pyxetabase 4.0.0.dev56__py3-none-any.whl

pyxetabase/rest_clients/_parent_rest_clients.py

@@ -0,0 +1,144 @@
+import os
+import requests
+
+from pyxetabase.commons import execute, _create_rest_url, snake_to_camel_case
+from pyxetabase.rest_response import RestResponse
+from pyxetabase.retry import retry
+
+
+class _ParentRestClient(object):
+    """Queries the REST service given the different query params"""
+
+    def __init__(self, configuration, token=None, login_handler=None,
+                 auto_refresh=True):
+        self.auto_refresh = auto_refresh
+        self._cfg = configuration
+        self.token = token
+        self.refresh_token = None
+        self.login_handler = login_handler
+        self.on_retry = None
+
+    def _client_login_handler(self):
+        if self.login_handler:
+            self.token, self.refresh_token = self.login_handler()
+
+    def _refresh_token_client(self):
+        if self.login_handler:
+            self.token, self.refresh_token = self.login_handler(refresh=True)
+
+    @staticmethod
+    def _get_query_id_str(query_ids):
+        if query_ids is None:
+            return None
+        elif isinstance(query_ids, list):
+            return ','.join(map(str, query_ids))
+        else:
+            return str(query_ids)
+
+    def _rest_retry(self, method, category, resource, query_id=None, subcategory=None,
+                    second_query_id=None, data=None, dont_retry=None,
+                    **options):
+
+        query_ids_str = self._get_query_id_str(query_id)
+
+        def exec_retry():
+            return execute(config=self._cfg,
+                           sid=self.token,
+                           category=category,
+                           subcategory=subcategory,
+                           method=method,
+                           query_id=query_ids_str,
+                           second_query_id=second_query_id,
+                           resource=resource,
+                           data=data,
+                           options=options)
+
+        def notify_retry(exc_type, exc_val, exc_tb):
+            if self.on_retry is not None:
+                self.on_retry(self, exc_type, exc_val, exc_tb, dict(
+                    method=method, resource=resource, query_id=query_id,
+                    category=category, subcategory=subcategory,
+                    second_query_id=second_query_id, data=data,
+                    options=options
+                ))
+
+        response = retry(
+            exec_retry, self._cfg.max_attempts, self._cfg.min_retry_secs,
+            self._cfg.max_retry_secs, login_handler=self.login_handler,
+            on_retry=notify_retry, dont_retry=dont_retry
+        )
+
+        if self.auto_refresh:
+            self._refresh_token_client()
+
+        if isinstance(response, dict):
+            return RestResponse(response)
+        else:  # Not a JSON (e.g. /{apiVersion}/files/{file}/download)
+            return response
+
+    def _get(self, category, resource, query_id=None, subcategory=None,
+             second_query_id=None, **options):
+        """Queries the REST service and returns the result"""
+        return self._rest_retry(
+            method='get', category=category, resource=resource, query_id=query_id,
+            subcategory=subcategory, second_query_id=second_query_id,
+            **options
+        )
+
+    def _post(self, category, resource, data=None, query_id=None, subcategory=None,
+              second_query_id=None, **options):
+        """Queries the REST service and returns the result"""
+        # Special treatment for the "/{apiVersion}/files/upload" endpoint
+        if category == 'files' and resource == 'upload':
+            response = self._upload(category=category, resource=resource, **options)
+            return RestResponse(response)
+        else:
+            if data is not None:
+                return self._rest_retry(
+                    method='post', category=category, resource=resource, query_id=query_id,
+                    subcategory=subcategory, second_query_id=second_query_id,
+                    data=data, **options
+                )
+            else:
+                return self._rest_retry(
+                    method='post', category=category, resource=resource, query_id=query_id,
+                    subcategory=subcategory, second_query_id=second_query_id,
+                    **options
+                )
+
+    def _delete(self, category, resource, query_id=None, subcategory=None,
+                second_query_id=None, **options):
+        """Queries the REST service and returns the result"""
+        return self._rest_retry(
+            method='delete', category=category, resource=resource, query_id=query_id,
+            subcategory=subcategory, second_query_id=second_query_id,
+            **options
+        )
+
+    def _upload(self, category, resource, **options):
+        """Upload files"""
+
+        # Checking that the parameter file contains the file path to upload
+        if 'file' not in options or not isinstance(options['file'], str):
+            raise ValueError('To upload a file, please specify the file path as the "file" parameter.')
+
+        # Creating URL and headers
+        url, header = _create_rest_url(host=self._cfg.host, version=self._cfg.version, sid=self.token,
+                                       category=category, resource=resource, options=options)
+
+        # Creating data
+        data = {}
+        for k, v in options.items():
+            if k == 'file':  # Param "file" is not included in data
+                continue
+            data[snake_to_camel_case(k)] = v
+
+        # Uploading
+        fpath = os.path.realpath(os.path.expanduser(options['file']))
+        with open(fpath, "rb") as f:
+            fhand = {"file": (fpath, f, "application/octet-stream")}
+            response = requests.post(url, headers=header, files=fhand, data=data or None)
+            if response.status_code != 200:
+                raise Exception(response.content)
+
+        return response.json()

pyxetabase/rest_clients/admin_client.py

@@ -0,0 +1,179 @@
+"""
+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 pyxetabase.rest_clients._parent_rest_clients import _ParentRestClient
+
+
+class Admin(_ParentRestClient):
+    """
+    This class contains methods for the 'Admin' webservices
+    PATH: /{apiVersion}/admin
+    """
+
+    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
+        super(Admin, self).__init__(configuration, token, login_handler, *args, **kwargs)
+
+    def group_by_audit(self, fields, entity, **options):
+        """
+        Group by operation.
+        PATH: /{apiVersion}/admin/audit/groupBy
+
+        :param str entity: Entity to be grouped by. 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 EXTERNAL_TOOL
+            RESOURCE'] (REQUIRED)
+        :param str fields: Comma separated list of fields by which to group
+            by. (REQUIRED)
+        :param bool count: Count the number of elements matching the group.
+        :param int limit: Maximum number of documents (groups) to be returned.
+        :param str action: Action performed.
+        :param str before: Object before update.
+        :param str after: Object after update.
+        :param str date: Date <,<=,>,>=(Format: yyyyMMddHHmmss) and
+            yyyyMMddHHmmss-yyyyMMddHHmmss.
+        """
+
+        options['fields'] = fields
+        options['entity'] = entity
+        return self._get(category='admin', resource='groupBy', subcategory='audit', **options)
+
+    def install_catalog(self, data=None, **options):
+        """
+        Install OpenCGA database.
+        PATH: /{apiVersion}/admin/catalog/install
+
+        :param dict data: JSON containing the mandatory parameters. (REQUIRED)
+        """
+
+        return self._post(category='admin', resource='install', subcategory='catalog', data=data, **options)
+
+    def update_catalog_workspace(self, data=None, **options):
+        """
+        Update the OpenCGA Catalog workspace.
+        PATH: /{apiVersion}/admin/catalog/workspace/update
+
+        :param dict data: JSON containing the workspace parameters. (REQUIRED)
+        """
+
+        return self._post(category='admin', resource='update', subcategory='catalog/workspace', data=data, **options)
+
+    def list_organizations(self, **options):
+        """
+        List current Organizations.
+        PATH: /{apiVersion}/admin/organizations/list
+        """
+
+        return self._get(category='admin', resource='list', subcategory='organizations', **options)
+
+    def fetch_resource(self, data=None, **options):
+        """
+        Fetch resources from the public server and save them into the OpenCGA
+            local installation.
+        PATH: /{apiVersion}/admin/resource/fetch
+
+        :param dict data: Download-resources tool parameters. (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_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :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='admin', resource='fetch', subcategory='resource', data=data, **options)
+
+    def create_users(self, data=None, **options):
+        """
+        Create a new user.
+        PATH: /{apiVersion}/admin/users/create
+
+        :param dict data: JSON containing the parameters. (REQUIRED)
+        """
+
+        return self._post(category='admin', resource='create', subcategory='users', data=data, **options)
+
+    def import_users(self, data=None, **options):
+        """
+        Import users or a group of users from LDAP or AAD.
+        PATH: /{apiVersion}/admin/users/import
+
+        :param dict data: JSON containing the parameters. (REQUIRED)
+        :param str organization: Organization id.
+        """
+
+        return self._post(category='admin', resource='import', subcategory='users', data=data, **options)
+
+    def permissions_users(self, **options):
+        """
+        User permissions.
+        PATH: /{apiVersion}/admin/users/permissions
+
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param str entry_ids: Comma separated list of entry ids.
+        :param str permissions: Comma separated list of permissions to be
+            retrieved.
+        :param str category: Category corresponding to the id's provided.
+        """
+
+        return self._get(category='admin', resource='permissions', subcategory='users', **options)
+
+    def search_users(self, **options):
+        """
+        User search method.
+        PATH: /{apiVersion}/admin/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 user: User ID.
+        :param str authentication_id: Authentication origin ID.
+        """
+
+        return self._get(category='admin', resource='search', subcategory='users', **options)
+
+    def sync_users(self, data=None, **options):
+        """
+        [DEPRECATED] Moved to /users/sync.
+        PATH: /{apiVersion}/admin/users/sync
+
+        :param dict data: JSON containing the parameters. (REQUIRED)
+        :param str organization: Organization id.
+        """
+
+        return self._post(category='admin', resource='sync', subcategory='users', data=data, **options)
+
+    def users_update_groups(self, user, data=None, **options):
+        """
+        Add or remove users from existing groups.
+        PATH: /{apiVersion}/admin/users/{user}/groups/update
+
+        :param dict data: JSON containing the parameters. (REQUIRED)
+        :param str user: User ID. (REQUIRED)
+        :param str organization: Organization id.
+        :param str action: Action to be performed: ADD or REMOVE user to/from
+            groups. Allowed values: ['ADD REMOVE']
+        """
+
+        return self._post(category='admin/users', resource='update', query_id=user, subcategory='groups', data=data, **options)
+