def report(self, file_id=None, run_id=None, output_file=None,
output_dir=None):
"""Upload single file."""
report = Reports(base_url=self.base_url,
api_key=self.api_key,
file_id=file_id,
run_id=run_id)
try:
file_obj = Files(base_url=self.base_url, api_key=self.api_key)
res = file_obj.get_file(file_id=file_id)
if not res:
raise CosmosidException('Response from service is empty '
'for file id {}'.format(file_id))
results = report.save_report(out_file=output_file,
out_dir=output_dir)
if results['status']:
return results
else:
raise CosmosidException('{} File id: {}'.format(
results['message'],
file_id))
except CosmosidException as err:
self.logger.error('Save report error')
utils.log_traceback(err)
def profile(self):
""""Get profile information for current user"""
try:
return auth.get_profile(self.base_url, self.api_key)
except Exception as err:
self.logger.error('Client exception occured')
utils.log_traceback(err)
raise
def __auth(self):
"""Read api_key for authentication."""
api_key = None
try:
auth = ApiKeyAuth()
api_key = auth()
if api_key is None:
raise ValidationError("Api Key is empty")
except (KeyError, ValueError) as err:
self.logger.info("Can't get Cosmosid Api Key")
utils.log_traceback(err)
return api_key
def __init__(self, api_key=None, base_url=BASE_URL):
"""Initialize a client with the given params."""
try:
if not api_key:
api_key = self.__auth()
api_key = utils.key_len(api_key)
except ValidationError as err:
utils.log_traceback(err)
base_url = base_url if base_url else self.BASE_URL
if base_url != self.BASE_URL:
self.logger.info("Using base URL: %s", base_url)
self.base_url = base_url
self.api_key = api_key
def pricing(self, data):
"""Get pricing information for the given list of samples and their sizes
data:
[ { "sample_key": "sample_name", "extension": "bam", "file_sizes": [100, 300]},
...
]
"""
try:
return upload.pricing(data=data, base_url=self.base_url, api_key=self.api_key)
except Exception as err:
self.logger.error(err)
utils.log_traceback(err)
def upload_files(self, files, file_type, parent_id=None):
"""Upload single file."""
error_msg = '\nError occurred on File upload: {}'.format(files)
try:
upload_res = upload.upload_and_save(files=files,
parent_id=parent_id,
file_type=file_type,
base_url=self.base_url,
api_key=self.api_key)
if upload_res:
return upload_res['id']
else:
self.logger.error(error_msg)
except UploadException as err:
self.logger.error(error_msg)
utils.log_traceback(err)
def get_file(self, file_id=None):
request_url = self.request_url + "/" + file_id
results = {}
try:
results = requests.get(request_url, headers=self.auth_header)
if results.status_code == 400:
if json.loads(results.text)['error_code'] == 'NotUUID':
raise NotFound('Wrong ID.')
if results.status_code == 404:
results = results.json()
results.update({'status': 0})
return results
if results.status_code == 403:
raise AuthenticationFailed('Authentication Failed. '
'Wrong API Key.')
results.raise_for_status()
if requests.codes.ok:
results = results.json()['items'].pop()
results.update({'status': 1})
return results
except AuthenticationFailed as err:
self.logger.error('AuthenticationFailed')
utils.log_traceback(err)
except NotFound as err:
self.logger.error('Not Found')
utils.log_traceback(err)
except requests.exceptions.RequestException as err:
self.logger.error('Error occured during request')
self.logger.error('Response Status Code: %s', results.status_code)
utils.log_traceback(err)
def get_list(self, parent_id=None):
data = {'folder_id': parent_id} if parent_id else {}
results = {}
try:
results = requests.get(self.request_url,
headers=self.auth_header,
params=data)
if results.status_code == 400:
if json.loads(results.text)['error_code'] == 'NotUUID':
raise NotFound('Wrong ID.')
if results.status_code == 404:
results = results.json()
results.update({'status': 0})
return results
if results.status_code == 403:
raise AuthenticationFailed('Authentication Failed. '
'Wrong API Key.')
results.raise_for_status()
if requests.codes.ok:
results = results.json()
results.update({'status': 1})
#microbiom standart doesnt have an export TODO:export var
results['items'] = [
i for i in results['items'] if i['content_type'] != 7
]
return results
except AuthenticationFailed as err:
utils.log_traceback(err)
except NotFound as err:
utils.log_traceback(err)
except requests.exceptions.RequestException as err:
self.logger.error('Error occured during request')
utils.log_traceback(err)
def get_single_run(self, run_id):
run_metadata_url = "{}{}".format(
self.base_url, self.__single_run_path.format(run_id=run_id))
results = {}
try:
results = requests.get(run_metadata_url, headers=self.auth_header)
if results.status_code == 400:
if json.loads(results.text)['error_code'] == 'NotUUID':
raise NotFound('Wrong ID.')
if results.status_code == 404:
results = results.json()
results.update({'status': 0})
return results
if results.status_code == 403:
raise AuthenticationFailed('Authentication Failed. '
'Wrong API Key.')
results.raise_for_status()
if requests.codes.ok:
results = results.json()
results.update({'status': 1})
return results
except AuthenticationFailed as err:
utils.log_traceback(err)
except NotFound as err:
utils.log_traceback(err)
except requests.exceptions.RequestException as err:
self.logger.error('Error occured during request')
self.logger.error('Response Status Code: %s', results.status_code)
utils.log_traceback(err)
def get_last_run_for_file(self, file_id):
try:
runs_list = self.get_runs_list(file_id=file_id)
if not runs_list:
raise CosmosidException('Error occurred on get list of runs '
'for a File: {}'.format(file_id))
if not runs_list['status']:
raise NotFoundException(runs_list['message'])
sorted_runs_list = sorted(runs_list['runs'],
key=itemgetter('created'),
reverse=True)
return sorted_runs_list[0]
except NotFoundException as err:
self.logger.error('NotFound')
utils.log_traceback(err)
except CosmosidException:
self.logger.error('Runs list exception.')
return None
except Exception as err:
self.logger.error('Client exception occured')
utils.log_traceback(err)
def directory_list(self, parent):
""""get listing of appropriate directory."""
file_obj = Files(base_url=self.base_url, api_key=self.api_key)
try:
res = file_obj.get_list(parent_id=parent)
if res:
if res['status']:
return res
else:
raise NotFoundException(res['message'])
else:
raise CosmosidException('Response from service is empty '
'for directory {}'.format(parent))
except NotFoundException as err:
utils.log_traceback(err)
except CosmosidException as err:
self.logger.error('Get directory list exception')
utils.log_traceback(err)
except Exception as err:
self.logger.error("Failed to get listing of directory %s", parent)
utils.log_traceback(err)
def sample_run_list(self, file_id):
"""Get list of runs for a given file id."""
sample_runs = Runs(base_url=self.base_url, api_key=self.api_key)
try:
sample_run_list = sample_runs.get_runs_list(file_id=file_id)
if sample_run_list:
if sample_run_list['status']:
return sample_run_list
else:
raise NotFoundException(sample_run_list['message'])
else:
raise CosmosidException('Error occurred on get list of runs '
'for a File: %s' % file_id)
except NotFoundException as err:
self.logger.error('NotFound')
utils.log_traceback(err)
except CosmosidException as err:
self.logger.error('Get runs list exception')
utils.log_traceback(err)
except Exception as err:
self.logger.error('Client exception occured')
utils.log_traceback(err)
def analysis_list(self, file_id=None, run_id=None):
"""Get list of analysis for a given file id."""
analysis = Analysis(base_url=self.base_url, api_key=self.api_key)
try:
analysis_list = analysis.get_list(file_id=file_id, run_id=run_id)
if analysis_list:
if analysis_list['status']:
return analysis_list
else:
raise NotFoundException(analysis_list['message'])
else:
raise CosmosidException('Error occurred on get list of '
'analysis for a File: %s'
% file_id)
except NotFoundException as err:
self.logger.error('NotFound')
utils.log_traceback(err)
except CosmosidException as err:
self.logger.error('Get analysis list exception')
utils.log_traceback(err)
except Exception as err:
self.logger.error('Client exception occured')
utils.log_traceback(err)
def get_runs_list(self, file_id=None):
sample_runs_url = "{}{}".format(
self.base_url, self.__resource_path.format(file_id=file_id))
results = {}
try:
file_metadata = self.get_file(file_id)
if not file_metadata:
raise CosmosidException('Response from service is empty '
'for file id {}'.format(file_id))
if not file_metadata['status']:
raise NotFoundException(file_metadata['message'])
results = requests.get(sample_runs_url, headers=self.auth_header)
if results.status_code == 400:
if json.loads(results.text)['error_code'] == 'NotUUID':
raise NotFound('Wrong ID.')
if results.status_code == 404:
results = results.json()
results.update({'status': 0})
results.update({'file_name': file_metadata['name']})
return results
if results.status_code == 403:
raise AuthenticationFailed('Authentication Failed. '
'Wrong API Key.')
results.raise_for_status()
if requests.codes.ok:
results = results.json()
results.update({'status': 1})
results.update({'file_name': file_metadata['name']})
return results
except AuthenticationFailed as err:
utils.log_traceback(err)
except NotFound as err:
utils.log_traceback(err)
except requests.exceptions.RequestException as err:
self.logger.error('Error occured during request')
self.logger.error('Response Status Code: %s', results.status_code)
utils.log_traceback(err)
except NotFoundException as err:
utils.log_traceback(err)
except CosmosidException as err:
self.logger.error('Got runs list exception')
utils.log_traceback(err)
except Exception as err:
self.logger.error('Client exception occured')
utils.log_traceback(err)