def execute_sql(self, *args, **kwargs):
"""Proxy to Labkey's Python API"""
try:
r = labkey.query.execute_sql(self._context, *args, **kwargs)
self._log.debug('Found %d rows' % r['rowCount'])
return r
except ServerNotFoundError as e:
self._log.debug('Invalid URL %r, username %r, or password' % (self._base_url, self._username))
raise LabkeyException('Invalid URL, username, or password')
except (QueryNotFoundError, RequestError) as e:
self._log.debug('Invalid schema %r, or query %r' % (args[0], args[1]))
raise LabkeyException('Invalid schema, or query')
def download_file(self, destination, file_location, create=False, overwrite=False):
response = self._session.get(self._construct_url('_webdav', self.project_name, '@files', file_location))
self._log.debug('status_code %r' % (response.status_code))
if response.status_code != 200:
raise LabkeyException('Error HTTP Code %d' % response.status_code)
if len(response.text) < 150:
# Labkey Webdav return 200 even on errors
# So we try to determine if the content represents an error response
# Error response is JSON, with success, and status keys
try:
text = self._get_json(response.text)
if 'success' in text and 'status' in text:
if text['success'] is False:
if text['status'] == 401:
raise AuthenticationException('Authentication failed')
elif text['status'] == 403:
raise AuthenticationException('Authorization failed')
elif text['status'] == 404:
raise LabkeyException('File not found on server')
else:
self._log.debug(response.text)
except ValueError:
pass
if not os.path.isdir(destination):
if create:
os.makedirs(destination)
else:
raise LabkeyException(
'Destination directory %s does not exist, to create directory set create flag' % os.path.abspath(
destination))
file_path = '%s' % os.path.join(destination, os.path.basename(file_location))
if os.path.isfile(file_path):
if not overwrite:
raise LabkeyException(
'File %s already exists, to overwrite the file set overwrite flag' % os.path.abspath(file_path))
with open(file_path, 'wb') as f:
f.write(response.text)
def _trigger_ms2_analysis(self, input_file, input_location, protocol_name, search_engine, run_search=True):
params = {
'path': input_location,
'file': [os.path.basename(one_input_file) for one_input_file in input_file],
'protocol': protocol_name,
'runSearch': run_search,
'Accept': 'application/json'
}
search_engine_map = {
'xtandem': 'XTandem'
}
response = self._session.post(
self._construct_url('ms2-pipeline', self.project_name, 'search%s.api' % search_engine_map[search_engine]),
params=params)
self._log.debug('status_code %s, text %s' % (response.status_code, response.text))
if response.status_code == 401:
raise AuthenticationException('Authentication failed')
elif response.status_code == 403:
raise AuthenticationException('Authorization failed')
elif response.status_code == 404:
raise LabkeyException('Either URL is invalid or the directory does not exist')
def upload_file(self, destination, input_file, create=False, overwrite=False):
# Sanity Checks
file_exists(input_file)
params = {
'Accept': 'application/json',
}
file_exist = self.check_location_exists(os.path.join(destination, os.path.basename(input_file)))
if overwrite is False and file_exist is True:
raise LabkeyException('File already exists, try setting overwrite flag')
if create is False and not self.check_location_exists(destination):
raise LabkeyException('Either URL is invalid or the directory does not exist')
response = self._session.put(
self._construct_url('_webdav', self.project_name, '@files', destination, os.path.basename(input_file)),
data=open(input_file, 'rb'),
params=params
)
self._log.debug('status_code %s, text %s' % (response.status_code, response.text))
if response.status_code != 207 and response.text:
text = self._get_json(response.text)
if text['success'] is False:
if text['status'] == 208:
raise LabkeyException(text['exception'])
elif text['status'] == 401:
raise AuthenticationException('Authentication failed')
elif text['status'] == 403:
raise AuthenticationException('Authorization failed')
elif text['status'] == 404:
if create:
self.create_directory(os.path.join('@files', destination))
self.upload_file(destination, input_file=input_file, create=False, overwrite=overwrite)
else:
raise LabkeyException('Either URL is invalid or the directory does not exist')
else:
self._log.error(text)
def download_other_file(self, destination, file_location, create=False, overwrite=False):
response = self._session.get(
self._construct_url(file_location % {'project-name': self.project_name}))
self._log.debug('status_code %r' % (response.status_code))
if response.status_code != 200:
raise LabkeyException('Error HTTP Code %d' % response.status_code)
if response.history:
# Labkey Webdav return 200 even on errors
# So we try to determine if the content represents an error response
last = response.history[-1]
if 300 <= last.status_code < 400 and (
last.headers.get('location', None) and '/login.view?' in last.headers.get('location')):
raise AuthenticationException('Authentication failed')
if not os.path.isdir(destination):
if create:
os.makedirs(destination)
else:
raise LabkeyException(
'Destination directory %s does not exist, to create directory set create flag' % os.path.abspath(
destination))
output_file = os.path.basename(file_location)
if response.headers.get('content-disposition', None):
output_file = response.headers['content-disposition'].strip()
p = re.match('^filename\w*=\w*"(.*)";?.*$', output_file)
if p:
output_file = p.group(1)
else:
output_file = os.path.basename(file_location)
file_path = os.path.join(destination, output_file)
self._log.info('Downloading to filename %s' % file_path)
if os.path.isfile(file_path):
if not overwrite:
raise LabkeyException(
'File %s already exists, to overwrite the file set overwrite flag' % os.path.abspath(file_path))
with open(file_path, 'wb') as f:
f.write(response.content)
def create_directory(self, destination):
params = {
'Accept': 'application/json'
}
dest = ''
last_status = False
for d in destination.split('/'):
response = self._session.request('MKCOL', self._construct_url('_webdav', self.project_name, dest, d),
params=params)
self._log.debug('status_code %s, text %s' % (response.status_code, response.text))
dest = os.path.join(dest, d)
if response.text:
text = self._get_json(response.text)
if text['success'] is False:
if text['status'] == 208:
raise LabkeyException(text['exception'])
elif text['status'] == 401:
raise AuthenticationException('Authentication failed')
elif text['status'] == 403:
raise AuthenticationException('Authorization failed')
elif text['status'] == 404:
raise LabkeyException(text['exception'])
else:
self._log.debug(response.text)
else:
last_status = True
if last_status is False:
raise LabkeyException('Directory creation failed')
def decorator(*args, **kwargs):
try:
return f(*args, **kwargs)
except MissingSchema as e:
raise LabkeyException(e)