def setUp(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/authenticate/",
body='{"access_token": "token", "token_type": "Bearer", '
'"expires_in": "3600"}')
self.tester = QiitaClient("https://test_server.com")
self._clean_up_files = []
self._old_fp = environ.get('QP_TARGET_GENE_CONFIG_FP')
def setUp(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/authenticate/",
body='{"access_token": "token", "token_type": "Bearer", '
'"expires_in": "3600"}')
self.qclient = QiitaClient("https://test_server.com")
def test_init(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/authenticate/",
body='{"access_token": "token", "token_type": "Bearer", '
'"expires_in": "3600"}')
obs = QiitaClient("https://test_server.com")
self.assertEqual(obs._server_url, "https://test_server.com")
self.assertTrue(obs._verify)
def setUp(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/authenticate/",
body='{"access_token": "token", "token_type": "Bearer", '
'"expires_in": "3600"}')
self.tester = QiitaClient("https://test_server.com")
self._clean_up_files = []
self._old_fp = environ.get('QP_TARGET_GENE_CONFIG_FP')
def execute_job(server_url, job_id, output_dir):
"""Starts the plugin and executes the assigned task
Parameters
----------
server_url : str
The url of the server
job_id : str
The job id
Raises
------
RuntimeError
If there is a problem gathering the job information
"""
qclient = QiitaClient(server_url)
# Request job information
job_info = qclient.get("/qiita_db/jobs/%s" % job_id)
# Check if we have received the job information so we can start it
if job_info and job_info['success']:
# Starting the heartbeat
start_heartbeat(qclient, job_id)
# Execute the given task
task_name = job_info['command']
task = TASK_DICT[task_name]
if not exists(output_dir):
makedirs(output_dir)
try:
payload = task(qclient, job_id, job_info['parameters'],
output_dir)
except Exception:
exc_str = repr(traceback.format_exception(*sys.exc_info()))
error_msg = ("Error executing %s:\n%s" % (task_name, exc_str))
payload = format_payload(False, error_msg=error_msg)
# The job completed
complete_job(qclient, job_id, payload)
else:
raise RuntimeError("Can't get job (%s) information" % job_id)
def execute_job(server_url, job_id, output_dir):
"""Starts the plugin and executes the assigned task
Parameters
----------
server_url : str
The url of the server
job_id : str
The job id
Raises
------
RuntimeError
If there is a problem gathering the job information
"""
qclient = QiitaClient(server_url)
# Request job information
job_info = qclient.get("/qiita_db/jobs/%s" % job_id)
# Check if we have received the job information so we can start it
if job_info and job_info['success']:
# Starting the heartbeat
start_heartbeat(qclient, job_id)
# Execute the given task
task_name = job_info['command']
task = TASK_DICT[task_name]
if not exists(output_dir):
makedirs(output_dir)
try:
payload = task(qclient, job_id, job_info['parameters'], output_dir)
except Exception:
exc_str = repr(traceback.format_exception(*sys.exc_info()))
error_msg = ("Error executing %s:\n%s" % (task_name, exc_str))
payload = format_payload(False, error_msg=error_msg)
# The job completed
complete_job(qclient, job_id, payload)
else:
raise RuntimeError("Can't get job (%s) information" % job_id)
def test_init_cert(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/authenticate/",
body='{"access_token": "token", "token_type": "Bearer", '
'"expires_in": "3600"}')
fd, cert_fp = mkstemp()
close(fd)
with open(cert_fp, 'w') as f:
f.write(CERT_FP)
fd, conf_fp = mkstemp()
close(fd)
with open(conf_fp, 'w') as f:
f.write(CONF_FP % cert_fp)
self._clean_up_files.append(conf_fp)
environ['QP_TARGET_GENE_CONFIG_FP'] = conf_fp
obs = QiitaClient("https://test_server.com")
self.assertEqual(obs._server_url, "https://test_server.com")
self.assertEqual(obs._verify, cert_fp)
class QiitaClientTests(TestCase):
@httpretty.activate
def setUp(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/authenticate/",
body='{"access_token": "token", "token_type": "Bearer", '
'"expires_in": "3600"}')
self.tester = QiitaClient("https://test_server.com")
self._clean_up_files = []
self._old_fp = environ.get('QP_TARGET_GENE_CONFIG_FP')
def tearDown(self):
for fp in self._clean_up_files:
if exists(fp):
remove(fp)
if self._old_fp:
environ['QP_TARGET_GENE_CONFIG_FP'] = self._old_fp
else:
del environ['QP_TARGET_GENE_CONFIG_FP']
@httpretty.activate
def test_init(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/authenticate/",
body='{"access_token": "token", "token_type": "Bearer", '
'"expires_in": "3600"}')
obs = QiitaClient("https://test_server.com")
self.assertEqual(obs._server_url, "https://test_server.com")
self.assertTrue(obs._verify)
@httpretty.activate
def test_init_cert(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/authenticate/",
body='{"access_token": "token", "token_type": "Bearer", '
'"expires_in": "3600"}')
fd, cert_fp = mkstemp()
close(fd)
with open(cert_fp, 'w') as f:
f.write(CERT_FP)
fd, conf_fp = mkstemp()
close(fd)
with open(conf_fp, 'w') as f:
f.write(CONF_FP % cert_fp)
self._clean_up_files.append(conf_fp)
environ['QP_TARGET_GENE_CONFIG_FP'] = conf_fp
obs = QiitaClient("https://test_server.com")
self.assertEqual(obs._server_url, "https://test_server.com")
self.assertEqual(obs._verify, cert_fp)
@httpretty.activate
def test_get(self):
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/artifacts/1/type/",
body='{"type": "FASTQ", "success": true, "error": ""}')
obs = self.tester.get("/qiita_db/artifacts/1/type/")
exp = {"type": "FASTQ", "success": True, "error": ""}
self.assertEqual(obs, exp)
@httpretty.activate
def test_get_error(self):
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/artifacts/1/type/",
status=500)
obs = self.tester.get("/qiita_db/artifacts/1/type/")
self.assertIsNone(obs)
@httpretty.activate
def test_post(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/artifacts/1/type/",
body='{"type": "FASTQ", "success": true, "error": ""}')
obs = self.tester.post("/qiita_db/artifacts/1/type/", data="")
exp = {"type": "FASTQ", "success": True, "error": ""}
self.assertEqual(obs, exp)
@httpretty.activate
def test_post_error(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/artifacts/1/type/",
status=500)
obs = self.tester.post("/qiita_db/artifacts/1/type/")
self.assertIsNone(obs)
class QiitaClientTests(TestCase):
@httpretty.activate
def setUp(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/authenticate/",
body='{"access_token": "token", "token_type": "Bearer", '
'"expires_in": "3600"}')
self.tester = QiitaClient("https://test_server.com")
self._clean_up_files = []
self._old_fp = environ.get('QP_TARGET_GENE_CONFIG_FP')
def tearDown(self):
for fp in self._clean_up_files:
if exists(fp):
remove(fp)
if self._old_fp:
environ['QP_TARGET_GENE_CONFIG_FP'] = self._old_fp
else:
del environ['QP_TARGET_GENE_CONFIG_FP']
@httpretty.activate
def test_init(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/authenticate/",
body='{"access_token": "token", "token_type": "Bearer", '
'"expires_in": "3600"}')
obs = QiitaClient("https://test_server.com")
self.assertEqual(obs._server_url, "https://test_server.com")
self.assertTrue(obs._verify)
@httpretty.activate
def test_init_cert(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/authenticate/",
body='{"access_token": "token", "token_type": "Bearer", '
'"expires_in": "3600"}')
fd, cert_fp = mkstemp()
close(fd)
with open(cert_fp, 'w') as f:
f.write(CERT_FP)
fd, conf_fp = mkstemp()
close(fd)
with open(conf_fp, 'w') as f:
f.write(CONF_FP % cert_fp)
self._clean_up_files.append(conf_fp)
environ['QP_TARGET_GENE_CONFIG_FP'] = conf_fp
obs = QiitaClient("https://test_server.com")
self.assertEqual(obs._server_url, "https://test_server.com")
self.assertEqual(obs._verify, cert_fp)
@httpretty.activate
def test_get(self):
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/artifacts/1/type/",
body='{"type": "FASTQ", "success": true, "error": ""}')
obs = self.tester.get("/qiita_db/artifacts/1/type/")
exp = {"type": "FASTQ", "success": True, "error": ""}
self.assertEqual(obs, exp)
@httpretty.activate
def test_get_error(self):
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/artifacts/1/type/",
status=500)
obs = self.tester.get("/qiita_db/artifacts/1/type/")
self.assertIsNone(obs)
@httpretty.activate
def test_post(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/artifacts/1/type/",
body='{"type": "FASTQ", "success": true, "error": ""}')
obs = self.tester.post("/qiita_db/artifacts/1/type/", data="")
exp = {"type": "FASTQ", "success": True, "error": ""}
self.assertEqual(obs, exp)
@httpretty.activate
def test_post_error(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/artifacts/1/type/",
status=500)
obs = self.tester.post("/qiita_db/artifacts/1/type/")
self.assertIsNone(obs)