def test_monitor2_images(self):
"""
Test the POST, GET and DELETE images APIs.
"""
# Upload image stack
url = _MON_IMAGES_URL
url = add_url_argument(url, STACK_TYPE, MONITOR2, True)
url = add_url_argument(url, NAME, 'monitor1_images_name')
url = add_url_argument(url, DESCRIPTION, 'monitor1 images description')
response = upload_file(self, _TEST_DIR, url, _MON2_IMAGES, 200)
image_stack_uuid = response[UUID]
# Ensure duplicate image stacks cannot be uploaded
upload_file(self, _TEST_DIR, url, _MON2_IMAGES, 403)
# Ensure image stack exists in the database and can be retrieved
response = get_data(self, _MON_IMAGES_URL, 200)
record_found = False
for record in response[MONITOR_IMAGES]:
if record[UUID] == image_stack_uuid:
record_found = True
msg = "Monitor image stack %s doesn't exist in the database." % image_stack_uuid
self.assertTrue(record_found, msg)
# Delete image stack
url = add_url_argument(_IMAGES_URL, UUID, image_stack_uuid, True)
delete_data(self, url, 200)
# Ensure image stack no longer exists in the database
response = get_data(self, _MON_IMAGES_URL, 200)
for record in response[MONITOR_IMAGES]:
msg = "Monitor image stack %s still exists in the database." % record[UUID]
self.assertNotEqual(image_stack_uuid, record[UUID], msg)
def exercise_file_upload_api(self, url, filename):
response_key = url.split("/")[-1]
# Test successful file upload
response = upload_file(self, _TEST_DIR, url, filename, 200)
uuid = response[UUID]
# Test error code 403: File already exists.
upload_file(self, _TEST_DIR, url, filename, 403)
# Test error code 415: File is not a valid FASTA file.
upload_file(self, _TEST_DIR, url, _INVALID_FASTA_FILENAME, 415)
# Test successful retrieval of uploaded file
response = get_data(self, url, 200)
retrieved_uuid = response[response_key][0][UUID]
msg = "Expected uuid (%s) doesn't match observed uuid (%s) for %s" % \
(uuid, retrieved_uuid, url)
self.assertEqual(uuid, retrieved_uuid, msg)
# Test successful deletion of uploaded file
delete_data(self, url + "?uuid=%s" % uuid, 200)
# Test unsuccessful deletion of non-existent file
delete_data(self, url + "?uuid=%s" % str(uuid4()), 404)
def test_images(self):
"""
Test the POST, GET and DELETE images APIs.
"""
# Upload image stack
url = _IMAGES_URL
url = add_url_argument(url, EXP_DEF, 'Beta_24b_p1_V6', True)
url = add_url_argument(url, NAME, 'golden_run')
url = add_url_argument(url, DESCRIPTION, 'Short description.')
response = upload_file(self, _TEST_DIR, url, _PNG_IMAGES, 200)
image_stack_uuid = response[UUID]
# Ensure duplicate image stacks cannot be uploaded
response = upload_file(self, _TEST_DIR, url, _PNG_IMAGES, 403)
# Ensure image stack exists in the database and can be retrieved
response = get_data(self, _IMAGES_URL, 200)
record_found = False
for record in response[IMAGES]:
if record[UUID] == image_stack_uuid:
record_found = True
msg = "Image stack %s doesn't exist in the database." % image_stack_uuid
self.assertTrue(record_found, msg)
# Delete image stack
url = add_url_argument(_IMAGES_URL, UUID, image_stack_uuid, True)
delete_data(self, url, 200)
# Ensure image stack no longer exists in the database
response = get_data(self, _IMAGES_URL, 200)
for record in response[IMAGES]:
msg = "Image stack %s still exists in the database." % record[UUID]
self.assertNotEqual(image_stack_uuid, record[UUID], msg)
def test_absorption(self):
# Upload targets and probes files
response = upload_file(self, _TEST_DIR, _PROBES_URL, _PROBES_FILENAME,
200)
probes_uuid = response[UUID]
response = upload_file(self, _TEST_DIR, _TARGETS_URL,
_TARGETS_FILENAME, 200)
targets_uuid = response[UUID]
# Post absorption job
url = _ABSORPTION_URL + "?probes=%s&targets=%s&job_name=%s&%s=%s" % \
(probes_uuid, targets_uuid, _JOB_NAME, STRICT, _STRICT)
response = post_data(self, url, 200)
abs_job_uuid = response[UUID]
running = True
job_details = None
while running:
time.sleep(10)
response = get_data(self, _ABSORPTION_URL, 200)
for job in response[_ABSORPTION]:
if abs_job_uuid == job[UUID]:
job_details = job
running = job_details[_STATUS] == 'running'
# Copy result file to cwd for bamboo to ingest as an artifact
absorption_path = None
if _RESULT in job_details:
absorption_path = job_details[_RESULT]
if absorption_path and os.path.isfile(absorption_path):
shutil.copy(absorption_path, "observed_absorption.txt")
# Clean up by removing targets and probes files
delete_data(self, _PROBES_URL + "?uuid=%s" % probes_uuid, 200)
delete_data(self, _TARGETS_URL + "?uuid=%s" % targets_uuid, 200)
msg = "Expected absorption job status succeeded, but found: %s" % \
job_details[_STATUS]
self.assertEquals(job_details[_STATUS], "succeeded", msg)
exp_result_path = os.path.join(
os.path.abspath(os.path.dirname(__file__)),
_EXPECTED_RESULT_FILENAME)
msg = "Observed result (%s) doesn't match expected result (%s)." % \
(absorption_path, exp_result_path)
self.assertTrue(filecmp.cmp(exp_result_path, absorption_path), msg)
# Delete absorption job
delete_data(self, _ABSORPTION_URL + "?uuid=%s" % abs_job_uuid, 200)
# Ensure job no longer exists in the database
response = get_data(self, _ABSORPTION_URL, 200)
for job in response[_ABSORPTION]:
msg = "Absorption job %s still exists in database." % abs_job_uuid
self.assertNotEqual(abs_job_uuid, job[UUID], msg)
def test_bin_images(self):
# Upload image stack
url = _IMAGES_URL
url = add_url_argument(url, EXP_DEF, 'Beta_24b_p1_V6', True)
url = add_url_argument(url, NAME, 'bin_images')
url = add_url_argument(url, DESCRIPTION, 'Binary image stack.')
response = upload_file(self, _TEST_DIR, url, _BIN_IMAGES, 200)
msg = "Expected number of images (%d) not equal to observed (%d)." % \
(4, response[NUM_IMAGES])
self.assertEqual(response[NUM_IMAGES], 4, msg)
# Delete image stack
url = add_url_argument(_IMAGES_URL, UUID, response[UUID], True)
delete_data(self, url, 200)
def test_invalid_ham_dir_name(self):
url = _IMAGES_URL
url = add_url_argument(url, EXP_DEF, 'Beta_24b_p1_V6', True)
url = add_url_argument(url, NAME, 'invalid ham dir name')
url = add_url_argument(url, DESCRIPTION, 'invalid ham dir name')
upload_file(self, _TEST_DIR, url, _INVALID_HAM_NAME, 415)
def test_not_an_archive(self):
url = _IMAGES_URL
url = add_url_argument(url, EXP_DEF, 'Beta_24b_p1_V6', True)
url = add_url_argument(url, NAME, 'not_an_archive')
url = add_url_argument(url, DESCRIPTION, 'Not an archive.')
upload_file(self, _TEST_DIR, url, _NOT_AN_ARCHIVE, 415)
def test_empty_archive(self):
url = _IMAGES_URL
url = add_url_argument(url, EXP_DEF, 'Beta_24b_p1_V6', True)
url = add_url_argument(url, NAME, 'empty_archive')
url = add_url_argument(url, DESCRIPTION, 'Empty archive.')
upload_file(self, _TEST_DIR, url, _NO_IMAGES, 415)
def test_invalid_exp_def(self):
url = _IMAGES_URL
url = add_url_argument(url, EXP_DEF, 'invalid_exp_def', True)
url = add_url_argument(url, NAME, 'invalid_exp_def')
url = add_url_argument(url, DESCRIPTION, 'Invalid exp def.')
upload_file(self, _TEST_DIR, url, _PNG_IMAGES, 404)
def test_replay(self):
"""
Test the POST, GET and DELETE images APIs.
"""
# Upload ham image stack
ham_url = _IMAGES_URL
ham_url = add_url_argument(ham_url, EXP_DEF, 'Beta_24b_p1_V6', True)
ham_url = add_url_argument(ham_url, NAME, 'golden_run')
ham_url = add_url_argument(ham_url, DESCRIPTION, 'Short description.')
ham_response = upload_file(self, _TEST_DIR, ham_url, _HAM_IMAGES, 200)
ham_uuid = ham_response[UUID]
# Upload monitor 1 image stack
mon1_url = _MON_IMAGES_URL
mon1_url = add_url_argument(mon1_url, STACK_TYPE, MONITOR1, True)
mon1_url = add_url_argument(mon1_url, NAME, 'monitor1_images_name')
mon1_url = add_url_argument(mon1_url, DESCRIPTION, 'monitor1 images description')
mon1_response = upload_file(self, _TEST_DIR, mon1_url, _MON1_IMAGES, 200)
mon1_uuid = mon1_response[UUID]
# Upload monitor 2 image stack
mon2_url = _MON_IMAGES_URL
mon2_url = add_url_argument(mon2_url, STACK_TYPE, MONITOR2, True)
mon2_url = add_url_argument(mon2_url, NAME, 'monitor2_images_name')
mon2_url = add_url_argument(mon2_url, DESCRIPTION, 'monitor2 images description')
mon2_response = upload_file(self, _TEST_DIR, mon2_url, _MON2_IMAGES, 200)
mon2_uuid = mon2_response[UUID]
# create a replay image stack from existing stacks
replay_url = _REPLAY_IMAGES_URL
replay_url = add_url_argument(replay_url, NAME, 'replay_images_name', True)
replay_url = add_url_argument(replay_url, HAM_NAME, 'golden_run')
replay_url = add_url_argument(replay_url, MON1_NAME, 'monitor1_images_name')
replay_url = add_url_argument(replay_url, MON2_NAME, 'monitor2_images_name')
replay_url = add_url_argument(replay_url, DESCRIPTION, 'replay images description')
replay_response = post_data(self, replay_url, 200)
replay_uuid = replay_response[UUID]
# try to add replay image stack with same name
replay_url = _REPLAY_IMAGES_URL
replay_url = add_url_argument(replay_url, NAME, 'replay_images_name', True)
replay_url = add_url_argument(replay_url, HAM_NAME, 'golden_run')
replay_url = add_url_argument(replay_url, MON1_NAME, 'monitor1_images_name')
replay_url = add_url_argument(replay_url, MON2_NAME, 'monitor2_images_name')
replay_url = add_url_argument(replay_url, DESCRIPTION, 'replay images description')
post_data(self, replay_url, 403)
# try to add replay image stack comprised of the same ham/mon image stacks
replay_url = _REPLAY_IMAGES_URL
replay_url = add_url_argument(replay_url, NAME, 'different_replay_images_name', True)
replay_url = add_url_argument(replay_url, HAM_NAME, 'golden_run')
replay_url = add_url_argument(replay_url, MON1_NAME, 'monitor1_images_name')
replay_url = add_url_argument(replay_url, MON2_NAME, 'monitor2_images_name')
replay_url = add_url_argument(replay_url, DESCRIPTION, 'replay images description')
post_data(self, replay_url, 403)
# Delete image stacks
url = add_url_argument(_IMAGES_URL, UUID, ham_uuid, True)
delete_data(self, url, 200)
url = add_url_argument(_IMAGES_URL, UUID, mon1_uuid, True)
delete_data(self, url, 200)
url = add_url_argument(_IMAGES_URL, UUID, mon2_uuid, True)
delete_data(self, url, 200)
url = add_url_argument(_IMAGES_URL, UUID, replay_uuid, True)
delete_data(self, url, 200)
def test_invalid_mon_bad_compression(self):
url = _MON_IMAGES_URL
url = add_url_argument(url, STACK_TYPE, MONITOR1, True)
url = add_url_argument(url, NAME, 'invalid monitor bad compression')
url = add_url_argument(url, DESCRIPTION, 'invalid monitor bad compression')
upload_file(self, _TEST_DIR, url, _INVALID_MON_BADCOMPRESS, 415)
def test_invalid_mon_uncropped(self):
url = _MON_IMAGES_URL
url = add_url_argument(url, STACK_TYPE, MONITOR1, True)
url = add_url_argument(url, NAME, 'invalid monitor crop on name')
url = add_url_argument(url, DESCRIPTION, 'invalid monitor crop on name')
upload_file(self, _TEST_DIR, url, _INVALID_MON_CROP_ON, 415)
def test_invalid_mon_no_images(self):
url = _MON_IMAGES_URL
url = add_url_argument(url, STACK_TYPE, MONITOR1, True)
url = add_url_argument(url, NAME, 'invalid monitor no images name')
url = add_url_argument(url, DESCRIPTION, 'invalid monitor no images name')
upload_file(self, _TEST_DIR, url, _INVALID_MON_NO_IMAGES, 415)
def test_invalid_mon_additional_files(self):
url = _MON_IMAGES_URL
url = add_url_argument(url, STACK_TYPE, MONITOR1, True)
url = add_url_argument(url, NAME, 'invalid monitor additional files name')
url = add_url_argument(url, DESCRIPTION, 'invalid monitor additional files name')
upload_file(self, _TEST_DIR, url, _INVALID_MON_ADD_FILES, 415)
def test_invalid_mon_dir_name(self):
url = _MON_IMAGES_URL
url = add_url_argument(url, STACK_TYPE, MONITOR1, True)
url = add_url_argument(url, NAME, 'invalid monitor root dir name')
url = add_url_argument(url, DESCRIPTION, 'invalid monitor root dir name')
upload_file(self, _TEST_DIR, url, _INVALID_MON_ROOT_NAME, 415)