pyxetabase 3.1.0.dev0__py3-none-any.whl

pyopencga/rest_clients/study_client.py

@@ -0,0 +1,433 @@
+"""
+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 Study(_ParentRestClient):
+    """
+    This class contains methods for the 'Studies' webservices
+    PATH: /{apiVersion}/studies
+    """
+
+    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
+        super(Study, 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}/studies/acl/{members}/update
+
+        :param dict data: JSON containing the parameters to modify ACLs.
+            'template' could be either 'admin', 'analyst' or 'view_only'.
+            (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)
+        """
+
+        options['action'] = action
+        return self._post(category='studies', resource='update', subcategory='acl', second_query_id=members, data=data, **options)
+
+    def create(self, data=None, **options):
+        """
+        Create a new study.
+        PATH: /{apiVersion}/studies/create
+
+        :param dict data: study. (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 project: Project [organization@]project where project can
+            be either the ID or the alias.
+        :param bool include_result: Flag indicating to include the created or
+            updated document result in the response.
+        """
+
+        return self._post(category='studies', resource='create', data=data, **options)
+
+    def search(self, project, **options):
+        """
+        Search studies.
+        PATH: /{apiVersion}/studies/search
+
+        :param str project: Project [organization@]project where project can
+            be either the ID or the alias. (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 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 name: Study name.
+        :param str id: Study ID.
+        :param str alias: Study alias.
+        :param str fqn: Study full qualified name.
+        :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 internal_status: Filter by internal status.
+        :param str status: Filter by status.
+        :param str attributes: Attributes.
+        :param str release: Release value.
+        """
+
+        options['project'] = project
+        return self._get(category='studies', resource='search', **options)
+
+    def acl(self, studies, **options):
+        """
+        Return the acl of the study. If member is provided, it will only
+            return the acl for the member.
+        PATH: /{apiVersion}/studies/{studies}/acl
+
+        :param str studies: Comma separated list of Studies
+            [[organization@]project:]study where study and project can be
+            either the ID or UUID up to a maximum of 100. (REQUIRED)
+        :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='studies', resource='acl', query_id=studies, **options)
+
+    def info(self, studies, **options):
+        """
+        Fetch study information.
+        PATH: /{apiVersion}/studies/{studies}/info
+
+        :param str studies: Comma separated list of Studies
+            [[organization@]project:]study where study and project can be
+            either the ID or UUID 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.
+        """
+
+        return self._get(category='studies', resource='info', query_id=studies, **options)
+
+    def search_audit(self, study, **options):
+        """
+        Search audit collection.
+        PATH: /{apiVersion}/studies/{study}/audit/search
+
+        :param str study: Study ID. (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 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 operation_id: Audit operation UUID.
+        :param str user_id: User ID.
+        :param str action: Action performed by the user.
+        :param str resource: Resource involved. Allowed values: ['AUDIT NOTE
+            ORGANIZATION USER PROJECT STUDY FILE SAMPLE JOB INDIVIDUAL COHORT
+            DISEASE_PANEL FAMILY CLINICAL_ANALYSIS INTERPRETATION VARIANT
+            ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL WORKFLOW RESOURCE']
+        :param str resource_id: Resource ID.
+        :param str resource_uuid: resource UUID.
+        :param str status: Filter by status. Allowed values: ['SUCCESS ERROR']
+        :param str date: Date. Format: yyyyMMddHHmmss. Examples: >2018,
+            2017-2018, <201805.
+        """
+
+        return self._get(category='studies', resource='search', query_id=study, subcategory='audit', **options)
+
+    def groups(self, study, **options):
+        """
+        Return the groups present in the study. For owners and administrators
+            only.
+        PATH: /{apiVersion}/studies/{study}/groups
+
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        :param str id: Group id. If provided, it will only fetch information
+            for the provided group.
+        :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='studies', resource='groups', query_id=study, **options)
+
+    def update_groups(self, study, data=None, **options):
+        """
+        Add or remove a group.
+        PATH: /{apiVersion}/studies/{study}/groups/update
+
+        :param dict data: JSON containing the parameters. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        :param str action: Action to be performed: ADD or REMOVE a group.
+            Allowed values: ['ADD REMOVE']
+        """
+
+        return self._post(category='studies', resource='update', query_id=study, subcategory='groups', data=data, **options)
+
+    def update_groups_users(self, study, group, data=None, **options):
+        """
+        Add, set or remove users from an existing group.
+        PATH: /{apiVersion}/studies/{study}/groups/{group}/users/update
+
+        :param dict data: JSON containing the parameters. (REQUIRED)
+        :param str group: Group name. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        :param str action: Action to be performed: ADD, SET or REMOVE users
+            to/from a group. Allowed values: ['ADD SET REMOVE']
+        """
+
+        return self._post(category='studies', resource='users/update', query_id=study, subcategory='groups', second_query_id=group, data=data, **options)
+
+    def create_notes(self, study, data=None, **options):
+        """
+        Create a new note.
+        PATH: /{apiVersion}/studies/{study}/notes/create
+
+        :param dict data: JSON containing the Note to be added. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (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 include_result: Flag indicating to include the created or
+            updated document result in the response.
+        """
+
+        return self._post(category='studies', resource='create', query_id=study, subcategory='notes', data=data, **options)
+
+    def search_notes(self, study, **options):
+        """
+        Search for notes of scope STUDY.
+        PATH: /{apiVersion}/studies/{study}/notes/search
+
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (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 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 id: Note unique identifier.
+        :param str type: Note type.
+        :param str uuid: Unique 32-character identifier assigned automatically
+            by OpenCGA.
+        :param str user_id: User that wrote that Note.
+        :param str tags: Note tags.
+        :param str visibility: Visibility of the Note.
+        :param str version: Autoincremental version assigned to the registered
+            entry. By default, updates does not create new versions. To enable
+            versioning, users must set the `incVersion` flag from the /update
+            web service when updating the document.
+        """
+
+        return self._get(category='studies', resource='search', query_id=study, subcategory='notes', **options)
+
+    def delete_notes(self, study, id, **options):
+        """
+        Delete note.
+        PATH: /{apiVersion}/studies/{study}/notes/{id}/delete
+
+        :param str id: Note unique identifier. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        :param bool include_result: Flag indicating to include the created or
+            updated document result in the response.
+        """
+
+        return self._delete(category='studies', resource='delete', query_id=study, subcategory='notes', second_query_id=id, **options)
+
+    def update_notes(self, study, id, data=None, **options):
+        """
+        Update a note.
+        PATH: /{apiVersion}/studies/{study}/notes/{id}/update
+
+        :param dict data: JSON containing the Note fields to be updated.
+            (REQUIRED)
+        :param str id: Note unique identifier. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (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 tags_action: Action to be performed if the array of tags 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.
+        """
+
+        return self._post(category='studies', resource='update', query_id=study, subcategory='notes', second_query_id=id, data=data, **options)
+
+    def permission_rules(self, study, entity, **options):
+        """
+        Fetch permission rules.
+        PATH: /{apiVersion}/studies/{study}/permissionRules
+
+        :param str entity: Entity where the permission rules should be applied
+            to. Allowed values: ['SAMPLES FILES COHORTS INDIVIDUALS FAMILIES
+            JOBS CLINICAL_ANALYSES DISEASE_PANELS'] (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        """
+
+        options['entity'] = entity
+        return self._get(category='studies', resource='permissionRules', query_id=study, **options)
+
+    def update_permission_rules(self, study, entity, data=None, **options):
+        """
+        Add or remove a permission rule.
+        PATH: /{apiVersion}/studies/{study}/permissionRules/update
+
+        :param dict data: JSON containing the permission rule to be created or
+            removed. (REQUIRED)
+        :param str entity: Entity where the permission rules should be applied
+            to. Allowed values: ['SAMPLES FILES COHORTS INDIVIDUALS FAMILIES
+            JOBS CLINICAL_ANALYSES DISEASE_PANELS'] (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        :param str action: Action to be performed: ADD to add a new permission
+            rule; REMOVE to remove all permissions assigned by an existing
+            permission rule (even if it overlaps any manual permission); REVERT
+            to remove all permissions assigned by an existing permission rule
+            (keep manual overlaps); NONE to remove an existing permission rule
+            without removing any permissions that could have been assigned
+            already by the permission rule. Allowed values: ['ADD REMOVE REVERT
+            NONE']
+        """
+
+        options['entity'] = entity
+        return self._post(category='studies', resource='update', query_id=study, subcategory='permissionRules', data=data, **options)
+
+    def run_templates(self, study, data=None, **options):
+        """
+        Execute template.
+        PATH: /{apiVersion}/studies/{study}/templates/run
+
+        :param dict data: Template loader parameters. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        :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.
+        """
+
+        return self._post(category='studies', resource='run', query_id=study, subcategory='templates', data=data, **options)
+
+    def upload_templates(self, study, **options):
+        """
+        Resource to upload a zipped template.
+        PATH: /{apiVersion}/studies/{study}/templates/upload
+
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        :param inputstream file: File to upload.
+        """
+
+        return self._post(category='studies', resource='upload', query_id=study, subcategory='templates', **options)
+
+    def delete_templates(self, study, template_id, **options):
+        """
+        Delete template.
+        PATH: /{apiVersion}/studies/{study}/templates/{templateId}/delete
+
+        :param str template_id: Template id. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        """
+
+        return self._delete(category='studies', resource='delete', query_id=study, subcategory='templates', second_query_id=template_id, **options)
+
+    def update(self, study, data=None, **options):
+        """
+        Update some study attributes.
+        PATH: /{apiVersion}/studies/{study}/update
+
+        :param dict data: JSON containing the params to be updated. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (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 include_result: Flag indicating to include the created or
+            updated document result in the response.
+        """
+
+        return self._post(category='studies', resource='update', query_id=study, data=data, **options)
+
+    def variable_sets(self, study, **options):
+        """
+        Fetch variableSets from a study.
+        PATH: /{apiVersion}/studies/{study}/variableSets
+
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        :param str id: Id of the variableSet to be retrieved. If no id is
+            passed, it will show all the variableSets of the study.
+        """
+
+        return self._get(category='studies', resource='variableSets', query_id=study, **options)
+
+    def update_variable_sets(self, study, data=None, **options):
+        """
+        Add or remove a variableSet.
+        PATH: /{apiVersion}/studies/{study}/variableSets/update
+
+        :param dict data: JSON containing the VariableSet to be created or
+            removed. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        :param str action: Action to be performed: ADD, REMOVE or FORCE_REMOVE
+            a variableSet. Allowed values: ['ADD REMOVE FORCE_REMOVE']
+        """
+
+        return self._post(category='studies', resource='update', query_id=study, subcategory='variableSets', data=data, **options)
+
+    def update_variable_sets_variables(self, study, variable_set, data=None, **options):
+        """
+        Add or remove variables to a VariableSet.
+        PATH: /{apiVersion}/studies/{study}/variableSets/{variableSet}/variables/update
+
+        :param dict data: JSON containing the variable to be added or removed.
+            For removing, only the variable id will be needed. (REQUIRED)
+        :param str variable_set: VariableSet id of the VariableSet to be
+            updated. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        :param str action: Action to be performed: ADD or REMOVE a variable.
+            Allowed values: ['ADD REMOVE']
+        """
+
+        return self._post(category='studies', resource='variables/update', query_id=study, subcategory='variableSets', second_query_id=variable_set, data=data, **options)
+

pyopencga/rest_clients/user_client.py

@@ -0,0 +1,192 @@
+"""
+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 User(_ParentRestClient):
+    """
+    This class contains methods for the 'Users' webservices
+    PATH: /{apiVersion}/users
+    """
+
+    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
+        super(User, self).__init__(configuration, token, login_handler, *args, **kwargs)
+
+    def anonymous(self, organization, **options):
+        """
+        Get an anonymous token to gain access to the system.
+        PATH: /{apiVersion}/users/anonymous
+
+        :param str organization: Organization id. (REQUIRED)
+        """
+
+        options['organization'] = organization
+        return self._post(category='users', resource='anonymous', **options)
+
+    def create(self, data=None, **options):
+        """
+        Create a new user.
+        PATH: /{apiVersion}/users/create
+
+        :param dict data: JSON containing the parameters. (REQUIRED)
+        """
+
+        return self._post(category='users', resource='create', data=data, **options)
+
+    def login(self, data=None, **options):
+        """
+        Get identified and gain access to the system.
+        PATH: /{apiVersion}/users/login
+
+        :param dict data: JSON containing the authentication parameters.
+        """
+
+        return self._post(category='users', resource='login', data=data, **options)
+
+    def password(self, data=None, **options):
+        """
+        Change the password of a user.
+        PATH: /{apiVersion}/users/password
+
+        :param dict data: JSON containing the change of password parameters.
+            (REQUIRED)
+        """
+
+        return self._post(category='users', resource='password', data=data, **options)
+
+    def search(self, **options):
+        """
+        User search method.
+        PATH: /{apiVersion}/users/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 organization: Organization id.
+        :param str id: Comma separated list user 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 authentication_id: Authentication origin ID.
+        """
+
+        return self._get(category='users', resource='search', **options)
+
+    def info(self, users, **options):
+        """
+        Return the user information including its projects and studies.
+        PATH: /{apiVersion}/users/{users}/info
+
+        :param str users: Comma separated list of user 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 organization: Organization id.
+        """
+
+        return self._get(category='users', resource='info', query_id=users, **options)
+
+    def configs(self, user, **options):
+        """
+        Fetch a user configuration.
+        PATH: /{apiVersion}/users/{user}/configs
+
+        :param str user: User ID. (REQUIRED)
+        :param str name: Unique name (typically the name of the application).
+        """
+
+        return self._get(category='users', resource='configs', query_id=user, **options)
+
+    def update_configs(self, user, data=None, **options):
+        """
+        Add or remove a custom user configuration.
+        PATH: /{apiVersion}/users/{user}/configs/update
+
+        :param dict data: JSON containing anything useful for the application
+            such as user or default preferences. When removing, only the id
+            will be necessary. (REQUIRED)
+        :param str user: User ID. (REQUIRED)
+        :param str action: Action to be performed: ADD or REMOVE a group.
+            Allowed values: ['ADD REMOVE']
+        """
+
+        return self._post(category='users', resource='update', query_id=user, subcategory='configs', data=data, **options)
+
+    def filters(self, user, **options):
+        """
+        Fetch user filters.
+        PATH: /{apiVersion}/users/{user}/filters
+
+        :param str user: User ID. (REQUIRED)
+        :param str id: Filter id. If provided, it will only fetch the
+            specified filter.
+        """
+
+        return self._get(category='users', resource='filters', query_id=user, **options)
+
+    def update_filters(self, user, data=None, **options):
+        """
+        Add or remove a custom user filter.
+        PATH: /{apiVersion}/users/{user}/filters/update
+
+        :param dict data: Filter parameters. When removing, only the 'name' of
+            the filter will be necessary. (REQUIRED)
+        :param str user: User ID. (REQUIRED)
+        :param str action: Action to be performed: ADD or REMOVE a group.
+            Allowed values: ['ADD REMOVE']
+        """
+
+        return self._post(category='users', resource='update', query_id=user, subcategory='filters', data=data, **options)
+
+    def update_filter(self, user, filter_id, data=None, **options):
+        """
+        Update a custom filter.
+        PATH: /{apiVersion}/users/{user}/filters/{filterId}/update
+
+        :param dict data: Filter parameters. (REQUIRED)
+        :param str filter_id: Filter id. (REQUIRED)
+        :param str user: User ID. (REQUIRED)
+        """
+
+        return self._post(category='users', resource='update', query_id=user, subcategory='filters', second_query_id=filter_id, data=data, **options)
+
+    def reset_password(self, user, **options):
+        """
+        Reset password.
+        PATH: /{apiVersion}/users/{user}/password/reset
+
+        :param str user: User ID. (REQUIRED)
+        """
+
+        return self._get(category='users', resource='reset', query_id=user, subcategory='password', **options)
+
+    def update(self, user, data=None, **options):
+        """
+        Update some user attributes.
+        PATH: /{apiVersion}/users/{user}/update
+
+        :param dict data: JSON containing the params to be updated. (REQUIRED)
+        :param str user: User ID. (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 include_result: Flag indicating to include the created or
+            updated document result in the response.
+        """
+
+        return self._post(category='users', resource='update', query_id=user, data=data, **options)
+