How to use the pyopencga.rest_clients._parent_rest_clients._ParentRestClient function in pyopencga

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github opencb / opencga / opencga-client / src / main / python / pyOpenCGA / pyopencga / rest_clients / alignment_client.py View on Github external
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)
        """
github opencb / opencga / opencga-client / src / main / python / pyOpenCGA / pyopencga / rest_clients / admin_client.py View on Github external
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.
github opencb / opencga / opencga-client / src / main / python / pyOpenCGA / pyopencga / rest_clients / meta_client.py View on Github external
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)
github opencb / opencga / opencga-client / src / main / python / pyOpenCGA / pyopencga / rest_clients / tool_client.py View on Github external
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)
github opencb / opencga / opencga-client / src / main / python / pyOpenCGA / pyopencga / rest_clients / variant_client.py View on Github external
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
github opencb / opencga / opencga-client / src / main / python / pyOpenCGA / pyopencga / rest_clients / ga4gh_client.py View on Github external
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
github opencb / opencga / opencga-client / src / main / python / pyOpenCGA / pyopencga / rest_clients / clinical_client.py View on Github external
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
        """