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

pyopencga/rest_clients/family_client.py

@@ -1,355 +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 Family(_ParentRestClient):
-    """
-    This class contains methods for the 'Families' webservices
-    PATH: /{apiVersion}/families
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(Family, 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}/families/acl/{members}/update
-
-        :param dict data: JSON containing the parameters to add ACLs.
-            (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.
-        :param str propagate: Propagate family permissions to related
-            individuals and samples. Allowed values: ['NO YES
-            YES_AND_VARIANT_VIEW']
-        """
-
-        options['action'] = action
-        return self._post(category='families', resource='update', subcategory='acl', second_query_id=members, data=data, **options)
-
-    def aggregation_stats(self, **options):
-        """
-        Fetch catalog family stats.
-        PATH: /{apiVersion}/families/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 family 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 name: Comma separated list family 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 uuid: Comma separated list family UUIDs up to a maximum of
-            100.
-        :param str members: Comma separated list of family members.
-        :param int expected_size: Expected size of the family (number of
-            members).
-        :param str samples: Comma separated list of member's samples.
-        :param str phenotypes: Comma separated list of phenotype 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.
-        :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.
-        :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 bool deleted: Boolean to retrieve deleted entries.
-        :param str internal_status: Filter by internal status.
-        :param str status: Filter by status.
-        :param str annotation: Annotation filters. Example:
-            age>30;gender=FEMALE. For more information, please visit
-            http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-        :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='families', resource='aggregationStats', **options)
-
-    def load_annotation_sets(self, variable_set_id, path, data=None, **options):
-        """
-        Load annotation sets from a TSV file.
-        PATH: /{apiVersion}/families/annotationSets/load
-
-        :param str path: Path where the TSV file is located in OpenCGA or
-            where it should be located. (REQUIRED)
-        :param str variable_set_id: Variable set ID or name. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param bool parents: Flag indicating whether to create parent
-            directories if they don't exist (only when TSV file was not
-            previously associated).
-        :param str annotation_set_id: Annotation set id. If not provided,
-            variableSetId will be used.
-        :param dict data: JSON containing the 'content' of the TSV file if
-            this has not yet been registered into OpenCGA.
-        """
-
-        options['variableSetId'] = variable_set_id
-        options['path'] = path
-        return self._post(category='families', resource='load', subcategory='annotationSets', data=data, **options)
-
-    def create(self, data=None, **options):
-        """
-        Create family and the individual objects if they do not exist.
-        PATH: /{apiVersion}/families/create
-
-        :param dict data: JSON containing family information. (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 members: Comma separated list of member ids to be
-            associated to the created family.
-        :param bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        """
-
-        return self._post(category='families', resource='create', data=data, **options)
-
-    def distinct(self, field, **options):
-        """
-        Family distinct method.
-        PATH: /{apiVersion}/families/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 family 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 name: Comma separated list family 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 uuid: Comma separated list family UUIDs up to a maximum of
-            100.
-        :param str members: Comma separated list of family members.
-        :param int expected_size: Expected size of the family (number of
-            members).
-        :param str samples: Comma separated list of member's samples.
-        :param str phenotypes: Comma separated list of phenotype 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.
-        :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.
-        :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 bool deleted: Boolean to retrieve deleted entries.
-        :param str internal_status: Filter by internal status.
-        :param str status: Filter by status.
-        :param str annotation: Annotation filters. Example:
-            age>30;gender=FEMALE. For more information, please visit
-            http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-        :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='families', resource='distinct', **options)
-
-    def search(self, **options):
-        """
-        Search families.
-        PATH: /{apiVersion}/families/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 bool flatten_annotations: Flatten the annotations?.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str id: Comma separated list family 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 name: Comma separated list family 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 uuid: Comma separated list family UUIDs up to a maximum of
-            100.
-        :param str members: Comma separated list of family members.
-        :param int expected_size: Expected size of the family (number of
-            members).
-        :param str samples: Comma separated list of member's samples.
-        :param str phenotypes: Comma separated list of phenotype 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.
-        :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.
-        :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 bool deleted: Boolean to retrieve deleted entries.
-        :param str internal_status: Filter by internal status.
-        :param str status: Filter by status.
-        :param str annotation: Annotation filters. Example:
-            age>30;gender=FEMALE. For more information, please visit
-            http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-        :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='families', resource='search', **options)
-
-    def acl(self, families, **options):
-        """
-        Returns the acl of the families. If member is provided, it will only
-            return the acl for the member.
-        PATH: /{apiVersion}/families/{families}/acl
-
-        :param str families: Comma separated list of family IDs or names 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='families', resource='acl', query_id=families, **options)
-
-    def delete(self, families, **options):
-        """
-        Delete existing families.
-        PATH: /{apiVersion}/families/{families}/delete
-
-        :param str families: Comma separated list of family ids. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._delete(category='families', resource='delete', query_id=families, **options)
-
-    def info(self, families, **options):
-        """
-        Get family information.
-        PATH: /{apiVersion}/families/{families}/info
-
-        :param str families: Comma separated list of family IDs or names 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 bool flatten_annotations: Flatten the annotations?.
-        :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 family versions. 'all' to
-            get all the family versions. Not supported if multiple family ids
-            are provided.
-        :param bool deleted: Boolean to retrieve deleted families.
-        """
-
-        return self._get(category='families', resource='info', query_id=families, **options)
-
-    def update(self, families, data=None, **options):
-        """
-        Update some family attributes.
-        PATH: /{apiVersion}/families/{families}/update
-
-        :param str families: Comma separated list of family 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 update_roles: Update the member roles within the family.
-        :param bool update_pedigree_graph: Update the family pedigree graph.
-        :param str annotation_sets_action: Action to be performed if the array
-            of annotationSets is being updated. Allowed values: ['ADD SET
-            REMOVE']
-        :param bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        :param dict data: body.
-        """
-
-        return self._post(category='families', resource='update', query_id=families, data=data, **options)
-
-    def update_annotation_sets_annotations(self, family, annotation_set, data=None, **options):
-        """
-        Update annotations from an annotationSet.
-        PATH: /{apiVersion}/families/{family}/annotationSets/{annotationSet}/annotations/update
-
-        :param str annotation_set: AnnotationSet ID to be updated. (REQUIRED)
-        :param str family: Family id. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str action: Action to be performed: ADD to add new annotations;
-            REPLACE to replace the value of an already existing annotation; SET
-            to set the new list of annotations removing any possible old
-            annotations; REMOVE to remove some annotations; RESET to set some
-            annotations to the default value configured in the corresponding
-            variables of the VariableSet if any. Allowed values: ['ADD SET
-            REMOVE RESET REPLACE']
-        :param dict data: Json containing the map of annotations when the
-            action is ADD, SET or REPLACE, a json with only the key 'remove'
-            containing the comma separated variables to be removed as a value
-            when the action is REMOVE or a json with only the key 'reset'
-            containing the comma separated variables that will be set to the
-            default value when the action is RESET.
-        """
-
-        return self._post(category='families', resource='annotations/update', query_id=family, subcategory='annotationSets', second_query_id=annotation_set, data=data, **options)
-