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from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient
class Alignment(_ParentRestClient):
"""
This class contains methods for the AnalysisAlignment webservices
"""
def __init__(self, configuration, session_id=None, login_handler=None, *args, **kwargs):
_category = 'analysis/alignment'
super(Alignment, self).__init__(configuration, _category, session_id, login_handler, *args, **kwargs)
def index(self, file, **options):
"""
Index alignment files
URL: /{apiVersion}/analysis/alignment/index
:param file: Comma separated list of file ids (files or directories)
"""
from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient
class Admin(_ParentRestClient):
"""
This class contains methods for the Admin webservices
"""
def __init__(self, configuration, session_id=None, login_handler=None, *args, **kwargs):
_category = 'admin'
super(Admin, self).__init__(configuration, _category, session_id, login_handler, *args, **kwargs)
def sync_users(self, data, **options):
"""
Synchronise groups of users with LDAP groups
URL: /{apiVersion}/admin/users/sync
# Mandatory fields:
- authOriginId: Authentication origin id defined in the main Catalog configuration.
from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient
class Meta(_ParentRestClient):
"""
This class contains methods for the Meta webservice
"""
def __init__(self, configuration, session_id=None, login_handler=None, *args, **kwargs):
_category = "meta"
super(Meta, self).__init__(configuration, _category, session_id, login_handler, *args, **kwargs)
def about(self, **options):
"""
Returns info about current OpenCGA code.
URL: /{apiVersion}/meta/about
"""
return self._get('about', **options)
from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient
class Tool(_ParentRestClient):
"""
This class contains methods for the Analysis - Tool webservices
"""
def __init__(self, configuration, session_id=None, login_handler=None, *args, **kwargs):
_category = 'analysis/tool'
super(Tool, self).__init__(configuration, _category, session_id, login_handler, *args, **kwargs)
def execute(self, data, **options):
"""
Execute an analysis using an internal or external tool
URL: /{apiVersion}/analysis/tool/execute
"""
return self._post('execute', data=data, **options)
from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient
class Variant(_ParentRestClient):
"""
This class contains method for AnalysisVariant ws
"""
def __init__(self, configuration, session_id=None, login_handler=None, *args, **kwargs):
_category = "analysis/variant"
super(Variant, self).__init__(configuration, _category, session_id, login_handler, *args, **kwargs)
def index(self, file, **options):
"""
Index variant files
URL: /{apiVersion}/analysis/variant/index
:param file: comma separated list of file ids (files or directories)
:param study: Study [[user@]project:]study where study and project can
be either the id or alias
from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient, _ParentBasicCRUDClient, _ParentAclRestClient, _ParentAnnotationSetRestClient
class GA4GH(_ParentRestClient):
"""
This class contains method for GA4GH ws
"""
def __init__(self, configuration, session_id=None, login_handler=None, *args, **kwargs):
_category = "ga4gh"
super(GA4GH, self).__init__(configuration, _category, session_id, login_handler, *args, **kwargs)
def responses(self, chrom, pos, allele, beacon, **options):
"""
Beacon webservices
URL: /{apiVersion}/ga4gh/responses
chrom: Chromosome ID. Accepted values: 1-22, X, Y, MT. Note:
For compatibility with conventions set by some of the existing
from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient, _ParentBasicCRUDClient, _ParentAclRestClient
class Interpretations(_ParentRestClient):
"""
This class contains the Interpretations client with methods for the
Analysis - Clinical webservices
"""
def __init__(self, configuration, session_id=None, login_handler=None, *args, **kwargs):
_category = 'analysis/clinical'
super(Interpretations, self).__init__(configuration, _category, session_id, login_handler, *args, **kwargs)
def tool_tiering(self, **options):
"""
GEL Tiering interpretation analysis (PENDING)
URL: /{apiVersion}/analysis/clinical/interpretation/tools/tiering
"""