pyxetabase 3.1.0.dev25__py3-none-any.whl → 3.1.1__py3-none-any.whl

pyopencga/rest_clients/disease_panel_client.py

@@ -1,352 +0,0 @@
-"""
-WARNING: AUTOGENERATED CODE
-
-    This code was generated by a tool.
-    
-    Manual changes to this file may cause unexpected behavior in your application.
-    Manual changes to this file will be overwritten if the code is regenerated.
-"""
-
-from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient
-
-
-class DiseasePanel(_ParentRestClient):
-    """
-    This class contains methods for the 'Disease Panels' webservices
-    PATH: /{apiVersion}/panels
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(DiseasePanel, self).__init__(configuration, token, login_handler, *args, **kwargs)
-
-    def update_acl(self, members, action, data=None, **options):
-        """
-        Update the set of permissions granted for the member.
-        PATH: /{apiVersion}/panels/acl/{members}/update
-
-        :param dict data: JSON containing the parameters to update the
-            permissions. (REQUIRED)
-        :param str action: Action to be performed [ADD, SET, REMOVE or RESET].
-            Allowed values: ['SET ADD REMOVE RESET'] (REQUIRED)
-        :param str members: Comma separated list of user or group ids.
-            (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        options['action'] = action
-        return self._post(category='panels', resource='update', subcategory='acl', second_query_id=members, data=data, **options)
-
-    def aggregation_stats(self, **options):
-        """
-        Fetch catalog panel stats.
-        PATH: /{apiVersion}/panels/aggregationStats
-
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str id: Comma separated list of panel IDs  up to a maximum of
-            100. Also admits basic regular expressions using the operator '~',
-            i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i'
-            for case insensitive search.
-        :param str uuid: Comma separated list of panel UUIDs  up to a maximum
-            of 100.
-        :param str name: Comma separated list of panel names  up to a maximum
-            of 100. Also admits basic regular expressions using the operator
-            '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive,
-            '~/value/i' for case insensitive search.
-        :param str internal_status: Filter by internal status.
-        :param str disorders: Comma separated list of disorder ids or names.
-            Also admits basic regular expressions using the operator '~', i.e.
-            '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for
-            case insensitive search.. Also admits basic regular expressions
-            using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case
-            sensitive, '~/value/i' for case insensitive search.
-        :param str variants: Comma separated list of variant ids. Also admits
-            basic regular expressions using the operator '~', i.e.
-            '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for
-            case insensitive search.
-        :param str genes: Comma separated list of gene ids. Also admits basic
-            regular expressions using the operator '~', i.e. '~{perl-regex}'
-            e.g. '~value' for case sensitive, '~/value/i' for case insensitive
-            search.
-        :param str source: Comma separated list of source ids or names.
-        :param str regions: Comma separated list of regions. Also admits basic
-            regular expressions using the operator '~', i.e. '~{perl-regex}'
-            e.g. '~value' for case sensitive, '~/value/i' for case insensitive
-            search.
-        :param str categories: Comma separated list of category names. Also
-            admits basic regular expressions using the operator '~', i.e.
-            '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for
-            case insensitive search.
-        :param str tags: Panel tags. Also admits basic regular expressions
-            using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case
-            sensitive, '~/value/i' for case insensitive search.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        :param str status: Filter by status.
-        :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
-            Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Modification date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str acl: Filter entries for which a user has the provided
-            permissions. Format: acl={user}:{permissions}. Example:
-            acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which
-            user john has both WRITE and WRITE_ANNOTATIONS permissions. Only
-            study owners or administrators can query by this field. .
-        :param str release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        :param str field: Field to apply aggregation statistics to (or a list
-            of fields separated by semicolons), e.g.:
-            studies;type;numSamples[0..10]:1;format:sum(size).
-        """
-
-        return self._get(category='panels', resource='aggregationStats', **options)
-
-    def create(self, data=None, **options):
-        """
-        Create a panel.
-        PATH: /{apiVersion}/panels/create
-
-        :param str include: Fields included in the response, whole JSON path
-            must be provided.
-        :param str exclude: Fields excluded in the response, whole JSON path
-            must be provided.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        :param dict data: Panel parameters.
-        """
-
-        return self._post(category='panels', resource='create', data=data, **options)
-
-    def distinct(self, field, **options):
-        """
-        Panel distinct method.
-        PATH: /{apiVersion}/panels/distinct
-
-        :param str field: Comma separated list of fields for which to obtain
-            the distinct values. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str id: Comma separated list of panel IDs  up to a maximum of
-            100. Also admits basic regular expressions using the operator '~',
-            i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i'
-            for case insensitive search.
-        :param str uuid: Comma separated list of panel UUIDs  up to a maximum
-            of 100.
-        :param str name: Comma separated list of panel names  up to a maximum
-            of 100. Also admits basic regular expressions using the operator
-            '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive,
-            '~/value/i' for case insensitive search.
-        :param str internal_status: Filter by internal status.
-        :param str disorders: Comma separated list of disorder ids or names.
-            Also admits basic regular expressions using the operator '~', i.e.
-            '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for
-            case insensitive search.. Also admits basic regular expressions
-            using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case
-            sensitive, '~/value/i' for case insensitive search.
-        :param str variants: Comma separated list of variant ids. Also admits
-            basic regular expressions using the operator '~', i.e.
-            '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for
-            case insensitive search.
-        :param str genes: Comma separated list of gene ids. Also admits basic
-            regular expressions using the operator '~', i.e. '~{perl-regex}'
-            e.g. '~value' for case sensitive, '~/value/i' for case insensitive
-            search.
-        :param str source: Comma separated list of source ids or names.
-        :param str regions: Comma separated list of regions. Also admits basic
-            regular expressions using the operator '~', i.e. '~{perl-regex}'
-            e.g. '~value' for case sensitive, '~/value/i' for case insensitive
-            search.
-        :param str categories: Comma separated list of category names. Also
-            admits basic regular expressions using the operator '~', i.e.
-            '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for
-            case insensitive search.
-        :param str tags: Panel tags. Also admits basic regular expressions
-            using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case
-            sensitive, '~/value/i' for case insensitive search.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        :param str status: Filter by status.
-        :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
-            Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Modification date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str acl: Filter entries for which a user has the provided
-            permissions. Format: acl={user}:{permissions}. Example:
-            acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which
-            user john has both WRITE and WRITE_ANNOTATIONS permissions. Only
-            study owners or administrators can query by this field. .
-        :param str release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        """
-
-        options['field'] = field
-        return self._get(category='panels', resource='distinct', **options)
-
-    def import_panels(self, data=None, **options):
-        """
-        Import panels.
-        PATH: /{apiVersion}/panels/import
-
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        :param dict data: Panel parameters.
-        """
-
-        return self._post(category='panels', resource='import', data=data, **options)
-
-    def search(self, **options):
-        """
-        Panel search.
-        PATH: /{apiVersion}/panels/search
-
-        :param str include: Fields included in the response, whole JSON path
-            must be provided.
-        :param str exclude: Fields excluded in the response, whole JSON path
-            must be provided.
-        :param int limit: Number of results to be returned.
-        :param int skip: Number of results to skip.
-        :param bool count: Get the total number of results matching the query.
-            Deactivated by default.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str id: Comma separated list of panel IDs  up to a maximum of
-            100. Also admits basic regular expressions using the operator '~',
-            i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i'
-            for case insensitive search.
-        :param str uuid: Comma separated list of panel UUIDs  up to a maximum
-            of 100.
-        :param str name: Comma separated list of panel names  up to a maximum
-            of 100. Also admits basic regular expressions using the operator
-            '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive,
-            '~/value/i' for case insensitive search.
-        :param str internal_status: Filter by internal status.
-        :param str disorders: Comma separated list of disorder ids or names.
-            Also admits basic regular expressions using the operator '~', i.e.
-            '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for
-            case insensitive search.. Also admits basic regular expressions
-            using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case
-            sensitive, '~/value/i' for case insensitive search.
-        :param str variants: Comma separated list of variant ids. Also admits
-            basic regular expressions using the operator '~', i.e.
-            '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for
-            case insensitive search.
-        :param str genes: Comma separated list of gene ids. Also admits basic
-            regular expressions using the operator '~', i.e. '~{perl-regex}'
-            e.g. '~value' for case sensitive, '~/value/i' for case insensitive
-            search.
-        :param str source: Comma separated list of source ids or names.
-        :param str regions: Comma separated list of regions. Also admits basic
-            regular expressions using the operator '~', i.e. '~{perl-regex}'
-            e.g. '~value' for case sensitive, '~/value/i' for case insensitive
-            search.
-        :param str categories: Comma separated list of category names. Also
-            admits basic regular expressions using the operator '~', i.e.
-            '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for
-            case insensitive search.
-        :param str tags: Panel tags. Also admits basic regular expressions
-            using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case
-            sensitive, '~/value/i' for case insensitive search.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        :param str status: Filter by status.
-        :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
-            Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Modification date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str acl: Filter entries for which a user has the provided
-            permissions. Format: acl={user}:{permissions}. Example:
-            acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which
-            user john has both WRITE and WRITE_ANNOTATIONS permissions. Only
-            study owners or administrators can query by this field. .
-        :param str release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        """
-
-        return self._get(category='panels', resource='search', **options)
-
-    def acl(self, panels, **options):
-        """
-        Returns the acl of the panels. If member is provided, it will only
-            return the acl for the member.
-        PATH: /{apiVersion}/panels/{panels}/acl
-
-        :param str panels: Comma separated list of panel IDs up to a maximum
-            of 100. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str member: User or group id.
-        :param bool silent: Boolean to retrieve all possible entries that are
-            queried for, false to raise an exception whenever one of the
-            entries looked for cannot be shown for whichever reason.
-        """
-
-        return self._get(category='panels', resource='acl', query_id=panels, **options)
-
-    def delete(self, panels, **options):
-        """
-        Delete existing panels.
-        PATH: /{apiVersion}/panels/{panels}/delete
-
-        :param str panels: Comma separated list of panel ids. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._delete(category='panels', resource='delete', query_id=panels, **options)
-
-    def info(self, panels, **options):
-        """
-        Panel info.
-        PATH: /{apiVersion}/panels/{panels}/info
-
-        :param str panels: Comma separated list of panel IDs up to a maximum
-            of 100. (REQUIRED)
-        :param str include: Fields included in the response, whole JSON path
-            must be provided.
-        :param str exclude: Fields excluded in the response, whole JSON path
-            must be provided.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str version: Comma separated list of panel versions. 'all' to
-            get all the panel versions. Not supported if multiple panel ids are
-            provided.
-        :param bool deleted: Boolean to retrieve deleted panels.
-        """
-
-        return self._get(category='panels', resource='info', query_id=panels, **options)
-
-    def update(self, panels, data=None, **options):
-        """
-        Update panel attributes.
-        PATH: /{apiVersion}/panels/{panels}/update
-
-        :param str panels: Comma separated list of panel ids. (REQUIRED)
-        :param str include: Fields included in the response, whole JSON path
-            must be provided.
-        :param str exclude: Fields excluded in the response, whole JSON path
-            must be provided.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        :param dict data: Panel parameters.
-        """
-
-        return self._post(category='panels', resource='update', query_id=panels, data=data, **options)
-