def test_dna(self):
"""test /dna route"""
# submit parameters
app = 'dna'
url = misc.URL + '/confirm'
dna = 'GATCACAGGTCTATCACCCTATTAACCACTCACGGGA'
values = {'app': app, 'cid': '', 'dna': dna}
(code, html) = misc.post(url, values)
self.assertEqual(code, httplib.OK)
self.assertIn("Execute simulation", html)
loc = html.find("cid:")
cid = html[loc + 4:loc + 10]
# test if input file was written
assert os.path.exists('user_data/guest/dna/' + cid + '/dna.in') == 1
# submit for execution
app = 'dna'
url = misc.URL + '/execute'
np = "1"
values = {'app': app, 'cid': cid, 'np': np}
(code, html) = misc.post(url, values)
self.assertEqual(code, httplib.OK)
# wait a second for scheduler to start job
# this may need to be increased to 2 or 3 seconds
time.sleep(1)
# test if output file was written
assert os.path.exists('user_data/guest/dna/' + cid + '/dna.out') == 1
def test_login_invalid(self):
url = misc.URL + '/login'
values = {'askjdfas': 'guest', 'passwd': 'guest'}
response = misc.post(url, values)
(code, html) = misc.post(url, values)
self.assertEqual(code, httplib.OK)
self.assertIn("failed", html)
async def consume(ws):
while True:
logger.info('ready to receive msg')
message = await ws.recv()
logger.info('received: %s', message)
job = json.loads(message)
# call gateway to execute task
url = 'http://%s:%s/%s' % (gateway['host'], gateway['port'],
job['task'])
if 'data' in job and job['data']:
misc.post(url, job['data'])
else:
misc.get(url)
def test_step0_exists(self):
appname = APP
url = misc.URL + '/app_exists/' + appname
values = {'appname': appname}
(code, html) = misc.post(url, values)
self.assertEqual(code, httplib.OK)
self.assertNotIn("true", html)
def put_file(self, id, files):
"""
Create files in the session with given id, where files is a
dictionary of filename:content pairs, and content is a string
or file-like object.
INPUT::
- ``id`` -- nonnegative integer
- ``files`` -- dictionary
EXAMPLES::
>>> from client import TestClient; c = TestClient()
First try to put a file into a session that doesn't exist::
>>> c.put_file(0, {'foo.txt':'stuff'})
Traceback (most recent call last):
...
ValueError: unknown session 0
>>> c.new_session()
0
>>> c.put_file(0, {'a/b/c.txt':'more stuff'})
>>> c.get_file(0, 'a/b/c.txt')
u'more stuff'
>>> c.quit()
"""
msg = post('%s/put_file/%s'%(self._url, id), files=files)
m = json.loads(msg)
if m['status'] == u'error':
raise ValueError(str(m['data']))
def test_step0(self):
"""enter app name"""
url = misc.URL + '/addapp/step1'
appname = APP
values = {'appname': appname}
(code, html) = misc.post(url, values)
self.assertEqual(code, httplib.OK)
self.assertIn("configure app", html)
def test_registration_valid(self):
url = misc.URL + '/register'
values = {
'user': user,
'password1': passwd,
'password2': passwd,
'email': '*****@*****.**'
}
(code, html) = misc.post(url, values)
#print html
self.assertEqual(code, httplib.OK)
self.assertNotIn("failed", html)
def test_step3(self):
url = misc.URL + '/addapp/step4'
appname = APP
input_format = 'ini'
# contents not used just for user to see
# so just pass dummy string in
values = {
'input_format': input_format,
'appname': appname,
'contents': 'blah'
}
(code, html) = misc.post(url, values)
self.assertEqual(code, httplib.OK)
self.assertIn("assign html input types", html)
def execute(self, session_id, code):
r"""
INPUT:
- ``session_id`` -- id of a session
- ``code`` -- string
OUTPUT:
- cell_id -- execution id number
- status message
EXAMPLES::
>>> from client import TestClient; c = TestClient()
>>> c.new_session()
0
>>> c.wait(0)
>>> c.new_session()
1
>>> c.wait(1)
>>> c.execute(0, 'print(2+3)')
(0, 'running')
>>> c.execute(1, 'print(5*8)')
(0, 'running')
>>> c.wait(0)
>>> c.cells(0)
[{u'code': u'print(2+3)', u'cell_id': 0}]
>>> c.output(0,0)
[{u'output': u'5\n', u'modified_files': None, u'done': False, u'number': 0}, {u'output': None, u'modified_files': None, u'done': True, u'number': 1}]
>>> c.wait(1)
>>> c.cells(1)
[{u'code': u'print(5*8)', u'cell_id': 0}]
>>> c.output(1,0)
[{u'output': u'40\n', u'modified_files': None, u'done': False, u'number': 0}, {u'output': None, u'modified_files': None, u'done': True, u'number': 1}]
>>> c.quit()
"""
msg = post('%s/execute/%s'%(self._url, session_id), {'code':code})
m = json.loads(msg)
if m['status'] == u'error':
raise RuntimeError(m['data'])
return int(m['cell_id']), str(m['cell_status'])
def test_step1(self):
"""enter config options about app"""
url = misc.URL + '/addapp/step2'
appname = APP
description = 'this is a test case'
category = 'bioinformatics'
command = '../../../../apps/' + appname + os.sep + appname
user = '******'
input_format = 'namelist'
values = {
'appname': appname,
'description': description,
'input_format': input_format,
'category': category,
'command': command,
'user': user
}
(code, html) = misc.post(url, values)
self.assertEqual(code, httplib.OK)
self.assertIn("Upload zip file", html)
def test_step4(self):
url = misc.URL + '/addapp/step5'
bool_rep = 'T'
appname = APP
input_format = 'ini'
html_tags = ['text', 'hidden', 'select', 'checkbox']
descriptions = [
'this is a textbox', 'this is a hidden input',
'this is a select tag', 'this is a checkbox'
]
keys = ['par1', 'par2', 'par3']
values = {
'bool_rep': bool_rep,
'input_format': input_format,
'appname': appname,
'descriptions': descriptions,
'html_tags': html_tags,
'keys': keys
}
(code, html) = misc.post(url, values)
self.assertEqual(code, httplib.OK)
self.assertIn("Template file successfully written", html)
def post(url, payload):
print('-------------------> req post')
print('-------------------> %s' % api['base'])
url = api['base'] + url
print('-------------------> %s' % url)
return misc.post(url, payload, True)
def test_check_user_false(self):
url = misc.URL + '/check_user'
values = {'user': '******'}
(code, html) = misc.post(url, values)
self.assertEqual(code, httplib.OK)
self.assertIn("false", html)
def test_check_user_true(self):
url = misc.URL + '/check_user'
values = {'user': '******'}
(code, html) = misc.post(url, values)
self.assertEqual(code, httplib.OK)
self.assertIn("true", html)
def send_status_mesg(id, frontend_uri, status):
uri = status_update_uri(frontend_uri)
data={'id':id, 'status':status}
log.debug("Sending status update to %s with data=%s"%(uri, data))
misc.post(uri, data=data)