JOBS_RUN_DIR, job_id)
self.assertTrue(
os.path.isdir(job_run_dir_must_be),
msg=
f'The run dir for the job ({job_run_dir_must_be}) has not been created!'
)
input_files_dir_must_be = os.path.join(
job_run_dir_must_be,
job_submission_service.INPUT_FILES_DIR_NAME)
self.assertTrue(
os.path.isdir(input_files_dir_must_be),
msg=
f'The input files dir for the job ({input_files_dir_must_be}) has not been created!'
)
# -----------------------------------------------
# Test Run Params
# -----------------------------------------------
params_file_must_be = os.path.join(
job_run_dir_must_be,
job_submission_service.RUN_PARAMS_FILENAME)
self.assertTrue(
os.path.isfile(params_file_must_be),
msg=
f'The run params file for the job ({params_file_must_be}) has not been created!'
)
params_file = open(params_file_must_be, 'r')
params_got = yaml.load(params_file, Loader=yaml.FullLoader)
params_file.close()
token_must_be = token_generator.generate_job_token(job_id)
token_got = params_got.get('job_token')
self.assertEqual(token_must_be,
token_got,
msg='The token was not generated correctly')
job_id_must_be = job_id
job_id_got = params_got.get('job_id')
self.assertEqual(job_id_must_be,
job_id_got,
msg='The job id was not generated correctly')
status_update_url_must_be = f'http://0.0.0.0:5000/status/{job_id}'
status_update_url_got = params_got.get(
'status_update_endpoint').get('url')
self.assertEqual(
status_update_url_must_be,
status_update_url_got,
msg='The status update url was not set correctly!')
status_update_method_must_be = 'PATCH'
status_update_method_got = params_got.get(
'status_update_endpoint').get('method')
self.assertEqual(
status_update_method_must_be,
status_update_method_got,
msg='The status update method was not set correctly!')
job_params_got = params_got.get('job_params')
raw_job_params_must_be = job_data.get('raw_params')
self.assertEqual(json.dumps(job_params_got, sort_keys=True),
raw_job_params_must_be,
msg='The job params were not set correctly')
custom_statistics_url_must_be = f'http://0.0.0.0:5000' \
f'/custom_statistics/submit_statistics/{job_type.lower()}_job/{job_id}'
custom_statistics_url_got = params_got.get(
'custom_statistics_endpoint', {}).get('url')
self.assertEqual(
custom_statistics_url_must_be,
custom_statistics_url_got,
msg='The status update method was not set correctly!')
custom_statistics_method_must_be = 'POST'
custom_statistics_method_got = params_got.get(
'custom_statistics_endpoint', {}).get('method')
self.assertEqual(
custom_statistics_method_must_be,
custom_statistics_method_got,
msg='The custom statistics method was not set correctly!')
# -----------------------------------------------
# Test Input Files
# -----------------------------------------------
job_input_files_desc_got = params_got.get('inputs')
for key, tmp_path in input_files_desc.items():
run_path_must_be = job_input_files_desc_got[key]
self.assertTrue(
os.path.isfile(run_path_must_be),
msg=
f'The input file for the job ({run_path_must_be}) has not been created!'
)
job_got = delayed_job_models.get_job_by_id(job_id)
input_files_got = job_got.input_files
num_inputs_files_must_be = len(os.listdir(input_files_dir_must_be))
self.assertEquals(
num_inputs_files_must_be,
len(input_files_got),
msg='The input files were not registered correctly!')
for input_file in input_files_got:
internal_path_got = input_file.internal_path
self.assertTrue(
os.path.isfile(internal_path_got),
msg=
f'The internal path of an input file {internal_path_got} '
f'seems that does not exist!')
# -----------------------------------------------
# Test Output Directory
# -----------------------------------------------
output_dir_must_be = Path(
job_submission_service.JOBS_OUTPUT_DIR).joinpath(job_id)
output_dir_got = params_got.get('output_dir')
self.assertEqual(str(output_dir_got),
str(output_dir_must_be),
msg='The job output dir was not set correctly')
self.assertTrue(
os.path.isdir(output_dir_must_be),
msg=
f'The output dir for the job ({output_dir_must_be}) has not been created!'
)
# -----------------------------------------------
# Submission script file
# -----------------------------------------------
submission_script_file_must_be = \
os.path.join(job_run_dir_must_be, job_submission_service.SUBMISSION_FILE_NAME)
self.assertTrue(
os.path.isfile(submission_script_file_must_be),
msg=
f'The script file for submitting the job ({submission_script_file_must_be}) '
f'has not been created!')
self.assertTrue(
os.access(submission_script_file_must_be, os.X_OK),
msg=
f'The script file for the job ({submission_script_file_must_be}) is not executable!'
)