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from pyopencga.rest_clients._parent_rest_clients import _ParentBasicCRUDClient, _ParentAclRestClient
class Panels(_ParentBasicCRUDClient, _ParentAclRestClient):
"""
This class contains the methods for Panels webservices
"""
def __init__(self, configuration, session_id=None, login_handler=None, *args, **kwargs):
_category = 'panels'
super(Panels, self).__init__(configuration, _category, session_id, login_handler, *args, **kwargs)
def search(self, **options):
"""
Panel search
URL: /{apiVersion}/panels/search
:param study: Study [[user@]project:]study
:param name: Panel name
from pyopencga.rest_clients._parent_rest_clients import _ParentBasicCRUDClient, _ParentAclRestClient
class Jobs(_ParentBasicCRUDClient, _ParentAclRestClient):
"""
This class cotains methods for the Jobs webservice
"""
def __init__(self, configuration, session_id=None, login_handler=None, *args, **kwargs):
_category = 'jobs'
super(Jobs, self).__init__(configuration, _category, session_id, login_handler, *args, **kwargs)
def search(self, **options):
"""
Job search method
URL: /{apiVersion}/jobs/search
:param study: study [[user@]project:]study where study and project can be either the id or alias
:param name: name
:param action: Action to be performed [ADD, SET, REMOVE]
"""
return self._post('interpretations', query_id=clinical_analysis, subquery_id=interpretation,
subcategory='comments/update', data=data, action=action, **options)
def update_reported_variants(self, clinical_analysis, interpretation, data, **options):
"""
Update reported variants of an interpretation
URL: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretations/{interpretation}/reportedVariants/update
"""
return self._post('interpretations', query_id=clinical_analysis, subquery_id=interpretation,
subcategory='reportedVariants/update', data=data, **options)
class Clinical(_ParentBasicCRUDClient, _ParentAclRestClient):
"""
This class contains methods for the Analysis - Clinical webservices
"""
def __init__(self, configuration, session_id=None, login_handler=None, *args, **kwargs):
_category = 'analysis/clinical'
super(Clinical, self).__init__(configuration, _category, session_id, login_handler, *args, **kwargs)
self.configuration = configuration
self.session_id = session_id
self.login_handler = login_handler
self._create_clients()
def _create_clients(self):
## undef all
from pyopencga.rest_clients._parent_rest_clients import _ParentBasicCRUDClient, _ParentAclRestClient
class Studies(_ParentBasicCRUDClient, _ParentAclRestClient):
"""
This class contains method for the Studies webservices
"""
def __init__(self, configuration, session_id=None, login_handler=None, *args, **kwargs):
_category = 'studies'
super(Studies, self).__init__(configuration, _category, session_id, login_handler, *args, **kwargs)
def aggregation_stats(self, study, **options):
"""
Fetch catalog study stats
URL: /{apiVersion}/studies/{studies}/aggregationStats
:param study: study id
:param default: calculate default stats (bool)