pyxetabase 4.0.0.dev0__py3-none-any.whl → 4.0.0.dev1__py3-none-any.whl

pyopencga/opencga_client.py

@@ -1,334 +0,0 @@
-import getpass
-import time
-import sys
-import re
-if sys.version_info >= (3, 8):
-    from importlib.metadata import version
-else:
-    from importlib_metadata import version
-
-from pyopencga.opencga_config import ClientConfiguration
-from pyopencga.rest_clients.admin_client import Admin
-from pyopencga.rest_clients.alignment_client import Alignment
-from pyopencga.rest_clients.clinical_analysis_client import ClinicalAnalysis
-from pyopencga.rest_clients.cohort_client import Cohort
-from pyopencga.rest_clients.family_client import Family
-from pyopencga.rest_clients.file_client import File
-from pyopencga.rest_clients.ga4gh_client import GA4GH
-from pyopencga.rest_clients.individual_client import Individual
-from pyopencga.rest_clients.job_client import Job
-from pyopencga.rest_clients.meta_client import Meta
-from pyopencga.rest_clients.disease_panel_client import DiseasePanel
-from pyopencga.rest_clients.project_client import Project
-from pyopencga.rest_clients.sample_client import Sample
-from pyopencga.rest_clients.study_client import Study
-from pyopencga.rest_clients.variant_operation_client import VariantOperation
-from pyopencga.rest_clients.user_client import User
-from pyopencga.rest_clients.variant_client import Variant
-from pyopencga.rest_clients.organization_client import Organization
-from pyopencga.rest_clients.workflow_client import Workflow
-
-
-class OpencgaClient(object):
-    def __init__(self, configuration, token=None, refresh_token=None, on_retry=None, auto_refresh=True):
-        """
-        :param on_retry: callback to be called with client retries an operation.
-            It must accept parameters: client, exc_type, exc_val, exc_tb, call
-        """
-
-        if not isinstance(configuration, ClientConfiguration):
-            raise ValueError('Expected ClientConfiguration instance')
-
-        self.configuration = configuration
-        self.auto_refresh = auto_refresh
-        self.on_retry = on_retry
-        self.clients = []
-        self._login_handler = None
-        self.token = token
-        self.refresh_token = refresh_token
-        self._create_clients()
-        self._check_versions()
-        if self.configuration.sso_login:
-            self._sso_login()
-
-    def __enter__(self):
-        return self
-
-    def __exit__(self, exc_type, exc_val, exc_tb):
-        self.logout()
-
-    def _check_versions(self):
-        # Getting client and server versions
-        client_version = version("pyopencga")
-        server_version = self.meta.about().get_result(0)['Version'].split('-')[0]
-
-        ansi_reset = "\033[0m"
-        ansi_red = "\033[31m"
-        ansi_yellow = "\033[33m"
-        if tuple(server_version.split('.')[:2]) < tuple(client_version.split('.')[:2]):
-            msg = '[WARNING]: Client version ({}) is higher than server version ({}).' \
-                  ' Some client features may not be implemented in the server.\n'.format(client_version, server_version)
-            sys.stdout.write('{}{}{}'.format(ansi_red, msg, ansi_reset))
-        elif tuple(server_version.split('.')[:2]) > tuple(client_version.split('.')[:2]):
-            msg = '[INFO]: Client version ({}) is lower than server version ({}).' \
-                   ' Some client features may not work as intended.\n'.format(client_version, server_version)
-            sys.stdout.write('{}{}{}'.format(ansi_yellow, msg, ansi_reset))
-
-    def _create_clients(self):
-        self.organizations = Organization(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.users = User(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.projects = Project(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.studies = Study(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.files = File(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.jobs = Job(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.samples = Sample(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.individuals = Individual(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.families = Family(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.cohorts = Cohort(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.disease_panels = DiseasePanel(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.alignments = Alignment(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.variants = Variant(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.clinical = ClinicalAnalysis(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.operations = VariantOperation(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.variant_operations = self.operations  # DEPRECATED: use 'self.operations'
-        self.meta = Meta(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.ga4gh = GA4GH(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.admin = Admin(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-        self.workflows = Workflow(self.configuration, self.token, self._login_handler, auto_refresh=self.auto_refresh)
-
-        self.clients = [
-            self.organizations, self.users, self.projects, self.studies, self.files, self.jobs,
-            self.samples, self.individuals, self.families, self.cohorts,
-            self.disease_panels, self.alignments, self.variants, self.clinical, self.operations,
-            self.variant_operations, self.meta, self.ga4gh, self.admin, self.workflows
-        ]
-
-        for client in self.clients:
-            client.on_retry = self.on_retry
-
-    def _make_login_handler(self, user=None, password=None, organization=None):
-        """
-        Returns a closure that performs the log-in. This will be called on retries
-        if the current session ever expires.
-        The reason for using a closure and not a normal function is that a normal
-        function would require storing the password in a field. It is more secure
-        not to do so. This way, the password stored in the closure is inaccessible
-        to other code
-        """
-        def login_handler(refresh=False):
-            if refresh:
-                data = {'refreshToken': self.refresh_token}
-            else:
-                data = {'user': user, 'password': password}
-            if organization:
-                data.update({'organization': organization})
-            tokens = User(self.configuration).login(data=data).get_result(0)
-            self.token = tokens['token']
-            self.refresh_token = tokens['refreshToken']
-            return self.token, self.refresh_token
-        return login_handler
-
-    def login(self, user=None, password=None, organization=None):
-        if user is not None and password is None:
-            password = getpass.getpass()
-        if not (user and password):
-            raise ValueError('User and password required')
-
-        self._login_handler = self._make_login_handler(user=user, password=password, organization=organization)
-        self._login_handler()
-        for client in self.clients:
-            client.token = self.token
-            client.refresh_token = self.refresh_token
-            client.login_handler = self._login_handler
-
-    def _sso_login(self):
-        # Getting token and refresh token from configuration
-        self.token = self.configuration.token
-        self.refresh_token = self.configuration.token
-
-        self._login_handler = self._make_login_handler()
-        for client in self.clients:
-            client.token = self.token
-            client.refresh_token = self.refresh_token
-            client.login_handler = self._login_handler
-
-    def logout(self):
-        self.token = None
-        self.refresh_token = None
-        for client in self.clients:
-            client.token = self.token
-            client.refresh_token = self.refresh_token
-
-    def wait_for_job(self, response=None, study_id=None, job_id=None, retry_seconds=10):
-        if response is not None:
-            study_id = response['results'][0]['study']['id']
-            job_id = response['results'][0]['id']
-
-        if response is None and (study_id is None or job_id is None):
-            raise ValueError('Argument "response" or arguments "study" and "job_id" must be provided')
-
-        if len(job_id.split(',')) > 1:
-            raise ValueError('Only one job ID is allowed')
-
-        retry_seconds = retry_seconds if retry_seconds >= 10 else 10
-        while True:
-            job_info = self.jobs.info(study=study_id, jobs=job_id).get_result(0)
-            if job_info['internal']['status']['id'] in ['ERROR', 'ABORTED']:
-                raise ValueError('{} ({}): {}'.format(
-                    job_info['internal']['status']['id'],
-                    job_info['internal']['status']['date'],
-                    job_info['internal']['status']['description']
-                ))
-            elif job_info['internal']['status']['id'] in ['DONE']:
-                break
-            time.sleep(retry_seconds)
-
-    def _get_help_info(self, client_name=None, parameters=False):
-        info = []
-        for client in self.clients:
-            # Name
-            cls_name = type(client).__name__
-            client_method = re.sub(r'(?<!^)(?=[A-Z])', '_', cls_name).lower() \
-                if cls_name != 'GA4GH' else cls_name.lower()
-            client_method = 'get_' + client_method + '_client'
-
-            if client_name is not None and client_name != cls_name:
-                continue
-
-            # Description and path
-            class_docstring = client.__doc__
-            cls_desc = re.findall('(This class contains methods .+)\n', class_docstring)[0]
-            cls_path = re.findall('PATH: (.+)\n', class_docstring)[0]
-
-            # Methods
-            methods = []
-            method_names = [method_name for method_name in dir(client)
-                            if callable(getattr(client, method_name))
-                            and not method_name.startswith('_') and method_name != 'login_handler']
-            for method_name in method_names:
-                if client_name is None:
-                    continue
-                method_docstring = getattr(client, method_name).__doc__
-                desc = re.findall('(.+)\n +PATH', method_docstring, re.DOTALL)
-                desc = re.sub(' +', ' ', desc[0].replace('\n', ' ').strip())
-                path = re.findall('PATH: (.+)\n', method_docstring)[0]
-
-                args = []
-                arguments = re.findall(
-                    ' +:param (.+)', method_docstring, re.DOTALL
-                )
-                if arguments and parameters:
-                    arguments = arguments[0].replace('\n', ' ').strip()
-                    arguments = re.sub(' +', ' ', arguments)
-                    arguments = arguments.split(' :param ')
-                    for parameter in arguments:
-                        param_info = parameter.split(' ', 2)
-                        args.append({
-                            'name': param_info[1].rstrip(':'),
-                            'type': param_info[0],
-                            'desc': param_info[2]
-                        })
-                methods.append({
-                    'name': method_name,
-                    'desc': desc,
-                    'path': path,
-                    'params': args
-                })
-
-            info.append(
-                {'class_name': cls_name, 'client_method': client_method,
-                 'desc': cls_desc, 'path': cls_path, 'methods': methods}
-            )
-        return info
-
-    def help(self, client_name=None, show_parameters=False):
-        help_txt = []
-
-        info = self._get_help_info(client_name, show_parameters)
-        if client_name is None:
-            help_txt += ['Available clients:']
-            for client in info:
-                txt = '{}- {}: {} ({}). USAGE: opencga_client.{}()'
-                help_txt += [txt.format(
-                    ' '*4, client['class_name'], client['desc'],
-                    client['path'], client['client_method']
-                )]
-        else:
-            for client in info:
-                help_txt += ['{}: {} ({}). USAGE: opencga_client.{}()'.format(
-                    client['class_name'], client['desc'], client['path'],
-                    client['client_method']
-                )]
-                help_txt += ['{}Available methods:'.format(' '*4)]
-                for method in client['methods']:
-                    help_txt += ['{}- {}: {} ({})'.format(
-                        ' '*8, method['name'], method['desc'], method['path']
-                    )]
-                    if not show_parameters:
-                        continue
-                    for param in method['params']:
-                        help_txt += ['{}* {} ({}): {}'.format(
-                            ' ' * 12, param['name'], param['type'],
-                            param['desc']
-                        )]
-        sys.stdout.write('\n'.join(help_txt) + '\n')
-
-    def get_organization_client(self):
-        return self.organizations
-
-    def get_user_client(self):
-        return self.users
-
-    def get_project_client(self):
-        return self.projects
-
-    def get_study_client(self):
-        return self.studies
-
-    def get_file_client(self):
-        return self.files
-
-    def get_job_client(self):
-        return self.jobs
-
-    def get_sample_client(self):
-        return self.samples
-
-    def get_individual_client(self):
-        return self.individuals
-
-    def get_family_client(self):
-        return self.families
-
-    def get_cohort_client(self):
-        return self.cohorts
-
-    def get_disease_panel_client(self):
-        return self.disease_panels
-
-    def get_alignment_client(self):
-        return self.alignments
-
-    def get_variant_client(self):
-        return self.variants
-
-    def get_clinical_client(self):
-        return self.clinical
-
-    def get_operations_client(self):
-        return self.operations
-
-    def get_variant_operation_client(self):
-        return self.variant_operations
-
-    def get_meta_client(self):
-        return self.meta
-
-    def get_ga4gh_client(self):
-        return self.ga4gh
-
-    def get_admin_client(self):
-        return self.admin
-
-    def get_workflows_client(self):
-        return self.workflows

pyopencga/opencga_config.py

@@ -1,211 +0,0 @@
-import os
-import json
-import requests
-import yaml
-
-
-class ClientConfiguration(object):
-    """PyOpenCGA configuration"""
-    
-    def __init__(self, config_input):
-        """
-        :param dict or str config_input: a dict, or a yaml/json file containing an OpenCGA valid client configuration.
-        """
-
-        if isinstance(config_input, dict):
-            self._config = config_input
-        else:
-            self._config = self._get_dictionary_from_file(config_input)
-
-        self.get_sso_login_info()
-
-        self._validate_configuration()
-
-    @staticmethod
-    def _get_dictionary_from_file(config_fpath):
-        config_fhand = open(config_fpath, 'r')
-
-        if config_fpath.endswith('.yml') or config_fpath.endswith('.yaml'):
-            config_dict = yaml.safe_load(config_fhand)
-        elif config_fpath.endswith('.json'):
-            config_dict = json.loads(config_fhand.read())
-        else:
-            raise NotImplementedError('Input must be a dictionary, a yaml file (.yml or .yaml) or a json file (.json)')
-
-        config_fhand.close()
-
-        return config_dict
-
-    def get_sso_login_info(self):
-        # Checking if SSO login is specified
-        if (('sso_login' in self._config and self._config['sso_login']) or
-                ('cookies' in self._config and self._config['cookies'])):
-
-            # Getting session file name
-            if 'name' in self._config['rest'] and self._config['rest']['name']:
-                host_name = self._config['rest']['name']
-            else:
-                host_name = 'opencga'
-            python_session_fhand = open(os.path.expanduser("~/.opencga/{}_session.json".format(host_name)), 'r')
-
-            # Loading info from session file
-            session_info = json.loads(python_session_fhand.read())
-            self._config['sso_login'] = True
-            self._config['cookies'] = session_info['attributes']['cookies']
-            self._config['token'] = session_info['token']
-
-    def _validate_configuration(self):
-        if self._config is None:
-            raise ValueError('Missing configuration dictionary.')
-
-        if 'rest' not in self._config:
-            raise ValueError('Missing configuration field "rest".')
-
-        if 'host' not in self._config['rest'] or not self._config['rest']['host']:
-            raise ValueError('Missing configuration field "host".')
-
-        self._validate_host()
-
-    def _validate_host(self):
-        try:
-            r = requests.head(self.host, timeout=2, verify=not self.tlsAllowInvalidCertificates)
-            if r.status_code == 302:
-                return
-        except requests.exceptions.SSLError:
-            raise Exception('Invalid SSL certificate from "{}"'.format(self.host))
-        except requests.ConnectionError:
-            raise Exception('Unreachable host "{}"'.format(self.host))
-
-    @property
-    def host(self):
-        return self._config['rest']['host']
-
-    @host.setter
-    def host(self, new_host):
-        self._config['rest']['host'] = new_host
-
-    @property
-    def tlsAllowInvalidCertificates(self):
-        if ('tlsAllowInvalidCertificates' in self._config['rest']
-                and self._config['rest']['tlsAllowInvalidCertificates'] is not None):
-            return self._config['rest']['tlsAllowInvalidCertificates']
-        else:
-            return False
-
-    @property
-    def version(self):
-        return self._config['version'] if 'version' in self._config else 'v2'
-
-    @property
-    def cookies(self):
-        if 'cookies' in self._config and self._config['cookies']:
-            python_session_fhand = open(os.path.expanduser("~/.opencga/python_session.json"), 'r')
-            session_info = json.loads(python_session_fhand.read())
-            return session_info['cookies']
-        else:
-            return None
-
-    @property
-    def configuration(self):
-        return self._config
-
-    @property
-    def host(self):
-        return self._config['rest']['host']
-
-    @host.setter
-    def host(self, host):
-        self._config['rest']['host'] = host
-        self._validate_host()
-
-    @property
-    def tlsAllowInvalidCertificates(self):
-        if ('tlsAllowInvalidCertificates' in self._config['rest'] and
-                self._config['rest']['tlsAllowInvalidCertificates'] is not None):
-            return self._config['rest']['tlsAllowInvalidCertificates']
-        else:
-            return False
-
-    @tlsAllowInvalidCertificates.setter
-    def tlsAllowInvalidCertificates(self, tlsAllowInvalidCertificates):
-        self._config['rest']['tlsAllowInvalidCertificates'] = tlsAllowInvalidCertificates
-
-    @property
-    def version(self):
-        return self._config['version'] if 'version' in self._config else 'v2'
-
-    @version.setter
-    def version(self, version):
-        self._config['version'] = version
-
-    @property
-    def sso_login(self):
-        if 'sso_login' in self._config and self._config['sso_login']:
-            return self._config['sso_login']
-        else:
-            return False
-
-    @sso_login.setter
-    def sso_login(self, sso_login):
-        if isinstance(str, sso_login):
-            self._config['sso_login'] = sso_login.lower() == 'true'
-        if isinstance(bool, sso_login):
-            self._config['sso_login'] = sso_login
-
-    @property
-    def cookies(self):
-        if 'cookies' in self._config and self._config['cookies']:
-            return self._config['cookies']
-        else:
-            return None
-
-    @cookies.setter
-    def cookies(self, cookies):
-        self._config['cookies'] = cookies
-
-    @property
-    def token(self):
-        if 'token' in self._config and self._config['token']:
-            return self._config['token']
-        else:
-            return None
-
-    @token.setter
-    def token(self, token):
-        self._config['token'] = token
-
-    @property
-    def max_attempts(self):
-        """Returns configured max_attempts or 1 if not configured"""
-        if 'max_attempts' in self._config and self._config['max_attempts']:
-            return self._config['max_attempts']
-        else:
-            return 1
-
-    @max_attempts.setter
-    def max_attempts(self, max_attempts):
-        self._config['max_attempts'] = max_attempts
-
-    @property
-    def min_retry_secs(self):
-        """Returns configured min_retry_seconds or 0 if not configured"""
-        if 'min_retry_secs' in self._config and self._config['min_retry_secs']:
-            return self._config['min_retry_secs']
-        else:
-            return 0
-
-    @min_retry_secs.setter
-    def min_retry_secs(self, min_retry_secs):
-        self._config['min_retry_secs'] = min_retry_secs
-
-    @property
-    def max_retry_secs(self):
-        """Returns configured max_retry_seconds or 0 if not configured"""
-        if 'max_retry_secs' in self._config and self._config['max_retry_secs']:
-            return self._config['max_retry_secs']
-        else:
-            return 0
-
-    @max_retry_secs.setter
-    def max_retry_secs(self, max_retry_secs):
-        self._config['max_retry_secs'] = max_retry_secs

pyopencga/rest_clients/_parent_rest_clients.py

@@ -1,110 +0,0 @@
-import json
-
-from pyopencga.commons import execute
-from pyopencga.rest_response import RestResponse
-from pyopencga.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"""
-        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
-        )